From 26358ac5ab612e3ba5cc965994853f4a6616220c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 20 Sep 2018 13:13:25 +0200
Subject: [PATCH 001/909] gnu: Add r-parmigene.

* gnu/packages/cran.scm (r-parmigene): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 5519b85d0b..58e9ad09c7 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5875,3 +5875,23 @@ score in order to detect blood doping.  The package also contains functions to
 calculate other scores used in anti-doping programs, such as the ratio of
 hemoglobin to reticulocytes (OFF-score), as well as example data.")
     (license license:gpl2+)))
+
+(define-public r-parmigene
+  (package
+    (name "r-parmigene")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "parmigene" version))
+       (sha256
+        (base32
+         "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/parmigene/")
+    (synopsis "Mutual information estimation for gene network reconstruction")
+    (description
+     "This package provides a parallel estimation of the mutual information
+based on entropy estimates from k-nearest neighbors distances and algorithms
+for the reconstruction of gene regulatory networks.")
+    (license license:agpl3+)))

From 391fc11f0e492b06fa6eb31535e1e34165040b7d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 20 Sep 2018 15:53:20 +0200
Subject: [PATCH 002/909] gnu: python2-scikit-learn: Fix check phase.

* gnu/packages/machine-learning.scm (python2-scikit-learn)[arguments]:
Override check phase to disable broken tests and pass environment variables.
---
 gnu/packages/machine-learning.scm | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 9aa61bd8f8..990a6c771a 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -750,7 +750,24 @@ data analysis.")
     (license license:bsd-3)))
 
 (define-public python2-scikit-learn
-  (package-with-python2 python-scikit-learn))
+  (let ((parent (package-with-python2 python-scikit-learn)))
+    (package (inherit parent)
+      (arguments
+       (substitute-keyword-arguments (package-arguments parent)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (replace 'check
+               (lambda _
+                 ;; Restrict OpenBLAS threads to prevent segfaults while testing!
+                 (setenv "OPENBLAS_NUM_THREADS" "1")
+                 ;; Some tests expect to be able to write to HOME.
+                 (setenv "HOME" "/tmp")
+                 ;; Disable tests that require network access
+                 (delete-file "sklearn/datasets/tests/test_kddcup99.py")
+                 (delete-file "sklearn/datasets/tests/test_mldata.py")
+                 (delete-file "sklearn/datasets/tests/test_rcv1.py")
+                 (invoke "pytest" "sklearn")
+                 #t)))))))))
 
 (define-public python-autograd
   (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")

From e30397dddb0c8ba130b9c77b3305f6da6508e766 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 20 Sep 2018 16:02:38 +0200
Subject: [PATCH 003/909] gnu: ghc-xml-conduit: Update to 1.8.0.1.

* gnu/packages/haskell.scm (ghc-xml-conduit): Update to 1.8.0.1.
[inputs]: Add ghc-doctest.
---
 gnu/packages/haskell.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index eb629cf138..0c6c30acd2 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6729,7 +6729,7 @@ documents.")
 (define-public ghc-xml-conduit
   (package
     (name "ghc-xml-conduit")
-    (version "1.7.1.2")
+    (version "1.8.0.1")
     (source
      (origin
        (method url-fetch)
@@ -6737,11 +6737,12 @@ documents.")
                            "xml-conduit-" version ".tar.gz"))
        (sha256
         (base32
-         "0n4k0rq9j5cc9kdvj9xbx8gmiqlyk5x6pw8yxzw5wfsw7qkych2s"))))
+         "177gmyigxql1pn3ncz0r8annwv5cbxnihbgrrg1dhm4gmc9jy2wq"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-conduit" ,ghc-conduit)
        ("ghc-conduit-extra" ,ghc-conduit-extra)
+       ("ghc-doctest" ,ghc-doctest)
        ("ghc-resourcet" ,ghc-resourcet)
        ("ghc-text" ,ghc-text)
        ("ghc-xml-types" ,ghc-xml-types)

From a235ea4f30785e42cedf9a52d22c1e6650901fdd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 20 Sep 2018 16:03:06 +0200
Subject: [PATCH 004/909] gnu: ghc-pandoc-citeproc: Update to 0.14.3.1.

* gnu/packages/haskell.scm (ghc-pandoc-citeproc): Update to 0.14.3.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0c6c30acd2..6b774c358a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6763,7 +6763,7 @@ the @code{conduit} package.")
 (define-public ghc-pandoc-citeproc
   (package
     (name "ghc-pandoc-citeproc")
-    (version "0.12.2.5")
+    (version "0.14.3.1")
     (source
      (origin
        (method url-fetch)
@@ -6772,7 +6772,7 @@ the @code{conduit} package.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1l58nbflcnlznc93qimkk7ghk2gv8kipf45zf88piqa2zys41yyx"))))
+         "0yj6rckwsc9vig40cm15ry0j3d01xpk04qma9n4byhal6v4b5h22"))))
     (build-system haskell-build-system)
     (arguments
      `(#:phases

From 89ee8a6edf7ceae66ff86e88778e07e80aa119fd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 20 Sep 2018 17:46:34 +0200
Subject: [PATCH 005/909] gnu: rsem: Update to 1.3.1.

* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                             |   1 -
 gnu/packages/bioinformatics.scm          |  91 +--
 gnu/packages/patches/rsem-makefile.patch | 682 -----------------------
 3 files changed, 52 insertions(+), 722 deletions(-)
 delete mode 100644 gnu/packages/patches/rsem-makefile.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 0ead43acd9..4bca986619 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1115,7 +1115,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/reptyr-fix-gcc-7.patch			\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
-  %D%/packages/patches/rsem-makefile.patch			\
   %D%/packages/patches/rtags-separate-rct.patch			\
   %D%/packages/patches/racket-store-checksum-override.patch	\
   %D%/packages/patches/ruby-rubygems-276-for-ruby24.patch	\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67f24a6170..10330cd8b2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4800,66 +4800,79 @@ phylogenies.")
 (define-public rsem
   (package
     (name "rsem")
-    (version "1.2.20")
+    (version "1.3.1")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
-                       version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/deweylab/RSEM.git")
+             (commit (string-append "v" version))))
        (sha256
-        (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
-       (patches (search-patches "rsem-makefile.patch"))
+        (base32 "1jlq11d1p8qp64w75yj8cnbbd1a93viq10pzsbwal7vdn8fg13j1"))
+       (file-name (git-file-name name version))
        (modules '((guix build utils)))
        (snippet
         '(begin
-           ;; remove bundled copy of boost
+           ;; remove bundled copy of boost and samtools
            (delete-file-recursively "boost")
+           (delete-file-recursively "samtools-1.3")
            #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
+       #:make-flags
+       (list (string-append "BOOST="
+                            (assoc-ref %build-inputs "boost")
+                            "/include/")
+             (string-append "SAMHEADERS="
+                            (assoc-ref %build-inputs "htslib")
+                            "/include/htslib/sam.h")
+             (string-append "SAMLIBS="
+                            (assoc-ref %build-inputs "htslib")
+                            "/lib/libhts.a"))
        #:phases
        (modify-phases %standard-phases
          ;; No "configure" script.
          ;; Do not build bundled samtools library.
          (replace 'configure
-                  (lambda _
-                    (substitute* "Makefile"
-                      (("^all : sam/libbam.a") "all : "))
-                    #t))
+           (lambda _
+             (substitute* "Makefile"
+               (("^all : \\$\\(PROGRAMS\\).*") "all: $(PROGRAMS)\n")
+               (("^\\$\\(SAMLIBS\\).*") ""))
+             #t))
          (replace 'install
-                  (lambda* (#:key outputs #:allow-other-keys)
-                    (let* ((out (string-append (assoc-ref outputs "out")))
-                           (bin (string-append out "/bin/"))
-                           (perl (string-append out "/lib/perl5/site_perl")))
-                      (mkdir-p bin)
-                      (mkdir-p perl)
-                      (for-each (lambda (file)
-                                  (install-file file bin))
-                                (find-files "." "rsem-.*"))
-                      (install-file "rsem_perl_utils.pm" perl))
-                    #t))
-         (add-after
-          'install 'wrap-program
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out")))
-              (for-each (lambda (prog)
-                          (wrap-program (string-append out "/bin/" prog)
-                            `("PERL5LIB" ":" prefix
-                              (,(string-append out "/lib/perl5/site_perl")))))
-                        '("rsem-plot-transcript-wiggles"
-                          "rsem-calculate-expression"
-                          "rsem-generate-ngvector"
-                          "rsem-run-ebseq"
-                          "rsem-prepare-reference")))
-            #t)))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (string-append (assoc-ref outputs "out")))
+                    (bin (string-append out "/bin/"))
+                    (perl (string-append out "/lib/perl5/site_perl")))
+               (mkdir-p bin)
+               (mkdir-p perl)
+               (for-each (lambda (file)
+                           (install-file file bin))
+                         (find-files "." "rsem-.*"))
+               (install-file "rsem_perl_utils.pm" perl))
+             #t))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each (lambda (prog)
+                           (wrap-program (string-append out "/bin/" prog)
+                             `("PERL5LIB" ":" prefix
+                               (,(string-append out "/lib/perl5/site_perl")))))
+                         '("rsem-calculate-expression"
+                           "rsem-control-fdr"
+                           "rsem-generate-data-matrix"
+                           "rsem-generate-ngvector"
+                           "rsem-plot-transcript-wiggles"
+                           "rsem-prepare-reference"
+                           "rsem-run-ebseq"
+                           "rsem-run-prsem-testing-procedure")))
+             #t)))))
     (inputs
      `(("boost" ,boost)
-       ("ncurses" ,ncurses)
        ("r-minimal" ,r-minimal)
        ("perl" ,perl)
-       ("samtools" ,samtools-0.1)
+       ("htslib" ,htslib-1.3)
        ("zlib" ,zlib)))
     (home-page "http://deweylab.biostat.wisc.edu/rsem/")
     (synopsis "Estimate gene expression levels from RNA-Seq data")
diff --git a/gnu/packages/patches/rsem-makefile.patch b/gnu/packages/patches/rsem-makefile.patch
deleted file mode 100644
index 5481dc685f..0000000000
--- a/gnu/packages/patches/rsem-makefile.patch
+++ /dev/null
@@ -1,682 +0,0 @@
-This patch simplifies the Makefile, making it much easier to build rsem
-without the bundled version of samtools.  It has already been submitted
-upstream: https://github.com/bli25wisc/RSEM/pull/11
-
-From 161894e91a16c7e15af57e4fcfe8cb613711c7fa Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 14:51:07 +0200
-Subject: [PATCH 1/7] remove all headers from Makefile
-
----
- Makefile | 95 +++++++++++-----------------------------------------------------
- 1 file changed, 16 insertions(+), 79 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 54e2603..3a55ed8 100644
---- a/Makefile
-+++ b/Makefile
-@@ -10,133 +10,70 @@ all : $(PROGRAMS)
- sam/libbam.a :
- 	cd sam ; ${MAKE} all
- 
--Transcript.h : utils.h
--
--Transcripts.h : utils.h my_assert.h Transcript.h
--
--rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp
-+rsem-extract-reference-transcripts : extractRef.cpp
- 	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
- 
--rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp
-+rsem-synthesis-reference-transcripts : synthesisRef.cpp
- 	$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
- 
--BowtieRefSeqPolicy.h : RefSeqPolicy.h
--
--RefSeq.h : utils.h
--
--Refs.h : utils.h RefSeq.h RefSeqPolicy.h PolyARules.h
--
--
- rsem-preref : preRef.o
- 	$(CC) preRef.o -o rsem-preref
- 
--preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp
-+preRef.o : preRef.cpp
- 	$(CC) $(COFLAGS) preRef.cpp
- 
--
--SingleRead.h : Read.h
--
--SingleReadQ.h : Read.h
--
--PairedEndRead.h : Read.h SingleRead.h
--
--PairedEndReadQ.h : Read.h SingleReadQ.h
--
--
--PairedEndHit.h : SingleHit.h
--
--HitContainer.h : GroupInfo.h
--
--
--SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h
--
--
- rsem-parse-alignments : parseIt.o sam/libbam.a
- 	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread 
- 
--parseIt.o : utils.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp
-+parseIt.o : parseIt.cpp
- 	$(CC) -Wall -O2 -c -I. parseIt.cpp
- 
--
--rsem-build-read-index : utils.h buildReadIndex.cpp
-+rsem-build-read-index : buildReadIndex.cpp
- 	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
--
--simul.h : boost/random.hpp
--
--ReadReader.h : SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h ReadIndex.h
--
--SingleModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h SingleHit.h ReadReader.h simul.h
--
--SingleQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h SingleHit.h ReadReader.h simul.h
--
--PairedEndModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h Profile.h NoiseProfile.h ModelParams.h RefSeq.h Refs.h SingleRead.h PairedEndRead.h PairedEndHit.h ReadReader.h simul.h 
--
--PairedEndQModel.h : utils.h my_assert.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h Refs.h SingleReadQ.h PairedEndReadQ.h PairedEndHit.h ReadReader.h simul.h
--
--HitWrapper.h : HitContainer.h
--
--sam_rsem_aux.h : sam/bam.h
--
--sam_rsem_cvt.h : sam/bam.h Transcript.h Transcripts.h
--
--BamWriter.h : sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h SingleHit.h PairedEndHit.h HitWrapper.h Transcript.h Transcripts.h
--
--sampling.h : boost/random.hpp
--
--WriteResults.h : utils.h my_assert.h GroupInfo.h Transcript.h Transcripts.h RefSeq.h Refs.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h
--
- rsem-run-em : EM.o sam/libbam.a
- 	$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
- 
--EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h EM.cpp
-+EM.o : EM.cpp
- 	$(CC) $(COFLAGS) EM.cpp
- 
--bc_aux.h : sam/bam.h
--
--BamConverter.h : utils.h my_assert.h sam/sam.h sam/bam.h sam_rsem_aux.h sam_rsem_cvt.h bc_aux.h Transcript.h Transcripts.h
--
--rsem-tbam2gbam : utils.h Transcripts.h Transcript.h bc_aux.h BamConverter.h sam/sam.h sam/bam.h sam/libbam.a sam_rsem_aux.h sam_rsem_cvt.h tbam2gbam.cpp sam/libbam.a
-+rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
- 	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
- 
--rsem-bam2wig : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2wig.cpp
-+rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
- 	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
--rsem-bam2readdepth : utils.h my_assert.h wiggle.h wiggle.o sam/libbam.a bam2readdepth.cpp
-+rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
- 	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
--wiggle.o: sam/bam.h sam/sam.h wiggle.cpp wiggle.h
-+wiggle.o: wiggle.cpp
- 	$(CC) $(COFLAGS) wiggle.cpp
- 
- rsem-simulate-reads : simulation.o
- 	$(CC) -o rsem-simulate-reads simulation.o
- 
--simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp
-+simulation.o : simulation.cpp
- 	$(CC) $(COFLAGS) simulation.cpp
- 
- rsem-run-gibbs : Gibbs.o
- 	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
- 
--#some header files are omitted
--Gibbs.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Gibbs.cpp 
-+Gibbs.o : Gibbs.cpp
- 	$(CC) $(COFLAGS) Gibbs.cpp
- 
--Buffer.h : my_assert.h
--
- rsem-calculate-credibility-intervals : calcCI.o
- 	$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
--#some header files are omitted
--calcCI.o : utils.h my_assert.h boost/random.hpp sampling.h Model.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h RefSeq.h RefSeqPolicy.h PolyARules.h Refs.h GroupInfo.h WriteResults.h Buffer.h calcCI.cpp
-+calcCI.o : calcCI.cpp
- 	$(CC) $(COFLAGS) calcCI.cpp
- 
--rsem-get-unique : sam/bam.h sam/sam.h getUnique.cpp sam/libbam.a
-+rsem-get-unique : getUnique.cpp sam/libbam.a
- 	$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
- 
--rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a
-+rsem-sam-validator : samValidator.cpp sam/libbam.a
- 	$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
- 
--rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
-+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
- 	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
- 
- ebseq :
-
-From ec136638a727632e20abfaeb65c22c46d15ca8c4 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:06:41 +0200
-Subject: [PATCH 2/7] include current dir, ./sam and ./boost by default
-
----
- Makefile | 48 ++++++++++++++++++++++++------------------------
- 1 file changed, 24 insertions(+), 24 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 3a55ed8..1dd97ca 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,6 +1,6 @@
- CC = g++
--CFLAGS = -Wall -c -I.
--COFLAGS = -Wall -O3 -ffast-math -c -I.
-+CFLAGS = -Wall -I. -I./sam -I./boost
-+COFLAGS = -O3 -ffast-math -c
- PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
- 
- .PHONY : all ebseq clean
-@@ -11,70 +11,70 @@ sam/libbam.a :
- 	cd sam ; ${MAKE} all
- 
- rsem-extract-reference-transcripts : extractRef.cpp
--	$(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
- 
- rsem-synthesis-reference-transcripts : synthesisRef.cpp
--	$(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
- 
- rsem-preref : preRef.o
--	$(CC) preRef.o -o rsem-preref
-+	$(CC) $(CFLAGS) preRef.o -o rsem-preref
- 
- preRef.o : preRef.cpp
--	$(CC) $(COFLAGS) preRef.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
- 
- rsem-parse-alignments : parseIt.o sam/libbam.a
--	$(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread 
-+	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
- 
- parseIt.o : parseIt.cpp
--	$(CC) -Wall -O2 -c -I. parseIt.cpp
-+	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
- 
- rsem-build-read-index : buildReadIndex.cpp
--	$(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index
-+	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
- rsem-run-em : EM.o sam/libbam.a
--	$(CC) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
-+	$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
- 
- EM.o : EM.cpp
--	$(CC) $(COFLAGS) EM.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
- 
- rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
--	$(CC) -O3 -Wall tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
- 
- rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
--	$(CC) -O3 -Wall bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
- rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
--	$(CC) -O3 -Wall bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
- wiggle.o: wiggle.cpp
--	$(CC) $(COFLAGS) wiggle.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
- 
- rsem-simulate-reads : simulation.o
--	$(CC) -o rsem-simulate-reads simulation.o
-+	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
- 
- simulation.o : simulation.cpp
--	$(CC) $(COFLAGS) simulation.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
- 
- rsem-run-gibbs : Gibbs.o
--	$(CC) -o rsem-run-gibbs Gibbs.o -lpthread
-+	$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
- 
- Gibbs.o : Gibbs.cpp
--	$(CC) $(COFLAGS) Gibbs.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
- 
- rsem-calculate-credibility-intervals : calcCI.o
--	$(CC) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-+	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
- calcCI.o : calcCI.cpp
--	$(CC) $(COFLAGS) calcCI.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
- 
- rsem-get-unique : getUnique.cpp sam/libbam.a
--	$(CC) -O3 -Wall getUnique.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
- 
- rsem-sam-validator : samValidator.cpp sam/libbam.a
--	$(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
- 
- rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
--	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
- 
- ebseq :
- 	cd EBSeq ; ${MAKE} all
-
-From d366614ea50f79fdd93e3c76383ccb6fcdeaa8e0 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:10:49 +0200
-Subject: [PATCH 3/7] separate object rules from rules for executables
-
----
- Makefile | 50 ++++++++++++++++++++++++++------------------------
- 1 file changed, 26 insertions(+), 24 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 1dd97ca..ae4de3b 100644
---- a/Makefile
-+++ b/Makefile
-@@ -10,6 +10,32 @@ all : $(PROGRAMS)
- sam/libbam.a :
- 	cd sam ; ${MAKE} all
- 
-+ebseq :
-+	cd EBSeq ; ${MAKE} all
-+
-+
-+calcCI.o : calcCI.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
-+
-+EM.o : EM.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
-+
-+Gibbs.o : Gibbs.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
-+
-+preRef.o : preRef.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
-+
-+parseIt.o : parseIt.cpp
-+	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
-+
-+simulation.o : simulation.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
-+
-+wiggle.o: wiggle.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
-+
-+
- rsem-extract-reference-transcripts : extractRef.cpp
- 	$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
- 
-@@ -19,24 +45,15 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
- rsem-preref : preRef.o
- 	$(CC) $(CFLAGS) preRef.o -o rsem-preref
- 
--preRef.o : preRef.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
--
- rsem-parse-alignments : parseIt.o sam/libbam.a
- 	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
- 
--parseIt.o : parseIt.cpp
--	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
--
- rsem-build-read-index : buildReadIndex.cpp
- 	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
- rsem-run-em : EM.o sam/libbam.a
- 	$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
- 
--EM.o : EM.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
--
- rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
- 	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
- 
-@@ -46,27 +63,15 @@ rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
- rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
- 	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
- 
--wiggle.o: wiggle.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
--
- rsem-simulate-reads : simulation.o
- 	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
- 
--simulation.o : simulation.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
--
- rsem-run-gibbs : Gibbs.o
- 	$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
- 
--Gibbs.o : Gibbs.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
--
- rsem-calculate-credibility-intervals : calcCI.o
- 	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
--calcCI.o : calcCI.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
--
- rsem-get-unique : getUnique.cpp sam/libbam.a
- 	$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
- 
-@@ -76,9 +81,6 @@ rsem-sam-validator : samValidator.cpp sam/libbam.a
- rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
- 	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
- 
--ebseq :
--	cd EBSeq ; ${MAKE} all
--
- clean :
- 	rm -f *.o *~ $(PROGRAMS)
- 	cd sam ; ${MAKE} clean
-
-From 6ba1c33cccdf7c8e7df7a3189e7db204be3b1e8d Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:28:30 +0200
-Subject: [PATCH 4/7] add ./sam to library directories, link with -lbam
-
----
- Makefile | 36 ++++++++++++++++++------------------
- 1 file changed, 18 insertions(+), 18 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index ae4de3b..a87cc4d 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,11 +1,11 @@
- CC = g++
--CFLAGS = -Wall -I. -I./sam -I./boost
-+CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
- COFLAGS = -O3 -ffast-math -c
- PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
- 
- .PHONY : all ebseq clean
- 
--all : $(PROGRAMS)
-+all : sam/libbam.a $(PROGRAMS)
- 
- sam/libbam.a :
- 	cd sam ; ${MAKE} all
-@@ -45,23 +45,23 @@ rsem-synthesis-reference-transcripts : synthesisRef.cpp
- rsem-preref : preRef.o
- 	$(CC) $(CFLAGS) preRef.o -o rsem-preref
- 
--rsem-parse-alignments : parseIt.o sam/libbam.a
--	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread
-+rsem-parse-alignments : parseIt.o
-+	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
- 
- rsem-build-read-index : buildReadIndex.cpp
- 	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
- 
--rsem-run-em : EM.o sam/libbam.a
--	$(CC) $(CFLAGS) -o rsem-run-em EM.o sam/libbam.a -lz -lpthread
-+rsem-run-em : EM.o
-+	$(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
- 
--rsem-tbam2gbam : tbam2gbam.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-tbam2gbam : tbam2gbam.cpp
-+	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
- 
--rsem-bam2wig : wiggle.o sam/libbam.a bam2wig.cpp
--	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2wig : wiggle.o bam2wig.cpp
-+	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
- 
--rsem-bam2readdepth : wiggle.o sam/libbam.a bam2readdepth.cpp
--	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o sam/libbam.a -lz -lpthread -o $@
-+rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
-+	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
- 
- rsem-simulate-reads : simulation.o
- 	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
-@@ -72,14 +72,14 @@ rsem-run-gibbs : Gibbs.o
- rsem-calculate-credibility-intervals : calcCI.o
- 	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
- 
--rsem-get-unique : getUnique.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 getUnique.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-get-unique : getUnique.cpp
-+	$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
- 
--rsem-sam-validator : samValidator.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 samValidator.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-sam-validator : samValidator.cpp
-+	$(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
- 
--rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp sam/libbam.a
--	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
-+rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
-+	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
- 
- clean :
- 	rm -f *.o *~ $(PROGRAMS)
-
-From 5402b88c269df79ee245c1c59e15f3c8282a0220 Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:33:02 +0200
-Subject: [PATCH 5/7] do not repeat target name, use $@ instead
-
----
- Makefile | 18 +++++++++---------
- 1 file changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index a87cc4d..7ec90a3 100644
---- a/Makefile
-+++ b/Makefile
-@@ -37,22 +37,22 @@ wiggle.o: wiggle.cpp
- 
- 
- rsem-extract-reference-transcripts : extractRef.cpp
--	$(CC) $(CFLAGS) -O3 extractRef.cpp -o rsem-extract-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
- 
- rsem-synthesis-reference-transcripts : synthesisRef.cpp
--	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts
-+	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
- 
- rsem-preref : preRef.o
--	$(CC) $(CFLAGS) preRef.o -o rsem-preref
-+	$(CC) $(CFLAGS) preRef.o -o $@
- 
- rsem-parse-alignments : parseIt.o
--	$(CC) $(CFLAGS) -o rsem-parse-alignments parseIt.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
- 
- rsem-build-read-index : buildReadIndex.cpp
--	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o rsem-build-read-index
-+	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
- 
- rsem-run-em : EM.o
--	$(CC) $(CFLAGS) -o rsem-run-em EM.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
- 
- rsem-tbam2gbam : tbam2gbam.cpp
- 	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
-@@ -64,13 +64,13 @@ rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
- 	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
- 
- rsem-simulate-reads : simulation.o
--	$(CC) $(CFLAGS) -o rsem-simulate-reads simulation.o
-+	$(CC) $(CFLAGS) -o $@ simulation.o
- 
- rsem-run-gibbs : Gibbs.o
--	$(CC) $(CFLAGS) -o rsem-run-gibbs Gibbs.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
- 
- rsem-calculate-credibility-intervals : calcCI.o
--	$(CC) $(CFLAGS) -o rsem-calculate-credibility-intervals calcCI.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
- 
- rsem-get-unique : getUnique.cpp
- 	$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
-
-From f60784bc7aa303cc825bd87dd3f5d7d26c51bded Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:44:53 +0200
-Subject: [PATCH 6/7] use automatic variables to refer to prerequisites
-
----
- Makefile | 44 ++++++++++++++++++++++----------------------
- 1 file changed, 22 insertions(+), 22 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 7ec90a3..6540d81 100644
---- a/Makefile
-+++ b/Makefile
-@@ -15,71 +15,71 @@ ebseq :
- 
- 
- calcCI.o : calcCI.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) calcCI.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- EM.o : EM.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) EM.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- Gibbs.o : Gibbs.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) Gibbs.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- preRef.o : preRef.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) preRef.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- parseIt.o : parseIt.cpp
--	$(CC) $(CFLAGS) -O2 -c parseIt.cpp
-+	$(CC) $(CFLAGS) -O2 -c $<
- 
- simulation.o : simulation.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) simulation.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- wiggle.o: wiggle.cpp
--	$(CC) $(CFLAGS) $(COFLAGS) wiggle.cpp
-+	$(CC) $(CFLAGS) $(COFLAGS) $<
- 
- 
- rsem-extract-reference-transcripts : extractRef.cpp
--	$(CC) $(CFLAGS) -O3 extractRef.cpp -o $@
-+	$(CC) $(CFLAGS) -O3 $< -o $@
- 
- rsem-synthesis-reference-transcripts : synthesisRef.cpp
--	$(CC) $(CFLAGS) -O3 synthesisRef.cpp -o $@
-+	$(CC) $(CFLAGS) -O3 $< -o $@
- 
- rsem-preref : preRef.o
--	$(CC) $(CFLAGS) preRef.o -o $@
-+	$(CC) $(CFLAGS) $< -o $@
- 
- rsem-parse-alignments : parseIt.o
--	$(CC) $(CFLAGS) -o $@ parseIt.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
- 
- rsem-build-read-index : buildReadIndex.cpp
--	$(CC) $(CFLAGS) -O3 buildReadIndex.cpp -o $@
-+	$(CC) $(CFLAGS) -O3 $< -o $@
- 
- rsem-run-em : EM.o
--	$(CC) $(CFLAGS) -o $@ EM.o -lbam -lz -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lbam -lz -lpthread
- 
- rsem-tbam2gbam : tbam2gbam.cpp
--	$(CC) $(CFLAGS) -O3 tbam2gbam.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- rsem-bam2wig : wiggle.o bam2wig.cpp
--	$(CC) $(CFLAGS) -O3 bam2wig.cpp wiggle.o -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
- 
- rsem-bam2readdepth : wiggle.o bam2readdepth.cpp
--	$(CC) $(CFLAGS) -O3 bam2readdepth.cpp wiggle.o -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $^ -lbam -lz -lpthread -o $@
- 
- rsem-simulate-reads : simulation.o
--	$(CC) $(CFLAGS) -o $@ simulation.o
-+	$(CC) $(CFLAGS) -o $@ $<
- 
- rsem-run-gibbs : Gibbs.o
--	$(CC) $(CFLAGS) -o $@ Gibbs.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lpthread
- 
- rsem-calculate-credibility-intervals : calcCI.o
--	$(CC) $(CFLAGS) -o $@ calcCI.o -lpthread
-+	$(CC) $(CFLAGS) -o $@ $< -lpthread
- 
- rsem-get-unique : getUnique.cpp
--	$(CC) $(CFLAGS) -O3 getUnique.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- rsem-sam-validator : samValidator.cpp
--	$(CC) $(CFLAGS) -O3 samValidator.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- rsem-scan-for-paired-end-reads : scanForPairedEndReads.cpp
--	$(CC) $(CFLAGS) -O3 scanForPairedEndReads.cpp -lbam -lz -lpthread -o $@
-+	$(CC) $(CFLAGS) -O3 $< -lbam -lz -lpthread -o $@
- 
- clean :
- 	rm -f *.o *~ $(PROGRAMS)
-
-From 0cf9721077f67fb4ca15fdc59cbfbf24a944debd Mon Sep 17 00:00:00 2001
-From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
-Date: Wed, 22 Apr 2015 15:49:19 +0200
-Subject: [PATCH 7/7] split long line
-
----
- Makefile | 17 ++++++++++++++++-
- 1 file changed, 16 insertions(+), 1 deletion(-)
-
-diff --git a/Makefile b/Makefile
-index 6540d81..0ab04a5 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,7 +1,22 @@
- CC = g++
- CFLAGS = -Wall -I. -I./sam -I./boost -L./sam
- COFLAGS = -O3 -ffast-math -c
--PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
-+PROGRAMS = \
-+  rsem-extract-reference-transcripts \
-+  rsem-synthesis-reference-transcripts \
-+  rsem-preref \
-+  rsem-parse-alignments \
-+  rsem-build-read-index \
-+  rsem-run-em \
-+  rsem-tbam2gbam \
-+  rsem-run-gibbs \
-+  rsem-calculate-credibility-intervals \
-+  rsem-simulate-reads \
-+  rsem-bam2wig \
-+  rsem-get-unique \
-+  rsem-bam2readdepth \
-+  rsem-sam-validator \
-+  rsem-scan-for-paired-end-reads
- 
- .PHONY : all ebseq clean
- 

From f5c10a94eff314ed985089719e817cd036a746f1 Mon Sep 17 00:00:00 2001
From: fis trivial <ybbs.daans@hotmail.com>
Date: Thu, 20 Sep 2018 13:37:26 +0000
Subject: [PATCH 006/909] gnu: gprolog: Update to 1.4.5.

* gnu/packages/gprolog.scm (gprolog): Update to 1.4.5.
[source]: Add an alternate source URL.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/gprolog.scm | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/gprolog.scm b/gnu/packages/gprolog.scm
index b27b080ca7..166bf33294 100644
--- a/gnu/packages/gprolog.scm
+++ b/gnu/packages/gprolog.scm
@@ -27,15 +27,18 @@
 (define-public gprolog
   (package
     (name "gprolog")
-    (version "1.4.4")
+    (version "1.4.5")
     (source
-     (origin
-      (method url-fetch)
-      (uri (string-append "mirror://gnu/gprolog/gprolog-" version
-                          ".tar.gz"))
-      (sha256
-       (base32
-        "13miyas47bmijmadm68cbvb21n4s156gjafz7kfx9brk9djfkh0q"))))
+      (origin
+        (method url-fetch)
+        ;; Recent versions are not hosted on the GNU mirrors.
+        (uri (list (string-append "http://gprolog.org/gprolog-" version
+                                  ".tar.gz")
+                   (string-append "mirror://gnu/gprolog/gprolog-" version
+                                  ".tar.gz")))
+        (sha256
+         (base32
+          "0z4cc42n3k6i35b8mr816iwsvrpxshw6d7dgz6s2h1hy0l7g1p5z"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

From ea2364621a57f4797a512caa53cbf0d4475c1c90 Mon Sep 17 00:00:00 2001
From: fis trivial <ybbs.daans@hotmail.com>
Date: Thu, 20 Sep 2018 13:29:15 +0000
Subject: [PATCH 007/909] gnu: qbittorrent: Update to 4.1.3.

* gnu/packages/bittorrent.scm (qbittorrent): Update to 4.1.3.
[inputs]: Use python-wrapper instead of python.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/bittorrent.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index 3937fac745..59fbd6906b 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -409,7 +409,7 @@ desktops.")
 (define-public qbittorrent
   (package
     (name "qbittorrent")
-    (version "4.0.4")
+    (version "4.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -418,7 +418,7 @@ desktops.")
               (file-name (string-append name "-release-" version ".tar.gz"))
               (sha256
                (base32
-                "145r4lv7rqdhrm5znn3ndxsfdf579n46zvj7c53c422am8ir5xhp"))))
+                "00zrpnwanq9f7maky2z4wnzw08xy902s77scm2gcvxxxankr4j92"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -434,7 +434,7 @@ desktops.")
      `(("boost" ,boost)
        ("libtorrent-rasterbar" ,libtorrent-rasterbar)
        ("openssl" ,openssl)
-       ("python" ,python)
+       ("python" ,python-wrapper)
        ("qtbase" ,qtbase)
        ("qtsvg" ,qtsvg)
        ("zlib" ,zlib)))

From c6ede267e64ea6b5e3546274fafd2afc84f8b140 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 20 Sep 2018 17:58:31 -0400
Subject: [PATCH 008/909] gnu: linux-libre@4.4: Update to 4.4.157.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.157.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index e34c67cb0f..1657ebc71a 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -452,8 +452,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.156"
-                    "13j4jb4hifh3fah2ysy2425fakwqqdh2z23lf4i0frxa1xl974h2"
+  (make-linux-libre "4.4.157"
+                    "00bnfqwkr0jfdabmwx5qk5bqxn5vwnnzwqbm5rfg7lggii74kk54"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 41d6afb266a7bf2f0df95915a0fefc714e191199 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 20 Sep 2018 17:59:10 -0400
Subject: [PATCH 009/909] gnu: linux-libre@4.9: Update to 4.9.128.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.128.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 1657ebc71a..7034291d02 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.127"
-                    "0q7h5gnl3ikic0pvwrxp78pz56yvijhz6s84gb92xywi1v3dd8mh"
+  (make-linux-libre "4.9.128"
+                    "0lww23xcyyg0dwzrap5x9d700gy3lbxln55n6sqqkm7m89dkqwha"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From c57a2a12b17fb3595a1a2c85da7c796e2ee9815c Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 20 Sep 2018 18:00:47 -0400
Subject: [PATCH 010/909] gnu: linux-libre@4.14: Update to 4.14.71.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.71.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 7034291d02..22cc7dff9b 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.70")
-(define %linux-libre-4.14-hash "138v51m6k57wnvlf9c22dad0w819mfb8f95i6w99mlg69qpwdvag")
+(define %linux-libre-4.14-version "4.14.71")
+(define %linux-libre-4.14-hash "1akvykaccy7ikl8v04grwxvgs4z2rrs7drf2s85ysqwq79mdh3gq")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From 83e8b1d7946d07d1c26dd7bd6e11e6e9396024ac Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 20 Sep 2018 18:01:38 -0400
Subject: [PATCH 011/909] gnu: linux-libre: Update to 4.18.9.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.9.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 22cc7dff9b..170c77374d 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.8")
-(define %linux-libre-hash "163awpba1yd0x33xzj5dczimk4y96xc28syc4w2ad0qafgapng8l")
+(define %linux-libre-version "4.18.9")
+(define %linux-libre-hash "0wwmhnfvcsdlqhzwwwyz1x5a3ldjky6l0xir1pi6pysr0lak402x")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch

From 1bfaae25fab372c8ff86e34024adf20240699b55 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Thu, 20 Sep 2018 22:12:10 +0200
Subject: [PATCH 012/909] gnu: rust@1.20.0: Fix tests.

* gnu/packages/rust.scm (rust-1.23)[arguments]<#:phases>
[patch-cargo-tests, ignore-glibc-2.27-incompatible-test,fix-mtime-bug]: Move
to...
(rust-1.20): ... here.
---
 gnu/packages/rust.scm | 57 ++++++++++++++++++++++---------------------
 1 file changed, 29 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm
index 74de6f3ae1..ec8b30d78f 100644
--- a/gnu/packages/rust.scm
+++ b/gnu/packages/rust.scm
@@ -514,6 +514,35 @@ safety and thread safety guarantees.")
        (substitute-keyword-arguments (package-arguments rust-1.19)
          ((#:phases phases)
           `(modify-phases ,phases
+             (add-after 'patch-tests 'patch-cargo-tests
+               (lambda _
+                 (substitute* "src/tools/cargo/tests/build.rs"
+                  (("/usr/bin/env") (which "env"))
+                  ;; Guix llvm is compiled without asmjs-unknown-emscripten.
+                  (("fn wasm32_final_outputs") "#[ignore]\nfn wasm32_final_outputs"))
+                 (substitute* "src/tools/cargo/tests/death.rs"
+                  ;; This is stuck when built in container.
+                  (("fn ctrl_c_kills_everyone") "#[ignore]\nfn ctrl_c_kills_everyone"))
+                 ;; Prints test output in the wrong order when built on
+                 ;; i686-linux.
+                 (substitute* "src/tools/cargo/tests/test.rs"
+                   (("fn cargo_test_env") "#[ignore]\nfn cargo_test_env"))
+                 #t))
+             (add-after 'patch-cargo-tests 'ignore-glibc-2.27-incompatible-test
+               ;; https://github.com/rust-lang/rust/issues/47863
+               (lambda _
+                 (substitute* "src/test/run-pass/out-of-stack.rs"
+                   (("// ignore-android") "// ignore-test\n// ignore-android"))
+                 #t))
+             (add-after 'ignore-glibc-2.27-incompatible-test 'fix-mtime-bug
+               (lambda* _
+                 (substitute* "src/build_helper/lib.rs"
+                   ;; Bug in Rust code.
+                   ;; Current implementation assume that if dst not exist then it's mtime
+                   ;; is 0, but in same time "src" have 0 mtime in guix build!
+                   (("let threshold = mtime\\(dst\\);")
+                    "if !dst.exists() {\nreturn false\n}\n let threshold = mtime(dst);"))
+                 #t))
              (replace 'configure
                (lambda* (#:key inputs outputs #:allow-other-keys)
                  (let* ((out (assoc-ref outputs "out"))
@@ -651,34 +680,6 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
                ;; XXX: Revisit this when we use gcc 6.
                (substitute* "src/binaryen/CMakeLists.txt"
                  (("ADD_COMPILE_FLAG\\(\\\"-march=native\\\"\\)") ""))
-               #t))
-           (add-after 'patch-tests 'patch-cargo-tests
-             (lambda _
-               (substitute* "src/tools/cargo/tests/build.rs"
-                (("/usr/bin/env") (which "env"))
-                ;; Guix llvm is compiled without asmjs-unknown-emscripten.
-                (("fn wasm32_final_outputs") "#[ignore]\nfn wasm32_final_outputs"))
-               (substitute* "src/tools/cargo/tests/death.rs"
-                ;; This is stuck when built in container.
-                (("fn ctrl_c_kills_everyone") "#[ignore]\nfn ctrl_c_kills_everyone"))
-               ;; Prints test output in the wrong order when built on
-               ;; i686-linux.
-               (substitute* "src/tools/cargo/tests/test.rs"
-                 (("fn cargo_test_env") "#[ignore]\nfn cargo_test_env"))
-               #t))
-           (add-after 'patch-cargo-tests 'ignore-glibc-2.27-incompatible-test
-             ;; https://github.com/rust-lang/rust/issues/47863
-             (lambda _
-               (substitute* "src/test/run-pass/out-of-stack.rs"
-                 (("// ignore-android") "// ignore-test\n// ignore-android"))))
-           (add-after 'ignore-glibc-2.27-incompatible-test 'fix-mtime-bug
-             (lambda* _
-               (substitute* "src/build_helper/lib.rs"
-                 ;; Bug in Rust code.
-                 ;; Current implementation assume that if dst not exist then it's mtime
-                 ;; is 0, but in same time "src" have 0 mtime in guix build!
-                 (("let threshold = mtime\\(dst\\);")
-                  "if !dst.exists() {\nreturn false\n}\n let threshold = mtime(dst);"))
                #t))))))))
 
 (define-public rust-1.24

From e0b07ccc1ab0b763f0e9da39f56f2a7aec6116d5 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Thu, 20 Sep 2018 22:16:45 +0200
Subject: [PATCH 013/909] gnu: rust: Work around mtime bug in rust build
 helpers.

* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[fix-mtime-bug]:
Delete.
[reset-timestamps-after-changes]: Modify.
(rust-1.24): Don't delete "fix-mtime-bug" since now it doesn't ever
get created.
---
 gnu/packages/rust.scm | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm
index ec8b30d78f..e8eca80aa6 100644
--- a/gnu/packages/rust.scm
+++ b/gnu/packages/rust.scm
@@ -534,15 +534,6 @@ safety and thread safety guarantees.")
                  (substitute* "src/test/run-pass/out-of-stack.rs"
                    (("// ignore-android") "// ignore-test\n// ignore-android"))
                  #t))
-             (add-after 'ignore-glibc-2.27-incompatible-test 'fix-mtime-bug
-               (lambda* _
-                 (substitute* "src/build_helper/lib.rs"
-                   ;; Bug in Rust code.
-                   ;; Current implementation assume that if dst not exist then it's mtime
-                   ;; is 0, but in same time "src" have 0 mtime in guix build!
-                   (("let threshold = mtime\\(dst\\);")
-                    "if !dst.exists() {\nreturn false\n}\n let threshold = mtime(dst);"))
-                 #t))
              (replace 'configure
                (lambda* (#:key inputs outputs #:allow-other-keys)
                  (let* ((out (assoc-ref outputs "out"))
@@ -608,10 +599,11 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
              (delete 'patch-cargo-tomls)
              (add-before 'build 'reset-timestamps-after-changes
                (lambda* _
-                 (define ref (stat "README.md"))
                  (for-each
                   (lambda (filename)
-                    (set-file-time filename ref))
+                    ;; Rust 1.20.0 treats timestamp 0 as "file doesn't exist".
+                    ;; Therefore, use timestamp 1.
+                    (utime filename 1 1 1 1))
                   (find-files "." #:directories? #t))
                  #t))
              (replace 'build
@@ -699,8 +691,7 @@ jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
                    ;; This test is known to fail on aarch64 and powerpc64le:
                    ;; https://github.com/rust-lang/rust/issues/45410
                    (("fn test_loading_cosine") "#[ignore]\nfn test_loading_cosine"))
-                 #t))
-             (delete 'fix-mtime-bug))))))))
+                 #t)))))))))
 
 (define-public rust-1.25
   (let ((base-rust

From eeecbe09cc497b1ed9a2000283a5767903ba2fb4 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 08:07:25 +0200
Subject: [PATCH 014/909] gnu: perl-dbd-mysql: Update to 4.048.

* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.048.
---
 gnu/packages/databases.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 9db892a0b7..9e8c9d8f9e 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -1458,15 +1458,15 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-mysql
   (package
     (name "perl-dbd-mysql")
-    (version "4.047")
+    (version "4.048")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/C/CA/CAPTTOFU/"
+       (uri (string-append "mirror://cpan/authors/id/M/MI/MICHIELB/"
                            "DBD-mysql-" version ".tar.gz"))
        (sha256
         (base32
-         "0idizgr0hr7sj92fbdlb3gv6cva15jkpaq28wrdw4j4p7awx2mls"))))
+         "1zqmch6c9gq06z90mkmk1skajk2kaggriw19ym5w04l7wv5gydqp"))))
     (build-system perl-build-system)
     (arguments
      `(#:phases

From 4aa64e3a819ca53629b1cbe58c079eefa7dd24b0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 08:09:35 +0200
Subject: [PATCH 015/909] gnu: ubuntu-keyring: Update to 2018.09.18.1.

* gnu/packages/debian.scm (ubuntu-keyring): Update to 2018.09.18.1.
---
 gnu/packages/debian.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
index 1974672fb6..185dacfe73 100644
--- a/gnu/packages/debian.scm
+++ b/gnu/packages/debian.scm
@@ -71,7 +71,7 @@ contains the archive keys used for that.")
 (define-public ubuntu-keyring
   (package
     (name "ubuntu-keyring")
-    (version "2018.02.28")
+    (version "2018.09.18.1")
     (source
       (origin
         (method url-fetch)
@@ -79,7 +79,7 @@ contains the archive keys used for that.")
                             "+files/" name "_" version ".tar.gz"))
         (sha256
          (base32
-          "1zj3012cz7rlx9pm39wnwa0lmi1h38n6bkgbz81vnmcsvqsc9a3a"))))
+          "0csx2n62rj9rxjv4y8qhby7l9rbybfwrb0406pc2cjr7f2yk91af"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))

From 1779aaa09a576401e35bf4a0d1534ee546b5506e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 08:19:42 +0200
Subject: [PATCH 016/909] Add 'GNU Guix' comment to all (gnu packages) headers.

* gnu/packages/debian.scm, gnu/packages/syndication.scm: Add comments.
---
 gnu/packages/debian.scm      | 3 +++
 gnu/packages/syndication.scm | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/gnu/packages/debian.scm b/gnu/packages/debian.scm
index 185dacfe73..5ea263149e 100644
--- a/gnu/packages/debian.scm
+++ b/gnu/packages/debian.scm
@@ -1,6 +1,9 @@
+;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
+;;; This file is part of GNU Guix.
+;;;
 ;;; GNU Guix is free software; you can redistribute it and/or modify it
 ;;; under the terms of the GNU General Public License as published by
 ;;; the Free Software Foundation; either version 3 of the License, or (at
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index f37c0eaac5..6247d1f3b6 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -1,6 +1,9 @@
+;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
+;;; This file is part of GNU Guix.
+;;;
 ;;; GNU Guix is free software; you can redistribute it and/or modify it
 ;;; under the terms of the GNU General Public License as published by
 ;;; the Free Software Foundation; either version 3 of the License, or (at

From 29ddbc5607c8ad7bb0622e10716e60396817a42d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 08:46:11 +0200
Subject: [PATCH 017/909] gnu: python-pydot: Update to 1.2.4.

* gnu/packages/graphviz.scm (python-pydot): Update to 1.2.4.
[arguments]: Run the test suite.
[native-inputs]: Add python-chardet.
---
 gnu/packages/graphviz.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 09f46fab84..569923d4e0 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -220,17 +220,18 @@ be used either as a standalone application, or as a python library.")
 (define-public python-pydot
   (package
     (name "python-pydot")
-    (version "1.2.3")
+    (version "1.2.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pydot" version))
        (sha256
         (base32
-         "00imlz0033dygb9gdag1xr0cybn33gk5jsdi9ffbszzr97rd7dgd"))))
+         "1dhy4jpp646jslh2yks6klwwbaxcs905byyny880gl1iap8y5llj"))))
     (build-system python-build-system)
-    ;; FIXME: No tests in PyPi release tarball.
-    (arguments '(#:tests? #f))
+    (native-inputs
+     ;; For tests.
+     `(("python-chardet" ,python-chardet)))
     (propagated-inputs
      `(("python-pyparsing" ,python-pyparsing)))
     (home-page "https://github.com/erocarrera/pydot")

From 3752b683dc16e172f57f8397a542e562f564fc30 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 09:13:45 +0200
Subject: [PATCH 018/909] gnu: openscenegraph: Update to 3.6.3.

* gnu/packages/graphics.scm (openscenegraph): Update to 3.6.3.
[source]: Use GIT-FILE-NAME.
[inputs]: Remove unused pth and qtbase.
---
 gnu/packages/graphics.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index 9c2869c12b..58c742b825 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -406,7 +406,7 @@ visual effects work for film.")
 (define-public openscenegraph
   (package
     (name "openscenegraph")
-    (version "3.6.2")
+    (version "3.6.3")
     (source
      (origin
        (method git-fetch)
@@ -415,8 +415,8 @@ visual effects work for film.")
              (commit (string-append "OpenSceneGraph-" version))))
        (sha256
         (base32
-         "03jk6lclyd4biniaw04w7j0z1spkm69f1c19i37b8v9x3zv1p1id"))
-       (file-name (string-append name "-" version "-checkout"))))
+         "0h32z15sa8sbq276j0iib0n707m8bs4p5ji9z2ah411446paad9q"))
+       (file-name (git-file-name name version))))
     (properties
      `((upstream-name . "OpenSceneGraph")))
     (build-system cmake-build-system)
@@ -437,8 +437,6 @@ visual effects work for film.")
        ("jasper" ,jasper)
        ("librsvg" ,librsvg)
        ("libxrandr" ,libxrandr)
-       ("pth" ,pth)
-       ("qtbase" ,qtbase)
        ("ffmpeg" ,ffmpeg)
        ("mesa" ,mesa)))
     (synopsis "High performance real-time graphics toolkit")

From 1df40d3dbff82c2990271b406b32633fe216d143 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Fri, 21 Sep 2018 11:52:12 +0200
Subject: [PATCH 019/909] gnu: emacs-orgalist: Update to 1.9.

* gnu/packages/emacs.scm (emacs-orgalist): Update to 1.9.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 9b3a90bd33..fc019cf241 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5252,7 +5252,7 @@ distribution, primarily targeting Clojure users")
 (define-public emacs-orgalist
   (package
     (name "emacs-orgalist")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
@@ -5260,7 +5260,7 @@ distribution, primarily targeting Clojure users")
                            "orgalist-" version ".el"))
        (sha256
         (base32
-         "1wqwnmn08i0qkxm8b2iclvf6cydcn68h1p3h7r1kig2bdn5b8948"))))
+         "1rmmcyiiqkq54hn74nhzxzl4nvd902hv6gq341jwhrm7yiagffi6"))))
     (build-system emacs-build-system)
     (home-page "http://elpa.gnu.org/packages/orgalist.html")
     (synopsis "Manage Org-like lists in non-Org buffers")

From 174988fa05fbda4a9cdaab77d59fe4ea187b0e6b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 12:18:55 +0200
Subject: [PATCH 020/909] gnu: perl-xml-compile: Update to 1.60.

* gnu/packages/xml.scm (perl-xml-compile): Update to 1.60.
[propagated-inputs]: Add perl-carp, perl-scalar-list-utils, and
perl-types-serialiser.
---
 gnu/packages/xml.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 9c8e3cef08..aa1395286f 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -665,20 +665,23 @@ This module provide functions which simplify writing tests for
 (define-public perl-xml-compile
   (package
     (name "perl-xml-compile")
-    (version "1.54")
+    (version "1.60")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/M/MA/MARKOV/"
                                   "XML-Compile-" version ".tar.gz"))
               (sha256
                (base32
-                "1hp41960bpqxvv1samv9hc0ghhmvs3i16r4rfl9yp54lp6jhsr2c"))))
+                "04vv7wy5v1l38xsfdbacvyd90qircvnrs2f3ysljm1nhq8mycmwm"))))
     (build-system perl-build-system)
     (propagated-inputs
-     `(("perl-log-report" ,perl-log-report)
+     `(("perl-carp" ,perl-carp)
+       ("perl-log-report" ,perl-log-report)
        ("perl-xml-compile-tester" ,perl-xml-compile-tester)
        ("perl-xml-libxml" ,perl-xml-libxml)
-       ("perl-test-deep" ,perl-test-deep)))
+       ("perl-scalar-list-utils" ,perl-scalar-list-utils)
+       ("perl-test-deep" ,perl-test-deep)
+       ("perl-types-serialiser" ,perl-types-serialiser)))
     (home-page "https://metacpan.org/release/XML-Compile")
     (synopsis "Compilation-based XML processing")
     (description

From 6f05556ba77def387d862ee44d6658d8d647ad3c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 12:21:38 +0200
Subject: [PATCH 021/909] gnu: s6: Update to 2.7.2.1.

* gnu/packages/skarnet.scm (s6): Update to 2.7.2.1.
---
 gnu/packages/skarnet.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/skarnet.scm b/gnu/packages/skarnet.scm
index 9a6733d8bc..6546d40597 100644
--- a/gnu/packages/skarnet.scm
+++ b/gnu/packages/skarnet.scm
@@ -105,7 +105,7 @@ complexity.")))
 (define-public s6
   (package
    (name "s6")
-   (version "2.7.2.0")
+   (version "2.7.2.1")
    (source
     (origin
      (method url-fetch)
@@ -113,7 +113,7 @@ complexity.")))
                          version ".tar.gz"))
      (sha256
       (base32
-       "02canrzmhr66gi16ldyylk378jlmyfl73vn72ayr12h2wyxgqm5g"))))
+       "0vyl4wr2l4mp9ams0dyg224qxhl8ksxsv2shs6606lhhp9g1rb6b"))))
    (build-system gnu-build-system)
    (inputs `(("skalibs" ,skalibs)
              ("execline" ,execline)))

From e36058634d1754ab6d69f01a448efd691c2a1637 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 12:47:38 +0200
Subject: [PATCH 022/909] gnu: python-hdf4: Use INVOKE.

* gnu/packages/python.scm (python-hdf4)[arguments]: Substitute INVOKE
for SYSTEM*.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 6927924a68..b8521fa0e4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -767,8 +767,8 @@ and verifies that it matches the intended target hostname.")
             (setenv "PYTHONPATH"
                     (string-append (getcwd) ":"
                                    (getenv "PYTHONPATH")))
-            (and (zero? (system* "./runexamples.sh"))
-                 (zero? (system* "nosetests" "-v"))))))))
+            (invoke "./runexamples.sh")
+            (invoke "nosetests" "-v"))))))
    (home-page "https://github.com/fhs/python-hdf4")
    (synopsis "Python interface to the NCSA HDF4 library")
    (description

From a1d6610e84f4ff61913e1e861093b38c2beb9614 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 12:58:02 +0200
Subject: [PATCH 023/909] gnu: python-rencode: Update to 1.0.5.

* gnu/packages/python.scm (python-rencode): Update to 1.0.5.
[arguments]: Add a 'delete-bogus-test' phase.
---
 gnu/packages/python.scm | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b8521fa0e4..64ee4e028e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12456,15 +12456,24 @@ library.")
 (define-public python-rencode
   (package
    (name "python-rencode")
-   (version "1.0.3")
+   (version "1.0.5")
    (source
     (origin
      (method url-fetch)
      (uri (pypi-uri "rencode" version))
      (sha256
       (base32
-       "08if5yax1xn5yfp8p3765ccjmfcv9di7i4m5jckgnwvdsgznwkbj"))))
+       "0mzwdq1is7kyyr32i5k4iz6g5xxdvmiyc132jnc60p9m6lnwjrpv"))))
    (build-system python-build-system)
+   (arguments
+    `(#:phases
+      (modify-phases %standard-phases
+        (add-before 'check 'delete-bogus-test
+          ;; This test requires /home/aresch/Downloads, which is not provided by
+          ;; the build environment.
+          (lambda _
+            (delete-file "rencode/t.py")
+            #t)))))
    (native-inputs `(("pkg-config" ,pkg-config)
                     ("python-cython" ,python-cython)))
    (home-page "https://github.com/aresch/rencode")

From 101ad242be256d6a5953187be56d61f89e1317d7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 13:13:45 +0200
Subject: [PATCH 024/909] gnu: python-paramiko: Use HTTPS home page.

* gnu/packages/python-crypto.scm (python-paramiko)[home-page]: Use HTTPS.
---
 gnu/packages/python-crypto.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 63dc1a54df..5dce8ffdda 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -220,7 +220,7 @@ This package provides a Python interface for BLAKE2.")
        ("python-pyasn1" ,python-pyasn1)
        ("python-pynacl" ,python-pynacl)
        ("python-cryptography" ,python-cryptography)))
-    (home-page "http://www.paramiko.org/")
+    (home-page "https://www.paramiko.org/")
     (synopsis "SSHv2 protocol library")
     (description "Paramiko is a python implementation of the SSHv2 protocol,
 providing both client and server functionality.  While it leverages a Python C

From 6569549dfa0c35e0f80869a630cd216d01c84590 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 13:15:55 +0200
Subject: [PATCH 025/909] gnu: python-paramiko: Update to 2.4.2 [security
 fixes].

* gnu/packages/python-crypto.scm (python-paramiko): Update to 2.4.2.
---
 gnu/packages/python-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm
index 5dce8ffdda..bda547417c 100644
--- a/gnu/packages/python-crypto.scm
+++ b/gnu/packages/python-crypto.scm
@@ -203,14 +203,14 @@ This package provides a Python interface for BLAKE2.")
 (define-public python-paramiko
   (package
     (name "python-paramiko")
-    (version "2.4.1")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "paramiko" version))
        (sha256
         (base32
-         "1wx4s95i2cdh8hhi1c3jb8lzk71jifa3z9wjfsx905y7lrsngqrk"))))
+         "1jqgj2gl1pz7bi2aab1r2xq0ml0gskmm9p235cg9y32nydymm5x8"))))
     (build-system python-build-system)
     (arguments
      `(;; FIXME: Tests require many unpackaged libraries, see dev-requirements.txt.

From c5327efb97208df569b4682ef5bfe4ac825d1c4f Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 21 Sep 2018 04:34:10 -0400
Subject: [PATCH 026/909] gnu: libvpx: Add upstream security fix.

* gnu/packages/patches/libvpx-use-after-free-in-postproc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/video.scm (libvpx)[source]: Add patch.
---
 gnu/local.mk                                  |  1 +
 .../libvpx-use-after-free-in-postproc.patch   | 34 +++++++++++++++++++
 gnu/packages/video.scm                        |  3 +-
 3 files changed, 37 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/libvpx-use-after-free-in-postproc.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 4bca986619..9c69fd4f35 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -916,6 +916,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libutils-remove-damaging-includes.patch	\
   %D%/packages/patches/libvdpau-va-gl-unbundle.patch		\
   %D%/packages/patches/libvpx-CVE-2016-2818.patch		\
+  %D%/packages/patches/libvpx-use-after-free-in-postproc.patch	\
   %D%/packages/patches/libxslt-generated-ids.patch		\
   %D%/packages/patches/libxt-guix-search-paths.patch		\
   %D%/packages/patches/lierolibre-check-unaligned-access.patch	\
diff --git a/gnu/packages/patches/libvpx-use-after-free-in-postproc.patch b/gnu/packages/patches/libvpx-use-after-free-in-postproc.patch
new file mode 100644
index 0000000000..04f2a953b7
--- /dev/null
+++ b/gnu/packages/patches/libvpx-use-after-free-in-postproc.patch
@@ -0,0 +1,34 @@
+From 52add5896661d186dec284ed646a4b33b607d2c7 Mon Sep 17 00:00:00 2001
+From: Jerome Jiang <jianj@google.com>
+Date: Wed, 23 May 2018 15:43:00 -0700
+Subject: [PATCH] VP8: Fix use-after-free in postproc.
+
+The pointer in vp8 postproc refers to show_frame_mi which is only
+updated on show frame. However, when there is a no-show frame which also
+changes the size (thus new frame buffers allocated), show_frame_mi is
+not updated with new frame buffer memory.
+
+Change the pointer in postproc to mi which is always updated.
+
+Bug: 842265
+Change-Id: I33874f2112b39f74562cba528432b5f239e6a7bd
+---
+ vp8/common/postproc.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/vp8/common/postproc.c b/vp8/common/postproc.c
+index d67ee8a57..8c292d616 100644
+--- a/vp8/common/postproc.c
++++ b/vp8/common/postproc.c
+@@ -65,7 +65,7 @@ void vp8_deblock(VP8_COMMON *cm, YV12_BUFFER_CONFIG *source,
+   double level = 6.0e-05 * q * q * q - .0067 * q * q + .306 * q + .0065;
+   int ppl = (int)(level + .5);
+ 
+-  const MODE_INFO *mode_info_context = cm->show_frame_mi;
++  const MODE_INFO *mode_info_context = cm->mi;
+   int mbr, mbc;
+ 
+   /* The pixel thresholds are adjusted according to if or not the macroblock
+-- 
+2.19.0
+
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 4882f0476a..448773e0d9 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1242,7 +1242,8 @@ access to mpv's powerful playback capabilities.")
               (sha256
                (base32
                 "0vvh89hvp8qg9an9vcmwb7d9k3nixhxaz6zi65qdjnd0i56kkcz6"))
-              (patches (search-patches "libvpx-CVE-2016-2818.patch"))))
+              (patches (search-patches "libvpx-use-after-free-in-postproc.patch"
+                                       "libvpx-CVE-2016-2818.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list "--enable-shared"

From e67ad5532f76b53e955149da2f1e237696ff0893 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 21 Sep 2018 03:28:03 -0400
Subject: [PATCH 027/909] gnu: icecat: Update to 60.2.0-gnu1 (pre-release).

* gnu/packages/gnuzilla.scm (icecat): Update to 60.2.0-gnu1.
[source]: Download pre-release from alpha.gnu.org.  Remove obsolete patches.
Comment out the code to delete the bundled copies of libevent, cairo,
harfbuzz, and graphite2.
[inputs]: Use the latest ffmpeg.  Comment out libevent, cairo, harfbuzz, and
graphite2.
[native-inputs]: Add rust and cargo.
[arguments]: Remove --enable-gio and --disable-gnomeui.  Add --disable-stylo.
Comment out --with-system-{libevent,harfbuzz,graphite2}, --enable-system-cairo.
Import %cargo-build-system-modules.  Add 'patch-cargo-checksums' phase.
* gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch,
gnu/packages/patches/icecat-bug-1413868-pt1.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
---
 gnu/local.mk                                  |   2 -
 gnu/packages/gnuzilla.scm                     | 160 ++---
 ...ecat-CVE-2018-5157-and-CVE-2018-5158.patch | 441 ------------
 .../patches/icecat-bug-1413868-pt1.patch      | 663 ------------------
 4 files changed, 49 insertions(+), 1217 deletions(-)
 delete mode 100644 gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch
 delete mode 100644 gnu/packages/patches/icecat-bug-1413868-pt1.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 9c69fd4f35..4097ad5fcd 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -811,8 +811,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
-  %D%/packages/patches/icecat-bug-1413868-pt1.patch		\
-  %D%/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch	\
   %D%/packages/patches/icecat-use-system-graphite2.patch	\
   %D%/packages/patches/icecat-use-system-harfbuzz.patch		\
   %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 77a74a0ec4..db8f85cfb1 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -35,6 +35,7 @@
   #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cargo)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages databases)
@@ -58,6 +59,7 @@
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages assembly)
+  #:use-module (gnu packages rust)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages video)
   #:use-module (gnu packages xdisorg)
@@ -478,112 +480,25 @@ security standards.")
 (define-public icecat
   (package
     (name "icecat")
-    (version "52.6.0-gnu1")
+    (version "60.2.0-gnu1")
     (source
      (origin
       (method url-fetch)
+      ;; Temporary URL pending official release:
+      (uri "https://alpha.gnu.org/gnu/gnuzilla/60.2.0/icecat-60.2.0-gnu1.tar.bz2")
+      #;
       (uri (string-append "mirror://gnu/gnuzilla/"
                           (first (string-split version #\-))
                           "/" name "-" version ".tar.bz2"))
       (sha256
        (base32
-        "09fn54glqg1aa93hnz5zdcy07cps09dbni2b4200azh6nang630a"))
+        "0lqx7g79x15941rhjr3qsfwsny6vzc7d7abdmvjy6jjbqkqlc1zl"))
       (patches
        (list
         (search-patch "icecat-avoid-bundled-libraries.patch")
-        (search-patch "icecat-use-system-harfbuzz.patch")
-        (search-patch "icecat-use-system-graphite2.patch")
-        (mozilla-patch "icecat-bug-546387.patch"         "d13e3fefb76e" "1b760r0bg2ydbl585wlmajljh1nlisrwxvjws5b28a3sgjy01i6k")
-        (mozilla-patch "icecat-bug-1350152.patch"        "f822bda79c28" "1wf56169ca874shr6r7qx40s17h2gwj7ngmpyylrpmd1c6hipvsj")
-        (mozilla-patch "icecat-bug-1411708.patch"        "34c968767eb7" "0l2jy201ikj3m3h66mvlsj4y0ki7cpm7x7nnfygbwnfxg42s1sip")
-        (mozilla-patch "icecat-bug-1375217.patch"        "00fc630c9a46" "17pcprp452nslk6sac6sili0p74zh8w3g0v1wsdn0ikm9xmnphhv")
-        (mozilla-patch "icecat-CVE-2018-5145.patch"      "f0ec180993d2" "0jiazxcwki83wr00fyh2g518ynsd33p7nk65zk4d1682gn22lc8v")
-        (mozilla-patch "icecat-CVE-2018-5130.patch"      "a6a9e26688c1" "0cvizvilb4k422j2gzqcbakznvsffmk6n6xn1ayj5rgxfaizkkqk")
-        (mozilla-patch "icecat-CVE-2018-5125-pt1.patch"  "198ad052621e" "1721zx8hifdlflrhvw6hmkdgjbvsmxl9n84iji5qywhlp2krdk9r")
-        (mozilla-patch "icecat-bug-1426087.patch"        "391ea77ebfdb" "1fhkvd0z6mvdkj7m0d3jlj42rsdw5r4x122c1wb1i428228ifw6n")
-        (mozilla-patch "icecat-bug-1416307.patch"        "54f2f7f93b30" "1ncjir16mqya37wgf6fy2rqki3vl433c4grjr3fypmlig6xfgg1l")
-        (mozilla-patch "icecat-CVE-2018-5127.patch"      "2c4d7a59041b" "178c6gid89cvw52yqs43i6x6s5w0hslj0rfa2r8b4762ij3civ92")
-        (mozilla-patch "icecat-CVE-2018-5125-pt2.patch"  "f87ef3774d5e" "0payf3az2w93nzl5qknqx290jbxk8v39rwhdgq7wyd5f245dywxk")
-        (mozilla-patch "icecat-CVE-2018-5125-pt3.patch"  "ac743923f81d" "0msyr45xr1j5q4x6ah4r907pwjngyi0k6pp9y8ixk21cnwbzrdwx")
-        (mozilla-patch "icecat-CVE-2018-5129.patch"      "456913d7e8b5" "0fx0s06kxxj7g4hllinaskgh41z3k48zml6yqqzxx485qk3hdh9x")
-        (mozilla-patch "icecat-bug-1334465-pt1.patch"    "f95c5b881442" "0iaddhf65jd9cycj4bw0b207n2jiqkr4q84jifzyqn4ygs75wdqd")
-        (mozilla-patch "icecat-bug-1334465-pt2.patch"    "8a4265c8fb41" "1d9zfdbrlw9wzr84b7pj7lxgy487lsx0kfd89287hjk0al8m6vrw")
-        (mozilla-patch "icecat-bug-1398021.patch"        "28855df568d8" "1kmq836gniplxpjnvq8lhbcc1aqi56al628r1mzdy94b5yb0lis3")
-        (mozilla-patch "icecat-bug-1388020.patch"        "e8ab2736499b" "0n28vcd65rxsyq3z22rfcfksryfndhm1i3g6ah3akg11jnagqf5v")
-        (mozilla-patch "icecat-CVE-2018-5125-pt4.patch"  "014877bf17ea" "0hk90pnf7h7kvidji6ydvva1zpyraipn03pjhvprdqr7k2fqzmsz")
-        (mozilla-patch "icecat-CVE-2018-5125-pt5.patch"  "5b3a5de48912" "1ifya05rcd34ryp9zawdacihhkkf2m0xn2q8m8c6v78bvxj0mgig")
-        (mozilla-patch "icecat-CVE-2018-5144.patch"      "1df9b4404acd" "1sd59vsarfsbh3vlrzrqv6n1ni7vxdzm83j6s6g0fygl1h8kwijg")
-        (mozilla-patch "icecat-bug-1430173-pt1.patch"    "9124c3972e2b" "13ns5yy39yzfx7lrkv4rgwdz6s6q0z4i09wkbxdvnkfsz17cd17i")
-        (mozilla-patch "icecat-bug-1430173-pt2.patch"    "9f6dc031be51" "0bv2p98z5ahp3x9wxnhwxn87g21djvzzp7jy55ik90hqixsbhwdl")
-        (mozilla-patch "icecat-CVE-2018-5131.patch"      "3102fbb97b32" "0kg0183v92gxjb9255xjwhxyd6gl77l9c0civx3040k975fybwlp")
-        (mozilla-patch "icecat-CVE-2018-5125-pt6.patch"  "4904c0f4a645" "0lsq62ynksy1fbw0m87f1d741fyvrrp1vrznx5hx0l2p4g4frhv3")
-        (mozilla-patch "icecat-CVE-2018-5125-pt7.patch"  "16b8073d5c30" "1dv94qqah1wjd3bxjvrkmjbb2f95d3d11zpm8mggdk52il575bwl")
-        (mozilla-patch "icecat-bug-1442127-pt1.patch"    "f931f85b09da" "02s380w8a73g4w2wm810lbigh4z4rrlfy10ywwhv4lpkbk8xg7pr")
-        (mozilla-patch "icecat-bug-1442127-pt2.patch"    "da5792b70f30" "116k9qja5ir9b3laazasp43f5jx59qq72nknmq5bn5v1ixya9r4l")
-        (mozilla-patch "icecat-CVE-2018-5125-pt8.patch"  "62b831df8269" "109pn0hqn7s27580glv4z7qv1pmjzii9szvf3wkn97k5wybrzgkx")
-        (mozilla-patch "icecat-bug-1442504.patch"        "8954ce68a364" "0bl65zw82bwqg0mmcri94pxqq6ibff7y5rclkzapb081p6yvf73q")
-        (mozilla-patch "icecat-CVE-2018-5125-pt9.patch"  "8a16f439117c" "108iarql6z7h1r4rlzac6n6lrzs78x7kcdbfa0b5dbr5xc66jmgb")
-        (mozilla-patch "icecat-bug-1426603.patch"        "ca0b92ecedee" "0dc3mdl4a3hrq4j384zjavf3splj6blv4masign710hk7svlgbhq")
-        (mozilla-patch "icecat-CVE-2018-5146.patch"      "494e5d5278ba" "1yb4lxjw499ppwhk31vz0vzl0cfqvj9d4jwqag7ayj53ybwsqgjr")
-        (mozilla-patch "icecat-CVE-2018-5147.patch"      "5cd5586a2f48" "10s774pwvj6xfk3kk6ivnhp2acc8x9sqq6na8z47nkhgwl2712i5")
-        (mozilla-patch "icecat-CVE-2018-5148.patch"      "c3e447e07077" "0gmwy631f8ip4gr1mpbjk8bx1n1748wdls5zq4y8hpmpnq5g1wyx")
-        (mozilla-patch "icecat-CVE-2018-5178.patch"      "17201199b18d" "1d0hcim1fwh0bklwpmnal1mv9d9kmyif1m15aj1nqkf1n3x4xc37")
-        (mozilla-patch "icecat-bug-1361699.patch"        "a07d6c3ff262" "1z8mjg2487r8pxi0x951v6fwwr696q84f6hlzimc3r7bn5ds9r83")
-        (mozilla-patch "icecat-CVE-2018-5150-pt01.patch" "7127ccf8f88c" "0m4my7aflpp0wlqilr2m4axd7k2fyrs7jqdcz2rrz5pwivz1anvd")
-        (mozilla-patch "icecat-bug-1444231.patch"        "57bd35fa8618" "0pl6x5amc5x6nhwl7qnmnff3jjjxmbs8r365bfzj58g7q5ihqwvf")
-        (mozilla-patch "icecat-CVE-2018-5150-pt02.patch" "2f3e1ccf1661" "0azl8g81kpc0w2xpjpgm1154ll12g0a8n6i7bl3s9nnrk2i26n74")
-        (mozilla-patch "icecat-CVE-2018-5159.patch"      "8ff2c4d68e36" "0kz1rqhnz8ca4z20hnpcafidhsrwhnm0h2gmlgchni33h8pisr1f")
-        (mozilla-patch "icecat-CVE-2018-5154.patch"      "b8c430253efd" "1arjcaps9axhxh5ff84n9bydhhzrihn7hbq7v69nvqwqrjp3lgg9")
-        (mozilla-patch "icecat-CVE-2018-5155.patch"      "05cadfa3ac39" "0q0vh7vy7x0l8jp6376fn10qljfp4mnp4m9zfn90j4m19pfl86a0")
-        (mozilla-patch "icecat-CVE-2018-5168.patch"      "48a678d7cb81" "1yfh7kxxxvqck2hpn98pwag4splyc6c9brc5haq28fp8x9r9qvlk")
-        (mozilla-patch "icecat-CVE-2018-5150-pt03.patch" "112032576872" "1x1hxyggbxlnlj0n9cbp03hjnfvm6cq8nqj0jizrd8cfyd5aig8p")
-        (mozilla-patch "icecat-CVE-2018-5150-pt04.patch" "ad9a885b0df4" "1hrk1q9mk59jww55g4lqmaflznk87x3vvjn2mxfgfbbjs8l1cyz4")
-        (mozilla-patch "icecat-bug-1452416.patch"        "f89ab96a2532" "1dqchxdyznhgyxhfq0hm0vg1p597hjqflfzigc7j3s5vxf9rg2nv")
-        (mozilla-patch "icecat-CVE-2018-5150-pt05.patch" "af885a1bd293" "1wfpqhm2dp4fsx6zbrncngsqz7g2x09b625zcighixrbpvybyww3")
-        (mozilla-patch "icecat-CVE-2018-5150-pt06.patch" "666fc84ec72d" "0lml2wqd4yqidhi364x8r90f78397k2y0kq5z5bv8l8j4bhcnb9v")
-        (search-patch  "icecat-CVE-2018-5157-and-CVE-2018-5158.patch")
-        (mozilla-patch "icecat-CVE-2018-5150-pt07.patch" "1ab40761a856" "1kgwypy7k5b33jwkni4025za4kcnv5m6klsx4wsswlixmljmkbc7")
-        (mozilla-patch "icecat-bug-1453339.patch"        "0edb8dca7087" "0b30pipqryh311sc97rcmwnx9n8qdlbbz90b2hkybjnprmbhfxrm")
-        (mozilla-patch "icecat-CVE-2018-5150-pt08.patch" "134c728799c1" "16hbwx6fx1hrddsyjjbd3z954ql3pg348xs13h9riyblq8crzmam")
-        (mozilla-patch "icecat-CVE-2018-5150-pt09.patch" "14eab155eaa8" "0wr4xgblxzk4c2gvlnpl7ic1196mrhry1hgwdl1jivq0ji5cbvbd")
-        (mozilla-patch "icecat-bug-1452619.patch"        "2b75d55ccf0e" "1g87aybw6ggv6hyk385bplv0lx63n020gwyq0d6d4pqld48hsm1i")
-        (mozilla-patch "icecat-CVE-2018-5156-pt1.patch"  "89857f35df29" "0gzi47svrw5ajdlm3i12193psm702zx70x5h1rwp4gb7gxh4m4d9")
-        (mozilla-patch "icecat-CVE-2018-5150-pt10.patch" "3f2ec03c0405" "0w02952dlxd2gmwghck2nm4rjjmc5ylg62bw6m1rvi35kcr134lr")
-        (mozilla-patch "icecat-CVE-2018-5183.patch"      "f729bf78fb3a" "0xkj6jwxwdqkvb5c7wi16b8cm8qrnlrd3s9jnd46jg03iykrx56f")
-        (mozilla-patch "icecat-CVE-2018-5188-pt01.patch" "eb896089db47" "10lppk4x2d3pim71a36ky1dmg08rs5ckfiljwvfnr1cw6934qxl4")
-        (mozilla-patch "icecat-CVE-2018-5188-pt02.patch" "2374dca97bde" "0y1g55wvj44nzb1qfkl271jcf8s1ik8lcl1785z0zim4qzn7qkpa")
-        (mozilla-patch "icecat-CVE-2018-5188-pt03.patch" "70b6298e0c9e" "0n5jfy6c421dkybk8m18vd61y95zz0r64g1p1zlya3fps5knfaqi")
-        (mozilla-patch "icecat-CVE-2018-12365-pt1.patch" "4ef79fe9b3b7" "1c32z1ki1i6xj1nbb0xlxwqnmz48ikmy8dmp37rkjz8ssn04wgfg")
-        (mozilla-patch "icecat-CVE-2018-12365-pt2.patch" "9ad16112044a" "0ayya67sx7avcb8bplfdxb92l9g4mjrb1s3hby283llhqv0ikg9b")
-        (mozilla-patch "icecat-CVE-2018-12359.patch"     "11d8a87fb6d6" "1rkmdk18llw0x1jakix75hlhy0hpsmlminnflagbzrzjli81gwm1")
-        (mozilla-patch "icecat-CVE-2018-5188-pt04.patch" "407b10ad1273" "16qzsfirw045xag96f1qvpdlibm8lwdj9l1mlli4n1vz0db91v9q")
-        (mozilla-patch "icecat-CVE-2018-6126.patch"      "e76e2e481b17" "0hnx13msjy28n3bpa2c24kpzalam4bdk5gnp0f9k671l48rs9yb3")
-        (mozilla-patch "icecat-CVE-2018-5188-pt05.patch" "2c75bfcd465c" "1pjinj8qypafqm2fk68s3hzcbzcijn09qzrpcxvzq6bl1yfc1xfd")
-        (mozilla-patch "icecat-CVE-2018-5188-pt06.patch" "042f80f3befd" "0av918kin4bkrq7gnjz0h9w8kkq8rk9l93250lfl5kqrinza1gsk")
-        (mozilla-patch "icecat-CVE-2018-5188-pt07+bugs-1455071+1433642+1456604+1458320.patch"
-                                                         "bb0451c9c4a0" "1lhm1b2a7c6jwhzsg3c830hfhp17p8j9zbcmgchpb8c5jkc3vw0x")
-        (mozilla-patch "icecat-CVE-2018-5188-pt08.patch" "8189b262e3b9" "13rh86ddwmj1bhv3ibbil3sv5xbqq1c9v1czgbsna5hxxkzc1y3b")
-        (mozilla-patch "icecat-CVE-2018-5188-pt09.patch" "9f81ae3f6e1d" "05vfg8a8jrzd93n1wvncmvdmqgf9cgsl8ryxgjs3032gbbjkga7q")
-        (mozilla-patch "icecat-CVE-2018-12360.patch"     "face7a3dd5d7" "0jclw30mf693w8lrmvn0iankggj21nh4j3zh51q5363rj5xncdzx")
-        (mozilla-patch "icecat-CVE-2018-5188-pt10.patch" "7afb58c046c8" "1r0569r76712x7x1sw6xr0x06ilv6iw3fncb0f8r8b9mp6wrpx34")
-        (mozilla-patch "icecat-CVE-2018-12362-pt1.patch" "f1a745f8c42d" "11q73pb7a8f09xjzil4rhg5nr49zrnz1vb0prni0kqvrnppf5s40")
-        (mozilla-patch "icecat-CVE-2018-12362-pt2.patch" "1f9a430881cc" "0f79rv7njliqxx33z07n60b50jg0a596d1km7ayz2hivbl2d0168")
-        (mozilla-patch "icecat-CVE-2018-5188-pt11.patch" "28f4fc0a5141" "1a8f9z6c80in8ccj82ysdrcr2lqypp29l4acs50kwncm0c0b01zl")
-        (mozilla-patch "icecat-CVE-2018-12363.patch"     "ad5a53a1d2b1" "0rhl4r39ydb3lkfp5pkwvhhzqgfh33s9r7b7jccgkrx6f13xyq78")
-        (mozilla-patch "icecat-CVE-2018-5188-pt12.patch" "0ddfc03c0454" "1b0xw2kj9765lvpl8iwr3wwcz40bdfp3dp4y9f546a61qsi9q9d6")
-        (mozilla-patch "icecat-CVE-2018-5156-pt2.patch"  "dbf36189a364" "1awbyhy0r79i03sns2p0m78f9hb6c7kp4hwia2khx4qszlsr4j95")
-        (mozilla-patch "icecat-CVE-2018-5188-pt13.patch" "32509dfde003" "0cc3c92dgf5qynk093prq610c9x815l2fa24ddrw9czdzbwblsdq")
-        (mozilla-patch "icecat-bug-1462912.patch"        "f18535a212da" "0zkqz9il89f1s1yrp5c6hj6kysy2x02iy50vgwdj30lr56gkpzmk")
-        (mozilla-patch "icecat-CVE-2018-5188-pt14.patch" "e8e9e1ef79f2" "0dc8p6fsppq3bhbpmp41f8mjxbr31pvgpga0a73dqdaicq5ydgj4")
-        (search-patch  "icecat-bug-1413868-pt1.patch")
-        (mozilla-patch "icecat-CVE-2018-5188-pt15.patch" "9d4d31b2630d" "1lcbmsyi09kp80h1jgxj5l45zl24xn22h1lq7drbyjxsn1kggq4g")
-        (mozilla-patch "icecat-CVE-2018-12366-pt1.patch" "edf2c7dff493" "06xmyk7nm54cm9m6qc59wz8cxxfa5r25mf2xzdzy74iq5hwa1ac8")
-        (mozilla-patch "icecat-CVE-2018-5188-pt16.patch" "05549a4d1b80" "10q68cllshmmhlrbirm9h4gyc3ffrcpsxihfpcbxh90nv2h16jci")
-        (mozilla-patch "icecat-CVE-2018-12364.patch"     "67b2d8924841" "197riigbb6l30959pygr0zlv7vaims78dg1mh0pg33pa7cbna0ds")
-        (mozilla-patch "icecat-CVE-2018-12366-pt2.patch" "528d4d997bb3" "0f375i96a404dkn0fanmd9pgfj3wyrhjfc5dwslw2s44gwfjhljb")
-        (mozilla-patch "icecat-bug-1369771.patch"        "fab16ad7f256" "0kd8qm04sjgfgfg8yw3ivcxazb1d7v430g86chw4n64qybsh9ka3")
-        (mozilla-patch "icecat-CVE-2018-5188-pt17.patch" "068e249d02b4" "1iy9by1mg5qhp8502h31m8zm99aq2hx0c5n3hadd5pk11lfnq6ll")
-        (mozilla-patch "icecat-bug-1413868-pt2.patch"    "755067c14b06" "089dwqwzcdg1l6aimi0i65q4dgb2iny5h8yjx63h9zgv77n0700a")))
+        ;; FIXME (search-patch "icecat-use-system-harfbuzz.patch")
+        ;; FIXME (search-patch "icecat-use-system-graphite2.patch")
+        ))
       (modules '((guix build utils)))
       (snippet
        '(begin
@@ -613,13 +528,13 @@ security standards.")
                       "modules/freetype2"
                       "modules/zlib"
                       "modules/libbz2"
-                      "ipc/chromium/src/third_party/libevent"
+                      ;; UNBUNDLE-ME "ipc/chromium/src/third_party/libevent"
                       "media/libjpeg"
                       "media/libvpx"
                       "security/nss"
-                      "gfx/cairo"
-                      "gfx/harfbuzz"
-                      "gfx/graphite2"
+                      ;; UNBUNDLE-ME "gfx/cairo"
+                      ;; UNBUNDLE-ME "gfx/harfbuzz"
+                      ;; UNBUNDLE-ME "gfx/graphite2"
                       "js/src/ctypes/libffi"
                       "db/sqlite3"))
           ;; Delete .pyc files, typically present in icecat source tarballs
@@ -633,29 +548,29 @@ security standards.")
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("bzip2" ,bzip2)
-       ("cairo" ,cairo)
+       ;; UNBUNDLE-ME ("cairo" ,cairo)
        ("cups" ,cups)
        ("dbus-glib" ,dbus-glib)
        ("gdk-pixbuf" ,gdk-pixbuf)
        ("glib" ,glib)
        ("gtk+" ,gtk+)
        ("gtk+-2" ,gtk+-2)
-       ("graphite2" ,graphite2)
+       ;; UNBUNDLE-ME ("graphite2" ,graphite2)
        ("pango" ,pango)
        ("freetype" ,freetype)
-       ("harfbuzz" ,harfbuzz)
+       ;; UNBUNDLE-ME ("harfbuzz" ,harfbuzz)
        ("hunspell" ,hunspell)
        ("libcanberra" ,libcanberra)
        ("libgnome" ,libgnome)
        ("libjpeg-turbo" ,libjpeg-turbo)
        ("libxft" ,libxft)
-       ("libevent" ,libevent-2.0)
+       ;; UNBUNDLE-ME ("libevent" ,libevent-2.0)
        ("libxinerama" ,libxinerama)
        ("libxscrnsaver" ,libxscrnsaver)
        ("libxcomposite" ,libxcomposite)
        ("libxt" ,libxt)
        ("libffi" ,libffi)
-       ("ffmpeg" ,ffmpeg-3.4)
+       ("ffmpeg" ,ffmpeg)
        ("libvpx" ,libvpx)
        ("icu4c" ,icu4c)
        ("pixman" ,pixman)
@@ -670,7 +585,9 @@ security standards.")
        ("zip" ,zip)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("perl" ,perl)
+     `(("rust" ,rust)
+       ("cargo" ,rust "cargo")
+       ("perl" ,perl)
        ("python" ,python-2) ; Python 3 not supported
        ("python2-pysqlite" ,python2-pysqlite)
        ("yasm" ,yasm)
@@ -687,11 +604,12 @@ security standards.")
        ;; practice somehow.  See <http://hydra.gnu.org/build/378133>.
        #:validate-runpath? #f
 
+       #:imported-modules ,%cargo-build-system-modules ;for `generate-checksums'
+
        #:configure-flags '("--enable-default-toolkit=cairo-gtk3"
 
                            "--with-distribution-id=org.gnu"
 
-                           "--enable-gio"
                            "--enable-startup-notification"
                            "--enable-pulseaudio"
 
@@ -701,7 +619,9 @@ security standards.")
                            "--disable-maintenance-service"
                            "--disable-eme"
                            "--disable-gconf"
-                           "--disable-gnomeui"
+
+                           ;; Stylo requires LLVM/clang.  For now, disable it.
+                           "--disable-stylo"
 
                            ;; Building with debugging symbols takes ~5GiB, so
                            ;; disable it.
@@ -716,15 +636,15 @@ security standards.")
                            "--with-system-zlib"
                            "--with-system-bz2"
                            "--with-system-jpeg"        ; must be libjpeg-turbo
-                           "--with-system-libevent"
+                           ;; UNBUNDLE-ME "--with-system-libevent"
                            "--with-system-libvpx"
                            "--with-system-icu"
                            "--with-system-nspr"
                            "--with-system-nss"
-                           "--with-system-harfbuzz"
-                           "--with-system-graphite2"
+                           ;; UNBUNDLE-ME "--with-system-harfbuzz"
+                           ;; UNBUNDLE-ME "--with-system-graphite2"
                            "--enable-system-pixman"
-                           "--enable-system-cairo"
+                           ;; UNBUNDLE-ME "--enable-system-cairo"
                            "--enable-system-ffi"
                            "--enable-system-hunspell"
                            "--enable-system-sqlite"
@@ -774,6 +694,24 @@ security standards.")
     'avcodec', 'avutil', 'pulse' ]\n\n"
                               all)))
             #t))
+         (add-after 'patch-source-shebangs 'patch-cargo-checksums
+           (lambda* _
+             (use-modules (guix build cargo-build-system))
+             (let ((null-file "/dev/null")
+                   (null-hash "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"))
+               (substitute* '("Cargo.lock" "servo/Cargo.lock")
+                 (("(\"checksum .* = )\".*\"" all name)
+                  (string-append name "\"" null-hash "\"")))
+               (for-each
+                (lambda (filename)
+                  (delete-file filename)
+                  (let ((dir (dirname filename)))
+                    (display (string-append
+                              "patch-cargo-checksums: generate-checksums for "
+                              dir "\n"))
+                    (generate-checksums dir null-file)))
+                (find-files "third_party/rust" ".cargo-checksum.json")))
+             #t))
          (replace
           'configure
           ;; configure does not work followed by both "SHELL=..." and
diff --git a/gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch b/gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch
deleted file mode 100644
index b776640133..0000000000
--- a/gnu/packages/patches/icecat-CVE-2018-5157-and-CVE-2018-5158.patch
+++ /dev/null
@@ -1,441 +0,0 @@
-Based on <https://hg.mozilla.org/releases/mozilla-esr52/rev/608e76ec5ba2>
-Adapted to apply cleanly to GNU IceCat.
-
-# HG changeset patch
-# User Ryan VanderMeulen <ryanvm@gmail.com>
-# Date 1523630807 14400
-# Node ID 608e76ec5ba25cec2271d2b400c7bce2d4c5ef79
-# Parent  10b7f43b536f93151201d44d304c991aa9af5d0c
-Bug 1452075 - Backport some upstream pdf.js fixes to ESR52. r=bdahl, r=yury, a=RyanVM
-
-diff --git a/browser/extensions/pdfjs/content/PdfStreamConverter.jsm b/browser/extensions/pdfjs/content/PdfStreamConverter.jsm
---- a/browser/extensions/pdfjs/content/PdfStreamConverter.jsm
-+++ b/browser/extensions/pdfjs/content/PdfStreamConverter.jsm
-@@ -24,17 +24,18 @@ const Cc = Components.classes;
- const Ci = Components.interfaces;
- const Cr = Components.results;
- const Cu = Components.utils;
- // True only if this is the version of pdf.js that is included with icecat.
- const MOZ_CENTRAL = JSON.parse('true');
- const PDFJS_EVENT_ID = 'pdf.js.message';
- const PDF_CONTENT_TYPE = 'application/pdf';
- const PREF_PREFIX = 'pdfjs';
--const PDF_VIEWER_WEB_PAGE = 'resource://pdf.js/web/viewer.html';
-+const PDF_VIEWER_ORIGIN = "resource://pdf.js";
-+const PDF_VIEWER_WEB_PAGE = "resource://pdf.js/web/viewer.html";
- const MAX_NUMBER_OF_PREFS = 50;
- const MAX_STRING_PREF_LENGTH = 128;
- 
- Cu.import('resource://gre/modules/XPCOMUtils.jsm');
- Cu.import('resource://gre/modules/Services.jsm');
- Cu.import('resource://gre/modules/NetUtil.jsm');
- 
- XPCOMUtils.defineLazyModuleGetter(this, 'NetworkManager',
-@@ -105,21 +106,25 @@ function log(aMsg) {
-   if (!getBoolPref(PREF_PREFIX + '.pdfBugEnabled', false)) {
-     return;
-   }
-   var msg = 'PdfStreamConverter.js: ' + (aMsg.join ? aMsg.join('') : aMsg);
-   Services.console.logStringMessage(msg);
-   dump(msg + '\n');
- }
- 
--function getDOMWindow(aChannel) {
-+function getDOMWindow(aChannel, aPrincipal) {
-   var requestor = aChannel.notificationCallbacks ?
-                   aChannel.notificationCallbacks :
-                   aChannel.loadGroup.notificationCallbacks;
-   var win = requestor.getInterface(Components.interfaces.nsIDOMWindow);
-+  // Ensure the window wasn't navigated to something that is not PDF.js.
-+  if (!win.document.nodePrincipal.equals(aPrincipal)) {
-+    return null;
-+  }
-   return win;
- }
- 
- function getLocalizedStrings(path) {
-   var stringBundle = Cc['@mozilla.org/intl/stringbundle;1'].
-       getService(Ci.nsIStringBundleService).
-       createBundle('chrome://pdf.js/locale/' + path);
- 
-@@ -627,31 +632,31 @@ var RangedChromeActions = (function Rang
-       data = this.dataListener.readData();
- 
-       this.dataListener.onprogress = function (loaded, total) {
-         self.domWindow.postMessage({
-           pdfjsLoadAction: 'progressiveRead',
-           loaded: loaded,
-           total: total,
-           chunk: self.dataListener.readData()
--        }, '*');
-+        }, PDF_VIEWER_ORIGIN);
-       };
-       this.dataListener.oncomplete = function () {
-         self.dataListener = null;
-       };
-     }
- 
-     this.domWindow.postMessage({
-       pdfjsLoadAction: 'supportsRangedLoading',
-       rangeEnabled: this.rangeEnabled,
-       streamingEnabled: this.streamingEnabled,
-       pdfUrl: this.pdfUrl,
-       length: this.contentLength,
-       data: data
--    }, '*');
-+    }, PDF_VIEWER_ORIGIN);
- 
-     return true;
-   };
- 
-   proto.requestDataRange = function RangedChromeActions_requestDataRange(args) {
-     if (!this.rangeEnabled) {
-       return;
-     }
-@@ -663,23 +668,23 @@ var RangedChromeActions = (function Rang
-     // errors from chrome code for non-range requests, so this doesn't
-     // seem high-pri
-     this.networkManager.requestRange(begin, end, {
-       onDone: function RangedChromeActions_onDone(args) {
-         domWindow.postMessage({
-           pdfjsLoadAction: 'range',
-           begin: args.begin,
-           chunk: args.chunk
--        }, '*');
-+        }, PDF_VIEWER_ORIGIN);
-       },
-       onProgress: function RangedChromeActions_onProgress(evt) {
-         domWindow.postMessage({
-           pdfjsLoadAction: 'rangeProgress',
-           loaded: evt.loaded,
--        }, '*');
-+        }, PDF_VIEWER_ORIGIN);
-       }
-     });
-   };
- 
-   proto.abortLoading = function RangedChromeActions_abortLoading() {
-     this.networkManager.abortAllRequests();
-     if (this.originalRequest) {
-       this.originalRequest.cancel(Cr.NS_BINDING_ABORTED);
-@@ -718,26 +723,26 @@ var StandardChromeActions = (function St
-     var self = this;
- 
-     this.dataListener.onprogress = function ChromeActions_dataListenerProgress(
-                                       loaded, total) {
-       self.domWindow.postMessage({
-         pdfjsLoadAction: 'progress',
-         loaded: loaded,
-         total: total
--      }, '*');
-+      }, PDF_VIEWER_ORIGIN);
-     };
- 
-     this.dataListener.oncomplete =
-         function StandardChromeActions_dataListenerComplete(data, errorCode) {
-       self.domWindow.postMessage({
-         pdfjsLoadAction: 'complete',
-         data: data,
-         errorCode: errorCode
--      }, '*');
-+      }, PDF_VIEWER_ORIGIN);
- 
-       self.dataListener = null;
-       self.originalRequest = null;
-     };
- 
-     return true;
-   };
- 
-@@ -972,31 +977,35 @@ PdfStreamConverter.prototype = {
-     var proxy = {
-       onStartRequest: function(request, context) {
-         listener.onStartRequest(aRequest, aContext);
-       },
-       onDataAvailable: function(request, context, inputStream, offset, count) {
-         listener.onDataAvailable(aRequest, aContext, inputStream,
-                                  offset, count);
-       },
--      onStopRequest: function(request, context, statusCode) {
--        // We get the DOM window here instead of before the request since it
--        // may have changed during a redirect.
--        var domWindow = getDOMWindow(channel);
-+      onStopRequest(request, context, statusCode) {
-+        var domWindow = getDOMWindow(channel, resourcePrincipal);
-+        if (!Components.isSuccessCode(statusCode) || !domWindow) {
-+          // The request may have been aborted and the document may have been
-+          // replaced with something that is not PDF.js, abort attaching.
-+          listener.onStopRequest(aRequest, context, statusCode);
-+          return;
-+        }
-         var actions;
-         if (rangeRequest || streamRequest) {
-           actions = new RangedChromeActions(
-             domWindow, contentDispositionFilename, aRequest,
-             rangeRequest, streamRequest, dataListener);
-         } else {
-           actions = new StandardChromeActions(
-             domWindow, contentDispositionFilename, aRequest, dataListener);
-         }
-         var requestListener = new RequestListener(actions);
--        domWindow.addEventListener(PDFJS_EVENT_ID, function(event) {
-+        domWindow.document.addEventListener(PDFJS_EVENT_ID, function(event) {
-           requestListener.receive(event);
-         }, false, true);
-         if (actions.supportsIntegratedFind()) {
-           var findEventManager = new FindEventManager(domWindow);
-           findEventManager.bind();
-         }
-         listener.onStopRequest(aRequest, aContext, statusCode);
- 
-diff --git a/browser/extensions/pdfjs/content/build/pdf.worker.js b/browser/extensions/pdfjs/content/build/pdf.worker.js
---- a/browser/extensions/pdfjs/content/build/pdf.worker.js
-+++ b/browser/extensions/pdfjs/content/build/pdf.worker.js
-@@ -41648,16 +41648,32 @@
-       var error = sharedUtil.error;
-       var info = sharedUtil.info;
-       var isArray = sharedUtil.isArray;
-       var isBool = sharedUtil.isBool;
-       var isDict = corePrimitives.isDict;
-       var isStream = corePrimitives.isStream;
-       var PostScriptLexer = corePsParser.PostScriptLexer;
-       var PostScriptParser = corePsParser.PostScriptParser;
-+      function toNumberArray(arr) {
-+        if (!Array.isArray(arr)) {
-+          return null;
-+        }
-+        var length = arr.length;
-+        for (var i = 0; i < length; i++) {
-+          if (typeof arr[i] !== 'number') {
-+            var result = new Array(length);
-+            for (var j = 0; j < length; j++) {
-+              result[j] = +arr[j];
-+            }
-+            return result;
-+          }
-+        }
-+        return arr;
-+      }
-       var PDFFunction = function PDFFunctionClosure() {
-         var CONSTRUCT_SAMPLED = 0;
-         var CONSTRUCT_INTERPOLATED = 2;
-         var CONSTRUCT_STICHED = 3;
-         var CONSTRUCT_POSTSCRIPT = 4;
-         return {
-           getSampleArray: function PDFFunction_getSampleArray(size, outputSize, bps, str) {
-             var i, ii;
-@@ -41747,43 +41763,43 @@
-                 out[index] = [
-                   arr[i],
-                   arr[i + 1]
-                 ];
-                 ++index;
-               }
-               return out;
-             }
--            var domain = dict.getArray('Domain');
--            var range = dict.getArray('Range');
-+            var domain = toNumberArray(dict.getArray('Domain'));
-+            var range = toNumberArray(dict.getArray('Range'));
-             if (!domain || !range) {
-               error('No domain or range');
-             }
-             var inputSize = domain.length / 2;
-             var outputSize = range.length / 2;
-             domain = toMultiArray(domain);
-             range = toMultiArray(range);
--            var size = dict.get('Size');
-+            var size = toNumberArray(dict.get('Size'));
-             var bps = dict.get('BitsPerSample');
-             var order = dict.get('Order') || 1;
-             if (order !== 1) {
-               // No description how cubic spline interpolation works in PDF32000:2008
-               // As in poppler, ignoring order, linear interpolation may work as good
-               info('No support for cubic spline interpolation: ' + order);
-             }
--            var encode = dict.getArray('Encode');
-+            var encode = toNumberArray(dict.getArray('Encode'));
-             if (!encode) {
-               encode = [];
-               for (var i = 0; i < inputSize; ++i) {
--                encode.push(0);
--                encode.push(size[i] - 1);
--              }
--            }
--            encode = toMultiArray(encode);
--            var decode = dict.getArray('Decode');
-+                encode.push([0, size[i] - 1]);
-+              }
-+            } else {
-+              encode = toMultiArray(encode);
-+            }
-+            var decode = toNumberArray(dict.getArray('Decode'));
-             if (!decode) {
-               decode = range;
-             } else {
-               decode = toMultiArray(decode);
-             }
-             var samples = this.getSampleArray(size, outputSize, bps, str);
-             return [
-               CONSTRUCT_SAMPLED,
-@@ -41868,22 +41884,19 @@
-                 //                    Decode_2j, Decode_2j+1)
-                 rj = interpolate(rj, 0, 1, decode[j][0], decode[j][1]);
-                 // y_j = min(max(r_j, range_2j), range_2j+1)
-                 dest[destOffset + j] = Math.min(Math.max(rj, range[j][0]), range[j][1]);
-               }
-             };
-           },
-           constructInterpolated: function PDFFunction_constructInterpolated(str, dict) {
--            var c0 = dict.getArray('C0') || [0];
--            var c1 = dict.getArray('C1') || [1];
-+            var c0 = toNumberArray(dict.getArray('C0')) || [0];
-+            var c1 = toNumberArray(dict.getArray('C1')) || [1];
-             var n = dict.get('N');
--            if (!isArray(c0) || !isArray(c1)) {
--              error('Illegal dictionary for interpolated function');
--            }
-             var length = c0.length;
-             var diff = [];
-             for (var i = 0; i < length; ++i) {
-               diff.push(c1[i] - c0[i]);
-             }
-             return [
-               CONSTRUCT_INTERPOLATED,
-               c0,
-@@ -41899,49 +41912,45 @@
-             return function constructInterpolatedFromIRResult(src, srcOffset, dest, destOffset) {
-               var x = n === 1 ? src[srcOffset] : Math.pow(src[srcOffset], n);
-               for (var j = 0; j < length; ++j) {
-                 dest[destOffset + j] = c0[j] + x * diff[j];
-               }
-             };
-           },
-           constructStiched: function PDFFunction_constructStiched(fn, dict, xref) {
--            var domain = dict.getArray('Domain');
-+            var domain = toNumberArray(dict.getArray('Domain'));
-             if (!domain) {
-               error('No domain');
-             }
-             var inputSize = domain.length / 2;
-             if (inputSize !== 1) {
-               error('Bad domain for stiched function');
-             }
-             var fnRefs = dict.get('Functions');
-             var fns = [];
-             for (var i = 0, ii = fnRefs.length; i < ii; ++i) {
--              fns.push(PDFFunction.getIR(xref, xref.fetchIfRef(fnRefs[i])));
--            }
--            var bounds = dict.getArray('Bounds');
--            var encode = dict.getArray('Encode');
-+              fns.push(PDFFunction.parse(xref, xref.fetchIfRef(fnRefs[i])));
-+            }
-+            var bounds = toNumberArray(dict.getArray('Bounds'));
-+            var encode = toNumberArray(dict.getArray('Encode'));
-             return [
-               CONSTRUCT_STICHED,
-               domain,
-               bounds,
-               encode,
-               fns
-             ];
-           },
-           constructStichedFromIR: function PDFFunction_constructStichedFromIR(IR) {
-             var domain = IR[1];
-             var bounds = IR[2];
-             var encode = IR[3];
--            var fnsIR = IR[4];
--            var fns = [];
-+            var fns = IR[4];
-             var tmpBuf = new Float32Array(1);
--            for (var i = 0, ii = fnsIR.length; i < ii; i++) {
--              fns.push(PDFFunction.fromIR(fnsIR[i]));
--            }
-             return function constructStichedFromIRResult(src, srcOffset, dest, destOffset) {
-               var clip = function constructStichedFromIRClip(v, min, max) {
-                 if (v > max) {
-                   v = max;
-                 } else if (v < min) {
-                   v = min;
-                 }
-                 return v;
-@@ -41968,18 +41977,18 @@
-               // Prevent the value from becoming NaN as a result
-               // of division by zero (fixes issue6113.pdf).
-               tmpBuf[0] = dmin === dmax ? rmin : rmin + (v - dmin) * (rmax - rmin) / (dmax - dmin);
-               // call the appropriate function
-               fns[i](tmpBuf, 0, dest, destOffset);
-             };
-           },
-           constructPostScript: function PDFFunction_constructPostScript(fn, dict, xref) {
--            var domain = dict.getArray('Domain');
--            var range = dict.getArray('Range');
-+            var domain = toNumberArray(dict.getArray('Domain'));
-+            var range = toNumberArray(dict.getArray('Range'));
-             if (!domain) {
-               error('No domain.');
-             }
-             if (!range) {
-               error('No range.');
-             }
-             var lexer = new PostScriptLexer(fn);
-             var parser = new PostScriptParser(lexer);
-@@ -42928,18 +42937,18 @@
-           case 'IndexedCS':
-             var baseIndexedCS = IR[1];
-             var hiVal = IR[2];
-             var lookup = IR[3];
-             return new IndexedCS(ColorSpace.fromIR(baseIndexedCS), hiVal, lookup);
-           case 'AlternateCS':
-             var numComps = IR[1];
-             var alt = IR[2];
--            var tintFnIR = IR[3];
--            return new AlternateCS(numComps, ColorSpace.fromIR(alt), PDFFunction.fromIR(tintFnIR));
-+            var tintFn = IR[3];
-+            return new AlternateCS(numComps, ColorSpace.fromIR(alt), tintFn);
-           case 'LabCS':
-             whitePoint = IR[1];
-             blackPoint = IR[2];
-             var range = IR[3];
-             return new LabCS(whitePoint, blackPoint, range);
-           default:
-             error('Unknown name ' + name);
-           }
-@@ -43067,22 +43076,22 @@
-               var name = xref.fetchIfRef(cs[1]);
-               numComps = 1;
-               if (isName(name)) {
-                 numComps = 1;
-               } else if (isArray(name)) {
-                 numComps = name.length;
-               }
-               alt = ColorSpace.parseToIR(cs[2], xref, res);
--              var tintFnIR = PDFFunction.getIR(xref, xref.fetchIfRef(cs[3]));
-+              var tintFn = PDFFunction.parse(xref, xref.fetchIfRef(cs[3]));
-               return [
-                 'AlternateCS',
-                 numComps,
-                 alt,
--                tintFnIR
-+                tintFn
-               ];
-             case 'Lab':
-               params = xref.fetchIfRef(cs[1]);
-               whitePoint = params.getArray('WhitePoint');
-               blackPoint = params.getArray('BlackPoint');
-               var range = params.getArray('Range');
-               return [
-                 'LabCS',
-@@ -52483,9 +52492,9 @@
-         initializeWorker();
-       }
-       exports.setPDFNetworkStreamClass = setPDFNetworkStreamClass;
-       exports.WorkerTask = WorkerTask;
-       exports.WorkerMessageHandler = WorkerMessageHandler;
-     }));
-   }.call(pdfjsLibs));
-   exports.WorkerMessageHandler = pdfjsLibs.pdfjsCoreWorker.WorkerMessageHandler;
--}));
-\ No newline at end of file
-+}));
-
diff --git a/gnu/packages/patches/icecat-bug-1413868-pt1.patch b/gnu/packages/patches/icecat-bug-1413868-pt1.patch
deleted file mode 100644
index 18382dc33a..0000000000
--- a/gnu/packages/patches/icecat-bug-1413868-pt1.patch
+++ /dev/null
@@ -1,663 +0,0 @@
-Based on <https://hg.mozilla.org/releases/mozilla-esr52/rev/431fa5dd4016>
-Adapted to apply cleanly to GNU IceCat.
-
-# HG changeset patch
-# User Honza Bambas <honzab.moz@firemni.cz>
-# Date 1528830658 14400
-# Node ID 431fa5dd4016bdab7e4bb0d3c4df85468fe337b0
-# Parent  e8e9e1ef79f2a18c61ec1b87cfb214c8d4960f8e
-Bug 1413868. r=valentin, a=RyanVM
-
-diff --git a/toolkit/xre/nsAppRunner.cpp b/toolkit/xre/nsAppRunner.cpp
---- a/toolkit/xre/nsAppRunner.cpp
-+++ b/toolkit/xre/nsAppRunner.cpp
-@@ -4,16 +4,17 @@
-  * file, You can obtain one at http://mozilla.org/MPL/2.0/. */
- 
- #include "mozilla/dom/ContentParent.h"
- #include "mozilla/dom/ContentChild.h"
- #include "mozilla/ipc/GeckoChildProcessHost.h"
- 
- #include "mozilla/ArrayUtils.h"
- #include "mozilla/Attributes.h"
-+#include "mozilla/FilePreferences.h"
- #include "mozilla/ChaosMode.h"
- #include "mozilla/IOInterposer.h"
- #include "mozilla/Likely.h"
- #include "mozilla/MemoryChecking.h"
- #include "mozilla/Poison.h"
- #include "mozilla/Preferences.h"
- #include "mozilla/ScopeExit.h"
- #include "mozilla/Services.h"
-@@ -4304,16 +4305,20 @@ XREMain::XRE_mainRun()
-       // Need to write out the fact that the profile has been removed and potentially
-       // that the selected/default profile changed.
-       mProfileSvc->Flush();
-     }
-   }
- 
-   mDirProvider.DoStartup();
- 
-+  // As FilePreferences need the profile directory, we must initialize right here.
-+  mozilla::FilePreferences::InitDirectoriesWhitelist();
-+  mozilla::FilePreferences::InitPrefs();
-+
-   OverrideDefaultLocaleIfNeeded();
- 
- #ifdef MOZ_CRASHREPORTER
-   nsCString userAgentLocale;
-   // Try a localized string first. This pref is always a localized string in
-   // IceCatMobile, and might be elsewhere, too.
-   if (NS_SUCCEEDED(Preferences::GetLocalizedCString("general.useragent.locale", &userAgentLocale))) {
-     CrashReporter::AnnotateCrashReport(NS_LITERAL_CSTRING("useragent_locale"), userAgentLocale);
-diff --git a/toolkit/xre/nsEmbedFunctions.cpp b/toolkit/xre/nsEmbedFunctions.cpp
---- a/toolkit/xre/nsEmbedFunctions.cpp
-+++ b/toolkit/xre/nsEmbedFunctions.cpp
-@@ -46,16 +46,17 @@
- #include "nsX11ErrorHandler.h"
- #include "nsGDKErrorHandler.h"
- #include "base/at_exit.h"
- #include "base/command_line.h"
- #include "base/message_loop.h"
- #include "base/process_util.h"
- #include "chrome/common/child_process.h"
- 
-+#include "mozilla/FilePreferences.h"
- #include "mozilla/ipc/BrowserProcessSubThread.h"
- #include "mozilla/ipc/GeckoChildProcessHost.h"
- #include "mozilla/ipc/IOThreadChild.h"
- #include "mozilla/ipc/ProcessChild.h"
- #include "ScopedXREEmbed.h"
- 
- #include "mozilla/plugins/PluginProcessChild.h"
- #include "mozilla/dom/ContentProcess.h"
-@@ -680,16 +681,18 @@ XRE_InitChildProcess(int aArgc,
-       ::SetProcessShutdownParameters(0x280 - 1, SHUTDOWN_NORETRY);
- #endif
- 
- #if defined(MOZ_SANDBOX) && defined(XP_WIN)
-       // We need to do this after the process has been initialised, as
-       // InitLoggingIfRequired may need access to prefs.
-       mozilla::sandboxing::InitLoggingIfRequired(aChildData->ProvideLogFunction);
- #endif
-+      mozilla::FilePreferences::InitDirectoriesWhitelist();
-+      mozilla::FilePreferences::InitPrefs();
- 
-       OverrideDefaultLocaleIfNeeded();
- 
- #if defined(MOZ_CRASHREPORTER)
- #if defined(MOZ_CONTENT_SANDBOX) && !defined(MOZ_WIDGET_GONK)
-       AddContentSandboxLevelAnnotation();
- #endif
- #endif
-diff --git a/xpcom/io/FilePreferences.cpp b/xpcom/io/FilePreferences.cpp
-new file mode 100644
---- /dev/null
-+++ b/xpcom/io/FilePreferences.cpp
-@@ -0,0 +1,271 @@
-+/* -*- Mode: C++; tab-width: 8; indent-tabs-mode: nil; c-basic-offset: 2 -*- */
-+/* vim: set ts=8 sts=2 et sw=2 tw=80: */
-+/* This Source Code Form is subject to the terms of the Mozilla Public
-+* License, v. 2.0. If a copy of the MPL was not distributed with this
-+* file, You can obtain one at http://mozilla.org/MPL/2.0/. */
-+
-+#include "FilePreferences.h"
-+
-+#include "mozilla/Preferences.h"
-+#include "nsAppDirectoryServiceDefs.h"
-+#include "nsDirectoryServiceDefs.h"
-+#include "nsDirectoryServiceUtils.h"
-+
-+namespace mozilla {
-+namespace FilePreferences {
-+
-+static bool sBlockUNCPaths = false;
-+typedef nsTArray<nsString> Paths;
-+
-+static Paths& PathArray()
-+{
-+  static Paths sPaths;
-+  return sPaths;
-+}
-+
-+static void AllowDirectory(char const* directory)
-+{
-+  nsCOMPtr<nsIFile> file;
-+  NS_GetSpecialDirectory(directory, getter_AddRefs(file));
-+  if (!file) {
-+    return;
-+  }
-+
-+  nsString path;
-+  if (NS_FAILED(file->GetTarget(path))) {
-+    return;
-+  }
-+
-+  // The whitelist makes sense only for UNC paths, because this code is used
-+  // to block only UNC paths, hence, no need to add non-UNC directories here
-+  // as those would never pass the check.
-+  if (!StringBeginsWith(path, NS_LITERAL_STRING("\\\\"))) {
-+    return;
-+  }
-+
-+  if (!PathArray().Contains(path)) {
-+    PathArray().AppendElement(path);
-+  }
-+}
-+
-+void InitPrefs()
-+{
-+  sBlockUNCPaths = Preferences::GetBool("network.file.disable_unc_paths", false);
-+}
-+
-+void InitDirectoriesWhitelist()
-+{
-+  // NS_GRE_DIR is the installation path where the binary resides.
-+  AllowDirectory(NS_GRE_DIR);
-+  // NS_APP_USER_PROFILE_50_DIR and NS_APP_USER_PROFILE_LOCAL_50_DIR are the two
-+  // parts of the profile we store permanent and local-specific data.
-+  AllowDirectory(NS_APP_USER_PROFILE_50_DIR);
-+  AllowDirectory(NS_APP_USER_PROFILE_LOCAL_50_DIR);
-+}
-+
-+namespace { // anon
-+
-+class Normalizer
-+{
-+public:
-+  Normalizer(const nsAString& aFilePath, const char16_t aSeparator);
-+  bool Get(nsAString& aNormalizedFilePath);
-+
-+private:
-+  bool ConsumeItem();
-+  bool ConsumeSeparator();
-+  bool IsEOF() { return mFilePathCursor == mFilePathEnd; }
-+
-+  bool ConsumeName();
-+  bool CheckParentDir();
-+  bool CheckCurrentDir();
-+
-+  nsString::const_char_iterator mFilePathCursor;
-+  nsString::const_char_iterator mFilePathEnd;
-+
-+  nsDependentSubstring mItem;
-+  char16_t const mSeparator;
-+  nsTArray<nsDependentSubstring> mStack;
-+};
-+
-+Normalizer::Normalizer(const nsAString& aFilePath, const char16_t aSeparator)
-+  : mFilePathCursor(aFilePath.BeginReading())
-+  , mFilePathEnd(aFilePath.EndReading())
-+  , mSeparator(aSeparator)
-+{
-+}
-+
-+bool Normalizer::ConsumeItem()
-+{
-+  if (IsEOF()) {
-+    return false;
-+  }
-+
-+  nsString::const_char_iterator nameBegin = mFilePathCursor;
-+  while (mFilePathCursor != mFilePathEnd) {
-+    if (*mFilePathCursor == mSeparator) {
-+      break; // don't include the separator
-+    }
-+    ++mFilePathCursor;
-+  }
-+
-+  mItem.Rebind(nameBegin, mFilePathCursor);
-+  return true;
-+}
-+
-+bool Normalizer::ConsumeSeparator()
-+{
-+  if (IsEOF()) {
-+    return false;
-+  }
-+
-+  if (*mFilePathCursor != mSeparator) {
-+    return false;
-+  }
-+
-+  ++mFilePathCursor;
-+  return true;
-+}
-+
-+bool Normalizer::Get(nsAString& aNormalizedFilePath)
-+{
-+  aNormalizedFilePath.Truncate();
-+
-+  if (IsEOF()) {
-+    return true;
-+  }
-+  if (ConsumeSeparator()) {
-+    aNormalizedFilePath.Append(mSeparator);
-+  }
-+
-+  if (IsEOF()) {
-+    return true;
-+  }
-+  if (ConsumeSeparator()) {
-+    aNormalizedFilePath.Append(mSeparator);
-+  }
-+
-+  while (!IsEOF()) {
-+    if (!ConsumeName()) {
-+      return false;
-+    }
-+  }
-+
-+  for (auto const& name : mStack) {
-+    aNormalizedFilePath.Append(name);
-+  }
-+
-+  return true;
-+}
-+
-+bool Normalizer::ConsumeName()
-+{
-+  if (!ConsumeItem()) {
-+    return true;
-+  }
-+
-+  if (CheckCurrentDir()) {
-+    return true;
-+  }
-+
-+  if (CheckParentDir()) {
-+    if (!mStack.Length()) {
-+      // This means there are more \.. than valid names
-+      return false;
-+    }
-+
-+    mStack.RemoveElementAt(mStack.Length() - 1);
-+    return true;
-+  }
-+
-+  if (mItem.IsEmpty()) {
-+    // this means an empty name (a lone slash), which is illegal
-+    return false;
-+  }
-+
-+  if (ConsumeSeparator()) {
-+    mItem.Rebind(mItem.BeginReading(), mFilePathCursor);
-+  }
-+  mStack.AppendElement(mItem);
-+
-+  return true;
-+}
-+
-+bool Normalizer::CheckCurrentDir()
-+{
-+  if (mItem == NS_LITERAL_STRING(".")) {
-+    ConsumeSeparator();
-+    // EOF is acceptable
-+    return true;
-+  }
-+
-+  return false;
-+}
-+
-+bool Normalizer::CheckParentDir()
-+{
-+  if (mItem == NS_LITERAL_STRING("..")) {
-+    ConsumeSeparator();
-+    // EOF is acceptable
-+    return true;
-+  }
-+
-+  return false;
-+}
-+
-+} // anon
-+
-+bool IsBlockedUNCPath(const nsAString& aFilePath)
-+{
-+  if (!sBlockUNCPaths) {
-+    return false;
-+  }
-+
-+  if (!StringBeginsWith(aFilePath, NS_LITERAL_STRING("\\\\"))) {
-+    return false;
-+  }
-+
-+  nsAutoString normalized;
-+  if (!Normalizer(aFilePath, L'\\').Get(normalized)) {
-+    // Broken paths are considered invalid and thus inaccessible
-+    return true;
-+  }
-+
-+  for (const auto& allowedPrefix : PathArray()) {
-+    if (StringBeginsWith(normalized, allowedPrefix)) {
-+      if (normalized.Length() == allowedPrefix.Length()) {
-+        return false;
-+      }
-+      if (normalized[allowedPrefix.Length()] == L'\\') {
-+        return false;
-+      }
-+
-+      // When we are here, the path has a form "\\path\prefixevil"
-+      // while we have an allowed prefix of "\\path\prefix".
-+      // Note that we don't want to add a slash to the end of a prefix
-+      // so that opening the directory (no slash at the end) still works.
-+      break;
-+    }
-+  }
-+
-+  return true;
-+}
-+
-+void testing::SetBlockUNCPaths(bool aBlock)
-+{
-+  sBlockUNCPaths = aBlock;
-+}
-+
-+void testing::AddDirectoryToWhitelist(nsAString const & aPath)
-+{
-+  PathArray().AppendElement(aPath);
-+}
-+
-+bool testing::NormalizePath(nsAString const & aPath, nsAString & aNormalized)
-+{
-+  Normalizer normalizer(aPath, L'\\');
-+  return normalizer.Get(aNormalized);
-+}
-+
-+} // ::FilePreferences
-+} // ::mozilla
-diff --git a/xpcom/io/FilePreferences.h b/xpcom/io/FilePreferences.h
-new file mode 100644
---- /dev/null
-+++ b/xpcom/io/FilePreferences.h
-@@ -0,0 +1,25 @@
-+/* -*- Mode: C++; tab-width: 8; indent-tabs-mode: nil; c-basic-offset: 2 -*- */
-+/* vim: set ts=8 sts=2 et sw=2 tw=80: */
-+/* This Source Code Form is subject to the terms of the Mozilla Public
-+* License, v. 2.0. If a copy of the MPL was not distributed with this
-+* file, You can obtain one at http://mozilla.org/MPL/2.0/. */
-+
-+#include "nsIObserver.h"
-+
-+namespace mozilla {
-+namespace FilePreferences {
-+
-+void InitPrefs();
-+void InitDirectoriesWhitelist();
-+bool IsBlockedUNCPath(const nsAString& aFilePath);
-+
-+namespace testing {
-+
-+void SetBlockUNCPaths(bool aBlock);
-+void AddDirectoryToWhitelist(nsAString const& aPath);
-+bool NormalizePath(nsAString const & aPath, nsAString & aNormalized);
-+
-+}
-+
-+} // FilePreferences
-+} // mozilla
-diff --git a/xpcom/io/moz.build b/xpcom/io/moz.build
---- a/xpcom/io/moz.build
-+++ b/xpcom/io/moz.build
-@@ -79,24 +79,26 @@ EXPORTS += [
-     'nsUnicharInputStream.h',
-     'nsWildCard.h',
-     'SlicedInputStream.h',
-     'SpecialSystemDirectory.h',
- ]
- 
- EXPORTS.mozilla += [
-     'Base64.h',
-+    'FilePreferences.h',
-     'SnappyCompressOutputStream.h',
-     'SnappyFrameUtils.h',
-     'SnappyUncompressInputStream.h',
- ]
- 
- UNIFIED_SOURCES += [
-     'Base64.cpp',
-     'crc32c.c',
-+    'FilePreferences.cpp',
-     'nsAnonymousTemporaryFile.cpp',
-     'nsAppFileLocationProvider.cpp',
-     'nsBinaryStream.cpp',
-     'nsDirectoryService.cpp',
-     'nsEscape.cpp',
-     'nsInputStreamTee.cpp',
-     'nsIOUtil.cpp',
-     'nsLinebreakConverter.cpp',
-diff --git a/xpcom/io/nsLocalFileWin.cpp b/xpcom/io/nsLocalFileWin.cpp
---- a/xpcom/io/nsLocalFileWin.cpp
-+++ b/xpcom/io/nsLocalFileWin.cpp
-@@ -41,16 +41,17 @@
- #include  <stdio.h>
- #include  <stdlib.h>
- #include  <mbstring.h>
- 
- #include "nsXPIDLString.h"
- #include "prproces.h"
- #include "prlink.h"
- 
-+#include "mozilla/FilePreferences.h"
- #include "mozilla/Mutex.h"
- #include "SpecialSystemDirectory.h"
- 
- #include "nsTraceRefcnt.h"
- #include "nsXPCOMCIDInternal.h"
- #include "nsThreadUtils.h"
- #include "nsXULAppAPI.h"
- 
-@@ -1162,16 +1163,20 @@ nsLocalFile::InitWithPath(const nsAStrin
-   char16_t secondChar = *(++begin);
- 
-   // just do a sanity check.  if it has any forward slashes, it is not a Native path
-   // on windows.  Also, it must have a colon at after the first char.
-   if (FindCharInReadable(L'/', begin, end)) {
-     return NS_ERROR_FILE_UNRECOGNIZED_PATH;
-   }
- 
-+  if (FilePreferences::IsBlockedUNCPath(aFilePath)) {
-+    return NS_ERROR_FILE_ACCESS_DENIED;
-+  }
-+
-   if (secondChar != L':' && (secondChar != L'\\' || firstChar != L'\\')) {
-     return NS_ERROR_FILE_UNRECOGNIZED_PATH;
-   }
- 
-   if (secondChar == L':') {
-     // Make sure we have a valid drive, later code assumes the drive letter
-     // is a single char a-z or A-Z.
-     if (PathGetDriveNumberW(aFilePath.Data()) == -1) {
-@@ -1974,16 +1979,20 @@ nsLocalFile::CopySingleFile(nsIFile* aSo
-     bool path1Remote, path2Remote;
-     if (!IsRemoteFilePath(filePath.get(), path1Remote) ||
-         !IsRemoteFilePath(destPath.get(), path2Remote) ||
-         path1Remote || path2Remote) {
-       dwCopyFlags |= COPY_FILE_NO_BUFFERING;
-     }
-   }
- 
-+  if (FilePreferences::IsBlockedUNCPath(destPath)) {
-+    return NS_ERROR_FILE_ACCESS_DENIED;
-+  }
-+
-   if (!move) {
-     copyOK = ::CopyFileExW(filePath.get(), destPath.get(), nullptr,
-                            nullptr, nullptr, dwCopyFlags);
-   } else {
-     copyOK = ::MoveFileExW(filePath.get(), destPath.get(),
-                            MOVEFILE_REPLACE_EXISTING);
- 
-     // Check if copying the source file to a different volume,
-diff --git a/xpcom/tests/gtest/TestFilePreferencesWin.cpp b/xpcom/tests/gtest/TestFilePreferencesWin.cpp
-new file mode 100644
---- /dev/null
-+++ b/xpcom/tests/gtest/TestFilePreferencesWin.cpp
-@@ -0,0 +1,141 @@
-+#include "gtest/gtest.h"
-+
-+#include "mozilla/FilePreferences.h"
-+#include "nsIFile.h"
-+#include "nsXPCOMCID.h"
-+
-+TEST(FilePreferencesWin, Normalization)
-+{
-+  nsAutoString normalized;
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("foo"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("foo"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\foo"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\foo"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("foo\\some"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("foo\\some"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\.\\foo"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\."), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\.\\"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\.\\."), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\."), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\.\\"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\bar\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\..\\"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\.."), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\foo\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\..\\bar\\..\\"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\..\\bar"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\bar"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\..\\..\\"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
-+
-+  mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\.\\..\\.\\..\\"), normalized);
-+  ASSERT_TRUE(normalized == NS_LITERAL_STRING("\\\\"));
-+
-+  bool result;
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\.."), normalized);
-+  ASSERT_FALSE(result);
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\..\\"), normalized);
-+  ASSERT_FALSE(result);
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\.\\..\\"), normalized);
-+  ASSERT_FALSE(result);
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\\\bar"), normalized);
-+  ASSERT_FALSE(result);
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\foo\\bar\\..\\..\\..\\..\\"), normalized);
-+  ASSERT_FALSE(result);
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\\\"), normalized);
-+  ASSERT_FALSE(result);
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\.\\\\"), normalized);
-+  ASSERT_FALSE(result);
-+
-+  result = mozilla::FilePreferences::testing::NormalizePath(
-+    NS_LITERAL_STRING("\\\\..\\\\"), normalized);
-+  ASSERT_FALSE(result);
-+}
-+
-+TEST(FilePreferencesWin, AccessUNC)
-+{
-+  nsCOMPtr<nsIFile> lf = do_CreateInstance(NS_LOCAL_FILE_CONTRACTID);
-+
-+  nsresult rv;
-+
-+  mozilla::FilePreferences::testing::SetBlockUNCPaths(false);
-+
-+  rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\..\\evil\\share"));
-+  ASSERT_EQ(rv, NS_OK);
-+
-+  mozilla::FilePreferences::testing::SetBlockUNCPaths(true);
-+
-+  rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\..\\evil\\share"));
-+  ASSERT_EQ(rv, NS_ERROR_FILE_ACCESS_DENIED);
-+
-+  mozilla::FilePreferences::testing::AddDirectoryToWhitelist(NS_LITERAL_STRING("\\\\nice"));
-+
-+  rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\share"));
-+  ASSERT_EQ(rv, NS_OK);
-+
-+  rv = lf->InitWithPath(NS_LITERAL_STRING("\\\\nice\\..\\evil\\share"));
-+  ASSERT_EQ(rv, NS_ERROR_FILE_ACCESS_DENIED);
-+}
-diff --git a/xpcom/tests/gtest/moz.build b/xpcom/tests/gtest/moz.build
---- a/xpcom/tests/gtest/moz.build
-+++ b/xpcom/tests/gtest/moz.build
-@@ -51,16 +51,21 @@ UNIFIED_SOURCES += [
- if CONFIG['MOZ_DEBUG'] and CONFIG['OS_ARCH'] not in ('WINNT') and CONFIG['OS_TARGET'] != 'Android':
-     # FIXME bug 523392: TestDeadlockDetector doesn't like Windows
-     # Bug 1054249: Doesn't work on Android
-     UNIFIED_SOURCES += [
-         'TestDeadlockDetector.cpp',
-         'TestDeadlockDetectorScalability.cpp',
-     ]
- 
-+if CONFIG['OS_TARGET'] == 'WINNT':
-+    UNIFIED_SOURCES += [
-+        'TestFilePreferencesWin.cpp',
-+    ]
-+
- if CONFIG['WRAP_STL_INCLUDES'] and not CONFIG['CLANG_CL']:
-     UNIFIED_SOURCES += [
-         'TestSTLWrappers.cpp',
-     ]
- 
- # Compile TestAllocReplacement separately so Windows headers don't pollute
- # the global namespace for other files.
- SOURCES += [
-

From 2aa137e261984b9762de5221459835eefb165fe7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 13:29:38 +0200
Subject: [PATCH 028/909] gnu: crossguid: Use INVOKE.

* gnu/packages/kodi.scm (crossguid)[arguments]: Substitute INVOKE for SYSTEM*.
---
 gnu/packages/kodi.scm | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 62a971a0a8..2df5735dd0 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -92,22 +93,22 @@
       (arguments
        '(#:phases
          (modify-phases %standard-phases
-           (delete 'configure) ; no configure script
+           (delete 'configure)          ; no configure script
            ;; There's no build system here, so we have to do it ourselves.
            (replace 'build
              (lambda _
-               (and (zero? (system* "g++" "-c" "guid.cpp" "-o" "guid.o"
-                                    "-std=c++11" "-DGUID_LIBUUID"))
-                    (zero? (system* "ar" "rvs" "libcrossguid.a" "guid.o")))))
+               (invoke "g++" "-c" "guid.cpp" "-o" "guid.o"
+                       "-std=c++11" "-DGUID_LIBUUID")
+               (invoke "ar" "rvs" "libcrossguid.a" "guid.o")))
            (replace 'check
              (lambda _
-               (and (zero? (system* "g++" "-c" "test.cpp" "-o" "test.o"
-                                    "-std=c++11"))
-                    (zero? (system* "g++" "-c" "testmain.cpp" "-o" "testmain.o"
-                                    "-std=c++11"))
-                    (zero? (system* "g++" "test.o" "guid.o" "testmain.o"
-                                    "-o" "test" "-luuid"))
-                    (zero? (system* (string-append (getcwd) "/test"))))))
+               (invoke "g++" "-c" "test.cpp" "-o" "test.o"
+                       "-std=c++11")
+               (invoke "g++" "-c" "testmain.cpp" "-o" "testmain.o"
+                       "-std=c++11")
+               (invoke "g++" "test.o" "guid.o" "testmain.o"
+                       "-o" "test" "-luuid")
+               (invoke (string-append (getcwd) "/test"))))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))

From 93ab9a5d76b8b84afd6823e2cdd1f62c9e6284f2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 13:29:54 +0200
Subject: [PATCH 029/909] gnu: kodi: Use INVOKE.

* gnu/packages/kodi.scm (kodi)[arguments]: Substitute INVOKE for SYSTEM*.
---
 gnu/packages/kodi.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 2df5735dd0..86ce914d53 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -295,7 +295,7 @@ generator library for C++.")
                            "lib/cpluff")))
                (every (lambda (third-party)
                         (with-directory-excursion third-party
-                          (zero? (system* "autoreconf" "-vif"))))
+                          (invoke "autoreconf" "-vif")))
                       dirs))))
          (add-after 'bootstrap-bundled-software 'patch-stuff
            (lambda* (#:key inputs #:allow-other-keys)
@@ -336,7 +336,7 @@ generator library for C++.")
              #t))
          (add-before 'check 'build-kodi-test
            (lambda _
-             (zero? (system* "make" "kodi-test")))))))
+             (invoke "make" "kodi-test"))))))
     ;; TODO: Add dependencies for:
     ;; - nfs
     ;; - cec

From eacb5dc4871aadac965024aeab06f48362abba47 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 13:54:32 +0200
Subject: [PATCH 030/909] gnu: emacs-mu4e-conversation: Fix typo in
 description.

* gnu/packages/emacs.scm (emacs-mu4e-conversation)[description]:
Fix 'correspondant' typo.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index fc019cf241..977f0c99b8 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -11705,8 +11705,8 @@ file.")
       (synopsis
        "Show a complete thread in a single buffer")
       (description
-       "This package offers an alternate view to mu4e e-mail display.  It
-shows all e-mails of a thread in a single view, where each correspondant has
+       "This package offers an alternate view to mu4e's e-mail display.  It
+shows all e-mails of a thread in a single view, where each correspondent has
 their own face.  Threads can be displayed linearly (in which case e-mails are
 displayed in chronological order) or as an Org document where the node tree
 maps the thread tree.")

From 41e551b2d3ea24ffd96023d1b6c3648de3aac90d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 14:00:53 +0200
Subject: [PATCH 031/909] gnu: python-pyparsing: Update home page.

* gnu/packages/python.scm (python-pyparsing)[home-page]: Update.
---
 gnu/packages/python.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 64ee4e028e..a11c7e315e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3382,7 +3382,7 @@ library, libgit2 implements Git plumbing.")
                 (list "docs" "htmldoc" "examples")
                 (list doc html-doc examples))
                #t))))))
-    (home-page "http://pyparsing.wikispaces.com")
+    (home-page "https://github.com/pyparsing/pyparsing")
     (synopsis "Python parsing class library")
     (description
      "The pyparsing module is an alternative approach to creating and

From 118a084531a546ccad0762b5ac7d564619183d6b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 14:55:20 +0200
Subject: [PATCH 032/909] gnu: libfilezilla: Update to 0.13.2.

* gnu/packages/ftp.scm (libfilezilla): Update to 0.13.2.
[source]: Use HTTPS.
---
 gnu/packages/ftp.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index d3f3ef711c..335c975d12 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -170,15 +170,15 @@ as required.")
 (define-public libfilezilla
   (package
     (name "libfilezilla")
-    (version "0.13.1")
+    (version "0.13.2")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "http://download.filezilla-project.org/"
+       (uri (string-append "https://download.filezilla-project.org/"
                            name "/" name "-" version ".tar.bz2"))
        (sha256
         (base32
-         "0347zkapp0wrhfm1yzw7wa1v3lww65ch176scifxn8f9068f1ixb"))))
+         "0z9cqscca4w94j9npgcknrrw8gfwn5ids903042fczlr977j0i19"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("cppunit" ,cppunit)

From 10e066f410d1ffb9505f4fd0b5cc73e8af2154b0 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Fri, 21 Sep 2018 15:21:24 +0200
Subject: [PATCH 033/909] gnu: rust: Remove unused "localstatedir" setting.

* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "localstatedir" setting.
---
 gnu/packages/rust.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm
index e8eca80aa6..40633854ae 100644
--- a/gnu/packages/rust.scm
+++ b/gnu/packages/rust.scm
@@ -562,7 +562,6 @@ submodules = false
 prefix = \"" out "\"
 docdir = \"" doc "/share/doc/rust" "\"
 sysconfdir = \"etc\"
-localstatedir = \"var/lib\"
 [rust]
 default-linker = \"" gcc "/bin/gcc" "\"
 channel = \"stable\"

From b0d1e60fff023e405c92c45b3c78538c3cbb7e6b Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Thu, 20 Sep 2018 18:59:56 +0100
Subject: [PATCH 034/909] gnu: hdf5: Allow for absence of utility script.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/maths.scm (hdf5)[arguments]: Add condition to 'split'
phase to check for existence of h5fc script.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/maths.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 736bac163e..30f1610c1d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -814,8 +814,11 @@ incompatible with HDF5.")
                 (mkdir-p flib)
                 (mkdir-p finc)
                 (mkdir-p fex)
-                (rename-file (string-append bin "/h5fc")
-                             (string-append fbin "/h5fc"))
+                ;; Note: When built with --enable-parallel, the 'h5fc' file
+                ;; doesn't exist, hence this condition.
+                (when (file-exists? (string-append bin "/h5fc"))
+                  (rename-file (string-append bin "/h5fc")
+                               (string-append fbin "/h5fc")))
                 (for-each (lambda (file)
                             (rename-file file
                                          (string-append flib "/" (basename file))))

From 45201bf245856954cb8368c328e54773a0a81156 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Thu, 20 Sep 2018 18:59:57 +0100
Subject: [PATCH 035/909] gnu: hdf5-parallel-openmpi: Really enable parallel
 build.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
in the file H5pubconf.h.

* gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
the "--enable-parallel" flag to the list of configure flags.  Remove
the incompatible "--enable-cxx" flag.  Add 'mpi-setup' phase.

Signed-off-by: Ludovic Courtès <ludovic.courtes@inria.fr>
---
 gnu/packages/maths.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 30f1610c1d..636b485260 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1037,10 +1037,13 @@ Swath).")
      `(("mpi" ,openmpi)
        ,@(package-inputs hdf5)))
     (arguments
-     (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
-                                     ,@(package-arguments hdf5))
+     (substitute-keyword-arguments (package-arguments hdf5)
+       ((#:configure-flags flags)
+        ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
        ((#:phases phases)
         `(modify-phases ,phases
+           (add-after 'build 'mpi-setup
+             ,%openmpi-setup)
            (add-before 'check 'patch-tests
              (lambda _
                ;; OpenMPI's mpirun will exit with non-zero status if it

From 7e27393f82ff5e7237f870ded09652b89e457faa Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 11 Sep 2018 16:54:32 +0200
Subject: [PATCH 036/909] gnu: Add r-pore.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/bioinformatics.scm (r-pore): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 10330cd8b2..9599e3096f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13736,3 +13736,32 @@ juicer) and single-resolution or multi-resolution @code{.cool} files (for
 cooler).  Both @code{hic} and @code{cool} files describe Hi-C contact
 matrices.")
     (license license:expat)))
+
+(define-public r-pore
+  (package
+    (name "r-pore")
+    (version "0.24")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "mirror://sourceforge/rpore/" version
+                       "/poRe_" version ".tar.gz"))
+       (sha256
+        (base32 "0pih9nljbv8g4x8rkk29i7aqq681b782r5s5ynp4nw9yzqnmmksv"))))
+    (properties `((upstream-name . "poRe")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bit64" ,r-bit64)
+       ("r-data-table" ,r-data-table)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-shiny" ,r-shiny)
+       ("r-svdialogs" ,r-svdialogs)))
+    (home-page "https://sourceforge.net/projects/rpore/")
+    (synopsis "Visualize Nanopore sequencing data")
+    (description
+     "This package provides graphical user interfaces to organize and visualize Nanopore
+sequencing data.")
+    ;; This is free software but the license variant is unclear:
+    ;; <https://github.com/mw55309/poRe_docs/issues/10>.
+    (license license:bsd-3)))

From 9daf046c5dd9256e45073dfd4647e12de10dcb3e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 14 Sep 2018 17:30:06 +0200
Subject: [PATCH 037/909] inferior: Add 'inferior-package-derivation'.

* guix/inferior.scm (read-inferior-response)
(send-inferior-request): New procedures.
(inferior-eval): Rewrite in terms of these.
(proxy, inferior-package-derivation, inferior-package->derivation)
(package-compiler): New procedures.
* tests/inferior.scm ("inferior-package-derivation"): New test.
---
 guix/inferior.scm  | 125 ++++++++++++++++++++++++++++++++++++++++++---
 tests/inferior.scm |  22 ++++++++
 2 files changed, 141 insertions(+), 6 deletions(-)

diff --git a/guix/inferior.scm b/guix/inferior.scm
index af37233a03..5bef964887 100644
--- a/guix/inferior.scm
+++ b/guix/inferior.scm
@@ -19,9 +19,21 @@
 (define-module (guix inferior)
   #:use-module (srfi srfi-9)
   #:use-module (srfi srfi-9 gnu)
-  #:use-module ((guix utils) #:select (source-properties->location))
+  #:use-module ((guix utils)
+                #:select (%current-system
+                          source-properties->location
+                          call-with-temporary-directory))
+  #:use-module ((guix store)
+                #:select (nix-server-socket
+                          nix-server-major-version
+                          nix-server-minor-version
+                          store-lift))
+  #:use-module ((guix derivations)
+                #:select (read-derivation-from-file))
+  #:use-module (guix gexp)
   #:use-module (ice-9 match)
   #:use-module (ice-9 popen)
+  #:use-module (ice-9 binary-ports)
   #:export (inferior?
             open-inferior
             close-inferior
@@ -36,7 +48,8 @@
             inferior-package-synopsis
             inferior-package-description
             inferior-package-home-page
-            inferior-package-location))
+            inferior-package-location
+            inferior-package-derivation))
 
 ;;; Commentary:
 ;;;
@@ -123,8 +136,7 @@ equivalent.  Return #f if the inferior could not be launched."
 
 (set-record-type-printer! <inferior-object> write-inferior-object)
 
-(define (inferior-eval exp inferior)
-  "Evaluate EXP in INFERIOR."
+(define (read-inferior-response inferior)
   (define sexp->object
     (match-lambda
       (('value value)
@@ -132,14 +144,21 @@ equivalent.  Return #f if the inferior could not be launched."
       (('non-self-quoting address string)
        (inferior-object address string))))
 
-  (write exp (inferior-socket inferior))
-  (newline (inferior-socket inferior))
   (match (read (inferior-socket inferior))
     (('values objects ...)
      (apply values (map sexp->object objects)))
     (('exception key objects ...)
      (apply throw key (map sexp->object objects)))))
 
+(define (send-inferior-request exp inferior)
+  (write exp (inferior-socket inferior))
+  (newline (inferior-socket inferior)))
+
+(define (inferior-eval exp inferior)
+  "Evaluate EXP in INFERIOR."
+  (send-inferior-request exp inferior)
+  (read-inferior-response inferior))
+
 
 ;;;
 ;;; Inferior packages.
@@ -216,3 +235,97 @@ record."
                                             (location->source-properties
                                              loc)))
                                      package-location))))
+
+(define (proxy client backend)                    ;adapted from (guix ssh)
+  "Proxy communication between CLIENT and BACKEND until CLIENT closes the
+connection, at which point CLIENT is closed (both CLIENT and BACKEND must be
+input/output ports.)"
+  (define (select* read write except)
+    ;; This is a workaround for <https://bugs.gnu.org/30365> in Guile < 2.2.4:
+    ;; since 'select' sometimes returns non-empty sets for no good reason,
+    ;; call 'select' a second time with a zero timeout to filter out incorrect
+    ;; replies.
+    (match (select read write except)
+      ((read write except)
+       (select read write except 0))))
+
+  ;; Use buffered ports so that 'get-bytevector-some' returns up to the
+  ;; whole buffer like read(2) would--see <https://bugs.gnu.org/30066>.
+  (setvbuf client _IOFBF 65536)
+  (setvbuf backend _IOFBF 65536)
+
+  (let loop ()
+    (match (select* (list client backend) '() '())
+      ((reads () ())
+       (when (memq client reads)
+         (match (get-bytevector-some client)
+           ((? eof-object?)
+            (close-port client))
+           (bv
+            (put-bytevector backend bv)
+            (force-output backend))))
+       (when (memq backend reads)
+         (match (get-bytevector-some backend)
+           (bv
+            (put-bytevector client bv)
+            (force-output client))))
+       (unless (port-closed? client)
+         (loop))))))
+
+(define* (inferior-package-derivation store package
+                                      #:optional
+                                      (system (%current-system))
+                                      #:key target)
+  "Return the derivation for PACKAGE, an inferior package, built for SYSTEM
+and cross-built for TARGET if TARGET is true.  The inferior corresponding to
+PACKAGE must be live."
+  ;; Create a named socket in /tmp and let the inferior of PACKAGE connect to
+  ;; it and use it as its store.  This ensures the inferior uses the same
+  ;; store, with the same options, the same per-session GC roots, etc.
+  (call-with-temporary-directory
+   (lambda (directory)
+     (chmod directory #o700)
+     (let* ((name     (string-append directory "/inferior"))
+            (socket   (socket AF_UNIX SOCK_STREAM 0))
+            (inferior (inferior-package-inferior package))
+            (major    (nix-server-major-version store))
+            (minor    (nix-server-minor-version store))
+            (proto    (logior major minor)))
+       (bind socket AF_UNIX name)
+       (listen socket 1024)
+       (send-inferior-request
+        `(let ((socket (socket AF_UNIX SOCK_STREAM 0)))
+           (connect socket AF_UNIX ,name)
+
+           ;; 'port->connection' appeared in June 2018 and we can hardly
+           ;; emulate it on older versions.  Thus fall back to
+           ;; 'open-connection', at the risk of talking to the wrong daemon or
+           ;; having our build result reclaimed (XXX).
+           (let* ((store   (if (defined? 'port->connection)
+                               (port->connection socket #:version ,proto)
+                               (open-connection)))
+                  (package (hashv-ref %package-table
+                                      ,(inferior-package-id package)))
+                  (drv     ,(if target
+                                `(package-cross-derivation store package
+                                                           ,target
+                                                           ,system)
+                                `(package-derivation store package
+                                                     ,system))))
+             (close-connection store)
+             (close-port socket)
+             (derivation-file-name drv)))
+        inferior)
+       (match (accept socket)
+         ((client . address)
+          (proxy client (nix-server-socket store))))
+       (close-port socket)
+       (read-derivation-from-file (read-inferior-response inferior))))))
+
+(define inferior-package->derivation
+  (store-lift inferior-package-derivation))
+
+(define-gexp-compiler (package-compiler (package <inferior-package>) system
+                                        target)
+  ;; Compile PACKAGE for SYSTEM, optionally cross-building for TARGET.
+  (inferior-package->derivation package system #:target target))
diff --git a/tests/inferior.scm b/tests/inferior.scm
index ff5cad4210..817fcb6c6b 100644
--- a/tests/inferior.scm
+++ b/tests/inferior.scm
@@ -17,9 +17,13 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (test-inferior)
+  #:use-module (guix tests)
   #:use-module (guix inferior)
   #:use-module (guix packages)
+  #:use-module (guix store)
+  #:use-module (guix derivations)
   #:use-module (gnu packages)
+  #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-64))
 
@@ -29,6 +33,9 @@
 (define %top-builddir
   (dirname (search-path %load-compiled-path "guix.go")))
 
+(define %store
+  (open-connection-for-tests))
+
 
 (test-begin "inferior")
 
@@ -72,4 +79,19 @@
            (close-inferior inferior)
            result))))
 
+(test-equal "inferior-package-derivation"
+  (map derivation-file-name
+       (list (package-derivation %store %bootstrap-guile "x86_64-linux")
+             (package-derivation %store %bootstrap-guile "armhf-linux")))
+  (let* ((inferior (open-inferior %top-builddir
+                                  #:command "scripts/guix"))
+         (packages (inferior-packages inferior))
+         (guile    (find (lambda (package)
+                           (string=? (package-name %bootstrap-guile)
+                                     (inferior-package-name package)))
+                         packages)))
+    (map derivation-file-name
+         (list (inferior-package-derivation %store guile "x86_64-linux")
+               (inferior-package-derivation %store guile "armhf-linux")))))
+
 (test-end "inferior")

From e1a4ffdab52f616f41de4ff783a712bcd50a5187 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sat, 15 Sep 2018 14:50:14 +0200
Subject: [PATCH 038/909] inferior: Add 'lookup-inferior-packages'.

* guix/inferior.scm (<inferior>)[packages, table]: New fields.
(open-inferior): Initialize these new fields.
(inferior-packages): Rename to...
(%inferior-packages): ... this.
(inferior-packages): New procedure; force the promise.
(%inferior-package-table, lookup-inferior-packages): New procedures.
* tests/inferior.scm ("lookup-inferior-packages")
("lookup-inferior-packages and eq?-ness"): New tests.
---
 guix/inferior.scm  | 47 ++++++++++++++++++++++++++++++++++++++++------
 tests/inferior.scm | 29 ++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 6 deletions(-)

diff --git a/guix/inferior.scm b/guix/inferior.scm
index 5bef964887..81b71d0c77 100644
--- a/guix/inferior.scm
+++ b/guix/inferior.scm
@@ -22,7 +22,8 @@
   #:use-module ((guix utils)
                 #:select (%current-system
                           source-properties->location
-                          call-with-temporary-directory))
+                          call-with-temporary-directory
+                          version>? version-prefix?))
   #:use-module ((guix store)
                 #:select (nix-server-socket
                           nix-server-major-version
@@ -31,8 +32,10 @@
   #:use-module ((guix derivations)
                 #:select (read-derivation-from-file))
   #:use-module (guix gexp)
+  #:use-module (srfi srfi-1)
   #:use-module (ice-9 match)
   #:use-module (ice-9 popen)
+  #:use-module (ice-9 vlist)
   #:use-module (ice-9 binary-ports)
   #:export (inferior?
             open-inferior
@@ -45,6 +48,7 @@
             inferior-package-version
 
             inferior-packages
+            lookup-inferior-packages
             inferior-package-synopsis
             inferior-package-description
             inferior-package-home-page
@@ -61,11 +65,13 @@
 
 ;; Inferior Guix process.
 (define-record-type <inferior>
-  (inferior pid socket version)
+  (inferior pid socket version packages table)
   inferior?
   (pid      inferior-pid)
   (socket   inferior-socket)
-  (version  inferior-version))                    ;REPL protocol version
+  (version  inferior-version)                    ;REPL protocol version
+  (packages inferior-package-promise)            ;promise of inferior packages
+  (table    inferior-package-table))             ;promise of vhash
 
 (define (inferior-pipe directory command)
   "Return an input/output pipe on the Guix instance in DIRECTORY.  This runs
@@ -109,7 +115,9 @@ equivalent.  Return #f if the inferior could not be launched."
 
   (match (read pipe)
     (('repl-version 0 rest ...)
-     (let ((result (inferior 'pipe pipe (cons 0 rest))))
+     (letrec ((result (inferior 'pipe pipe (cons 0 rest)
+                                (delay (%inferior-packages result))
+                                (delay (%inferior-package-table result)))))
        (inferior-eval '(use-modules (guix)) result)
        (inferior-eval '(use-modules (gnu)) result)
        (inferior-eval '(define %package-table (make-hash-table))
@@ -181,8 +189,8 @@ equivalent.  Return #f if the inferior could not be launched."
 
 (set-record-type-printer! <inferior-package> write-inferior-package)
 
-(define (inferior-packages inferior)
-  "Return the list of packages known to INFERIOR."
+(define (%inferior-packages inferior)
+  "Compute the list of inferior packages from INFERIOR."
   (let ((result (inferior-eval
                  '(fold-packages (lambda (package result)
                                    (let ((id (object-address package)))
@@ -198,6 +206,33 @@ equivalent.  Return #f if the inferior could not be launched."
             (inferior-package inferior name version id)))
          result)))
 
+(define (inferior-packages inferior)
+  "Return the list of packages known to INFERIOR."
+  (force (inferior-package-promise inferior)))
+
+(define (%inferior-package-table inferior)
+  "Compute a package lookup table for INFERIOR."
+  (fold (lambda (package table)
+          (vhash-cons (inferior-package-name package) package
+                      table))
+        vlist-null
+        (inferior-packages inferior)))
+
+(define* (lookup-inferior-packages inferior name #:optional version)
+  "Return the sorted list of inferior packages matching NAME in INFERIOR, with
+highest version numbers first.  If VERSION is true, return only packages with
+a version number prefixed by VERSION."
+  ;; This is the counterpart of 'find-packages-by-name'.
+  (sort (filter (lambda (package)
+                  (or (not version)
+                      (version-prefix? version
+                                       (inferior-package-version package))))
+                (vhash-fold* cons '() name
+                             (force (inferior-package-table inferior))))
+        (lambda (p1 p2)
+          (version>? (inferior-package-version p1)
+                     (inferior-package-version p2)))))
+
 (define (inferior-package-field package getter)
   "Return the field of PACKAGE, an inferior package, accessed with GETTER."
   (let ((inferior (inferior-package-inferior package))
diff --git a/tests/inferior.scm b/tests/inferior.scm
index 817fcb6c6b..791e30b179 100644
--- a/tests/inferior.scm
+++ b/tests/inferior.scm
@@ -79,6 +79,35 @@
            (close-inferior inferior)
            result))))
 
+(test-equal "lookup-inferior-packages"
+  (let ((->list (lambda (package)
+                  (list (package-name package)
+                        (package-version package)
+                        (package-location package)))))
+    (list (map ->list (find-packages-by-name "guile" #f))
+          (map ->list (find-packages-by-name "guile" "2.2"))))
+  (let* ((inferior (open-inferior %top-builddir
+                                  #:command "scripts/guix"))
+         (->list   (lambda (package)
+                     (list (inferior-package-name package)
+                           (inferior-package-version package)
+                           (inferior-package-location package))))
+         (lst1     (map ->list
+                        (lookup-inferior-packages inferior "guile")))
+         (lst2     (map ->list
+                        (lookup-inferior-packages inferior
+                                                  "guile" "2.2"))))
+    (close-inferior inferior)
+    (list lst1 lst2)))
+
+(test-assert "lookup-inferior-packages and eq?-ness"
+  (let* ((inferior (open-inferior %top-builddir
+                                  #:command "scripts/guix"))
+         (lst1     (lookup-inferior-packages inferior "guile"))
+         (lst2     (lookup-inferior-packages inferior "guile")))
+    (close-inferior inferior)
+    (every eq? lst1 lst2)))
+
 (test-equal "inferior-package-derivation"
   (map derivation-file-name
        (list (package-derivation %store %bootstrap-guile "x86_64-linux")

From 6030396aec325b3c3287a472014bc2d530abb99d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 17 Sep 2018 09:55:31 +0200
Subject: [PATCH 039/909] inferior: Add 'inferior-package-inputs' & co.

* guix/inferior.scm (open-inferior): Use (ice-9 match).
(inferior-package-input-field, inferior-package-inputs):
(inferior-package-native-inputs)
(inferior-package-propagated-inputs)
(inferior-package-transitive-propagated-inputs): New procedures.
* tests/inferior.scm ("inferior-package-inputs"): New test.

inputs fixlet
---
 guix/inferior.scm  | 51 ++++++++++++++++++++++++++++++++++++++++++++++
 tests/inferior.scm | 34 ++++++++++++++++++++++++++++++-
 2 files changed, 84 insertions(+), 1 deletion(-)

diff --git a/guix/inferior.scm b/guix/inferior.scm
index 81b71d0c77..ca819c6eff 100644
--- a/guix/inferior.scm
+++ b/guix/inferior.scm
@@ -33,6 +33,7 @@
                 #:select (read-derivation-from-file))
   #:use-module (guix gexp)
   #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
   #:use-module (ice-9 popen)
   #:use-module (ice-9 vlist)
@@ -53,6 +54,10 @@
             inferior-package-description
             inferior-package-home-page
             inferior-package-location
+            inferior-package-inputs
+            inferior-package-native-inputs
+            inferior-package-propagated-inputs
+            inferior-package-transitive-propagated-inputs
             inferior-package-derivation))
 
 ;;; Commentary:
@@ -120,6 +125,7 @@ equivalent.  Return #f if the inferior could not be launched."
                                 (delay (%inferior-package-table result)))))
        (inferior-eval '(use-modules (guix)) result)
        (inferior-eval '(use-modules (gnu)) result)
+       (inferior-eval '(use-modules (ice-9 match)) result)
        (inferior-eval '(define %package-table (make-hash-table))
                       result)
        result))
@@ -271,6 +277,51 @@ record."
                                              loc)))
                                      package-location))))
 
+(define (inferior-package-input-field package field)
+  "Return the input field FIELD (e.g., 'native-inputs') of PACKAGE, an
+inferior package."
+  (define field*
+    `(compose (lambda (inputs)
+                (map (match-lambda
+                       ;; XXX: Origins are not handled.
+                       ((label (? package? package) rest ...)
+                        (let ((id (object-address package)))
+                          (hashv-set! %package-table id package)
+                          `(,label (package ,id
+                                            ,(package-name package)
+                                            ,(package-version package))
+                                   ,@rest)))
+                       (x
+                        x))
+                     inputs))
+              ,field))
+
+  (define inputs
+    (inferior-package-field package field*))
+
+  (define inferior
+    (inferior-package-inferior package))
+
+  (map (match-lambda
+         ((label ('package id name version) . rest)
+          ;; XXX: eq?-ness of inferior packages is not preserved here.
+          `(,label ,(inferior-package inferior name version id)
+                   ,@rest))
+         (x x))
+       inputs))
+
+(define inferior-package-inputs
+  (cut inferior-package-input-field <> 'package-inputs))
+
+(define inferior-package-native-inputs
+  (cut inferior-package-input-field <> 'package-native-inputs))
+
+(define inferior-package-propagated-inputs
+  (cut inferior-package-input-field <> 'package-propagated-inputs))
+
+(define inferior-package-transitive-propagated-inputs
+  (cut inferior-package-input-field <> 'package-transitive-propagated-inputs))
+
 (define (proxy client backend)                    ;adapted from (guix ssh)
   "Proxy communication between CLIENT and BACKEND until CLIENT closes the
 connection, at which point CLIENT is closed (both CLIENT and BACKEND must be
diff --git a/tests/inferior.scm b/tests/inferior.scm
index 791e30b179..03170a19c9 100644
--- a/tests/inferior.scm
+++ b/tests/inferior.scm
@@ -24,8 +24,10 @@
   #:use-module (guix derivations)
   #:use-module (gnu packages)
   #:use-module (gnu packages bootstrap)
+  #:use-module (gnu packages guile)
   #:use-module (srfi srfi-1)
-  #:use-module (srfi srfi-64))
+  #:use-module (srfi srfi-64)
+  #:use-module (ice-9 match))
 
 (define %top-srcdir
   (dirname (search-path %load-path "guix.scm")))
@@ -108,6 +110,36 @@
     (close-inferior inferior)
     (every eq? lst1 lst2)))
 
+(test-equal "inferior-package-inputs"
+  (let ((->list (match-lambda
+                  ((label (? package? package) . rest)
+                   `(,label
+                     (package ,(package-name package)
+                              ,(package-version package)
+                              ,(package-location package))
+                     ,@rest)))))
+    (list (map ->list (package-inputs guile-2.2))
+          (map ->list (package-native-inputs guile-2.2))
+          (map ->list (package-propagated-inputs guile-2.2))))
+  (let* ((inferior (open-inferior %top-builddir
+                                  #:command "scripts/guix"))
+         (guile    (first (lookup-inferior-packages inferior "guile")))
+         (->list   (match-lambda
+                     ((label (? inferior-package? package) . rest)
+                      `(,label
+                        (package ,(inferior-package-name package)
+                                 ,(inferior-package-version package)
+                                 ,(inferior-package-location package))
+                        ,@rest))))
+         (result   (list (map ->list (inferior-package-inputs guile))
+                         (map ->list
+                              (inferior-package-native-inputs guile))
+                         (map ->list
+                              (inferior-package-propagated-inputs
+                               guile)))))
+    (close-inferior inferior)
+    result))
+
 (test-equal "inferior-package-derivation"
   (map derivation-file-name
        (list (package-derivation %store %bootstrap-guile "x86_64-linux")

From eee8b303f6d82c1400fd8fd3b097406358ed7875 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 17 Sep 2018 10:04:15 +0200
Subject: [PATCH 040/909] inferior: Add 'inferior-package-search-paths' & co.

* guix/inferior.scm (%inferior-package-search-paths)
(inferior-package-native-search-paths)
(inferior-package-search-paths)
(inferior-package-transitive-native-search-paths): New procedures.
* tests/inferior.scm ("inferior-package-search-paths"): New test.
---
 guix/inferior.scm  | 26 ++++++++++++++++++++++++++
 tests/inferior.scm |  9 +++++++++
 2 files changed, 35 insertions(+)

diff --git a/guix/inferior.scm b/guix/inferior.scm
index ca819c6eff..3fa4930095 100644
--- a/guix/inferior.scm
+++ b/guix/inferior.scm
@@ -32,6 +32,7 @@
   #:use-module ((guix derivations)
                 #:select (read-derivation-from-file))
   #:use-module (guix gexp)
+  #:use-module (guix search-paths)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
@@ -58,6 +59,9 @@
             inferior-package-native-inputs
             inferior-package-propagated-inputs
             inferior-package-transitive-propagated-inputs
+            inferior-package-native-search-paths
+            inferior-package-transitive-native-search-paths
+            inferior-package-search-paths
             inferior-package-derivation))
 
 ;;; Commentary:
@@ -322,6 +326,28 @@ inferior package."
 (define inferior-package-transitive-propagated-inputs
   (cut inferior-package-input-field <> 'package-transitive-propagated-inputs))
 
+(define (%inferior-package-search-paths package field)
+  "Return the list of search path specificiations of PACKAGE, an inferior
+package."
+  (define paths
+    (inferior-package-field package
+                            `(compose (lambda (paths)
+                                        (map (@ (guix search-paths)
+                                                search-path-specification->sexp)
+                                             paths))
+                                      ,field)))
+
+  (map sexp->search-path-specification paths))
+
+(define inferior-package-native-search-paths
+  (cut %inferior-package-search-paths <> 'package-native-search-paths))
+
+(define inferior-package-search-paths
+  (cut %inferior-package-search-paths <> 'package-search-paths))
+
+(define inferior-package-transitive-native-search-paths
+  (cut %inferior-package-search-paths <> 'package-transitive-native-search-paths))
+
 (define (proxy client backend)                    ;adapted from (guix ssh)
   "Proxy communication between CLIENT and BACKEND until CLIENT closes the
 connection, at which point CLIENT is closed (both CLIENT and BACKEND must be
diff --git a/tests/inferior.scm b/tests/inferior.scm
index 03170a19c9..99d736bd40 100644
--- a/tests/inferior.scm
+++ b/tests/inferior.scm
@@ -140,6 +140,15 @@
     (close-inferior inferior)
     result))
 
+(test-equal "inferior-package-search-paths"
+  (package-native-search-paths guile-2.2)
+  (let* ((inferior (open-inferior %top-builddir
+                                  #:command "scripts/guix"))
+         (guile    (first (lookup-inferior-packages inferior "guile")))
+         (result   (inferior-package-native-search-paths guile)))
+    (close-inferior inferior)
+    result))
+
 (test-equal "inferior-package-derivation"
   (map derivation-file-name
        (list (package-derivation %store %bootstrap-guile "x86_64-linux")

From 2e6d64e122ad2745154a38122785895d1b66c2ff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 18 Sep 2018 09:56:34 +0200
Subject: [PATCH 041/909] inferior: Add 'inferior-package->manifest-entry'.

* guix/inferior.scm (inferior-package->manifest-entry): New procedure.
* tests/inferior.scm (manifest-entry->list): New procedure.
("inferior-package->manifest-entry"): New test.
---
 guix/inferior.scm  | 42 ++++++++++++++++++++++++++++++++++++++----
 tests/inferior.scm | 18 ++++++++++++++++++
 2 files changed, 56 insertions(+), 4 deletions(-)

diff --git a/guix/inferior.scm b/guix/inferior.scm
index 3fa4930095..c86fdd3ec1 100644
--- a/guix/inferior.scm
+++ b/guix/inferior.scm
@@ -33,6 +33,7 @@
                 #:select (read-derivation-from-file))
   #:use-module (guix gexp)
   #:use-module (guix search-paths)
+  #:use-module (guix profiles)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
   #:use-module (ice-9 match)
@@ -45,12 +46,12 @@
             inferior-eval
             inferior-object?
 
+            inferior-packages
+            lookup-inferior-packages
+
             inferior-package?
             inferior-package-name
             inferior-package-version
-
-            inferior-packages
-            lookup-inferior-packages
             inferior-package-synopsis
             inferior-package-description
             inferior-package-home-page
@@ -62,7 +63,9 @@
             inferior-package-native-search-paths
             inferior-package-transitive-native-search-paths
             inferior-package-search-paths
-            inferior-package-derivation))
+            inferior-package-derivation
+
+            inferior-package->manifest-entry))
 
 ;;; Commentary:
 ;;;
@@ -441,3 +444,34 @@ PACKAGE must be live."
                                         target)
   ;; Compile PACKAGE for SYSTEM, optionally cross-building for TARGET.
   (inferior-package->derivation package system #:target target))
+
+
+;;;
+;;; Manifest entries.
+;;;
+
+(define* (inferior-package->manifest-entry package
+                                           #:optional (output "out")
+                                           #:key (parent (delay #f))
+                                           (properties '()))
+  "Return a manifest entry for the OUTPUT of package PACKAGE."
+  ;; For each dependency, keep a promise pointing to its "parent" entry.
+  (letrec* ((deps  (map (match-lambda
+                          ((label package)
+                           (inferior-package->manifest-entry package
+                                                             #:parent (delay entry)))
+                          ((label package output)
+                           (inferior-package->manifest-entry package output
+                                                             #:parent (delay entry))))
+                        (inferior-package-propagated-inputs package)))
+            (entry (manifest-entry
+                     (name (inferior-package-name package))
+                     (version (inferior-package-version package))
+                     (output output)
+                     (item package)
+                     (dependencies (delete-duplicates deps))
+                     (search-paths
+                      (inferior-package-transitive-native-search-paths package))
+                     (parent parent)
+                     (properties properties))))
+    entry))
diff --git a/tests/inferior.scm b/tests/inferior.scm
index 99d736bd40..6f6abd28a1 100644
--- a/tests/inferior.scm
+++ b/tests/inferior.scm
@@ -21,6 +21,7 @@
   #:use-module (guix inferior)
   #:use-module (guix packages)
   #:use-module (guix store)
+  #:use-module (guix profiles)
   #:use-module (guix derivations)
   #:use-module (gnu packages)
   #:use-module (gnu packages bootstrap)
@@ -38,6 +39,13 @@
 (define %store
   (open-connection-for-tests))
 
+(define (manifest-entry->list entry)
+  (list (manifest-entry-name entry)
+        (manifest-entry-version entry)
+        (manifest-entry-output entry)
+        (manifest-entry-search-paths entry)
+        (map manifest-entry->list (manifest-entry-dependencies entry))))
+
 
 (test-begin "inferior")
 
@@ -164,4 +172,14 @@
          (list (inferior-package-derivation %store guile "x86_64-linux")
                (inferior-package-derivation %store guile "armhf-linux")))))
 
+(test-equal "inferior-package->manifest-entry"
+  (manifest-entry->list (package->manifest-entry
+                         (first (find-best-packages-by-name "guile" #f))))
+  (let* ((inferior (open-inferior %top-builddir
+                                  #:command "scripts/guix"))
+         (guile    (first (lookup-inferior-packages inferior "guile")))
+         (entry    (inferior-package->manifest-entry guile)))
+    (close-inferior inferior)
+    (manifest-entry->list entry)))
+
 (test-end "inferior")

From 811b21fb15d36b06fde994ca7ef5916a9a19f250 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludovic.courtes@inria.fr>
Date: Tue, 18 Sep 2018 10:21:28 +0200
Subject: [PATCH 042/909] profiles: 'packages->manifest' now accepts inferior
 packages.

* guix/profiles.scm (packages->manifest)[inferiors-loaded?]: New
variable.
[inferior->entry]: New procedure.
Accept inferior packages when INFERIORS-LOADED? is true.
* tests/guix-package.sh: Add test using a manifest with an inferior.
* tests/inferior.scm ("packages->manifest"): New test.
---
 guix/profiles.scm     | 27 +++++++++++++++++++++++----
 tests/guix-package.sh | 15 +++++++++++++++
 tests/inferior.scm    | 11 +++++++++++
 3 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/guix/profiles.scm b/guix/profiles.scm
index 8acfcff8c1..669ebe04e5 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -314,12 +314,31 @@ file name."
   "Return a list of manifest entries, one for each item listed in PACKAGES.
 Elements of PACKAGES can be either package objects or package/string tuples
 denoting a specific output of a package."
+  (define inferiors-loaded?
+    ;; This hack allows us to provide seamless integration for inferior
+    ;; packages while not having a hard dependency on (guix inferior).
+    (resolve-module '(guix inferior) #f #f #:ensure #f))
+
+  (define (inferior->entry)
+    (module-ref (resolve-interface '(guix inferior))
+                'inferior-package->manifest-entry))
+
   (manifest
    (map (match-lambda
-         ((package output)
-          (package->manifest-entry package output))
-         ((? package? package)
-          (package->manifest-entry package)))
+          ((package output)
+           (package->manifest-entry package output))
+          ((? package? package)
+           (package->manifest-entry package))
+          ((thing output)
+           (if inferiors-loaded?
+               ((inferior->entry) thing output)
+               (throw 'wrong-type-arg 'packages->manifest
+                      "Wrong package object: ~S" (list thing) (list thing))))
+          (thing
+           (if inferiors-loaded?
+               ((inferior->entry) thing)
+               (throw 'wrong-type-arg 'packages->manifest
+                      "Wrong package object: ~S" (list thing) (list thing)))))
         packages)))
 
 (define (manifest->gexp manifest)
diff --git a/tests/guix-package.sh b/tests/guix-package.sh
index cef3b3452e..f7dfbfad00 100644
--- a/tests/guix-package.sh
+++ b/tests/guix-package.sh
@@ -358,6 +358,21 @@ EOF
 guix package --bootstrap -m "$module_dir/manifest.scm"
 guix package -I | grep guile
 test `guix package -I | wc -l` -eq 1
+guix package --rollback --bootstrap
+
+# Applying a manifest file with inferior packages.
+cat > "$module_dir/manifest.scm"<<EOF
+(use-modules (guix inferior))
+
+(define i
+  (open-inferior "$abs_top_srcdir" #:command "scripts/guix"))
+
+(let ((guile (car (lookup-inferior-packages i "guile-bootstrap"))))
+  (packages->manifest (list guile)))
+EOF
+guix package --bootstrap -m "$module_dir/manifest.scm"
+guix package -I | grep guile
+test `guix package -I | wc -l` -eq 1
 
 # Error reporting.
 cat > "$module_dir/manifest.scm"<<EOF
diff --git a/tests/inferior.scm b/tests/inferior.scm
index 6f6abd28a1..d1d5c00a77 100644
--- a/tests/inferior.scm
+++ b/tests/inferior.scm
@@ -182,4 +182,15 @@
     (close-inferior inferior)
     (manifest-entry->list entry)))
 
+(test-equal "packages->manifest"
+  (map manifest-entry->list
+       (manifest-entries (packages->manifest
+                          (find-best-packages-by-name "guile" #f))))
+  (let* ((inferior (open-inferior %top-builddir
+                                  #:command "scripts/guix"))
+         (guile    (first (lookup-inferior-packages inferior "guile")))
+         (manifest (packages->manifest (list guile))))
+    (close-inferior inferior)
+    (map manifest-entry->list (manifest-entries manifest))))
+
 (test-end "inferior")

From c37f38bde69c072cfd0006ba89f30f0d0ad24448 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 18 Sep 2018 12:08:05 +0200
Subject: [PATCH 043/909] channels: Add 'channel-instances->derivation'.

* guix/channels.scm (channel-instances->derivation): New procedure.
(latest-channel-derivation): Use it.
(channel-instance-derivations): Make private.
---
 guix/channels.scm | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/guix/channels.scm b/guix/channels.scm
index 2e7bffae9f..82389eb583 100644
--- a/guix/channels.scm
+++ b/guix/channels.scm
@@ -47,9 +47,9 @@
             channel-instance-checkout
 
             latest-channel-instances
-            channel-instance-derivations
             latest-channel-derivation
-            channel-instances->manifest))
+            channel-instances->manifest
+            channel-instances->derivation))
 
 ;;; Commentary:
 ;;;
@@ -294,13 +294,17 @@ channel instances."
                                           (zip instances derivations))))
     (return (manifest entries))))
 
+(define (channel-instances->derivation instances)
+  "Return the derivation of the profile containing INSTANCES, a list of
+channel instances."
+  (mlet %store-monad ((manifest (channel-instances->manifest instances)))
+    (profile-derivation manifest)))
+
 (define latest-channel-instances*
   (store-lift latest-channel-instances))
 
 (define* (latest-channel-derivation #:optional (channels %default-channels))
   "Return as a monadic value the derivation that builds the profile for the
 latest instances of CHANNELS."
-  (mlet* %store-monad ((instances ((store-lift latest-channel-instances)
-                                   channels))
-                       (manifest  (channel-instances->manifest instances)))
-    (profile-derivation manifest)))
+  (mlet %store-monad ((instances (latest-channel-instances* channels)))
+    (channel-instances->derivation instances)))

From 2dad0313753c4b506eb1f401136b6fcb4785a3b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 18 Sep 2018 13:30:48 +0200
Subject: [PATCH 044/909] inferior: Add 'inferior-for-channels'.

* guix/inferior.scm (%inferior-cache-directory): New variable.
(inferior-for-channels): New procedure.
---
 guix/inferior.scm | 85 +++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 83 insertions(+), 2 deletions(-)

diff --git a/guix/inferior.scm b/guix/inferior.scm
index c86fdd3ec1..1dbb9e1699 100644
--- a/guix/inferior.scm
+++ b/guix/inferior.scm
@@ -23,7 +23,8 @@
                 #:select (%current-system
                           source-properties->location
                           call-with-temporary-directory
-                          version>? version-prefix?))
+                          version>? version-prefix?
+                          cache-directory))
   #:use-module ((guix store)
                 #:select (nix-server-socket
                           nix-server-major-version
@@ -34,12 +35,23 @@
   #:use-module (guix gexp)
   #:use-module (guix search-paths)
   #:use-module (guix profiles)
+  #:use-module (guix channels)
+  #:use-module (guix monads)
+  #:use-module (guix store)
+  #:use-module (guix derivations)
+  #:use-module (guix base32)
+  #:use-module (gcrypt hash)
+  #:autoload   (guix cache) (maybe-remove-expired-cache-entries)
+  #:autoload   (guix ui) (show-what-to-build*)
+  #:autoload   (guix build utils) (mkdir-p)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
+  #:autoload   (ice-9 ftw) (scandir)
   #:use-module (ice-9 match)
   #:use-module (ice-9 popen)
   #:use-module (ice-9 vlist)
   #:use-module (ice-9 binary-ports)
+  #:use-module ((rnrs bytevectors) #:select (string->utf8))
   #:export (inferior?
             open-inferior
             close-inferior
@@ -65,7 +77,10 @@
             inferior-package-search-paths
             inferior-package-derivation
 
-            inferior-package->manifest-entry))
+            inferior-package->manifest-entry
+
+            %inferior-cache-directory
+            inferior-for-channels))
 
 ;;; Commentary:
 ;;;
@@ -475,3 +490,69 @@ PACKAGE must be live."
                      (parent parent)
                      (properties properties))))
     entry))
+
+
+;;;
+;;; Cached inferiors.
+;;;
+
+(define %inferior-cache-directory
+  ;; Directory for cached inferiors (GC roots).
+  (make-parameter (string-append (cache-directory #:ensure? #f)
+                                 "/inferiors")))
+
+(define* (inferior-for-channels channels
+                                #:key
+                                (cache-directory (%inferior-cache-directory))
+                                (ttl (* 3600 24 30)))
+  "Return an inferior for CHANNELS, a list of channels.  Use the cache at
+CACHE-DIRECTORY, where entries can be reclaimed after TTL seconds.  This
+procedure opens a new connection to the build daemon.
+
+This is a convenience procedure that people may use in manifests passed to
+'guix package -m', for instance."
+  (with-store store
+    (let ()
+      (define instances
+        (latest-channel-instances store channels))
+
+      (define key
+        (bytevector->base32-string
+         (sha256
+          (string->utf8
+           (string-concatenate (map channel-instance-commit instances))))))
+
+      (define cached
+        (string-append cache-directory "/" key))
+
+      (define (base32-encoded-sha256? str)
+        (= (string-length str) 52))
+
+      (define (cache-entries directory)
+        (map (lambda (file)
+               (string-append directory "/" file))
+             (scandir directory base32-encoded-sha256?)))
+
+      (define symlink*
+        (lift2 symlink %store-monad))
+
+      (define add-indirect-root*
+        (store-lift add-indirect-root))
+
+      (mkdir-p cache-directory)
+      (maybe-remove-expired-cache-entries cache-directory
+                                          cache-entries
+                                          #:entry-expiration
+                                          (file-expiration-time ttl))
+
+      (if (file-exists? cached)
+          (open-inferior cached)
+          (run-with-store store
+            (mlet %store-monad ((profile
+                                 (channel-instances->derivation instances)))
+              (mbegin %store-monad
+                (show-what-to-build* (list profile))
+                (built-derivations (list profile))
+                (symlink* (derivation->output-path profile) cached)
+                (add-indirect-root* cached)
+                (return (open-inferior cached)))))))))

From 92a9f14b9d2ae08f5d8f30149963c1e326dd37a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 21 Sep 2018 17:03:52 +0200
Subject: [PATCH 045/909] doc: Add section about inferiors.

* doc/guix.texi (Inferiors): New node.
(Channels): Add xref to "Inferiors".
---
 doc/guix.texi | 131 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 131 insertions(+)

diff --git a/doc/guix.texi b/doc/guix.texi
index b925485be5..76ec718b07 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -147,6 +147,7 @@ Package Management
 * Invoking guix gc::            Running the garbage collector.
 * Invoking guix pull::          Fetching the latest Guix and distribution.
 * Channels::                    Customizing the package collection.
+* Inferiors::                   Interacting with another revision of Guix.
 * Invoking guix describe::      Display information about your Guix revision.
 * Invoking guix pack::          Creating software bundles.
 * Invoking guix archive::       Exporting and importing store files.
@@ -1699,6 +1700,7 @@ guix package -i emacs-guix
 * Invoking guix gc::            Running the garbage collector.
 * Invoking guix pull::          Fetching the latest Guix and distribution.
 * Channels::                    Customizing the package collection.
+* Inferiors::                   Interacting with another revision of Guix.
 * Invoking guix describe::      Display information about your Guix revision.
 * Invoking guix pack::          Creating software bundles.
 * Invoking guix archive::       Exporting and importing store files.
@@ -3053,6 +3055,135 @@ package it defines.
 This gives you super powers, allowing you to track the provenance of binary
 artifacts with very fine grain, and to reproduce software environments at
 will---some sort of ``meta reproducibility'' capabilities, if you will.
+@xref{Inferiors}, for another way to take advantage of these super powers.
+
+@node Inferiors
+@section Inferiors
+
+@c TODO: Remove this once we're more confident about API stability.
+@quotation Note
+The functionality described here is a ``technology preview'' as of version
+@value{VERSION}.  As such, the interface is subject to change.
+@end quotation
+
+@cindex inferiors
+@cindex composition of Guix revisions
+Sometimes you might need to mix packages from the revision of Guix you're
+currently running with packages available in a different revision of Guix.
+Guix @dfn{inferiors} allow you to achieve that by composing different Guix
+revisions in arbitrary ways.
+
+@cindex inferior packages
+Technically, an ``inferior'' is essentially a separate Guix process connected
+to your main Guix process through a REPL (@pxref{Invoking guix repl}).  The
+@code{(guix inferior)} module allows you to create inferiors and to
+communicate with them.  It also provides a high-level interface to browse and
+manipulate the packages that an inferior provides---@dfn{inferior packages}.
+
+When combined with channels (@pxref{Channels}), inferiors provide a simple way
+to interact with a separate revision of Guix.  For example, let's assume you
+want to install in your profile the current @code{guile} package, along with
+the @code{guile-json} as it existed in an older revision of Guix---perhaps
+because the newer @code{guile-json} has an incompatible API and you want to
+run your code against the old API@.  To do that, you could write a manifest for
+use by @code{guix package --manifest} (@pxref{Invoking guix package}); in that
+manifest, you would create an inferior for that old Guix revision you care
+about, and you would look up the @code{guile-json} package in the inferior:
+
+@lisp
+(use-modules (guix inferior) (guix channels)
+             (srfi srfi-1))   ;for 'first'
+
+(define channels
+  ;; This is the old revision from which we want to
+  ;; extract guile-json.
+  (list (channel
+         (name 'guix)
+         (url "https://git.savannah.gnu.org/git/guix.git")
+         (commit
+          "65956ad3526ba09e1f7a40722c96c6ef7c0936fe"))))
+
+(define inferior
+  ;; An inferior representing the above revision.
+  (inferior-for-channels channels))
+
+;; Now create a manifest with the current "guile" package
+;; and the old "guile-json" package.
+(packages->manifest
+ (list (first (lookup-inferior-packages inferior "guile-json"))
+       (specification->package "guile")))
+@end lisp
+
+On its first run, @command{guix package --manifest} might have to build the
+channel you specified before it can create the inferior; subsequent runs will
+be much faster because the Guix revision will be cached.
+
+The @code{(guix inferior)} module provides the following procedures to open an
+inferior:
+
+@deffn {Scheme Procedure} inferior-for-channels @var{channels} @
+   [#:cache-directory] [#:ttl]
+Return an inferior for @var{channels}, a list of channels.  Use the cache at
+@var{cache-directory}, where entries can be reclaimed after @var{ttl} seconds.
+This procedure opens a new connection to the build daemon.
+
+As a side effect, this procedure may build or substitute binaries for
+@var{channels}, which can take time.
+@end deffn
+
+@deffn {Scheme Procedure} open-inferior @var{directory} @
+  [#:command "bin/guix"]
+Open the inferior Guix in @var{directory}, running
+@code{@var{directory}/@var{command} repl} or equivalent.  Return @code{#f} if
+the inferior could not be launched.
+@end deffn
+
+@cindex inferior packages
+The procedures listed below allow you to obtain and manipulate inferior
+packages.
+
+@deffn {Scheme Procedure} inferior-packages @var{inferior}
+Return the list of packages known to @var{inferior}.
+@end deffn
+
+@deffn {Scheme Procedure} lookup-inferior-packages @var{inferior} @var{name} @
+   [@var{version}]
+Return the sorted list of inferior packages matching @var{name} in
+@var{inferior}, with highest version numbers first.  If @var{version} is true,
+return only packages with a version number prefixed by @var{version}.
+@end deffn
+
+@deffn {Scheme Procedure} inferior-package? @var{obj}
+Return true if @var{obj} is an inferior package.
+@end deffn
+
+@deffn {Scheme Procedure} inferior-package-name @var{package}
+@deffnx {Scheme Procedure} inferior-package-version @var{package}
+@deffnx {Scheme Procedure} inferior-package-synopsis @var{package}
+@deffnx {Scheme Procedure} inferior-package-description @var{package}
+@deffnx {Scheme Procedure} inferior-package-home-page @var{package}
+@deffnx {Scheme Procedure} inferior-package-location @var{package}
+@deffnx {Scheme Procedure} inferior-package-inputs @var{package}
+@deffnx {Scheme Procedure} inferior-package-native-inputs @var{package}
+@deffnx {Scheme Procedure} inferior-package-propagated-inputs @var{package}
+@deffnx {Scheme Procedure} inferior-package-transitive-propagated-inputs @var{package}
+@deffnx {Scheme Procedure} inferior-package-native-search-paths @var{package}
+@deffnx {Scheme Procedure} inferior-package-transitive-native-search-paths @var{package}
+@deffnx {Scheme Procedure} inferior-package-search-paths @var{package}
+These procedures are the counterpart of package record accessors
+(@pxref{package Reference}).  Most of them work by querying the inferior
+@var{package} comes from, so the inferior must still be live when you call
+these procedures.
+@end deffn
+
+Inferior packages can be used transparently like any other package or
+file-like object in G-expressions (@pxref{G-Expressions}).  They are also
+transparently handled by the @code{packages->manifest} procedure, which is
+commonly use in manifests (@pxref{Invoking guix package, the
+@option{--manifest} option of @command{guix package}}).  Thus you can insert
+an inferior package pretty much anywhere you would insert a regular package:
+in manifests, in the @code{packages} field of your @code{operating-system}
+declaration, and so on.
 
 @node Invoking guix describe
 @section Invoking @command{guix describe}

From ec944a1de97c8a523d6e1089b8c4430424297f93 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Fri, 21 Sep 2018 15:42:56 +0200
Subject: [PATCH 046/909] gnu: rust: Remove unused "ar" setting.

* gnu/packages/rust.scm (rust-1.20)[arguments]<#:phases>[configure]: Remove
unused "ar" setting.
---
 gnu/packages/rust.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm
index 40633854ae..cc33a0d3b9 100644
--- a/gnu/packages/rust.scm
+++ b/gnu/packages/rust.scm
@@ -574,7 +574,6 @@ rpath = true
 llvm-config = \"" llvm "/bin/llvm-config" "\"
 cc = \"" gcc "/bin/gcc" "\"
 cxx = \"" gcc "/bin/g++" "\"
-ar = \"" binutils "/bin/ar" "\"
 jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
 [dist]
 ") port)))

From 199d72e32759b0b0a0514d1bb667f0f1f2a6cbb4 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 14:26:30 +0200
Subject: [PATCH 047/909] gnu: python-pyparsing: Update to 2.2.1.

* gnu/packages/python.scm (python-pyparsing): Update to 2.2.1.
[source]: Use PYPI-URI.
---
 gnu/packages/python.scm | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index a11c7e315e..26829f050e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3350,16 +3350,13 @@ library, libgit2 implements Git plumbing.")
 (define-public python-pyparsing
   (package
     (name "python-pyparsing")
-    (version "2.2.0")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://sourceforge/pyparsing/pyparsing"
-                           "/pyparsing-" version
-                           "/pyparsing-" version ".tar.gz"))
+       (uri (pypi-uri "pyparsing" version))
        (sha256
-        (base32
-         "016b9gh606aa44sq92jslm89bg874ia0yyiyb643fa6dgbsbqch8"))))
+        (base32 "06dgd0iilvf8m0ssmfpcbh8l6jf0zkp8adbb84llksg17crfx4zl"))))
     (build-system python-build-system)
     (outputs '("out" "doc"))
     (arguments

From 9a32bdf8a9b56eec84310a809820eadd1a33f45f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 17:12:36 +0200
Subject: [PATCH 048/909] gnu: wxwidgets: Update to 3.0.4.

* gnu/packages/wxwidgets.scm (wxwidgets): Update to 3.0.4.
---
 gnu/packages/wxwidgets.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm
index f1a61329e8..6cbfd76e10 100644
--- a/gnu/packages/wxwidgets.scm
+++ b/gnu/packages/wxwidgets.scm
@@ -49,7 +49,7 @@
 (define-public wxwidgets
   (package
     (name "wxwidgets")
-    (version "3.0.3")
+    (version "3.0.4")
     (source
      (origin
        (method url-fetch)
@@ -57,7 +57,7 @@
                            "releases/download/v" version
                            "/wxWidgets-" version ".tar.bz2"))
        (sha256
-        (base32 "0yrhp5cs2g33cpbdwdzicmm5m4mfnlvxwv031x9266zc90zh7j08"))))
+        (base32 "1w7pgfqjab7n84lc4aarydl3g55d1hdgl2ilwml766r6inc7y5cn"))))
     (build-system glib-or-gtk-build-system)
     (inputs
      `(("glu" ,glu)

From 10fadd1e3d2e67ed8bc34a91a587d4862f6055e5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 17:13:13 +0200
Subject: [PATCH 049/909] gnu: filezilla: Update to 3.37.1.

* gnu/packages/ftp.scm (filezilla): Update to 3.37.1.
---
 gnu/packages/ftp.scm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index 335c975d12..faf9f5dd10 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -207,16 +207,14 @@ output.
 (define-public filezilla
   (package
     (name "filezilla")
-    (version "3.31.0")
+    (version "3.37.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://sourceforge.net/projects/" name
-                           "/files/FileZilla_Client/" version
-                           "/FileZilla_" version "_src" ".tar.bz2"))
+       (uri (string-append "https://download.filezilla-project.org/client/"
+                           "FileZilla_" version "_src.tar.bz2"))
        (sha256
-        (base32
-         "1rfysb8dil35a7bzj2kw0mzzkys39d7yn6ipsbk8l6rkwfvnii8l"))))
+        (base32 "1bbxlm8gc0r5jing8xmkdbhj5a1qfbjn8varhny3mrk1am4m7s7l"))))
     (build-system gnu-build-system)
     (arguments
       ;; Don't let filezilla phone home to check for updates.

From 43726c522f4b3802ce66c0f17160314569b1d673 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 20:13:14 +0200
Subject: [PATCH 050/909] gnu: emacs-password-store: Update to 1.7.3.

* gnu/packages/emacs.scm (emacs-password-store): Update to 1.7.3.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 977f0c99b8..4662c11cff 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -8394,7 +8394,7 @@ close, copy, cut, paste, undo, redo.")
 (define-public emacs-password-store
   (package
     (name "emacs-password-store")
-    (version "1.7.2")
+    (version "1.7.3")
     (source (origin
               (method url-fetch)
               (uri
@@ -8402,7 +8402,7 @@ close, copy, cut, paste, undo, redo.")
                               "password-store-" version ".tar.xz"))
               (sha256
                (base32
-                "1sl0d7nc85c6c2bmmmyb8rpmn47vhkj831l153mjlkawjvhwas27"))))
+                "1x53k5dn3cdmvy8m4fqdld4hji5n676ksl0ql4armkmsds26av1b"))))
     (build-system emacs-build-system)
     (arguments
      `(#:phases

From 1302837f6b9ba4364ed06cdbe55fb54e8fe7de0f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 20:22:51 +0200
Subject: [PATCH 051/909] gnu: workrave: Update to 1.10.21.

* gnu/packages/gnome.scm (workrave): Update to 1.10.21.
[source]: Use GIT-FILE-NAME.
---
 gnu/packages/gnome.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 99f4c1271a..65716ce413 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -7224,7 +7224,7 @@ mp3, Ogg Vorbis and FLAC")
     (license license:gpl2+)))
 
 (define-public workrave
-  (let ((commit "v1_10_20"))
+  (let ((commit "v1_10_21"))
     (package
       (name "workrave")
       (version (string-map (match-lambda
@@ -7236,10 +7236,10 @@ mp3, Ogg Vorbis and FLAC")
                 (uri (git-reference
                       (url "https://github.com/rcaelers/workrave.git")
                       (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
+                (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "099a87zkrkmsgfz9isrfm89dh545x52891jh6qxmn19h6wwsi941"))))
+                  "150qca8c552fakjlzkgarsxgp87l1xcwn19svqsa9d0cygqxjgia"))))
       (build-system glib-or-gtk-build-system)
       (arguments
        `(#:phases

From a255142af3288ff76e37ac30b6b6f9acdcd2ca01 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Fri, 21 Sep 2018 21:55:28 +0200
Subject: [PATCH 052/909] gnu: emacs-org: Update to 9.1.14.

* gnu/packages/emacs.scm (emacs-org): Update to 9.1.14.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 4662c11cff..28d97f82c1 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5318,14 +5318,14 @@ passive voice.")
     (name "emacs-org")
     ;; emacs-org-contrib inherits from this package.  Please update its sha256
     ;; checksum as well.
-    (version "9.1.13")
+    (version "9.1.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://elpa.gnu.org/packages/org-"
                                   version ".tar"))
               (sha256
                (base32
-                "1vx0n32gvrgy2bl2b4pvxf00cywxwm57gi46f2b2zlrnmd5n85pr"))))
+                "17vd9hig26rqv90l6y92hc2i0x29g44lsdsp0xd4m53s8r3zdikz"))))
     (build-system emacs-build-system)
     (home-page "https://orgmode.org/")
     (synopsis "Outline-based notes management and organizer")

From 78b7b9dbe9098c9c47c7acba363223bb6c5bb1c8 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Fri, 21 Sep 2018 22:22:09 +0200
Subject: [PATCH 053/909] gnu: snap: Update to 4.2.1.4.

* gnu/packages/education.scm (snap): Update to 4.2.1.4.
---
 gnu/packages/education.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index 52dde26f44..8b02adc182 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -243,7 +243,7 @@ easy.")
 (define-public snap
   (package
     (name "snap")
-    (version "4.2.1.3")
+    (version "4.2.1.4")
     (source
      (origin
        (method git-fetch)
@@ -253,7 +253,7 @@ easy.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0n32hg8rx6alk5j58l76gzmicrg1bp7jagz5mh1zrg7591aicjal"))))
+         "0yc0w0cdhvi0nwqqrann2v3y0n7shxh7irgixqvlavp4k49d7aqj"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))

From 05fb1e0017030f1c0cbc7e9a1adeccca57ef1d9d Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 22 Sep 2018 08:19:09 +1000
Subject: [PATCH 054/909] gnu: hmmer: Update to 3.2.1.

* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                  |  1 -
 gnu/packages/bioinformatics.scm               | 19 ++++++----------
 .../hmmer-remove-cpu-specificity.patch        | 22 -------------------
 3 files changed, 7 insertions(+), 35 deletions(-)
 delete mode 100644 gnu/packages/patches/hmmer-remove-cpu-specificity.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 4097ad5fcd..daf96ea4b6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -805,7 +805,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/hdf-eos5-remove-gctp.patch		\
   %D%/packages/patches/hdf-eos5-fix-szip.patch			\
   %D%/packages/patches/hdf-eos5-fortrantests.patch		\
-  %D%/packages/patches/hmmer-remove-cpu-specificity.patch	\
   %D%/packages/patches/higan-remove-march-native-flag.patch	\
   %D%/packages/patches/hubbub-sort-entities.patch		\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9599e3096f..b619866ba3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2936,18 +2936,15 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
 (define-public hmmer
   (package
     (name "hmmer")
-    (version "3.1b2")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append
-             "http://eddylab.org/software/hmmer"
-             (version-major version) "/"
-             version "/hmmer-" version ".tar.gz"))
+             "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz"))
        (sha256
         (base32
-         "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
-       (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
+         "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5"))))
     (build-system gnu-build-system)
     (native-inputs `(("perl" ,perl)))
     (home-page "http://hmmer.org/")
@@ -2957,12 +2954,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
 sequences, and for making protein sequence alignments.  It implements methods
 using probabilistic models called profile hidden Markov models (profile
 HMMs).")
-    (license (list license:gpl3+
-                   ;; The bundled library 'easel' is distributed
-                   ;; under The Janelia Farm Software License.
-                   (license:non-copyleft
-                    "file://easel/LICENSE"
-                    "See easel/LICENSE in the distribution.")))))
+    ;; hmmer uses non-portable SSE intrinsics so building fails on other
+    ;; platforms.
+    (supported-systems '("x86_64-linux" "i686-linux"))
+    (license license:bsd-3)))
 
 (define-public htseq
   (package
diff --git a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
deleted file mode 100644
index ba98db4d0e..0000000000
--- a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-This patch removes compilation flags which make the build for the machine
-where compilation takes place, rendering the build not reproducible.
-
-diff --git a/configure b/configure
-index 8b6aaef..49a6afc 100755
---- a/configure
-+++ b/configure
-@@ -6125,14 +6125,6 @@ fi # guess arch
- 
- if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then
- for arch in $ax_gcc_arch; do
--  if test "x$acx_maxopt_portable" = xyes; then # if we require portable code
--    flags="-mtune=$arch"
--    # -mcpu=$arch and m$arch generate nonportable code on every arch except
--    # x86.  And some other arches (e.g. Alpha) don't accept -mtune.  Grrr.
--    case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac
--  else
--    flags="-march=$arch -mcpu=$arch -m$arch"
--  fi
-   for flag in $flags; do
-     as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $flag" >&5

From 91294b53619995712a6f8d497d650bfc02b4c952 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sat, 22 Sep 2018 10:07:50 +0200
Subject: [PATCH 055/909] Revert 'gnu: rust: Remove unused "ar" setting.'.

Some versions of Rust do need it and others complain about it.
For now, revert the removal entirely.

This reverts commit ec944a1de97c8a523d6e1089b8c4430424297f93.
---
 gnu/packages/rust.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm
index cc33a0d3b9..40633854ae 100644
--- a/gnu/packages/rust.scm
+++ b/gnu/packages/rust.scm
@@ -574,6 +574,7 @@ rpath = true
 llvm-config = \"" llvm "/bin/llvm-config" "\"
 cc = \"" gcc "/bin/gcc" "\"
 cxx = \"" gcc "/bin/g++" "\"
+ar = \"" binutils "/bin/ar" "\"
 jemalloc = \"" jemalloc "/lib/libjemalloc_pic.a" "\"
 [dist]
 ") port)))

From ae71cd8ac93245360ffe73d6ab260975ec0d742f Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 22 Sep 2018 04:47:54 -0400
Subject: [PATCH 056/909] gnu: icecat: Add fixes from upstream mozilla-esr60
 [security fixes].

Includes fixes for CVE-2018-12383 and CVE-2018-12385.

* gnu/packages/patches/icecat-CVE-2018-12383.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/patches/icecat-avoid-bundled-libraries.patch: Adapt to apply
cleanly to IceCat 60.
* gnu/packages/gnuzilla.scm (mozilla-patch): Update to fetch from
mozilla-esr60.
(icecat): Add selected changesets from upstream mozilla-esr60.
---
 gnu/local.mk                                  |   1 +
 gnu/packages/gnuzilla.scm                     |   8 +-
 .../patches/icecat-CVE-2018-12383.patch       | 103 ++++++++++++++++++
 .../icecat-avoid-bundled-libraries.patch      |  20 ++--
 4 files changed, 119 insertions(+), 13 deletions(-)
 create mode 100644 gnu/packages/patches/icecat-CVE-2018-12383.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index daf96ea4b6..fe2b573dd5 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -810,6 +810,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch        \
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
+  %D%/packages/patches/icecat-CVE-2018-12383.patch		\
   %D%/packages/patches/icecat-use-system-graphite2.patch	\
   %D%/packages/patches/icecat-use-system-harfbuzz.patch		\
   %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index db8f85cfb1..653cee93d5 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -469,10 +469,10 @@ security standards.")
     (license license:mpl2.0)))
 
 (define (mozilla-patch file-name changeset hash)
-  "Return an origin for CHANGESET from the mozilla-esr52 repository."
+  "Return an origin for CHANGESET from the mozilla-esr60 repository."
   (origin
     (method url-fetch)
-    (uri (string-append "https://hg.mozilla.org/releases/mozilla-esr52/raw-rev/"
+    (uri (string-append "https://hg.mozilla.org/releases/mozilla-esr60/raw-rev/"
                         changeset))
     (sha256 (base32 hash))
     (file-name file-name)))
@@ -498,7 +498,9 @@ security standards.")
         (search-patch "icecat-avoid-bundled-libraries.patch")
         ;; FIXME (search-patch "icecat-use-system-harfbuzz.patch")
         ;; FIXME (search-patch "icecat-use-system-graphite2.patch")
-        ))
+        (mozilla-patch "icecat-CVE-2018-12385.patch"      "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5")
+        (search-patch  "icecat-CVE-2018-12383.patch")
+        (mozilla-patch "icecat-bug-1489744.patch"         "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")))
       (modules '((guix build utils)))
       (snippet
        '(begin
diff --git a/gnu/packages/patches/icecat-CVE-2018-12383.patch b/gnu/packages/patches/icecat-CVE-2018-12383.patch
new file mode 100644
index 0000000000..17ca0f3773
--- /dev/null
+++ b/gnu/packages/patches/icecat-CVE-2018-12383.patch
@@ -0,0 +1,103 @@
+Based on upstream changeset:
+  https://hg.mozilla.org/releases/mozilla-esr60/rev/300efdbc9fe1
+but with the git binary patch and related test changes omitted,
+and adapted to apply cleanly to GNU IceCat.
+
+# HG changeset patch
+# User David Keeler <dkeeler@mozilla.com>
+# Date 1531860660 25200
+# Node ID 300efdbc9fe1f9165428c7934861033935b5abfa
+# Parent  80a4a7ef281374dbb2afda8edac54665b14b9ef8
+Bug 1475775 - Clean up old NSS DB file after upgrade if necessary. r=franziskus, r=mattn, a=RyanVM
+
+Reviewers: franziskus, mattn
+
+Bug #: 1475775
+
+Differential Revision: https://phabricator.services.mozilla.com/D2202
+
+diff --git a/security/manager/ssl/nsNSSComponent.cpp b/security/manager/ssl/nsNSSComponent.cpp
+--- a/security/manager/ssl/nsNSSComponent.cpp
++++ b/security/manager/ssl/nsNSSComponent.cpp
+@@ -1935,16 +1935,61 @@ AttemptToRenameBothPKCS11ModuleDBVersion
+   NS_NAMED_LITERAL_CSTRING(sqlModuleDBFilename, "pkcs11.txt");
+   nsresult rv = AttemptToRenamePKCS11ModuleDB(profilePath,
+                                               legacyModuleDBFilename);
+   if (NS_FAILED(rv)) {
+     return rv;
+   }
+   return AttemptToRenamePKCS11ModuleDB(profilePath, sqlModuleDBFilename);
+ }
++
++// When we changed from the old dbm database format to the newer sqlite
++// implementation, the upgrade process left behind the existing files. Suppose a
++// user had not set a password for the old key3.db (which is about 99% of
++// users). After upgrading, both the old database and the new database are
++// unprotected. If the user then sets a password for the new database, the old
++// one will not be protected. In this scenario, we should probably just remove
++// the old database (it would only be relevant if the user downgraded to a
++// version of IceCat before 58, but we have to trade this off against the
++// user's old private keys being unexpectedly unprotected after setting a
++// password).
++// This was never an issue on Android because we always used the new
++// implementation.
++static void
++MaybeCleanUpOldNSSFiles(const nsACString& profilePath)
++{
++  UniquePK11SlotInfo slot(PK11_GetInternalKeySlot());
++  if (!slot) {
++    return;
++  }
++  // Unfortunately we can't now tell the difference between "there already was a
++  // password when the upgrade happened" and "there was not a password but then
++  // the user added one after upgrading".
++  bool hasPassword = PK11_NeedLogin(slot.get()) &&
++                     !PK11_NeedUserInit(slot.get());
++  if (!hasPassword) {
++    return;
++  }
++  nsCOMPtr<nsIFile> dbFile = do_CreateInstance("@mozilla.org/file/local;1");
++  if (!dbFile) {
++    return;
++  }
++  nsresult rv = dbFile->InitWithNativePath(profilePath);
++  if (NS_FAILED(rv)) {
++    return;
++  }
++  NS_NAMED_LITERAL_CSTRING(keyDBFilename, "key3.db");
++  rv = dbFile->AppendNative(keyDBFilename);
++  if (NS_FAILED(rv)) {
++    return;
++  }
++  // Since this isn't a directory, the `recursive` argument to `Remove` is
++  // irrelevant.
++  Unused << dbFile->Remove(false);
++}
+ #endif // ifndef ANDROID
+ 
+ // Given a profile directory, attempt to initialize NSS. If nocertdb is true,
+ // (or if we don't have a profile directory) simply initialize NSS in no DB mode
+ // and return. Otherwise, first attempt to initialize in read/write mode, and
+ // then read-only mode if that fails. If both attempts fail, we may be failing
+ // to initialize an NSS DB collection that has FIPS mode enabled. Attempt to
+ // ascertain if this is the case, and if so, rename the offending PKCS#11 module
+@@ -1966,16 +2011,19 @@ InitializeNSSWithFallbacks(const nsACStr
+ 
+   // Try read/write mode. If we're in safeMode, we won't load PKCS#11 modules.
+ #ifndef ANDROID
+   PRErrorCode savedPRErrorCode1;
+ #endif // ifndef ANDROID
+   SECStatus srv = ::mozilla::psm::InitializeNSS(profilePath, false, !safeMode);
+   if (srv == SECSuccess) {
+     MOZ_LOG(gPIPNSSLog, LogLevel::Debug, ("initialized NSS in r/w mode"));
++#ifndef ANDROID
++    MaybeCleanUpOldNSSFiles(profilePath);
++#endif // ifndef ANDROID
+     return NS_OK;
+   }
+ #ifndef ANDROID
+   savedPRErrorCode1 = PR_GetError();
+   PRErrorCode savedPRErrorCode2;
+ #endif // ifndef ANDROID
+   // That failed. Try read-only mode.
+   srv = ::mozilla::psm::InitializeNSS(profilePath, true, !safeMode);
diff --git a/gnu/packages/patches/icecat-avoid-bundled-libraries.patch b/gnu/packages/patches/icecat-avoid-bundled-libraries.patch
index 114631517a..b5e9fb887e 100644
--- a/gnu/packages/patches/icecat-avoid-bundled-libraries.patch
+++ b/gnu/packages/patches/icecat-avoid-bundled-libraries.patch
@@ -1,8 +1,8 @@
 Fixes needed when avoiding bundled libraries.
 
---- icecat-52.0.2/xpcom/build/moz.build.orig
-+++ icecat-52.0.2/xpcom/build/moz.build
-@@ -93,10 +93,5 @@
+--- icecat-60.2.0/xpcom/build/moz.build.orig	2018-09-13 17:46:49.000000000 -0400
++++ icecat-60.2.0/xpcom/build/moz.build	2018-09-22 04:26:50.659564554 -0400
+@@ -99,10 +99,5 @@
      '/docshell/base',
  ]
  
@@ -13,9 +13,9 @@ Fixes needed when avoiding bundled libraries.
 -
  if CONFIG['MOZ_WIDGET_TOOLKIT'] == 'cocoa':
      CXXFLAGS += CONFIG['TK_CFLAGS']
---- icecat-52.0.2/storage/moz.build.orig
-+++ icecat-52.0.2/storage/moz.build
-@@ -114,7 +114,6 @@
+--- icecat-60.2.0/storage/moz.build.orig	2018-09-13 17:51:11.000000000 -0400
++++ icecat-60.2.0/storage/moz.build	2018-09-22 04:26:50.659564554 -0400
+@@ -117,7 +117,6 @@
      DEFINES['MOZ_MEMORY_TEMP_STORE_PRAGMA'] = True
  
  LOCAL_INCLUDES += [
@@ -23,13 +23,13 @@ Fixes needed when avoiding bundled libraries.
      '/dom/base',
  ]
  
---- icecat-52.0.2/dom/indexedDB/moz.build.orig
-+++ icecat-52.0.2/dom/indexedDB/moz.build
-@@ -101,7 +101,6 @@
+--- icecat-60.2.0/dom/indexedDB/moz.build.orig	2018-09-13 17:49:42.000000000 -0400
++++ icecat-60.2.0/dom/indexedDB/moz.build	2018-09-22 04:26:50.663564574 -0400
+@@ -102,7 +102,6 @@
      CXXFLAGS += ['-Wno-error=shadow']
  
  LOCAL_INCLUDES += [
 -    '/db/sqlite3/src',
      '/dom/base',
      '/dom/storage',
-     '/dom/workers',
+     '/ipc/glue',

From 21280a8cd805ace5f95cd2580b8a6ca1e25050d7 Mon Sep 17 00:00:00 2001
From: Katherine Cox-Buday <cox.katherine.e@gmail.com>
Date: Tue, 18 Sep 2018 21:52:58 -0500
Subject: [PATCH 057/909] gnu: Add Go 1.11.

* gnu/packages/golang.scm (go-1.11): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/golang.scm | 119 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 119 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index fd4c362d36..bba03e77f2 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -12,6 +12,7 @@
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
+;;; Copyright @ 2018 Katherine Cox-Buday <cox.katherine.e@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -499,6 +500,124 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                  (setenv "HOME" "/tmp")
                  #t)))))))))
 
+(define-public go-1.11
+  (package
+    (inherit go-1.10)
+    (name "go")
+    (version "1.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://storage.googleapis.com/golang/"
+                           name version ".src.tar.gz"))
+       (sha256
+        (base32
+         "1ysj04jzds6xa8kdflkdsgyv3mg9fdn90zdf78g4g6p4bwpy3hdg"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments go-1.10)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (replace 'prebuild
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((gcclib (string-append (assoc-ref inputs "gcc:lib") "/lib"))
+                      (ld (string-append (assoc-ref inputs "libc") "/lib"))
+                      (loader (car (find-files ld "^ld-linux.+")))
+                      (net-base (assoc-ref inputs "net-base"))
+                      (tzdata-path
+                       (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo"))
+                      (output (assoc-ref outputs "out")))
+
+                 (for-each delete-file
+                           ;; Removing net/ tests, which fail when attempting to access
+                           ;; network resources not present in the build container.
+                           '("net/listen_test.go"
+                             "net/parse_test.go"
+                             "net/cgo_unix_test.go"
+                             ;; A side affect of these test scripts is testing
+                             ;; cgo. Attempts at using cgo flags and
+                             ;; directives with these scripts as specified
+                             ;; here (https://golang.org/cmd/cgo/) have not
+                             ;; worked. The tests continue to state that they
+                             ;; can not find crt1.o despite being present.
+                             "cmd/go/testdata/script/list_compiled_imports.txt"
+                             "cmd/go/testdata/script/mod_case_cgo.txt"
+                             ;; https://github.com/golang/go/issues/24884
+                             "os/user/user_test.go"))
+
+                 (substitute* "os/os_test.go"
+                   (("/usr/bin") (getcwd))
+                   (("/bin/pwd") (which "pwd"))
+                   (("/bin/sh") (which "sh")))
+
+                 (substitute* "cmd/vendor/golang.org/x/sys/unix/syscall_unix_test.go"
+                   (("/usr/bin") "/tmp"))
+
+                 ;; Add libgcc to runpath
+                 (substitute* "cmd/link/internal/ld/lib.go"
+                   (("!rpath.set") "true"))
+                 (substitute* "cmd/go/internal/work/gccgo.go"
+                   (("cgoldflags := \\[\\]string\\{\\}")
+                    (string-append "cgoldflags := []string{"
+                                   "\"-rpath=" gcclib "\""
+                                   "}"))
+                   (("\"-lgcc_s\", ")
+                    (string-append
+                     "\"-Wl,-rpath=" gcclib "\", \"-lgcc_s\", ")))
+                 (substitute* "cmd/go/internal/work/gc.go"
+                   (("ldflags = setextld\\(ldflags, compiler\\)")
+                    (string-append
+                     "ldflags = setextld(ldflags, compiler)\n"
+                     "ldflags = append(ldflags, \"-r\")\n"
+                     "ldflags = append(ldflags, \"" gcclib "\")\n")))
+
+                 ;; Disable failing tests: these tests attempt to access
+                 ;; commands or network resources which are neither available
+                 ;; nor necessary for the build to succeed.
+                 (for-each
+                  (match-lambda
+                    ((file regex)
+                     (substitute* file
+                       ((regex all before test_name)
+                        (string-append before "Disabled" test_name)))))
+                  '(("net/net_test.go" "(.+)(TestShutdownUnix.+)")
+                    ("net/dial_test.go" "(.+)(TestDialTimeout.+)")
+                    ("os/os_test.go" "(.+)(TestHostname.+)")
+                    ("time/format_test.go" "(.+)(TestParseInSydney.+)")
+                    ("time/format_test.go" "(.+)(TestParseInLocation.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestEcho.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestCommandRelativeName.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestCatStdin.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestCatGoodAndBadFile.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExitStatus.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestPipes.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestStdinClose.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestIgnorePipeErrorOnSuccess.+)")
+                    ("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)")
+                    ("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)")
+                    ("cmd/go/go_test.go" "(.+)(TestTwoPkgConfigs.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)")
+                    ("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)")
+                    ("net/lookup_test.go" "(.+)(TestLookupPort.+)")
+                    ("syscall/exec_linux_test.go"
+                     "(.+)(TestCloneNEWUSERAndRemapNoRootDisableSetgroups.+)")))
+
+                 ;; fix shebang for testar script
+                 ;; note the target script is generated at build time.
+                 (substitute* "../misc/cgo/testcarchive/carchive_test.go"
+                   (("#!/usr/bin/env") (string-append "#!" (which "env"))))
+
+                 (substitute* "net/lookup_unix.go"
+                   (("/etc/protocols") (string-append net-base "/etc/protocols")))
+                 (substitute* "net/port_unix.go"
+                   (("/etc/services") (string-append net-base "/etc/services")))
+                 (substitute* "time/zoneinfo_unix.go"
+                   (("/usr/share/zoneinfo/") tzdata-path))
+                 (substitute* (find-files "cmd" "\\.go")
+                   (("/lib(64)?/ld-linux.*\\.so\\.[0-9]") loader))
+                 #t)))))))))
+
 (define-public go go-1.9)
 
 (define-public go-github-com-alsm-ioprogress

From 844cc6f876b8dcadf210398e68b3f3f824cb7144 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 22 Sep 2018 19:17:29 -0400
Subject: [PATCH 058/909] gnu: webkitgtk: Add version 2.22.2.

* gnu/packages/webkit.scm (webkitgtk-2.22): New variable.
---
 gnu/packages/webkit.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index b671e44d18..976411dbbc 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -24,6 +24,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix utils)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
@@ -32,6 +33,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages enchant)
   #:use-module (gnu packages flex)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages glib)
@@ -149,3 +151,34 @@ HTML/CSS applications to full-fledged web browsers.")
                    license:lgpl2.1+
                    license:bsd-2
                    license:bsd-3))))
+
+;; This version of webkitgtk needs to be kept separate, because it requires a
+;; newer version of GCC than our default compiler, and this causes problems
+;; when linked with C++ libraries built using our default compiler.  For now,
+;; we use this newer webkitgtk only for selected packages, e.g. epiphany.
+(define-public webkitgtk-2.22
+  (package/inherit webkitgtk
+    (name "webkitgtk")
+    (version "2.22.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.webkitgtk.org/releases/"
+                                  name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1flrbr8pzbrlwv09b4pmgh6vklw7jghd2lgrhcb72vl9s7a8fm1l"))))
+    (native-inputs
+     `(("gcc" ,gcc-7)  ; webkitgtk-2.22 requires gcc-6 or newer
+       ,@(package-native-inputs webkitgtk)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments webkitgtk)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'add-gst-plugins-base-include-path
+               'work-around-gcc-7-include-path-issue
+             ;; FIXME: Work around a problem with gcc-7 includes (see
+             ;; <https://bugs.gnu.org/30756>).
+             (lambda _
+               (unsetenv "C_INCLUDE_PATH")
+               (unsetenv "CPLUS_INCLUDE_PATH")
+               #t))))))))

From 480d39a600701621e4d5938c8753b8487baa2c7f Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 22 Sep 2018 19:21:16 -0400
Subject: [PATCH 059/909] gnu: epiphany: Use webkitgtk-2.22.

* gnu/packages/gnome.scm (epiphany)[native-inputs]: Add gcc-7.
[inputs]: Replace webkitgtk with webkitgtk-2.22.
---
 gnu/packages/gnome.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 65716ce413..f9c9f1cf5c 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -4187,6 +4187,7 @@ a secret password store, an adblocker, and a modern UI.")
      `(("dconf" ,dconf)))
     (native-inputs
      `(("desktop-file-utils" ,desktop-file-utils) ; for update-desktop-database
+       ("gcc" ,gcc-7)  ; needed because webkitgtk-2.22 is compiled with gcc-7
        ("glib:bin" ,glib "bin") ; for glib-mkenums
        ("gtk+:bin" ,gtk+ "bin") ; for gtk-update-icon-cache
        ("intltool" ,intltool)
@@ -4207,7 +4208,7 @@ a secret password store, an adblocker, and a modern UI.")
        ("libxslt" ,libxslt)
        ("nettle" ,nettle) ; for hogweed
        ("sqlite" ,sqlite)
-       ("webkitgtk" ,webkitgtk)))
+       ("webkitgtk" ,webkitgtk-2.22)))
     (home-page "https://wiki.gnome.org/Apps/Web")
     (synopsis "GNOME web browser")
     (description

From 84b334362ebb7fb2e8bc0ec4df1d8b28aabe2413 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 22 Sep 2018 19:25:36 -0400
Subject: [PATCH 060/909] gnu: eolie: Use webkitgtk-2.22.

* gnu/packages/gnome.scm (eolie)[native-inputs]: Add gcc-7:lib.
[inputs]: Replace webkitgtk with webkitgtk-2.22.
[arguments]: Add "gcc:lib" to the list of libraries to add to
LD_LIBRARY_PATH.  Use invoke.
---
 gnu/packages/gnome.scm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index f9c9f1cf5c..9f5ede8b07 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -4104,19 +4104,20 @@ work and the interface is well tested.")
          (delete 'configure)
          (replace 'build
            (lambda* (#:key outputs #:allow-other-keys)
-             (zero? (system* "meson" "build"
-                             "--prefix" (assoc-ref outputs "out")))))
+             (invoke "meson" "build"
+                      "--prefix" (assoc-ref outputs "out"))))
          (replace 'check
-           (lambda _ (zero? (system* "ninja" "-C" "build" "test"))))
+           (lambda _ (invoke "ninja" "-C" "build" "test")))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
-             (zero? (system* "ninja" "-C" "build" "install"))))
+             (invoke "ninja" "-C" "build" "install")))
          (add-after 'wrap 'wrap-more
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out  (assoc-ref outputs "out"))
                     ;; These libraries must be on LD_LIBRARY_PATH.
                     (libs '("gtkspell3" "webkitgtk" "libsoup" "libsecret"
                             "atk" "gtk+" "gsettings-desktop-schemas"
+                            "gcc:lib" ; needed b/c webkitgtk is built with gcc-7
                             "gobject-introspection"))
                     (path (string-join
                            (map (lambda (lib)
@@ -4129,7 +4130,8 @@ work and the interface is well tested.")
                  `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))))
              #t)))))
     (native-inputs
-     `(("intltool" ,intltool)
+     `(("gcc:lib" ,gcc-7 "lib") ; needed because webkitgtk is built with gcc-7
+       ("intltool" ,intltool)
        ("itstool" ,itstool)
        ("pkg-config" ,pkg-config)
        ("meson" ,meson-for-build)
@@ -4149,7 +4151,7 @@ work and the interface is well tested.")
        ("libsecret" ,libsecret)
        ("gtkspell3" ,gtkspell3)
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)
-       ("webkitgtk" ,webkitgtk)))
+       ("webkitgtk" ,webkitgtk-2.22)))
     (home-page "https://wiki.gnome.org/Apps/Eolie")
     (synopsis "Web browser for GNOME")
     (description

From 94676ded5f2a68b07b94d83d2cfb768038c9c6c1 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Sun, 23 Sep 2018 13:13:50 +0200
Subject: [PATCH 061/909] gnu: xpra: Update to 2.3.4.

* gnu/packages/xorg.scm (xpra): Update to 2.3.4.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 90f4bf4f59..7c80e70dac 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5936,7 +5936,7 @@ basic eye-candy effects.")
 (define-public xpra
   (package
     (name "xpra")
-    (version "2.3.3")
+    (version "2.3.4")
     (source
      (origin
        (method url-fetch)
@@ -5944,7 +5944,7 @@ basic eye-candy effects.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "1azvvddjfq7lb5kmbn0ilgq2nf7pmymsc3b9lhbjld6w156qdv01"))))
+         "0wa3kx54himy3i1b2801hlzfilh3cf4kjk40k1cjl0ds28m5hija"))))
     (build-system python-build-system)
     (inputs `(("ffmpeg" ,ffmpeg)
               ("flac" ,flac)

From e10bf49668472dcfc17ad10a2b5704fce838570d Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Sun, 23 Sep 2018 17:19:56 +0200
Subject: [PATCH 062/909] gnu: Add emacs-synosaurus.

* gnu/packages/emacs.scm (emacs-synosaurus): New variable.
---
 gnu/packages/emacs.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 28d97f82c1..cff1898d72 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -118,6 +118,7 @@
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages video)
   #:use-module (gnu packages haskell)
+  #:use-module (gnu packages wordnet)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
   #:use-module (ice-9 match))
@@ -12197,3 +12198,41 @@ wrapper around all Imagemagick commands with descriptions, autocompletion (for
 some commands) and hints displayed in prompt using @command{eimp.el} to
 execute its commands and resize images.")
       (license license:gpl3+))))
+
+(define-public emacs-synosaurus
+  (let ((commit "8bf95b935976ec0a1964cf175ed57cc5f6f93bdb"))
+    (package
+      (name "emacs-synosaurus")
+      (version (git-version "0.1.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/hpdeifel/synosaurus")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "15by9jccab6kyplxa6k0glzaivxkqdigl33gl2qi2cvy6f2q7gva"))))
+      (build-system emacs-build-system)
+      (propagated-inputs
+       `(("wordnet" ,wordnet)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'configure
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((wn (assoc-ref inputs "wordnet")))
+                 ;; .el is read-only in git.
+                 (chmod "synosaurus-wordnet.el" #o644)
+                 ;; Specify the absolute file names of the various
+                 ;; programs so that everything works out-of-the-box.
+                 (emacs-substitute-variables
+                     "synosaurus-wordnet.el"
+                   ("wordnet-command"
+                    (string-append wn "/bin/wn")))))))))
+      (home-page "https://github.com/hpdeifel/synosaurus")
+      (synopsis "Extensible thesaurus mode for Emacs")
+      (description "Synosaurus is a thesaurus fontend for Emacs with pluggable
+backends, including the @command{wordnet} offline backend.")
+      (license license:gpl3+))))

From 88600acc939365b4ffd45a8be74117a8cf8dc3dd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 23 Sep 2018 22:10:50 +0200
Subject: [PATCH 063/909] system: Mention '--skip-checks' in initrd
 diagnostics.

* gnu/system/mapped-devices.scm (check-device-initrd-modules): Add note
about '--skip-checks'.
---
 gnu/system/mapped-devices.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/system/mapped-devices.scm b/gnu/system/mapped-devices.scm
index af73dc608c..a874666463 100644
--- a/gnu/system/mapped-devices.scm
+++ b/gnu/system/mapped-devices.scm
@@ -157,7 +157,10 @@ these lines:
    ;; @dots{}
    (initrd-modules (append (list~{ ~s~})
                            %base-initrd-modules)))
-@end example\n")
+@end example
+
+If you think this diagnostic is inaccurate, use the @option{--skip-checks}
+option of @command{guix system}.\n")
                                missing)))
                 (&error-location
                  (location (source-properties->location location)))))))))

From c122a2e509df98c4391750a066fecba37465eab3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 23 Sep 2018 22:11:35 +0200
Subject: [PATCH 064/909] serialization: Remove redundancy in 'write-file'.

* guix/serialization.scm (write-file): Remove redundant 'member' call.
---
 guix/serialization.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/guix/serialization.scm b/guix/serialization.scm
index 129374f541..87ad7eeec0 100644
--- a/guix/serialization.scm
+++ b/guix/serialization.scm
@@ -301,8 +301,7 @@ result of 'lstat'; exclude entries for which SELECT? does not return true."
                      (filter-map (lambda (base)
                                    (let ((file (string-append directory
                                                               "/" base)))
-                                     (and (not (member base '("." "..")))
-                                          (select? file (lstat file))
+                                     (and (select? file (lstat file))
                                           base)))
                                  basenames))
 

From a387b0bebb151a766ca6a454a891f2370c96703c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 23 Sep 2018 22:24:07 +0200
Subject: [PATCH 065/909] store-copy: Display a progress bar when copying store
 items.

* guix/build/store-copy.scm (populate-store): Add #:log-port parameter.
Use 'progress-reporter/bar' to report progress.
---
 guix/build/store-copy.scm | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/guix/build/store-copy.scm b/guix/build/store-copy.scm
index 2d9590d16f..64ade7885c 100644
--- a/guix/build/store-copy.scm
+++ b/guix/build/store-copy.scm
@@ -19,6 +19,7 @@
 (define-module (guix build store-copy)
   #:use-module (guix build utils)
   #:use-module (guix sets)
+  #:use-module (guix progress)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9)
   #:use-module (srfi srfi-26)
@@ -167,7 +168,8 @@ REFERENCE-GRAPHS, a list of reference-graph files."
 
   (reduce + 0 (map file-size items)))
 
-(define* (populate-store reference-graphs target)
+(define* (populate-store reference-graphs target
+                         #:key (log-port (current-error-port)))
   "Populate the store under directory TARGET with the items specified in
 REFERENCE-GRAPHS, a list of reference-graph files."
   (define store
@@ -183,9 +185,20 @@ REFERENCE-GRAPHS, a list of reference-graph files."
 
   (mkdir-p store)
   (chmod store #o1775)
-  (for-each (lambda (thing)
-              (copy-recursively thing
-                                (string-append target thing)))
-            (things-to-copy)))
+
+  (let* ((things   (things-to-copy))
+         (len      (length things))
+         (progress (progress-reporter/bar len
+                                          (format #f "copying ~a store items"
+                                                  len)
+                                          log-port)))
+    (call-with-progress-reporter progress
+      (lambda (report)
+        (for-each (lambda (thing)
+                    (copy-recursively thing
+                                      (string-append target thing)
+                                      #:log (%make-void-port "w"))
+                    (report))
+                  things)))))
 
 ;;; store-copy.scm ends here

From f0addd6461658d13eadf5f6e3bdb89aa02a6e902 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 23 Sep 2018 22:51:51 +0200
Subject: [PATCH 066/909] database: 'register-items' shows a progress bar.

* guix/store/database.scm (register-items): Add #:log-port.  Use
'progress-reporter/bar' to show a progress report.
(register-path): Pass #:log-port to 'register-items'.
---
 guix/store/database.scm | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/guix/store/database.scm b/guix/store/database.scm
index 0879a95d0b..5d094faaf3 100644
--- a/guix/store/database.scm
+++ b/guix/store/database.scm
@@ -23,6 +23,7 @@
   #:use-module (guix serialization)
   #:use-module (guix store deduplication)
   #:use-module (guix base16)
+  #:use-module (guix progress)
   #:use-module (guix build syscalls)
   #:use-module ((guix build utils)
                 #:select (mkdir-p executable-file?))
@@ -234,7 +235,8 @@ be used internally by the daemon's build hook."
                   #:prefix prefix #:state-directory state-directory
                   #:deduplicate? deduplicate?
                   #:reset-timestamps? reset-timestamps?
-                  #:schema schema))
+                  #:schema schema
+                  #:log-port (%make-void-port "w")))
 
 (define %epoch
   ;; When it all began.
@@ -245,12 +247,14 @@ be used internally by the daemon's build hook."
                          (deduplicate? #t)
                          (reset-timestamps? #t)
                          registration-time
-                         (schema (sql-schema)))
+                         (schema (sql-schema))
+                         (log-port (current-error-port)))
   "Register all of ITEMS, a list of <store-info> records as returned by
 'read-reference-graph', in the database under PREFIX/STATE-DIRECTORY.  ITEMS
 must be in topological order (with leaves first.)  If the database is
 initially empty, apply SCHEMA to initialize it.  REGISTRATION-TIME must be the
-registration time to be recorded in the database; #f means \"now\"."
+registration time to be recorded in the database; #f means \"now\".
+Write a progress report to LOG-PORT."
 
   ;; Priority for options: first what is given, then environment variables,
   ;; then defaults. %state-directory, %store-directory, and
@@ -302,4 +306,12 @@ registration time to be recorded in the database; #f means \"now\"."
   (mkdir-p db-dir)
   (parameterize ((sql-schema schema))
     (with-database (string-append db-dir "/db.sqlite") db
-      (for-each (cut register db <>) items))))
+      (let* ((prefix   (format #f "registering ~a items" (length items)))
+             (progress (progress-reporter/bar (length items)
+                                              prefix log-port)))
+        (call-with-progress-reporter progress
+          (lambda (report)
+            (for-each (lambda (item)
+                        (register db item)
+                        (report))
+                      items)))))))

From bb3b6ccb05550fbfbeb459c68819a752327d6e1e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 23 Sep 2018 23:11:30 +0200
Subject: [PATCH 067/909] database: Register each store item only once.

Fixes <https://bugs.gnu.org/32600>.
Reported by Leo Famulari.

* guix/store/database.scm (register-items): Check whether TO-REGISTER is
in DB by calling 'path-id',  and skip the reset-timestamps,
registration, and deduplication phases when it is.
---
 guix/store/database.scm | 24 ++++++++++++++----------
 1 file changed, 14 insertions(+), 10 deletions(-)

diff --git a/guix/store/database.scm b/guix/store/database.scm
index 5d094faaf3..341276bc30 100644
--- a/guix/store/database.scm
+++ b/guix/store/database.scm
@@ -290,18 +290,22 @@ Write a progress report to LOG-PORT."
     (define real-file-name
       (string-append store-dir "/" (basename (store-info-item item))))
 
-    (let-values (((hash nar-size) (nar-sha256 real-file-name)))
+    ;; When TO-REGISTER is already registered, skip it.  This makes a
+    ;; significant differences when 'register-closures' is called
+    ;; consecutively for overlapping closures such as 'system' and 'bootcfg'.
+    (unless (path-id db to-register)
       (when reset-timestamps?
         (reset-timestamps real-file-name))
-      (sqlite-register db #:path to-register
-                       #:references (store-info-references item)
-                       #:deriver (store-info-deriver item)
-                       #:hash (string-append "sha256:"
-                                             (bytevector->base16-string hash))
-                       #:nar-size nar-size
-                       #:time registration-time)
-      (when deduplicate?
-        (deduplicate real-file-name hash #:store store-dir))))
+      (let-values (((hash nar-size) (nar-sha256 real-file-name)))
+        (sqlite-register db #:path to-register
+                         #:references (store-info-references item)
+                         #:deriver (store-info-deriver item)
+                         #:hash (string-append "sha256:"
+                                               (bytevector->base16-string hash))
+                         #:nar-size nar-size
+                         #:time registration-time)
+        (when deduplicate?
+          (deduplicate real-file-name hash #:store store-dir)))))
 
   (mkdir-p db-dir)
   (parameterize ((sql-schema schema))

From b5460d95e970608bee7a794590be1b051b57d3a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 23 Sep 2018 23:29:31 +0200
Subject: [PATCH 068/909] vm: Disable deduplication for 'guix system vm-image'.

* gnu/system/vm.scm (qemu-image): Pass #:deduplicate? #f to
'root-partition-initializer'.
---
 gnu/system/vm.scm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm
index 91e117b9f3..435501d726 100644
--- a/gnu/system/vm.scm
+++ b/gnu/system/vm.scm
@@ -390,7 +390,12 @@ the image."
                                  #:closures graphs
                                  #:copy-closures? #$copy-inputs?
                                  #:register-closures? #$register-closures?
-                                 #:system-directory #$os-drv))
+                                 #:system-directory #$os-drv
+
+                                 ;; Disable deduplication to speed things up,
+                                 ;; and because it doesn't help much for a
+                                 ;; single system generation.
+                                 #:deduplicate? #f))
                     (root-size  #$(if (eq? 'guess disk-image-size)
                                       #~(max
                                          ;; Minimum 20 MiB root size

From fce225471128c4a5246342b3aa1b7e53a8066211 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 23 Sep 2018 23:31:52 +0200
Subject: [PATCH 069/909] vm: Use "cache=loose" for all 9p mounts.

This significantly improves read throughput when running things like
"guix hash -r ...".

* gnu/system/vm.scm (%linux-vm-file-systems): Add 'flags' for "store".
Add "cache=loose" to every file system.
---
 gnu/system/vm.scm | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm
index 435501d726..a1b595d45d 100644
--- a/gnu/system/vm.scm
+++ b/gnu/system/vm.scm
@@ -99,21 +99,28 @@
           (device "store")
           (type "9p")
           (needed-for-boot? #t)
-          (options "trans=virtio")
+          (flags '(read-only))
+          (options "trans=virtio,cache=loose")
           (check? #f))
+
+        ;; The 9p documentation says that cache=loose is "intended for
+        ;; exclusive, read-only mounts", without additional details.  In
+        ;; practice it seems to work well for these, and it's much faster than
+        ;; the default cache=none, especially when copying and registering
+        ;; store items.
         (file-system
           (mount-point "/xchg")
           (device "xchg")
           (type "9p")
           (needed-for-boot? #t)
-          (options "trans=virtio")
+          (options "trans=virtio,cache=loose")
           (check? #f))
         (file-system
           (mount-point "/tmp")
           (device "tmp")
           (type "9p")
           (needed-for-boot? #t)
-          (options "trans=virtio")
+          (options "trans=virtio,cache=loose")
           (check? #f))))
 
 (define not-config?

From 8fa361ce63235335e266cb5ff21bf9da73f4d8dd Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 00:23:19 +0200
Subject: [PATCH 070/909] gnu: fping: Update to 4.1.

* gnu/packages/networking.scm (fping): Update to 4.1.
---
 gnu/packages/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index abc616de3c..d1765cc46f 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -651,7 +651,7 @@ network frames.")
 (define-public fping
   (package
     (name "fping")
-    (version "4.0")
+    (version "4.1")
     (source
      (origin
        (method url-fetch)
@@ -659,7 +659,7 @@ network frames.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1kp81wchi79l8z8rrj602fpjrd8bi84y3i7fsaclzlwap5943sv7"))))
+         "0wxbvm480vij8dy4v1pi8f0c7010rx6bidg3qhsvkdf2ijhy4cr7"))))
     (build-system gnu-build-system)
     (home-page "http://fping.org/")
     (synopsis "Send ICMP ECHO_REQUEST packets to network hosts")

From 25706b8fc9aa36085ecec085f08d5ad1808d4a96 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 00:23:58 +0200
Subject: [PATCH 071/909] gnu: fping: Use HTTPS home page.

* gnu/packages/networking.scm (fping)[home-page]: Use HTTPS.
---
 gnu/packages/networking.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index d1765cc46f..84224374c6 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -661,7 +661,7 @@ network frames.")
         (base32
          "0wxbvm480vij8dy4v1pi8f0c7010rx6bidg3qhsvkdf2ijhy4cr7"))))
     (build-system gnu-build-system)
-    (home-page "http://fping.org/")
+    (home-page "https://fping.org/")
     (synopsis "Send ICMP ECHO_REQUEST packets to network hosts")
     (description
      "fping is a ping like program which uses the Internet Control Message

From 0604d3cfceea13fad33c6188fa54f5fd16c74406 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 00:29:46 +0200
Subject: [PATCH 072/909] gnu: nano: Update to 3.1.

* gnu/packages/nano.scm (nano): Update to 3.1.
---
 gnu/packages/nano.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm
index 9396588fc8..8f96b605a6 100644
--- a/gnu/packages/nano.scm
+++ b/gnu/packages/nano.scm
@@ -30,7 +30,7 @@
 (define-public nano
   (package
     (name "nano")
-    (version "3.0")
+    (version "3.1")
     (source
      (origin
       (method url-fetch)
@@ -38,7 +38,7 @@
                           version ".tar.xz"))
       (sha256
        (base32
-        "1868hg9s584fwjrh0fzdrixmxc2qhw520z4q5iv68kjiajivr9g0"))))
+        "17kinzyv6vwgyx2d0ym1kp65qbf7kxzwpyg21ic1rijv1aj2rh0l"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gettext-minimal)

From 899e1974a6f4a4ff041c035ff3494bd10a8069ac Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 21:31:52 +0200
Subject: [PATCH 073/909] gnu: python-gitdb: Update to 2.0.4.

* gnu/packages/version-control.scm (python-gitdb): Update to 2.0.4.
[arguments]: Replace AND with equivalent but more 'accurate' BEGIN.
---
 gnu/packages/version-control.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 58c870df5a..204ec403f6 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -712,13 +712,13 @@ default) of the repository.")
 (define-public python-gitdb
   (package
     (name "python-gitdb")
-    (version "2.0.3")
+    (version "2.0.4")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "gitdb2" version))
               (sha256
                (base32
-                "02azg62mr99b7cllyjrly77np3vw32y8nrxpa2xjapiyaga2j3mn"))))
+                "0i608q9c47rdsmyac1cn6s0hzwwj7cb957y8fc9wacc5lnw8ak5v"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -733,7 +733,7 @@ default) of the repository.")
                                                   "file" (number->string filecount))
                             (lambda (port)
                               (format port "~a" filecount))))
-                        (and
+                        (begin
                          (invoke "git" "init")
                          (invoke "git" "config" "user.name" "Total Git")
                          (invoke "git" "config" "user.email" "git@localhost")

From 2f7ad2a788fa190dbe97038020322ce1c772feec Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 21 Sep 2018 20:24:51 +0200
Subject: [PATCH 074/909] gnu: workrave: Use Guix's built-in bootstrap phase.

* gnu/packages/gnome.scm (workrave)[arguments]: Remove
'autoconf' phase.
---
 gnu/packages/gnome.scm | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 9f5ede8b07..ac898fb294 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -7244,13 +7244,6 @@ mp3, Ogg Vorbis and FLAC")
                  (base32
                   "150qca8c552fakjlzkgarsxgp87l1xcwn19svqsa9d0cygqxjgia"))))
       (build-system glib-or-gtk-build-system)
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'autogen
-             (lambda _
-               (invoke "sh" "autogen.sh")
-               #t)))))
       (propagated-inputs `(("glib" ,glib)
                            ("gtk+" ,gtk+)
                            ("gdk-pixbuf" ,gdk-pixbuf)

From 2c36baa56ffeaf451f42e5f5ff3b60705e17a30b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 23 Sep 2018 14:58:06 +0200
Subject: [PATCH 075/909] gnu: parallel: Update to 20180922.

* gnu/packages/parallel.scm (parallel): Update to 20180922.
---
 gnu/packages/parallel.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index ec1fae6470..3dba2b8c00 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -48,7 +48,7 @@
 (define-public parallel
   (package
     (name "parallel")
-    (version "20180822")
+    (version "20180922")
     (source
      (origin
       (method url-fetch)
@@ -56,7 +56,7 @@
                           version ".tar.bz2"))
       (sha256
        (base32
-        "0jjs7fpvdjjb5v0j39a6k7hq9h5ap3db1j7vg1r2dq4swk23h9bm"))))
+        "07q7lzway2qf8mx6fb4q45jmirsc8pw6rgv03ifrp32jw3q8w1za"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -66,7 +66,7 @@
              (for-each
               (lambda (file)
                 (substitute* file
-                  ;; Patch hard coded '/bin/sh' in the lin ending in:
+                  ;; Patch hard coded '/bin/sh' in the line ending in:
                   ;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
                   ;;  parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
                   (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))

From c30fd002c8fe568d7a22ec2939825e68c88f8e31 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 23 Sep 2018 15:06:12 +0200
Subject: [PATCH 076/909] gnu: virtualgl: Update to 2.6.

* gnu/packages/gl.scm (virtualgl): Update to 2.6.
[inputs]: Add libxtst.
---
 gnu/packages/gl.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/gl.scm b/gnu/packages/gl.scm
index 28e283640d..b88fab4929 100644
--- a/gnu/packages/gl.scm
+++ b/gnu/packages/gl.scm
@@ -725,7 +725,7 @@ mixed vector/bitmap output.")
 (define-public virtualgl
   (package
     (name "virtualgl")
-    (version "2.5.2")
+    (version "2.6")
     (source
      (origin
        (method url-fetch)
@@ -734,16 +734,17 @@ mixed vector/bitmap output.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0rnid3hwrry9d5d4m7sygq00xxx976rgk00a3557m9r5kxbmy476"))))
+         "1ck1d0w19cgyqvrb9mdlj6l5db90xf18yln71kdninlqxvpgj6h7"))))
     (arguments
-     `(#:tests? #f ;; no tests are available
+     `(#:tests? #f                      ; no tests are available
        #:configure-flags (list
-                           (string-append "-DCMAKE_INSTALL_LIBDIR="
-                                          (assoc-ref %outputs "out") "/lib")
-                           "-DVGL_USESSL=1"))) ;; use OpenSSL
+                          (string-append "-DCMAKE_INSTALL_LIBDIR="
+                                         (assoc-ref %outputs "out") "/lib")
+                          "-DVGL_USESSL=1"))) ; use OpenSSL
     (build-system cmake-build-system)
     (inputs `(("glu" ,glu)
               ("libjpeg-turbo" ,libjpeg-turbo)
+              ("libxtst" ,libxtst)
               ("mesa" ,mesa)
               ("openssl" ,openssl)))
     (native-inputs `(("pkg-config" ,pkg-config)))

From a42b68480b3e73b8486ce808f6451ca880860574 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 23 Sep 2018 15:41:01 +0200
Subject: [PATCH 077/909] gnu: libiptcdata: Update to 1.0.5.

* gnu/packages/image.scm (libiptcdata): Update to 1.0.5.
[home-page]: Follow Debian's maintained upstream.
---
 gnu/packages/image.scm | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index c3eb48ad0d..b367e0799c 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -1368,16 +1368,18 @@ medical image data, e.g. magnetic resonance image (MRI) and functional MRI
 (define-public libiptcdata
   (package
     (name "libiptcdata")
-    (version "1.0.4")
+    (version "1.0.5")
     (source (origin
               (method url-fetch)
-              (uri (string-append "mirror://sourceforge/" name "/" name "/"
-                                  version "/" name "-" version ".tar.gz"))
+              (uri (string-append "https://github.com/ianw/libiptcdata"
+                                  "/releases/download/release_"
+                                  (string-join (string-split version #\.) "_")
+                                  "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "03pfvkmmx762iydq0q207x2028d275pbdysfsgpmrr0ywy63pxkr"))))
+                "17m2bscc76r1bymjgb44fbbfrdsjfqyb2ivg9wchyllm8pgx1560"))))
     (build-system gnu-build-system)
-    (home-page "http://libiptcdata.sourceforge.net/")
+    (home-page "https://github.com/ianw/libiptcdata")
     (synopsis "IPTC metadata manipulation library")
     (description
      "Libiptcdata is a C library for manipulating the International Press

From 3715e79ec8a310a0a957105b57d58b178f2f9d1a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 23 Sep 2018 20:10:13 +0200
Subject: [PATCH 078/909] gnu: python-marshmallow: Update to 3.0.0b14.

* gnu/packages/python.scm (python-marshmallow): Update to 3.0.0b14.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 26829f050e..30bde632fb 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12179,14 +12179,14 @@ address is valid and really exists.")
 (define-public python-marshmallow
   (package
     (name "python-marshmallow")
-    (version "3.0.0b3")
+    (version "3.0.0b14")
     (source
      (origin
       (method url-fetch)
       (uri (pypi-uri "marshmallow" version))
       (sha256
        (base32
-        "07mcrij1yvk85lvgx44wwr9pc80xryghvlgayb057g1cazcypysd"))))
+        "1digk3f5cfk7wmlka65mc7bzsd96pbsgcsvp6pimd5b4ff9zb5p3"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)

From 68cbec027e8e48f1047b7cb1bfdd9b0dd65937ac Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 23 Sep 2018 23:58:51 +0200
Subject: [PATCH 079/909] gnu: python-decorator: Update to 4.3.0.

* gnu/packages/python.scm (python-decorator): Update to 4.3.0.
[arguments]: Run the test suite.
---
 gnu/packages/python.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 30bde632fb..0bd8086473 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4340,15 +4340,14 @@ PNG, PostScript, PDF, and SVG file output.")
 (define-public python-decorator
   (package
     (name "python-decorator")
-    (version "4.2.1")
+    (version "4.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "decorator" version))
        (sha256
-        (base32 "03iaf116rm3w8b4agb8hzf6z9331mrvi4khfxq35zkx17sgxsikx"))))
+        (base32 "0308djallnh00v112y5b7nadl657ysmkp6vc8xn51d6yzc9zm7n3"))))
     (build-system python-build-system)
-    (arguments '(#:tests? #f)) ; no test target
     (home-page "https://pypi.python.org/pypi/decorator/")
     (synopsis "Python module to simplify usage of decorators")
     (description

From dd29bd4ebcbfcdcb4c62e2c6c5cf4fd54c74af3b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 00:12:59 +0200
Subject: [PATCH 080/909] gnu: python-networkx: Update to 2.2.

* gnu/packages/python.scm (python-networkx): Update to 2.2.
---
 gnu/packages/python.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0bd8086473..69d87c6e17 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5194,15 +5194,15 @@ interfaces in an easy and portable manner.")
 (define-public python-networkx
   (package
     (name "python-networkx")
-    (version "2.1")
+    (version "2.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "networkx" version ".zip"))
        (sha256
-        (base32 "1ccb8mfz4m821k9y0cigkbq42q2sbb4dj5fbjshp0awp32j2q9v4"))))
+        (base32 "12swxb15299v9vqjsq4z8rgh5sdhvpx497xwnhpnb0gynrx6zra5"))))
     (build-system python-build-system)
-    ;; python-decorator is needed at runtime
+    ;; python-decorator is needed at runtime.
     (propagated-inputs
      `(("python-decorator" ,python-decorator)))
     (native-inputs

From cd8aa06093f6491edc17b65608d1f528742f11a6 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 00:15:18 +0200
Subject: [PATCH 081/909] gnu: python-networkx: Use HTTPS home page.

* gnu/packages/python.scm (python-networkx)[home-page]: Use HTTPS.
---
 gnu/packages/python.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 69d87c6e17..ea641b8213 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5208,7 +5208,7 @@ interfaces in an easy and portable manner.")
     (native-inputs
      `(("python-nose" ,python-nose)
        ("unzip" ,unzip)))
-    (home-page "http://networkx.github.io/")
+    (home-page "https://networkx.github.io/")
     (synopsis "Python module for creating and manipulating graphs and networks")
     (description
       "NetworkX is a Python package for the creation, manipulation, and study

From 5c8031ff7382ec9079040d08ae5a05b4dd2352b7 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 17 Sep 2018 18:31:33 +0200
Subject: [PATCH 082/909] gnu: Prefix all Emacs packages with "emacs-".

* gnu/packages/emacs.scm: Prefix all Emacs packages with "emacs-".
This is to enforce consistency and so that `emacs-packages?' can reliably
detect Emacs packages based on the "emacs-" prefix.
---
 gnu/packages/emacs.scm | 119 +++++++++++++++++++++++++++--------------
 1 file changed, 79 insertions(+), 40 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index cff1898d72..fbedd2f48d 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -335,9 +335,9 @@ editor (without an X toolkit)" )
 ;;; Emacs hacking.
 ;;;
 
-(define-public geiser
+(define-public emacs-geiser
   (package
-    (name "geiser")
+    (name "emacs-geiser")
     (version "0.10")
     (source (origin
              (method url-fetch)
@@ -370,7 +370,10 @@ implementation, Emacs and, ultimately, the schemer, giving them access to live
 metadata.")
     (license license:bsd-3)))
 
-(define-public paredit
+(define-public geiser
+  (deprecated-package "geiser" emacs-geiser))
+
+(define-public emacs-paredit
   (package
     (name "emacs-paredit")
     (version "24")
@@ -395,6 +398,9 @@ for those who may want transient periods of unbalanced parentheses, such as
 when typing parentheses directly or commenting out code line by line.")
     (license license:gpl3+)))
 
+(define-public paredit
+  (deprecated-package "paredit" emacs-paredit))
+
 (define-public git-modes
   (package
     (name "emacs-git-modes")
@@ -444,9 +450,9 @@ For remote processes a substitute is provided, which communicates with Emacs
 on stdout instead of using a socket as the Emacsclient does.")
     (license license:gpl3+)))
 
-(define-public magit
+(define-public emacs-magit
   (package
-    (name "magit")
+    (name "emacs-magit")
     (version "2.13.0")
     (source (origin
              (method url-fetch)
@@ -512,9 +518,12 @@ cherry picking, reverting, merging, rebasing, and other common Git
 operations.")
     (license license:gpl3+)))
 
-(define-public magit-svn
+(define-public magit
+  (deprecated-package "magit" emacs-magit))
+
+(define-public emacs-magit-svn
   (package
-    (name "magit-svn")
+    (name "emacs-magit-svn")
     (version "2.2.0")
     (source (origin
               (method url-fetch)
@@ -531,7 +540,7 @@ operations.")
                      ("gzip" ,gzip)))
     (propagated-inputs `(("dash" ,emacs-dash)
                          ("with-editor" ,emacs-with-editor)
-                         ("magit" ,magit)))
+                         ("magit" ,emacs-magit)))
     (arguments
      `(#:modules ((guix build utils)
                   (guix build emacs-utils))
@@ -577,6 +586,9 @@ operations.")
 support for Git-SVN.")
     (license license:gpl3+)))
 
+(define-public magit-svn
+  (deprecated-package "magit-svn" emacs-magit-svn))
+
 (define-public emacs-magit-popup
   (package
     (name "emacs-magit-popup")
@@ -641,9 +653,9 @@ Gitlab APIs from Emacs packages.  It abstracts access to API resources using
 only a handful of functions that are not resource-specific.")
     (license license:gpl3+)))
 
-(define-public haskell-mode
+(define-public emacs-haskell-mode
   (package
-    (name "haskell-mode")
+    (name "emacs-haskell-mode")
     (version "16.1")
     (source (origin
               (method url-fetch)
@@ -731,7 +743,10 @@ only a handful of functions that are not resource-specific.")
 programs.")
     (license license:gpl3+)))
 
-(define-public flycheck
+(define-public haskell-mode
+  (deprecated-package "haskell-mode" emacs-haskell-mode))
+
+(define-public emacs-flycheck
   (package
     (name "emacs-flycheck")
     (version "31")
@@ -767,6 +782,9 @@ different tools.  It highlights errors and warnings inline in the buffer, and
 provides an optional IDE-like error list.")
     (license license:gpl3+)))                     ;+GFDLv1.3+ for the manual
 
+(define-public flycheck
+  (deprecated-package "flycheck" emacs-flycheck))
+
 
 ;;;
 ;;; Web browsing.
@@ -910,7 +928,7 @@ provides an optional IDE-like error list.")
 ;;; Multimedia.
 ;;;
 
-(define-public emms
+(define-public emacs-emms
   (package
     (name "emacs-emms")
     (version "5.0")
@@ -1048,9 +1066,12 @@ light user interface.")
     (home-page "https://www.gnu.org/software/emms/")
     (license license:gpl3+)))
 
+(define-public emms
+  (deprecated-package "emacs-emms" emacs-emms))
+
 (define-public emacs-emms-player-mpv
   ;; A new mpv backend is included in Emms from 5.0.
-  (deprecated-package "emacs-emms-player-mpv" emms))
+  (deprecated-package "emacs-emms-player-mpv" emacs-emms))
 
 (define-public emacs-emms-mode-line-cycle
   (package
@@ -1080,9 +1101,9 @@ within a specified width.  It is useful for displaying long track titles.")
 ;;; Miscellaneous.
 ;;;
 
-(define-public bbdb
+(define-public emacs-bbdb
   (package
-    (name "bbdb")
+    (name "emacs-bbdb")
     (version "3.1.2")
     (source (origin
               (method url-fetch)
@@ -1121,6 +1142,9 @@ like.  It can be linked with various Emacs mail clients (Message and Mail
 mode, Rmail, Gnus, MH-E, and VM).  BBDB is fully customizable.")
     (license license:gpl3+)))
 
+(define-public bbdb
+  (deprecated-package "bbdb" emacs-bbdb))
+
 (define-public emacs-aggressive-indent
   (package
     (name "emacs-aggressive-indent")
@@ -1721,7 +1745,7 @@ type, for example: packages, buffers, files, etc.")
      `(("guile" ,guile-2.2)
        ("guix" ,guix)))
     (propagated-inputs
-     `(("geiser" ,geiser)
+     `(("geiser" ,emacs-geiser)
        ("guile-gcrypt" ,guile-gcrypt)
        ("dash" ,emacs-dash)
        ("bui" ,emacs-bui)
@@ -2377,7 +2401,7 @@ in Lisp modes.")
                 "1k0sm552iawi49v4zis6dbb81d1rzgky9v0dpv7nj31gnb7bmy7k"))))
     (build-system emacs-build-system)
     (native-inputs
-     `(("ert-runner" ,ert-runner)))
+     `(("ert-runner" ,emacs-ert-runner)))
     (arguments
      `(#:tests? #t
        #:test-command '("ert-runner")))
@@ -2663,7 +2687,7 @@ framework for Emacs Lisp to be used with @code{ert}.")
     (native-inputs
      `(("emacs-ert-expectations" ,emacs-ert-expectations)
        ("emacs-undercover" ,emacs-undercover)
-       ("ert-runner" ,ert-runner)))
+       ("ert-runner" ,emacs-ert-runner)))
     (synopsis "Simple asynchronous functions for Emacs Lisp")
     (description
      "The @code{deferred.el} library provides support for asynchronous tasks.
@@ -2672,7 +2696,7 @@ The API is almost the same as that of
 for asynchronous tasks.")
     (license license:gpl3+)))
 
-(define-public butler
+(define-public emacs-butler
   (package
     (name "emacs-butler")
     (version "0.2.4")
@@ -2698,6 +2722,9 @@ view the build status of those servers' build jobs, and possibly to trigger
 build jobs.")
     (license license:gpl3+)))
 
+(define-public butler
+  (deprecated-package "emacs-butler" emacs-butler))
+
 (define-public emacs-company
   (package
     (name "emacs-company")
@@ -2823,7 +2850,7 @@ completion candidate when using the Company text completion framework.")
 simultaneous cursors.")
     (license license:gpl3+)))
 
-(define-public typo
+(define-public emacs-typo
   (package
     (name "emacs-typo")
     (version "1.1")
@@ -2847,6 +2874,9 @@ automatically inserts a Unicode opening or closing quotation mark, depending
 on context.")
     (license license:gpl3+)))
 
+(define-public typo
+  (deprecated-package "emacs-typo" emacs-typo))
+
 (define-public emacs-scheme-complete
   (let ((commit "9b5cf224bf2a5994bc6d5b152ff487517f1a9bb5"))
     (package
@@ -3982,7 +4012,7 @@ state and will work even without lispy being enabled.")
     (native-inputs
      `(("emacs-dash" ,emacs-dash)
        ("emacs-s" ,emacs-s)
-       ("ert-runner" ,ert-runner)))
+       ("ert-runner" ,emacs-ert-runner)))
     (arguments
      `(#:tests? #t
        #:test-command '("ert-runner")))
@@ -4354,7 +4384,7 @@ indentation and filling of comments and C preprocessor fontification.")
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)
        ("emacs-s" ,emacs-s)
-       ("emacs-flycheck" ,flycheck)
+       ("emacs-flycheck" ,emacs-flycheck)
        ("emacs-typescript-mode" ,emacs-typescript-mode)))
     (home-page "https://github.com/ananthakumaran/tide")
     (synopsis "Typescript IDE for Emacs")
@@ -4519,7 +4549,7 @@ provide the historic behavior of @code{flet}, as well as
      `(#:tests? #t
        #:test-command '("ert-runner")))
     (native-inputs
-     `(("ert-runner" ,ert-runner)))
+     `(("ert-runner" ,emacs-ert-runner)))
     (propagated-inputs
      `(("emacs-el-x" ,emacs-el-x)))
     (home-page "https://github.com/sigma/mocker.el")
@@ -4585,7 +4615,7 @@ functions to assist in reviewing changes on files.")
        #:tests? #t
        #:test-command '("ert-runner")))
     (native-inputs
-     `(("ert-runner" ,ert-runner)
+     `(("ert-runner" ,emacs-ert-runner)
        ("emacs-mocker" ,emacs-mocker)))
     (home-page "https://github.com/jorgenschaefer/pyvenv")
     (synopsis "Virtualenv minor mode for Emacs")
@@ -4670,7 +4700,7 @@ indentation (space indentation only).
        ("pyvenv" ,emacs-pyvenv)
        ("s" ,emacs-s)))
     (native-inputs
-     `(("ert-runner" ,ert-runner)
+     `(("ert-runner" ,emacs-ert-runner)
        ("emacs-f" ,emacs-f)
        ("python" ,python-wrapper)
        ("python-autopep8" ,python-autopep8)
@@ -6932,9 +6962,9 @@ Emacs.")
 
 ;; Tests for ert-runner have a circular dependency with ecukes, and therefore
 ;; cannot be run
-(define-public ert-runner
+(define-public emacs-ert-runner
   (package
-    (name "ert-runner")
+    (name "emacs-ert-runner")
     (version "0.7.0")
     (source
      (origin
@@ -6977,6 +7007,9 @@ using ERT.  It assumes a certain test structure setup and can therefore make
 running tests easier.")
     (license license:gpl3+)))
 
+(define-public ert-runner
+  (deprecated-package "ert-runner" emacs-ert-runner))
+
 (define-public emacs-disable-mouse
   (package
     (name "emacs-disable-mouse")
@@ -7020,7 +7053,7 @@ running a customisable handler command (@code{ignore} by default). ")
     (native-inputs
      `(("emacs-dash" ,emacs-dash)
        ("emacs-shut-up" ,emacs-shut-up)
-       ("ert-runner" ,ert-runner)))
+       ("ert-runner" ,emacs-ert-runner)))
     (arguments
      `(#:tests? #t
        #:test-command '("ert-runner")))
@@ -7251,7 +7284,7 @@ settings).")
                 "1a4b0lsmwq84qfx51c5xy4fryhb1ysld4fhgw2vr37izf53379sb"))))
     (build-system emacs-build-system)
     (native-inputs
-     `(("ert-runner" ,ert-runner)))
+     `(("ert-runner" ,emacs-ert-runner)))
     (arguments
      `(#:tests? #t
        #:test-command '("ert-runner" "tests")))
@@ -7507,7 +7540,7 @@ Idris.")
      `(("emacs-f" ,emacs-f)
        ("emacs-s" ,emacs-s)))
     (native-inputs
-     `(("ert-runner" ,ert-runner)))
+     `(("ert-runner" ,emacs-ert-runner)))
     (arguments
      `(#:tests? #t
        #:test-command '("ert-runner")))
@@ -7977,9 +8010,9 @@ supports multiple backends such as @code{vlc}, @code{mpg123},
 @code{afplay}.")
     (license license:gpl2+)))
 
-(define-public groovy-emacs-modes
+(define-public emacs-groovy-modes
   (package
-    (name "groovy-emacs-modes")
+    (name "emacs-groovy-modes")
     (version "2.0")
     (source (origin
               (method url-fetch)
@@ -8001,7 +8034,10 @@ Groovy source files, REPL integration with run-groovy and Grails project
 navigation with the grails mode.")
     (license license:gpl3+)))
 
-(define-public org-tree-slide
+(define-public groovy-emacs-modes
+  (deprecated-package "groovy-emacs-modes" emacs-groovy-modes))
+
+(define-public emacs-org-tree-slide
   (let ((commit "dff8f1a4a64c8dd0a1fde0b0131e2fe186747134")
         (revision "0"))
     (package
@@ -8023,6 +8059,9 @@ navigation with the grails mode.")
 @kbd{C-<} to jump to the next and previous slide.")
       (license license:gpl3+))))
 
+(define-public org-tree-slide
+  (deprecated-package "emacs-org-tree-slide" emacs-org-tree-slide))
+
 (define-public emacs-scratch-el
   (let ((commit "2cdf2b841ce7a0987093f65b0cc431947549f897")
         (revision "1"))
@@ -10095,7 +10134,7 @@ time is being spent during Emacs startup in order to optimize startup time.")
 
 (define-public emacs-emms-player-simple-mpv
   ;; A new mpv backend is included in Emms from 5.0.
-  (deprecated-package "emacs-emms-player-simple-mpv" emms))
+  (deprecated-package "emacs-emms-player-simple-mpv" emacs-emms))
 
 (define-public emacs-magit-org-todos-el
   (let ((commit "df206287737b9671f2e36ae7b1474ebbe9940d2a"))
@@ -10113,7 +10152,7 @@ time is being spent during Emacs startup in order to optimize startup time.")
           (base32
            "0kdp7k7jnnrkhsg0xh1c3h7iz0vgi120gf5xwl1hxy61avivnxrn"))))
       (propagated-inputs
-       `(("magit" ,magit)))
+       `(("magit" ,emacs-magit)))
       (build-system emacs-build-system)
       (home-page "https://github.com/danielma/magit-org-todos.el")
       (synopsis "Get todo.org into Emacs Magit status")
@@ -10952,7 +10991,7 @@ through the symbol: @command{this-fn}.")
      `(("emacs-el-mock" ,emacs-el-mock)
        ("emacs-noflet" ,emacs-noflet)
        ("emacs-undercover" ,emacs-undercover)
-       ("ert-runner" ,ert-runner)))
+       ("ert-runner" ,emacs-ert-runner)))
     (propagated-inputs
      `(("emacs-f" ,emacs-f)
        ("emacs-popup" ,emacs-popup)))
@@ -11139,7 +11178,7 @@ Org-mode file, and citations of Zotero items in Pandoc Markdown files.")
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-evil" ,emacs-evil)
-         ("magit" ,magit)))
+         ("magit" ,emacs-magit)))
       (home-page
        "https://github.com/emacs-evil/evil-magit")
       (synopsis "Evil-based key bindings for Magit")
@@ -11412,7 +11451,7 @@ you searched for and execute it, or view its documentation.")
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-helm" ,emacs-helm)
-         ("emacs-emms" ,emms)))
+         ("emacs-emms" ,emacs-emms)))
       (home-page
        "https://github.com/emacs-helm/helm-emms")
       (synopsis "Emms for Helm")
@@ -11467,7 +11506,7 @@ See @code{helm-exwm-switch-browser} for an example.")
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-dash" ,emacs-dash)
-         ("emacs-flycheck" ,flycheck)
+         ("emacs-flycheck" ,emacs-flycheck)
          ("emacs-helm" ,emacs-helm)))
       (home-page "https://github.com/yasuyk/helm-flycheck")
       (synopsis "Show Flycheck errors with Helm")
@@ -12029,7 +12068,7 @@ buffers – other modes on the TODO list).
        ("emacs-dash" ,emacs-dash)
        ("emacs-f" ,emacs-f)
        ("emacs-hl-todo" ,emacs-hl-todo)
-       ("magit" ,magit)
+       ("magit" ,emacs-magit)
        ("emacs-pcre2el" ,emacs-pcre2el)
        ("emacs-s" ,emacs-s)))
     (home-page "https://github.com/alphapapa/magit-todos")

From a434730f2ebc39fcda7a8d0709c7f5adffa69299 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 24 Sep 2018 13:23:32 +0200
Subject: [PATCH 083/909] gnu: Add r-xbioc.

* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b619866ba3..d92fbd7de9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13760,3 +13760,36 @@ sequencing data.")
     ;; This is free software but the license variant is unclear:
     ;; <https://github.com/mw55309/poRe_docs/issues/10>.
     (license license:bsd-3)))
+
+(define-public r-xbioc
+  (let ((revision "1")
+        (commit "f798c187e376fd1ba27abd559f47bbae7e3e466b"))
+    (package
+      (name "r-xbioc")
+      (version (git-version "0.1.15" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/renozao/xbioc.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "03hffh2f6z71y6l6dqpa5cql3hdaw7zigdi8sm2dzgx379k9rgrr"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-annotationdbi" ,r-annotationdbi)
+         ("r-assertthat" ,r-assertthat)
+         ("r-biobase" ,r-biobase)
+         ("r-biocinstaller" ,r-biocinstaller)
+         ("r-digest" ,r-digest)
+         ("r-pkgmaker" ,r-pkgmaker)
+         ("r-plyr" ,r-plyr)
+         ("r-reshape2" ,r-reshape2)
+         ("r-stringr" ,r-stringr)))
+      (home-page "https://github.com/renozao/xbioc/")
+      (synopsis "Extra base functions for Bioconductor")
+      (description "This package provides extra utility functions to perform
+common tasks in the analysis of omics data, leveraging and enhancing features
+provided by Bioconductor packages.")
+      (license license:gpl3+))))

From 28829c040f92399c0705f968f232543e97e5f5f9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 24 Sep 2018 13:23:44 +0200
Subject: [PATCH 084/909] gnu: Add r-cssam.

* gnu/packages/bioinformatics.scm (r-cssam): New variable.
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d92fbd7de9..2366843d87 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13793,3 +13793,34 @@ sequencing data.")
 common tasks in the analysis of omics data, leveraging and enhancing features
 provided by Bioconductor packages.")
       (license license:gpl3+))))
+
+(define-public r-cssam
+  (let ((revision "1")
+        (commit "9ec58c982fa551af0d80b1a266890d92954833f2"))
+    (package
+      (name "r-cssam")
+      (version (git-version "1.4" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/shenorrLab/csSAM.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "128syf9v39gk0z3ip000qpsjbg6l1siyq6c8b0hz41dzg5achyb3"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-formula" ,r-formula)
+         ("r-ggplot2" ,r-ggplot2)
+         ("r-pkgmaker" ,r-pkgmaker)
+         ("r-plyr" ,r-plyr)
+         ("r-rngtools" ,r-rngtools)
+         ("r-scales" ,r-scales)))
+      (home-page "https://github.com/shenorrLab/csSAM/")
+      (synopsis "Cell type-specific statistical analysis of microarray")
+      (description "This package implements the method csSAM that computes
+cell-specific differential expression from measured cell proportions using
+SAM.")
+      ;; Any version
+      (license license:lgpl2.1+))))

From e72702475da2379e10ca09e724e10a9bceceef1b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 24 Sep 2018 13:24:13 +0200
Subject: [PATCH 085/909] gnu: Add r-bseqsc.

* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
---
 gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2366843d87..e74abf005f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13824,3 +13824,48 @@ cell-specific differential expression from measured cell proportions using
 SAM.")
       ;; Any version
       (license license:lgpl2.1+))))
+
+(define-public r-bseqsc
+  (let ((revision "1")
+        (commit "fef3f3e38dcf3df37103348b5780937982b43b98"))
+    (package
+      (name "r-bseqsc")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/shenorrLab/bseqsc.git")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "1prw13wa20f7wlc3gkkls66n1kxz8d28qrb8icfqdwdnnv8w5qg8"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-abind" ,r-abind)
+         ("r-annotationdbi" ,r-annotationdbi)
+         ("r-biobase" ,r-biobase)
+         ("r-cssam" ,r-cssam)
+         ("r-dplyr" ,r-dplyr)
+         ("r-e1071" ,r-e1071)
+         ("r-edger" ,r-edger)
+         ("r-ggplot2" ,r-ggplot2)
+         ("r-nmf" ,r-nmf)
+         ("r-openxlsx" ,r-openxlsx)
+         ("r-pkgmaker" ,r-pkgmaker)
+         ("r-plyr" ,r-plyr)
+         ("r-preprocesscore" ,r-preprocesscore)
+         ("r-rngtools" ,r-rngtools)
+         ("r-scales" ,r-scales)
+         ("r-stringr" ,r-stringr)
+         ("r-xbioc" ,r-xbioc)))
+      (home-page "https://github.com/shenorrLab/bseqsc")
+      (synopsis "Deconvolution of bulk sequencing experiments using single cell data")
+      (description "BSeq-sc is a bioinformatics analysis pipeline that
+leverages single-cell sequencing data to estimate cell type proportion and
+cell type-specific gene expression differences from RNA-seq data from bulk
+tissue samples.  This is a companion package to the publication \"A
+single-cell transcriptomic map of the human and mouse pancreas reveals inter-
+and intra-cell population structure.\" Baron et al. Cell Systems (2016)
+@url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.")
+      (license license:gpl2+))))

From 94282358fd5ca5be85dbf3ccadc7693259f7a72f Mon Sep 17 00:00:00 2001
From: Arun Isaac <arunisaac@systemreboot.net>
Date: Mon, 24 Sep 2018 17:46:18 +0530
Subject: [PATCH 086/909] gnu: m17n-db: Update to 1.8.0.

* gnu/packages/emacs.scm (m17n-db): Update to 1.8.0.
---
 gnu/packages/emacs.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index fbedd2f48d..cc2560dffa 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5538,14 +5538,15 @@ extensibility.")
 (define-public m17n-db
   (package
     (name "m17n-db")
-    (version "1.7.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://savannah/m17n/m17n-db-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1w08hnsbknrcjlzp42c99bgwc9hzsnf5m4apdv0dacql2s09zfm2"))))
+        (base32
+         "0vfw7z9i2s9np6nmx1d4dlsywm044rkaqarn7akffmb6bf1j6zv5"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gettext-minimal)))

From 53c64d7c9303d52cbacdaca5d182175d472c53db Mon Sep 17 00:00:00 2001
From: Arun Isaac <arunisaac@systemreboot.net>
Date: Mon, 24 Sep 2018 17:46:47 +0530
Subject: [PATCH 087/909] gnu: m17n-lib: Update to 1.8.0.

* gnu/packages/emacs.scm (m17n-lib): Update to 1.8.0.
---
 gnu/packages/emacs.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index cc2560dffa..f29040c372 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5573,14 +5573,15 @@ This package contains the library database.")
 (define-public m17n-lib
   (package
     (name "m17n-lib")
-    (version "1.7.0")
+    (version "1.8.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://savannah/m17n/m17n-lib-"
                            version ".tar.gz"))
        (sha256
-        (base32 "10yv730i25g1rpzv6q49m6xn4p8fjm7jdwvik2h70sn8w3hm7f4f"))))
+        (base32
+         "0jp61y09xqj10mclpip48qlfhniw8gwy8b28cbzxy8hq8pkwmfkq"))))
     (build-system gnu-build-system)
     (inputs
      `(("fribidi" ,fribidi)

From d08b3258435254cc6ade95b84a6c53e59cc191e6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 24 Sep 2018 16:20:19 +0200
Subject: [PATCH 088/909] gnu: Add python-grequests.

* gnu/packages/python-web.scm (python-grequests): New variable.
---
 gnu/packages/python-web.scm | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 226b9b631b..6ded2f75ab 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2016, 2017 Danny Milosavljevic <dannym+a@scratchpost.org>
 ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2016, 2017 Nils Gillmann <ng0@n0.is>
@@ -1592,6 +1592,29 @@ library.")
 (define-public python2-responses
   (package-with-python2 python-responses))
 
+(define-public python-grequests
+  (package
+    (name "python-grequests")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "grequests" version))
+       (sha256
+        (base32
+         "1j9icncllbkv7x5719b20mx670c6q1jrdx1sakskkarvx3pc8h8g"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-gevent" ,python-gevent)
+       ("python-requests" ,python-requests)))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "https://github.com/kennethreitz/grequests")
+    (synopsis "Python library for asynchronous HTTP requests")
+    (description "GRequests is a Python library that allows you to use
+@code{Requests} with @code{Gevent} to make asynchronous HTTP Requests easily")
+    (license license:bsd-2)))
+
 (define-public python-geventhttpclient
   (package
     (name "python-geventhttpclient")

From 0750f344eceb10e8ddd81ed146ae2e1aa897f2d4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 24 Sep 2018 16:20:32 +0200
Subject: [PATCH 089/909] gnu: Add python-hawkauthlib.

* gnu/packages/python-web.scm (python-hawkauthlib): New variable.
---
 gnu/packages/python-web.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6ded2f75ab..c38ccea216 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2649,3 +2649,25 @@ for URL parsing and changing.")
 
 (define-public python2-google-api-client
   (package-with-python2 python-google-api-client))
+
+(define-public python-hawkauthlib
+  (package
+    (name "python-hawkauthlib")
+    (version "2.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "hawkauthlib" version))
+       (sha256
+        (base32
+         "03ai47s4h8nfnrf25shbfvkm1b9n1ccd4nmmj280sg1fayi69zgg"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)
+       ("python-webob" ,python-webob)))
+    (home-page "https://github.com/mozilla-services/hawkauthlib")
+    (synopsis "Hawk Access Authentication protocol")
+    (description
+     "This is a low-level Python library for implementing Hawk Access Authentication,
+a simple HTTP request-signing scheme.")
+    (license license:mpl2.0)))

From 084e14cc37d893703b526d8f8f9220f7ee3aa0b3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 24 Sep 2018 16:20:42 +0200
Subject: [PATCH 090/909] gnu: Add python-pybrowserid.

* gnu/packages/python-web.scm (python-pybrowserid): New variable.
---
 gnu/packages/python-web.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index c38ccea216..68a0d78db5 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2671,3 +2671,26 @@ for URL parsing and changing.")
      "This is a low-level Python library for implementing Hawk Access Authentication,
 a simple HTTP request-signing scheme.")
     (license license:mpl2.0)))
+
+(define-public python-pybrowserid
+  (package
+    (name "python-pybrowserid")
+    (version "0.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PyBrowserID" version))
+       (sha256
+        (base32
+         "1qvi79kfb8x9kxkm5lw2mp42hm82cpps1xknmsb5ghkwx1lpc8kc"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)))
+    (native-inputs
+     `(("python-mock" ,python-mock)))
+    (home-page "https://github.com/mozilla/PyBrowserID")
+    (synopsis "Python library for the BrowserID protocol")
+    (description
+     "This is a Python client library for the BrowserID protocol that
+underlies Mozilla Persona.")
+    (license license:mpl2.0)))

From f45bb3cc0fc4e687f966a8f2fabce73e0c6f31f7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 24 Sep 2018 16:20:51 +0200
Subject: [PATCH 091/909] gnu: Add python-pyfxa.

* gnu/packages/python-web.scm (python-pyfxa): New variable.
---
 gnu/packages/python-web.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 68a0d78db5..6df33fe41d 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2694,3 +2694,34 @@ a simple HTTP request-signing scheme.")
      "This is a Python client library for the BrowserID protocol that
 underlies Mozilla Persona.")
     (license license:mpl2.0)))
+
+(define-public python-pyfxa
+  (package
+    (name "python-pyfxa")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PyFxA" version))
+       (sha256
+        (base32
+         "0axl16fyrz2r88gnw4b12mk7dpkqscv8c4wsc1y5hicl7bsbc4fm"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #f)) ; 17 tests require network access
+    (propagated-inputs
+     `(("python-cryptography" ,python-cryptography)
+       ("python-hawkauthlib" ,python-hawkauthlib)
+       ("python-pybrowserid" ,python-pybrowserid)
+       ("python-requests" ,python-requests)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("python-grequests" ,python-grequests)
+       ("python-mock" ,python-mock)
+       ("python-responses" ,python-responses)
+       ("python-unittest2" ,python-unittest2)))
+    (home-page "https://github.com/mozilla/PyFxA")
+    (synopsis "Firefox Accounts client library for Python")
+    (description
+     "This is a Python library for interacting with the Firefox Accounts
+ecosystem.")
+    (license license:mpl2.0)))

From 000147811b15465cd0f67d2635ba7d807d865afd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 24 Sep 2018 16:21:11 +0200
Subject: [PATCH 092/909] gnu: eolie: Update to 0.9.37.

* gnu/packages/gnome.scm (eolie): Update to 0.9.37.
[source]: Fetch from gitlab.
[build-system]: Use meson-build-system.
[arguments]: Remove custom phases; set #:glib-or-gtk?.
[native-inputs]: Remove meson-for-build and ninja; add glib:bin.
[inputs]: Add python-pyfxa and python-pycrypto.
---
 gnu/packages/gnome.scm | 32 +++++++++++++-------------------
 1 file changed, 13 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index ac898fb294..1ca354a432 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -115,6 +115,8 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages rdesktop)
   #:use-module (gnu packages scanner)
   #:use-module (gnu packages selinux)
@@ -4088,29 +4090,20 @@ work and the interface is well tested.")
 (define-public eolie
   (package
     (name "eolie")
-    (version "0.9.15")
+    (version "0.9.37")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/gnumdk/eolie/"
-                                  "releases/download/" version
-                                  "/eolie-" version ".tar.xz"))
+              (uri (string-append "https://gitlab.gnome.org/World/eolie/"
+                                  "uploads/4341cb428b7a45670308ee3fb3fa07dd/"
+                                  "eolie-" version ".tar.xz"))
               (sha256
                (base32
-                "0glydxp1xh85gfidk1l9miqn6qxdbvvk5s3iy0pjlv8nrs3263jd"))))
-    (build-system glib-or-gtk-build-system)
+                "126m0nwwy3lqv7z8aj9hiwangih03b1nlkg3xja9p7wbf7zcvp2n"))))
+    (build-system meson-build-system)
     (arguments
-     `(#:phases
+     `(#:glib-or-gtk? #t
+       #:phases
        (modify-phases %standard-phases
-         (delete 'configure)
-         (replace 'build
-           (lambda* (#:key outputs #:allow-other-keys)
-             (invoke "meson" "build"
-                      "--prefix" (assoc-ref outputs "out"))))
-         (replace 'check
-           (lambda _ (invoke "ninja" "-C" "build" "test")))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (invoke "ninja" "-C" "build" "install")))
          (add-after 'wrap 'wrap-more
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out  (assoc-ref outputs "out"))
@@ -4134,9 +4127,8 @@ work and the interface is well tested.")
        ("intltool" ,intltool)
        ("itstool" ,itstool)
        ("pkg-config" ,pkg-config)
-       ("meson" ,meson-for-build)
-       ("ninja" ,ninja)
        ("python" ,python)
+       ("glib:bin" ,glib "bin")
        ("gtk+" ,gtk+ "bin")))
     (inputs
      `(("gobject-introspection" ,gobject-introspection)
@@ -4146,8 +4138,10 @@ work and the interface is well tested.")
        ("atk" ,atk)    ; propagated by gtk+, but we need it in LD_LIBRARY_PATH
        ("python" ,python-wrapper)
        ("python-dateutil" ,python-dateutil)
+       ("python-pyfxa" ,python-pyfxa)
        ("python-pygobject" ,python-pygobject)
        ("python-pycairo" ,python-pycairo)
+       ("python-pycrypto" ,python-pycrypto)
        ("libsecret" ,libsecret)
        ("gtkspell3" ,gtkspell3)
        ("gsettings-desktop-schemas" ,gsettings-desktop-schemas)

From 8ae540a2c024f9b1b8bce65dbe1dfbf4e926bc77 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 00:54:39 +0200
Subject: [PATCH 093/909] gnu: ocaml-ssl: Don't use unstable tarball.

* gnu/packages/ocaml.scm (ocaml-ssl)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
---
 gnu/packages/ocaml.scm | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 7859696406..0756aecd6d 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -65,6 +65,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system ocaml)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix svn-download)
@@ -1650,12 +1651,13 @@ lets the client choose the concrete timeline.")
     (version "0.5.5")
     (source
       (origin
-        (method url-fetch)
-        (uri (string-append "https://github.com/savonet/ocaml-ssl/archive/"
-                            version ".tar.gz"))
-        (file-name (string-append name "-" version ".tar.gz"))
+        (method git-fetch)
+        (uri (git-reference
+              (url "https://github.com/savonet/ocaml-ssl.git")
+              (commit version)))
+        (file-name (git-file-name name version))
         (sha256 (base32
-                  "15p7652cvzdrlqxc1af11mg07wasxr1fsaj44gcmmh6bmav7wfzq"))))
+                  "0fviq8xhp3qk7pmkl7knchywsipxgb7p0z489hj8qnf2sx8xzdmy"))))
     (build-system ocaml-build-system)
     (arguments `(#:tests? #f
                  #:make-flags (list "OCAMLFIND_LDCONF=ignore")

From c60d5a25280d77ae22061ac08677e07db38e8fbd Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 01:08:09 +0200
Subject: [PATCH 094/909] gnu: libmesode: Don't use unstable tarball.

* gnu/packages/messaging.scm (libmesode)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
---
 gnu/packages/messaging.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 42a0847b7a..3174b4ef4e 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -1474,13 +1474,14 @@ is also scriptable and extensible via Guile.")
     (name "libmesode")
     (version "0.9.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/boothj5/libmesode/archive/"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/boothj5/libmesode.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0iaj56fkd5bjvqpvq3324ni895rmbj1akbfqipjydnghfwaym4z6"))))
+                "1zb1x422zkpnxrz9d2b7pmi8ms60lbw49yh78mydqfypsmj2iyfh"))))
     (build-system gnu-build-system)
     (inputs
      `(("expat" ,expat)

From b44a18c8f26e66c2cbfff4740bff29949a9eb684 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 01:12:00 +0200
Subject: [PATCH 095/909] gnu: libmesode: Update to 0.9.2.

* gnu/packages/messaging.scm (libmesode): Update to 0.9.2.
---
 gnu/packages/messaging.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 3174b4ef4e..33e9d2ffe3 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -1472,7 +1472,7 @@ is also scriptable and extensible via Guile.")
 (define-public libmesode
   (package
     (name "libmesode")
-    (version "0.9.1")
+    (version "0.9.2")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1481,7 +1481,7 @@ is also scriptable and extensible via Guile.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1zb1x422zkpnxrz9d2b7pmi8ms60lbw49yh78mydqfypsmj2iyfh"))))
+                "06f5nfaypvxrbsinxa1k2vrxrs7kqmg38g4wwwk5d63hpn1pj8ak"))))
     (build-system gnu-build-system)
     (inputs
      `(("expat" ,expat)

From 25ab91c85c8901e6e9b36042fa126e24ceb57263 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 01:35:17 +0200
Subject: [PATCH 096/909] gnu: gloox: Update to 1.0.21.

* gnu/packages/messaging.scm (gloox): Update to 1.0.21.
---
 gnu/packages/messaging.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 33e9d2ffe3..9b1aea788c 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -1135,7 +1135,7 @@ with several different talk daemons at the same time.")
 (define-public gloox
   (package
     (name "gloox")
-    (version "1.0.17")
+    (version "1.0.21")
     (source
      (origin
        (method url-fetch)
@@ -1143,7 +1143,7 @@ with several different talk daemons at the same time.")
                            version ".tar.bz2"))
        (sha256
         (base32
-         "09c01jr5nrm7f1ly42wg0pqqscmp48pv8y2fjx1vwbavjxdq59ri"))))
+         "1k57qgif1yii515m6jaqaibkdysfab6394bpawd2l67321f1a4rw"))))
     (build-system gnu-build-system)
     (inputs
      `(("libidn" ,libidn)

From 4cb4af797a08047b5ca894fcb7930519dd2ef466 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 01:37:35 +0200
Subject: [PATCH 097/909] gnu: lxterminal: Update to 0.3.2.

* gnu/packages/lxde.scm (lxterminal): Update to 0.3.2.
---
 gnu/packages/lxde.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/lxde.scm b/gnu/packages/lxde.scm
index 19938fa93c..c45beb8bbb 100644
--- a/gnu/packages/lxde.scm
+++ b/gnu/packages/lxde.scm
@@ -164,7 +164,7 @@ toolkit.  It allows users to monitor and control of running processes.")
 (define-public lxterminal
   (package
     (name "lxterminal")
-    (version "0.3.1")
+    (version "0.3.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/lxde/LXTerminal"
@@ -172,7 +172,7 @@ toolkit.  It allows users to monitor and control of running processes.")
                                   version "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0jrc3m0hbxcmcgahwjlm46s2350gh80ggb6a90xy0h6xqa3z73fd"))))
+                "1124pghrhnx6q4391ri8nvi6bsmvbj1dx81an08mird8jf2b2rii"))))
     (build-system gnu-build-system)
     (inputs `(("gtk+" ,gtk+-2)
               ("vte"  ,vte/gtk+-2)))

From e6dcf9ca5f386c98fc03093032d65559c03164e2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 13:11:24 +0200
Subject: [PATCH 098/909] gnu: rename: Update to 1.00.

* gnu/packages/admin.scm (rename): Update to 1.00.
[arguments]: Wrap executable to find its own library.
---
 gnu/packages/admin.scm | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index e7e34ab97f..8f504cafef 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -869,7 +869,7 @@ over ssh connections.")
 (define-public rename
   (package
     (name "rename")
-    (version "0.35")
+    (version "1.00")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -877,8 +877,24 @@ over ssh connections.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "052iqmn7ya3w1nadpiyavmr3rx566r0lbflx94y8b5wx9q5c16rq"))))
+                "03yhf8nmqsb0zyliv501fdvwlp589jqfn44yqkrflmpzrbik3zxl"))))
     (build-system perl-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'find-itself
+           ;; Fix run-time 'Can't locate File/Rename.pm in @INC' failure.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin")))
+               (with-directory-excursion bin
+                 (for-each
+                  (lambda (program)
+                    (wrap-program program
+                      `("PERL5LIB" ":" prefix
+                        (,(string-append out "/lib/perl5/site_perl")))))
+                  (find-files "." ".*")))
+               #t))))))
     (native-inputs
      `(("perl-module-build" ,perl-module-build)
        ("perl-test-pod" ,perl-test-pod)

From a68b45142373dd75bc96f9c4f8151bcd4e972888 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 19 Sep 2018 22:23:59 +0200
Subject: [PATCH 099/909] gnu: Add gandi.cli.

* gnu/packages/networking.scm (gandi.cli): New public variable.
---
 gnu/packages/networking.scm | 50 +++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 84224374c6..4800c2496b 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -87,6 +87,7 @@
   #:use-module (gnu packages perl-check)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages ssh)
@@ -673,6 +674,55 @@ send out a ping packet and move on to the next target in a round-robin
 fashion.")
     (license license:expat)))
 
+(define-public gandi.cli
+  (package
+    (name "gandi.cli")
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri name version))
+       (sha256
+        (base32 "0vfzkw1avybjkf6fwqpf5m4kjz4c0qkkmj62f3jd0zx00vh5ly1d"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'embed-store-file-names
+           (lambda _
+             (substitute* (list "gandi/cli/modules/cert.py"
+                                "gandi/cli/tests/commands/test_certificate.py")
+               (("openssl") (which "openssl")))
+             #t))
+         (add-after 'install 'install-documentation
+           ;; The included man page may be outdated but we install it anyway,
+           ;; since it's mentioned in 'gandi --help' and better than nothing.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out  (assoc-ref outputs "out"))
+                    (man1 (string-append out "/share/man/man1")))
+               (mkdir-p man1)
+               (with-output-to-file (string-append man1 "/gandi.1")
+                 (lambda _
+                   (invoke "rst2man.py" "gandicli.man.rst")))
+               #t))))))
+    (native-inputs
+     `(("python-docutils" ,python-docutils)   ; for rst2man.py
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-tox" ,python-tox)))
+    (inputs
+     `(("openssl" ,openssl)
+       ("python-click" ,python-click)
+       ("python-ipy" ,python-ipy)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-requests" ,python-requests)))
+    (home-page "https://cli.gandi.net")
+    (synopsis "Command-line interface to the Gandi.net Web API")
+    (description
+     "This package provides a command-line client (@command{gandi}) to buy,
+manage, and delete Internet resources from Gandi.net such as domain names,
+virtual machines, and certificates.")
+    (license license:gpl3+)))
+
 (define-public httping
   (package
     (name "httping")

From 116af86f14f7789831d79815d5b4532afa82058c Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sun, 16 Sep 2018 22:17:06 -0400
Subject: [PATCH 100/909] gnu: octave: Add a search path for CURLOPT_CAPATH.

* gnu/packages/maths.scm (octave)[native-search-paths]: New field.
---
 gnu/packages/maths.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 636b485260..b7d669ccea 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1402,6 +1402,13 @@ can solve two kinds of problems:
        ("less" ,less)
        ("ghostscript" ,ghostscript)
        ("gnuplot" ,gnuplot)))
+    ;; Octave code uses this variable to detect directories holding multiple CA
+    ;; certificates to verify peers with.  This is required for the networking
+    ;; functions that require encryption to work properly.
+    (native-search-paths
+     (list (search-path-specification
+            (variable "CURLOPT_CAPATH")
+            (files '("etc/ssl/certs")))))
     (arguments
      `(#:configure-flags
        (list (string-append "--with-shell="

From f1ea0759f414084a62e29a0740f48d508f3dee73 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 25 Sep 2018 08:18:03 +0200
Subject: [PATCH 101/909] gnu: qjackctl: Update to 0.5.4.

* gnu/packages/audio.scm (qjackctl): Update to 0.5.4.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 8bce6fa2c2..4465872732 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2013,14 +2013,14 @@ and ALSA.")
 (define-public qjackctl
   (package
     (name "qjackctl")
-    (version "0.5.3")
+    (version "0.5.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/qjackctl/qjackctl/"
                                   version "/qjackctl-" version ".tar.gz"))
               (sha256
                (base32
-                "0x08af8m5l8qy9av3dlldsg58ny9nc69h1s4i6hqkvj24jwy6fw1"))))
+                "0qr71nb93gkz5q53nfcl5g168z173wc6s8w1yjs3rfn3m4hg0bcq"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f))                    ; no check target

From 932839ff124ff3b0dd3070914fb1c5beec69bf32 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 25 Sep 2018 11:20:32 +0200
Subject: [PATCH 102/909] gnu: ibus: Update to 1.5.19.

* gnu/packages/ibus.scm (ibus): Update to 1.5.19.
[arguments]: Add configure flags to disable Python 2 support while building
Python 3 bindings; adjust make flags; add phase prepare-ucd-dir.
[inputs]: Replace python2-pygobject with python-pygobject; replace python-2
with python.
[native-inputs]: Add unicode files.
---
 gnu/packages/ibus.scm | 37 ++++++++++++++++++++++++++++---------
 1 file changed, 28 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 9f7e1f88b4..08fce5f6fb 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -44,7 +44,7 @@
 (define-public ibus
   (package
    (name "ibus")
-   (version "1.5.17")
+   (version "1.5.19")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/ibus/ibus/"
@@ -52,22 +52,29 @@
                                  version "/ibus-" version ".tar.gz"))
              (sha256
               (base32
-               "06fj7lawww5d5w73pk249191lvmpz7shlxfxia74bjkpb42shiq3"))))
+               "0a94bnpm24581317hdnihwr4cniriml10p4ffgxg14xhvaccfrjb"))))
    (build-system glib-or-gtk-build-system)
    (arguments
     `(#:tests? #f  ; tests fail because there's no connection to dbus
-      #:configure-flags '("--disable-emoji-dict" ; cannot find emoji.json path
+      #:configure-flags `("--disable-emoji-dict" ; cannot find emoji.json path
+                          "--disable-python2"
+                          "--enable-python-library"
+                          ,(string-append "--with-ucd-dir="
+                                          (getcwd) "/ucd")
                           "--enable-wayland")
       #:make-flags
       (list "CC=gcc"
             (string-append "pyoverridesdir="
                            (assoc-ref %outputs "out")
-                           "/lib/python2.7/site-packages/gi/overrides/")
-            (string-append "py2overridesdir="
-                           (assoc-ref %outputs "out")
-                           "/lib/python2.7/site-packages/gi/overrides/"))
+                           "/lib/python3.6/site-packages/gi/overrides/"))
       #:phases
       (modify-phases %standard-phases
+        (add-after 'unpack 'prepare-ucd-dir
+          (lambda* (#:key inputs #:allow-other-keys)
+            (mkdir-p "../ucd")
+            (symlink (assoc-ref inputs "unicode-blocks") "../ucd/Blocks.txt")
+            (symlink (assoc-ref inputs "unicode-nameslist") "../ucd/NamesList.txt")
+            #t))
         (add-before 'configure 'disable-dconf-update
           (lambda _
             (substitute* "data/dconf/Makefile.in"
@@ -117,11 +124,23 @@
       ("wayland" ,wayland)
       ("xmodmap" ,xmodmap)
       ("iso-codes" ,iso-codes)
-      ("pygobject2" ,python2-pygobject)
-      ("python2" ,python-2)))
+      ("pygobject2" ,python-pygobject)
+      ("python" ,python)))
    (native-inputs
     `(("glib" ,glib "bin") ; for glib-genmarshal
       ("gobject-introspection" ,gobject-introspection) ; for g-ir-compiler
+      ("unicode-nameslist"
+       ,(origin
+          (method url-fetch)
+          (uri "https://www.unicode.org/Public/UNIDATA/NamesList.txt")
+          (sha256
+           (base32 "0yr2h0nfqhirfi3bxl33z6cc94qqshlpgi06c25xh9754irqsgv8"))))
+      ("unicode-blocks"
+       ,(origin
+          (method url-fetch)
+          (uri "https://www.unicode.org/Public/UNIDATA/Blocks.txt")
+          (sha256
+           (base32 "0lnh9iazikpr548bd7nkaq9r3vfljfvz0rg2462prac8qxk7ni8b"))))
       ("vala" ,vala)
       ("pkg-config" ,pkg-config)))
    (native-search-paths

From 79374801d08c8b3e0df264340fd7212a3dac10ab Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 03:44:19 +0200
Subject: [PATCH 103/909] gnu: python-flask-login: Don't use unstable tarball.

* gnu/packages/python-web.scm (python-flask-login)[source]:
Use GIT-FETCH and GIT-FILE-NAME.
---
 gnu/packages/python-web.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6df33fe41d..e3de0a0824 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2056,13 +2056,13 @@ It comes with safe defaults and easily configurable options.")
     (version "0.4.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/maxcountryman/flask-login/archive/"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/maxcountryman/flask-login.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "1pdqp7a2gyb7k06xda004x0fi2w66s6kn2i0ndkqndmg12d83f9w"))))
+        (base32 "0sjbmk8m4mmd9g99n6c6lx9nv2jwwqp6qsqhl945w2m0f1sknwdh"))))
     (arguments
      ;; Tests fail PEP8 compliance. See:
      ;; https://github.com/maxcountryman/flask-login/issues/340

From bbc69023d86f5bd4ffec994453e5bdfbf5c429f4 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 10:13:01 +0200
Subject: [PATCH 104/909] gnu: Add python-semantic-version.

* gnu/packages/python.scm (python-semantic-version)
(python2-semantic-version): New public variables.
---
 gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ea641b8213..86ce70254d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -907,6 +907,34 @@ API for locking files.")
 (define-public python2-lockfile
   (package-with-python2 python-lockfile))
 
+(define-public python-semantic-version
+  (package
+    (name "python-semantic-version")
+    (version "2.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "semantic_version" version))
+       (sha256
+        (base32
+         "1h2l9xyg1zzsda6kjcmfcgycbvrafwci283vcr1v5sbk01l2hhra"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f))                    ; PyPI tarball lacks tests
+    (home-page "https://github.com/rbarrois/python-semanticversion")
+    (synopsis "Semantic versioning module for Python")
+    (description
+     "The @code{semantic_version} class is a small library for handling
+@uref{https://semver.org/, semantic versioning} (@dfn{SemVer}) in Python.
+
+It can compare versions, generate a new version that represents a bump in one of
+the version levels, and check whether any given string is a proper semantic
+version identifier.")
+    (license license:bsd-3)))
+
+(define-public python2-semantic-version
+  (package-with-python2 python-semantic-version))
+
 (define-public python-setuptools
   (package
     (name "python-setuptools")

From d6ab1d0ac3047931a4e4daf0d48f23d2468a7341 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 10:19:13 +0200
Subject: [PATCH 105/909] gnu: python-flask-login: Update to 0.4.1.

* gnu/packages/python-web.scm (python-flask-login): Update to 0.4.1.
[arguments]: Run the test suite.
[propagated-inputs]: Add python-flask.
[native-inputs]: Add test dependencies.
---
 gnu/packages/python-web.scm | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index e3de0a0824..456134c1ce 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2053,7 +2053,7 @@ It comes with safe defaults and easily configurable options.")
 (define-public python-flask-login
   (package
     (name "python-flask-login")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
      (origin
        (method git-fetch)
@@ -2062,12 +2062,27 @@ It comes with safe defaults and easily configurable options.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0sjbmk8m4mmd9g99n6c6lx9nv2jwwqp6qsqhl945w2m0f1sknwdh"))))
+        (base32 "1rj0qwyxapxnp84fi4lhmvh3d91fdiwz7hibw77x3d5i72knqaa9"))))
     (arguments
-     ;; Tests fail PEP8 compliance. See:
-     ;; https://github.com/maxcountryman/flask-login/issues/340
-     `(#:tests? #f))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'avoid-yanc
+           ;; Work around '.nosetests-real: error: no such option: --with-yanc'.
+           (lambda _
+             (setenv "NOCOLOR" "set")
+             #t)))))
     (build-system python-build-system)
+    (propagated-inputs
+     `(("python-flask" ,python-flask)))
+    (native-inputs
+     ;; For tests.
+     `(("python-blinker" ,python-blinker)
+       ("python-mock" ,python-mock)
+       ("python-nose" ,python-nose)
+       ("python-pep8" ,python-pep8)
+       ("python-pyflakes" ,python-pyflakes)
+       ("python-semantic-version" ,python-semantic-version)
+       ("python-werkzeug" ,python-werkzeug)))
     (home-page "https://github.com/maxcountryman/flask-login")
     (synopsis "User session management for Flask")
     (description

From 238d950b79b78365337e625d2a06247fe464d765 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 13:52:11 +0200
Subject: [PATCH 106/909] gnu: python-nose-timer: Update to 0.7.3.

* gnu/packages/check.scm (python-nose-timer): Update to 0.7.3.
---
 gnu/packages/check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index f4596010ea..866fa801c0 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1926,14 +1926,14 @@ create data based on random numbers and yet remain repeatable.")
 (define-public python-nose-timer
   (package
     (name "python-nose-timer")
-    (version "0.7.2")
+    (version "0.7.3")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "nose-timer" version))
         (sha256
           (base32
-            "0ywg223p528014z5s0vzck74r4xyw3kvcp2casfnc85dkvir1zj7"))))
+            "0hfz5aqnhf493i9kyb6prm4zm8vx7wmfsyg3nvsnh24lzh2kwx44"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-nose" ,python-nose)

From 6d7ca74ba60053ddd53636d5850d8ee97fb4ccf5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 11:39:12 +0200
Subject: [PATCH 107/909] gnu: 389-ds-base: Fix build.

* gnu/packages/openldap.scm (389-ds-base)[inputs]: Add openssl.
---
 gnu/packages/openldap.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/openldap.scm b/gnu/packages/openldap.scm
index 4b615b5d32..962a9c8cfe 100644
--- a/gnu/packages/openldap.scm
+++ b/gnu/packages/openldap.scm
@@ -295,6 +295,7 @@ servers from Python programs.")
        ("nspr" ,nspr)
        ("nss" ,nss)
        ("openldap" ,openldap)
+       ("openssl" ,openssl)             ; #included by net-snmp
        ("pcre" ,pcre)
        ("perl" ,perl)
        ("python" ,python)

From 06e6b17bd7ab0258536c62c3639fba38134d84ae Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 10:14:58 +0200
Subject: [PATCH 108/909] gnu: python-pexpect: Use INVOKE.

* gnu/packages/python.scm (python-pexpect)[arguments]: Substitute INVOKE
for SYSTEM*.
---
 gnu/packages/python.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 86ce70254d..5c6c79da88 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4550,7 +4550,7 @@ displayed.")
              ;; Why does it not work? Delete for now.
              (delete-file "tests/test_socket.py")
              #t))
-         (replace 'check (lambda _ (zero? (system* "nosetests" "-v")))))))
+         (replace 'check (lambda _ (invoke "nosetests" "-v"))))))
     (native-inputs
      `(("python-nose" ,python-nose)
        ("python-pytest" ,python-pytest)

From 38e1095d8294e824444c8669765da2358c9b13bd Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 03:38:24 +0200
Subject: [PATCH 109/909] gnu: python-wsgiproxy2: Update to 0.4.5.

* gnu/packages/python-web.scm (python-wsgiproxy2): Update to 0.4.5.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 456134c1ce..2a7487202a 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1351,14 +1351,14 @@ Amazon Web Services (AWS) API.")
 (define-public python-wsgiproxy2
   (package
     (name "python-wsgiproxy2")
-    (version "0.4.4")
+    (version "0.4.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "WSGIProxy2" version ".tar.gz"))
        (sha256
         (base32
-         "16532rjc94h3w74x52jfckf3yzsp8h6z34522jk4xgjy82hpnd7r"))))
+         "19d9dva282vfjs784i0zkxp078lxfz4h3f621z30ij9wbf5rba6a"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-webtest" ,python-webtest)))

From 35f903778a658f9778e945acb8b26d47ca240163 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 24 Sep 2018 13:59:35 +0200
Subject: [PATCH 110/909] gnu: Add guile-next.

* gnu/packages/guile.scm (guile-next): Rewrite to refer to Guile 3.0.
---
 gnu/packages/guile.scm | 40 +++++++++++++++++++++++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index c66183b9db..6d8ab71c78 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -317,7 +317,45 @@ without requiring the source code to be rewritten.")
                 "07p3g0v2ba2vlfbfidqzlgbhnzdx46wh2rgc5gszq1mjyx5bks6r"))))))
 
 (define-public guile-next
-  (deprecated-package "guile-next" guile-2.2))
+  ;; This is the upcoming Guile 3.0, with JIT support.
+  (let ((commit "a74b4a45fab1a78e34954bce5f031e8a9765f827")
+        (revision "0"))
+    (package
+      (inherit guile-2.2)
+      (name "guile-next")
+      (version (git-version "2.99" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://git.savannah.gnu.org/git/guile.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "0kq6mabv7j4gdlwmpz3iaddv98sc7awkl2358sg8j50sg10yw8nx"))
+                (file-name (git-file-name name version))))
+      (native-inputs
+       `(("autoconf", autoconf)
+         ("automake" ,automake)
+         ("libtool" ,libtool)
+         ("gettext" ,gnu-gettext)
+         ("texinfo" ,texinfo)
+         ("flex" ,flex)
+         ,@(package-native-inputs guile-2.2)))
+      (arguments
+       (substitute-keyword-arguments (package-arguments guile-2.2)
+         ((#:phases phases '%standard-phases)
+          ;; XXX: The default 'bootstrap' phase tries to execute the
+          ;; ./bootstrap directory.
+          `(modify-phases ,phases
+             (replace 'bootstrap
+               (lambda _
+                 (patch-shebang "build-aux/git-version-gen")
+                 (invoke "autoreconf" "-vfi")))
+             (add-before 'check 'skip-version-test
+               (lambda _
+                 ;; Remove this test that's bound to fail.
+                 (delete-file "test-suite/tests/version.test")
+                 #t)))))))))
 
 (define (make-guile-readline guile)
   (package

From a7a887718ad0624940d782f9e9b25d275a8f40d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 24 Sep 2018 14:08:40 +0200
Subject: [PATCH 111/909] gnu: diffoscope: Update to 102.

* gnu/packages/package-management.scm (diffoscope): Update to 102.
---
 gnu/packages/package-management.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 5edfb5dffb..3bc8ac6073 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -568,13 +568,13 @@ transactions from C or Python.")
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "100")
+    (version "102")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri name version))
               (sha256
                (base32
-                "0sh7g26i5ndpa8l7xq6rnijbi3jz5izjn0b98zcnm6wpgghszw48"))))
+                "0v2z98xx7n4viw12yq83flpb9ir5ahy1gn44pic0i3dam18xhcm6"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases

From 2e3a6250f8b1232c7f49f84ee7320bcd9869508a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 24 Sep 2018 14:16:13 +0200
Subject: [PATCH 112/909] gnupg: Change default keyserver.

* guix/gnupg.scm (%openpgp-key-server): Change default to
"pool.sks-keyservers.net".
---
 guix/gnupg.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/gnupg.scm b/guix/gnupg.scm
index b30ce461b4..40feb44561 100644
--- a/guix/gnupg.scm
+++ b/guix/gnupg.scm
@@ -57,7 +57,7 @@
 (define %openpgp-key-server
   ;; The default key server.  Note that keys.gnupg.net appears to be
   ;; unreliable.
-  (make-parameter "pgp.mit.edu"))
+  (make-parameter "pool.sks-keyservers.net"))
 
 (define* (gnupg-verify sig file
                        #:optional (keyring (current-keyring)))

From cfe19684ea21feaee97d5c31e248b5a69921f784 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 25 Sep 2018 10:22:59 +0200
Subject: [PATCH 113/909] progress: 'progress-reporter-report!' takes any
 number of arguments.

* guix/progress.scm (progress-reporter-report!): Accept an arbitrary
number of arguments and pass them to REPORT.
---
 guix/progress.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/guix/progress.scm b/guix/progress.scm
index c9c3cd12a0..53aea1c56d 100644
--- a/guix/progress.scm
+++ b/guix/progress.scm
@@ -70,11 +70,11 @@ stopped."
     (($ <progress-reporter> start report stop)
      (start))))
 
-(define (progress-reporter-report! reporter)
+(define (progress-reporter-report! reporter . args)
   "Low-level procedure to lead REPORTER to emit a report."
   (match reporter
     (($ <progress-reporter> start report stop)
-     (report))))
+     (apply report args))))
 
 (define (stop-progress-reporter! reporter)
   "Low-level procedure to stop REPORTER."

From f85dbc4f3bcdc9f11cea9cca4feffee2e57a4412 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 25 Sep 2018 12:28:55 +0200
Subject: [PATCH 114/909] substitute: Progress port really closes underlying
 port.

* guix/scripts/substitute.scm (progress-report-port): Use 'close-port'
instead of 'close-connection'.  Move 'stop' call first.
---
 guix/scripts/substitute.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index 6d31dfdaa4..50c6a22064 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -837,8 +837,8 @@ REPORTER, which should be a <progress-reporter> object."
        (make-custom-binary-input-port "progress-port-proc"
                                       read! #f #f
                                       (lambda ()
-                                        (close-connection port)
-                                        (stop)))))))
+                                        (stop)
+                                        (close-port port)))))))
 
 (define-syntax with-networking
   (syntax-rules ()

From 88268a34bc76c88c5c5e4ecc244924f3c8503d16 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 25 Sep 2018 18:44:38 +0200
Subject: [PATCH 115/909] pull: Try harder to use the host's X.509
 certificates.

* guix/scripts/pull.scm (honor-x509-certificates): Use commonly-found
certificate bundles.
---
 guix/scripts/pull.scm | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 10e1a99e54..39aebb18e2 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -180,9 +180,25 @@ Download and deploy the latest version of Guix.\n"))
 
 (define (honor-x509-certificates store)
   "Use the right X.509 certificates for Git checkouts over HTTPS."
-  (let ((file      (getenv "SSL_CERT_FILE"))
+  ;; On distros such as CentOS 7, /etc/ssl/certs contains only a couple of
+  ;; files (instead of all the certificates) among which "ca-bundle.crt".  On
+  ;; other distros /etc/ssl/certs usually contains the whole set of
+  ;; certificates along with "ca-certificates.crt".  Try to choose the right
+  ;; one.
+  (let ((file      (letrec-syntax ((choose
+                                    (syntax-rules ()
+                                      ((_ file rest ...)
+                                       (let ((f file))
+                                         (if (and f (file-exists? f))
+                                             f
+                                             (choose rest ...))))
+                                      ((_)
+                                       #f))))
+                     (choose (getenv "SSL_CERT_FILE")
+                             "/etc/ssl/certs/ca-certificates.crt"
+                             "/etc/ssl/certs/ca-bundle.crt")))
         (directory (or (getenv "SSL_CERT_DIR") "/etc/ssl/certs")))
-    (if (or (and file (file-exists? file))
+    (if (or file
             (and=> (stat directory #f)
                    (lambda (st)
                      (> (stat:nlink st) 2))))

From 280fc8351230a8fea086d9bbce919ba8395f312c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 15 Sep 2018 11:53:40 +0200
Subject: [PATCH 116/909] git-download: Don't assume the working directory is
 the parent of ".git".

This makes it do the right thing w.r.t. git worktrees.

* guix/git-download.scm (git-file-list): Use REPOSITORY-WORKING-DIRECTORY to
locate checkout.  Rename from "top" to "workdir".
---
 guix/git-download.scm | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/guix/git-download.scm b/guix/git-download.scm
index 24cf11be5e..fa94fad8f8 100644
--- a/guix/git-download.scm
+++ b/guix/git-download.scm
@@ -156,22 +156,23 @@ HASH-ALGO (a symbol).  Use NAME as the file name, or a generic name if #f."
 The result is similar to that of the 'git ls-files' command, except that it
 also includes directories, not just regular files.  The returned file names
 are relative to DIRECTORY, which is not necessarily the root of the checkout."
-  (let* ((directory  (canonicalize-path directory))
+  (let* (;; 'repository-working-directory' always returns a trailing "/",
+         ;; so add one here to ease the comparisons below.
+         (directory  (string-append (canonicalize-path directory) "/"))
          (dot-git    (repository-discover directory))
-         (top        (dirname dot-git))
          (repository (repository-open dot-git))
+         ;; XXX: This procedure is mistakenly private in Guile-Git 0.1.0.
+         (workdir    ((@@ (git repository) repository-working-directory)
+                      repository))
          (head       (repository-head repository))
          (oid        (reference-target head))
          (commit     (commit-lookup repository oid))
          (tree       (commit-tree commit))
          (files      (tree-list tree)))
     (repository-close! repository)
-    (if (string=? top directory)
+    (if (string=? workdir directory)
         files
-        (let ((relative (string-append
-                         (string-drop directory
-                                      (+ 1 (string-length top)))
-                         "/")))
+        (let ((relative (string-drop directory (string-length workdir))))
           (filter-map (lambda (file)
                         (and (string-prefix? relative file)
                              (string-drop file (string-length relative))))

From 52b87855ea64f02a254f6b510346dfb0e20dd5a7 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 28 Aug 2018 02:07:56 +0200
Subject: [PATCH 117/909] gnu: enchant: Update home page.

* gnu/packages/enchant.scm (enchant)[home-page]: Set to URL mentioned on the
legacy home page.
---
 gnu/packages/enchant.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/enchant.scm b/gnu/packages/enchant.scm
index 8b2796d0e2..1c6506ebf1 100644
--- a/gnu/packages/enchant.scm
+++ b/gnu/packages/enchant.scm
@@ -57,5 +57,5 @@ Enchant steps in to provide uniformity and conformity on top of these libraries,
 and implement certain features that may be lacking in any individual provider
 library.  Everything should \"just work\" for any and every definition of \"just
 working\".")
-    (home-page "http://www.abisource.com/projects/enchant")
+    (home-page "https://abiword.github.io/enchant/")
     (license lgpl2.1+)))

From 18ef85b64a3433bccf8dc8b32d338de91fd85a8a Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 28 Aug 2018 03:47:45 +0200
Subject: [PATCH 118/909] gnu: enchant: Don't build libenchant.a.

* gnu/packages/enchant.scm (enchant)[arguments]: Add #:configure-flags.
---
 gnu/packages/enchant.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/enchant.scm b/gnu/packages/enchant.scm
index 1c6506ebf1..b5e9084a42 100644
--- a/gnu/packages/enchant.scm
+++ b/gnu/packages/enchant.scm
@@ -40,6 +40,8 @@
           (base32 "0zq9yw1xzk8k9s6x83n1f9srzcwdavzazn3haln4nhp9wxxrxb1g"))))
 
     (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags '("--disable-static")))
     (inputs
       `(("aspell" ,aspell)    ;; Currently, the only supported backend in Guix
         ("glib" ,glib)))      ;; is aspell. (This information might be old)

From 9a59b29411e2f007a6ba32b88d3b6f50bd6c1f45 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 28 Aug 2018 17:15:00 +0200
Subject: [PATCH 119/909] gnu: enchant: Propagate Glib.

* gnu/packages/enchant.scm (enchant)[inputs]: Move GLIB ...
[propagated-inputs]: ... here.  New field.
---
 gnu/packages/enchant.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/enchant.scm b/gnu/packages/enchant.scm
index b5e9084a42..c3f75ccf2e 100644
--- a/gnu/packages/enchant.scm
+++ b/gnu/packages/enchant.scm
@@ -43,8 +43,10 @@
     (arguments
      '(#:configure-flags '("--disable-static")))
     (inputs
-      `(("aspell" ,aspell)    ;; Currently, the only supported backend in Guix
-        ("glib" ,glib)))      ;; is aspell. (This information might be old)
+     `(("aspell" ,aspell)))   ;; Currently, the only supported backend in Guix
+    (propagated-inputs        ;; is aspell. (This information might be old)
+     ;; Required by enchant.pc.
+     `(("glib" ,glib)))
     (native-inputs
      `(("glib:bin" ,glib "bin")
        ("pkg-config" ,pkg-config)))

From c1d59b3c2a88427aa268a405116a01958db84a5b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 28 Aug 2018 04:03:23 +0200
Subject: [PATCH 120/909] gnu: enchant: Update to 2.2.3.

* gnu/packages/enchant.scm (enchant): Update to 2.2.3.
[arguments]: Add "--enable-relocatable" to #:configure-flags.
[native-inputs]: Add UNITTEST-CPP.
(enchant-1.6): New public variable.
* gnu/packages/fcitx.scm (fcitx)[inputs]: Change ENCHANT to ENCHANT-1.6.
* gnu/packages/gnome.scm (gspell): Likewise.
* gnu/packages/mate.scm (pluma): Likewise.
* gnu/packages/gtk.scm (gtkspell3)[propagated-inputs]: Likewise.
[inputs]: Remove duplicate ENCHANT.
---
 gnu/packages/enchant.scm | 50 +++++++++++++++++++++++++++++-----------
 gnu/packages/fcitx.scm   |  2 +-
 gnu/packages/gnome.scm   |  2 +-
 gnu/packages/gtk.scm     |  5 ++--
 gnu/packages/mate.scm    |  2 +-
 5 files changed, 41 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/enchant.scm b/gnu/packages/enchant.scm
index c3f75ccf2e..0392a709e2 100644
--- a/gnu/packages/enchant.scm
+++ b/gnu/packages/enchant.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Marek Benc <merkur32@gmail.com>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,29 +20,32 @@
 (define-module (gnu packages enchant)
   #:use-module (gnu packages)
   #:use-module (gnu packages aspell)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages pkg-config)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
-  #:use-module (guix licenses))
+  #:use-module (guix licenses)
+  #:use-module (srfi srfi-1))
 
 (define-public enchant
   (package
     (name "enchant")
-    (version "1.6.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri
-          (string-append "http://www.abisource.com/downloads/" name "/" version
-                         "/" name "-" version ".tar.gz"))
-        (sha256
-          (base32 "0zq9yw1xzk8k9s6x83n1f9srzcwdavzazn3haln4nhp9wxxrxb1g"))))
-
+    (version "2.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/AbiWord/enchant/releases"
+                                  "/download/v" version "/enchant-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0v87p1ls0gym95qirijpclk650sjbkcjjl6ssk059zswcwaykn5b"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:configure-flags '("--disable-static")))
+     '(#:configure-flags '("--disable-static"
+                           ;; Tests require a relocatable build.
+                           "--enable-relocatable")))
     (inputs
      `(("aspell" ,aspell)))   ;; Currently, the only supported backend in Guix
     (propagated-inputs        ;; is aspell. (This information might be old)
@@ -49,8 +53,8 @@
      `(("glib" ,glib)))
     (native-inputs
      `(("glib:bin" ,glib "bin")
-       ("pkg-config" ,pkg-config)))
-
+       ("pkg-config" ,pkg-config)
+       ("unittest-cpp" ,unittest-cpp)))
     (synopsis "Multi-backend spell-checking library wrapper")
     (description
       "On the surface, Enchant appears to be a generic spell checking library.
@@ -63,3 +67,21 @@ library.  Everything should \"just work\" for any and every definition of \"just
 working\".")
     (home-page "https://abiword.github.io/enchant/")
     (license lgpl2.1+)))
+
+;; Some packages are not ready for the 2.x API yet, so we keep this version
+;; around.  The library and executables of Enchant 2 have been designed not to
+;; conflict with 1.x, so it's OK if both end up in the same profile.
+(define-public enchant-1.6
+  (package
+    (inherit enchant)
+    (version "1.6.0")
+    (arguments '(#:configure-flags '("--disable-static")))
+    (native-inputs (alist-delete "unittest-cpp"
+                                 (package-native-inputs enchant)))
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://www.abisource.com/downloads/enchant/"
+                                  version "/enchant-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0zq9yw1xzk8k9s6x83n1f9srzcwdavzazn3haln4nhp9wxxrxb1g"))))))
diff --git a/gnu/packages/fcitx.scm b/gnu/packages/fcitx.scm
index bcd5f12dd1..b05d9b7146 100644
--- a/gnu/packages/fcitx.scm
+++ b/gnu/packages/fcitx.scm
@@ -75,7 +75,7 @@
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("dbus"             ,dbus)
-       ("enchant"          ,enchant)
+       ("enchant"          ,enchant-1.6)
        ("gettext"          ,gettext-minimal)
        ("gtk2"             ,gtk+-2)
        ("gtk3"             ,gtk+)
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 1ca354a432..8d684cd36d 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -6969,7 +6969,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
        ("aspell-dict-en" ,aspell-dict-en)
        ("xorg-server" ,xorg-server)))
     (propagated-inputs
-     `(("enchant" ,enchant)))           ; enchant.pc is required by gspell-1.pc
+     `(("enchant" ,enchant-1.6)))       ; enchant.pc is required by gspell-1.pc
     (home-page "https://wiki.gnome.org/Projects/gspell")
     (synopsis "GNOME's alternative spell checker")
     (description
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 0b85a1723f..76e64b36bc 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -1582,12 +1582,11 @@ glass artworks done by Venicians glass blowers.")
      `(("intltool" ,intltool)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("enchant" ,enchant)
-       ("gobject-introspection" ,gobject-introspection)
+     `(("gobject-introspection" ,gobject-introspection)
        ("gtk+" ,gtk+)
        ("pango" ,pango)))
     (propagated-inputs
-     `(("enchant" ,enchant))) ; gtkspell3-3.0.pc refers to it.
+     `(("enchant" ,enchant-1.6)))          ;gtkspell3-3.0.pc refers to it
     (home-page "http://gtkspell.sourceforge.net")
     (synopsis "Spell-checking addon for GTK's TextView widget")
     (description
diff --git a/gnu/packages/mate.scm b/gnu/packages/mate.scm
index 88f64fdb66..5919c714ee 100644
--- a/gnu/packages/mate.scm
+++ b/gnu/packages/mate.scm
@@ -1411,7 +1411,7 @@ can be used as backgrounds in the MATE Desktop environment.")
     (inputs
      `(("atk" ,atk)
        ("cairo" ,cairo)
-       ("enchant" ,enchant)
+       ("enchant" ,enchant-1.6)
        ("glib" ,glib)
        ("gtk+" ,gtk+)
        ("gtksourceview" ,gtksourceview)

From 9b1bb75781118b1460563171aae503aa9ba702a8 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 28 Aug 2018 05:49:30 +0200
Subject: [PATCH 121/909] gnu: gspell: Update to 1.8.1.

* gnu/packages/gnome.scm (gspell): Update to 1.8.1.
[propagated-inputs]: Change ENCHANT-1.6 to ENCHANT.
---
 gnu/packages/gnome.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 8d684cd36d..1e8522c500 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -6927,7 +6927,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
 (define-public gspell
   (package
     (name "gspell")
-    (version "1.4.2")
+    (version "1.8.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -6935,7 +6935,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1683vyyfq3q0ph665jj6id8hnlyid4qxzmqiwpv97gmz8zksg6x5"))
+                "1rdv873ixhwr15jwgc2z6k6y0hj353fqnwsy7zkh0c30qwiiv6l1"))
               (patches (search-patches "gspell-dash-test.patch"))))
     (build-system glib-or-gtk-build-system)
     (arguments
@@ -6969,7 +6969,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).")
        ("aspell-dict-en" ,aspell-dict-en)
        ("xorg-server" ,xorg-server)))
     (propagated-inputs
-     `(("enchant" ,enchant-1.6)))       ; enchant.pc is required by gspell-1.pc
+     `(("enchant" ,enchant)))            ;enchant.pc is required by gspell-1.pc
     (home-page "https://wiki.gnome.org/Projects/gspell")
     (synopsis "GNOME's alternative spell checker")
     (description

From a0c9ba1d64be641192a22de3284aee2acb69214e Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 20 Sep 2018 16:56:15 +0200
Subject: [PATCH 122/909] gnu: webkitgtk: Remove obsolete phase.

* gnu/packages/webkit.scm (webkitgtk)[arguments]: Remove #:phases.
(webkitgtk-2.22)[arguments]: Don't reference removed phase.
---
 gnu/packages/webkit.scm | 38 ++++++++++----------------------------
 1 file changed, 10 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index 976411dbbc..c5238a8a65 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -87,23 +87,7 @@
                           ;; XXX Disable WOFF2 ‘web fonts’.  These were never
                           ;; supported in our previous builds.  Enabling them
                           ;; requires building libwoff2 and possibly woff2dec.
-                          "-DUSE_WOFF2=OFF")
-       #:phases
-       (modify-phases %standard-phases
-         (add-after
-          'set-paths 'add-gst-plugins-base-include-path
-          (lambda* (#:key inputs #:allow-other-keys)
-            ;; XXX Work around a problem in the build system, which neglects
-            ;; to add -I for gst-plugins-base when compiling
-            ;; Source/WebKit2/UIProcess/WebPageProxy.cpp, apparently assuming
-            ;; that it will be in the same directory as gstreamer's header
-            ;; files.
-            (setenv "CPATH"
-                    (string-append (getenv "C_INCLUDE_PATH")
-                                   ":"
-                                   (assoc-ref inputs "gst-plugins-base")
-                                   "/include/gstreamer-1.0"))
-            #t)))))
+                          "-DUSE_WOFF2=OFF")))
     (native-inputs
      `(("bison" ,bison)
        ("gettext" ,gettext-minimal)
@@ -171,14 +155,12 @@ HTML/CSS applications to full-fledged web browsers.")
      `(("gcc" ,gcc-7)  ; webkitgtk-2.22 requires gcc-6 or newer
        ,@(package-native-inputs webkitgtk)))
     (arguments
-     (substitute-keyword-arguments (package-arguments webkitgtk)
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (add-after 'add-gst-plugins-base-include-path
-               'work-around-gcc-7-include-path-issue
-             ;; FIXME: Work around a problem with gcc-7 includes (see
-             ;; <https://bugs.gnu.org/30756>).
-             (lambda _
-               (unsetenv "C_INCLUDE_PATH")
-               (unsetenv "CPLUS_INCLUDE_PATH")
-               #t))))))))
+     `(#:phases (modify-phases %standard-phases
+                  (add-before 'configure 'work-around-gcc-7-include-path-issue
+                    ;; FIXME: Work around a problem with gcc-7 includes (see
+                    ;; <https://bugs.gnu.org/30756>).
+                    (lambda _
+                      (unsetenv "C_INCLUDE_PATH")
+                      (unsetenv "CPLUS_INCLUDE_PATH")
+                      #t)))
+       ,@(package-arguments webkitgtk)))))

From 020c4ef18e2a1ab877de803d697ca96acfa46624 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 24 Sep 2018 14:43:53 +0200
Subject: [PATCH 123/909] gnu: node: Delete expired tests.

* gnu/packages/node.scm (node)[arguments]: Delete tests for which the TLS
certificates have expired.
---
 gnu/packages/node.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index d1de7a536c..de7d59c6b5 100644
--- a/gnu/packages/node.scm
+++ b/gnu/packages/node.scm
@@ -125,6 +125,14 @@
                          "test/sequential/test-child-process-emfile.js"
                          "test/sequential/test-benchmark-child-process.js"
                          "test/sequential/test-http-regr-gh-2928.js"))
+
+             ;; These tests have an expiry date: they depend on the validity of
+             ;; TLS certificates that are bundled with the source.  We want this
+             ;; package to be reproducible forever, so remove those.
+             ;; TODO: Regenerate certs instead.
+             (for-each delete-file
+                       '("test/parallel/test-tls-passphrase.js"
+                         "test/parallel/test-tls-server-verify.js"))
              #t))
          (replace 'configure
            ;; Node's configure script is actually a python script, so we can't

From e789b85841aa013c4f6bd18f4dff99b30bf0b3a4 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 23 Sep 2018 13:12:23 +0200
Subject: [PATCH 124/909] gnu: Add Node LTS.

* gnu/packages/node.scm (node)[arguments]: Adjust 'patch-files' phase to
ignore missing files.
(node-lts): New public variable.
---
 gnu/packages/node.scm | 28 +++++++++++++++++++++++++---
 1 file changed, 25 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index de7d59c6b5..b525804bdb 100644
--- a/gnu/packages/node.scm
+++ b/gnu/packages/node.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mike Gerwitz <mtg@gnu.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -86,6 +87,14 @@
        (modify-phases %standard-phases
          (add-before 'configure 'patch-files
            (lambda* (#:key inputs #:allow-other-keys)
+
+             ;; This phase is inherited by Node LTS, which does not have all
+             ;; the files listed here.  Use this helper for convenience.
+             (define (delete-if-exists file)
+               (if (file-exists? file)
+                   (delete-file file)
+                   '()))
+
              ;; Fix hardcoded /bin/sh references.
              (substitute* '("lib/child_process.js"
                             "lib/internal/v8_prof_polyfill.js"
@@ -103,7 +112,7 @@
 
              ;; FIXME: These tests depend on being able to install eslint.
              ;; See https://github.com/nodejs/node/issues/17098.
-             (for-each delete-file
+             (for-each delete-if-exists
                        '("test/parallel/test-eslint-alphabetize-errors.js"
                          "test/parallel/test-eslint-buffer-constructor.js"
                          "test/parallel/test-eslint-documented-errors.js"
@@ -111,7 +120,7 @@
 
              ;; FIXME: These tests fail in the build container, but they don't
              ;; seem to be indicative of real problems in practice.
-             (for-each delete-file
+             (for-each delete-if-exists
                        '("test/async-hooks/test-ttywrap.readstream.js"
                          "test/parallel/test-util-inspect.js"
                          "test/parallel/test-v8-serdes.js"
@@ -130,7 +139,7 @@
              ;; TLS certificates that are bundled with the source.  We want this
              ;; package to be reproducible forever, so remove those.
              ;; TODO: Regenerate certs instead.
-             (for-each delete-file
+             (for-each delete-if-exists
                        '("test/parallel/test-tls-passphrase.js"
                          "test/parallel/test-tls-server-verify.js"))
              #t))
@@ -188,3 +197,16 @@ devices.")
     (home-page "https://nodejs.org/")
     (license expat)
     (properties '((timeout . 3600))))) ; 1 h
+
+(define-public node-lts
+  (package
+    (inherit node)
+    (name "node-lts")
+    (version "8.12.0")
+    (source (origin
+              (inherit (package-source node))
+              (uri (string-append "https://nodejs.org/dist/v" version
+                                  "/node-v" version ".tar.xz"))
+              (sha256
+               (base32
+                "16j1rrxkhmvpcw689ndw1raql1gz4jqn7n82z55zn63c05cgz7as"))))))

From 5f33e9063b9b047801d0206e7a74eee8bf6fc52d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 26 Aug 2018 23:31:10 +0200
Subject: [PATCH 125/909] gnu: varnish: Use absolute file name of "rm".

* gnu/packages/web.scm (varnish)[arguments]: Rename 'patch-bin-sh-phase to
'use-absolute-file-names and add substitution.
---
 gnu/packages/web.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index b6bee57f9f..26c2e9128a 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5019,12 +5019,14 @@ deployments.")
                                "--localstatedir=/var")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'patch-/bin/sh
+         (add-after 'unpack 'use-absolute-file-names
            (lambda _
              (substitute* '("bin/varnishtest/vtc_varnish.c"
                             "bin/varnishtest/vtc_process.c"
                             "bin/varnishd/mgt/mgt_vcc.c")
                (("/bin/sh") (which "sh")))
+             (substitute* "bin/varnishd/mgt/mgt_shmem.c"
+               (("rm -rf") (string-append (which "rm") " -rf")))
              #t))
          (add-before 'install 'patch-Makefile
            (lambda _

From 3b97a1779f3b65d582b8edc8c154b6414314b946 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 26 Aug 2018 23:33:48 +0200
Subject: [PATCH 126/909] services: Add Varnish service.

* gnu/services/web.scm (<varnish-configuration>): New record type.
(%varnish-accounts, %varnish-service-type): New variables.
(varnish-shepherd-service): New procedure.
* gnu/tests/web.scm (%varnish-vcl, %varnish-os): New variables.
(%test-varnish): New test.
* doc/guix.texi (Web Services): Document it.
---
 doc/guix.texi        | 80 ++++++++++++++++++++++++++++++++++++
 gnu/services/web.scm | 96 +++++++++++++++++++++++++++++++++++++++++++-
 gnu/tests/web.scm    | 41 +++++++++++++++++++
 3 files changed, 216 insertions(+), 1 deletion(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 76ec718b07..6b4b06f46d 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -16888,6 +16888,86 @@ body of a named location block cannot contain location blocks.
 @end table
 @end deftp
 
+@subsubheading Varnish Cache
+@cindex Varnish
+Varnish is a fast cache server that sits in between web applications
+and end users.  It proxies requests from clients and caches the
+accessed URLs such that multiple requests for the same resource only
+creates one request to the back-end.
+
+@defvr {Scheme Variable} varnish-service-type
+Service type for the Varnish daemon.
+@end defvr
+
+@deftp {Data Type} varnish-configuration
+Data type representing the @code{varnish} service configuration.
+This type has the following parameters:
+
+@table @asis
+@item @code{package} (default: @code{varnish})
+The Varnish package to use.
+
+@item @code{name} (default: @code{"default"})
+A name for this Varnish instance.  Varnish will create a directory in
+@file{/var/varnish/} with this name and keep temporary files there.  If
+the name starts with a forward slash, it is interpreted as an absolute
+directory name.
+
+Pass the @code{-n} argument to other Varnish programs to connect to the
+named instance, e.g. @command{varnishncsa -n default}.
+
+@item @code{backend} (default: @code{"localhost:8080"})
+The backend to use.  This option has no effect if @code{vcl} is set.
+
+@item @code{vcl} (default: #f)
+The @dfn{VCL} (Varnish Configuration Language) program to run.  If this
+is @code{#f}, Varnish will proxy @code{backend} using the default
+configuration.  Otherwise this must be a file-like object with valid
+VCL syntax.
+
+@c Varnish does not support HTTPS, so keep this URL to avoid confusion.
+For example, to mirror @url{http://www.gnu.org,www.gnu.org} with VCL you
+can do something along these lines:
+
+@example
+(define %gnu-mirror
+  (plain-file
+   "gnu.vcl"
+   "vcl 4.1;
+backend gnu @{ .host = "www.gnu.org"; @}"))
+
+(operating-system
+  ...
+  (services (cons (service varnish-service-type
+                           (varnish-configuration
+                            (listen '(":80"))
+                            (vcl %gnu-mirror)))
+                  %base-services)))
+@end example
+
+The configuration of an already running Varnish instance can be inspected
+and changed using the @command{varnishadm} program.
+
+Consult the @url{https://varnish-cache.org/docs/,Varnish User Guide} and
+@url{https://book.varnish-software.com/4.0/,Varnish Book} for
+comprehensive documentation on Varnish and its configuration language.
+
+@item @code{listen} (default: @code{'("localhost:80")})
+List of addresses Varnish will listen on.
+
+@item @code{storage} (default: @code{'("malloc,128m")})
+List of storage backends that will be available in VCL.
+
+@item @code{parameters} (default: @code{'()})
+List of run-time parameters in the form @code{'(("parameter" . "value"))}.
+
+@item @code{extra-options} (default: @code{'()})
+Additional arguments to pass to the @command{varnishd} process.
+
+@end table
+@end deftp
+
+@subsubheading FastCGI
 @cindex fastcgi
 @cindex fcgiwrap
 FastCGI is an interface between the front-end and the back-end of a web
diff --git a/gnu/services/web.scm b/gnu/services/web.scm
index 1c38e7d8d3..1edb1f4d34 100644
--- a/gnu/services/web.scm
+++ b/gnu/services/web.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -190,7 +191,21 @@
             tailon-configuration-config-file
             tailon-configuration-package
 
-            tailon-service-type))
+            tailon-service-type
+
+            <varnish-configuration>
+            varnish-configuration
+            varnish-configuration?
+            varnish-configuration-package
+            varnish-configuration-name
+            varnish-configuration-backend
+            varnish-configuration-vcl
+            varnish-configuration-listen
+            varnish-configuration-storage
+            varnish-configuration-parameters
+            varnish-configuration-extra-options
+
+            varnish-service-type))
 
 ;;; Commentary:
 ;;;
@@ -1162,3 +1177,82 @@ files.")
                   (files (append (tailon-configuration-file-files old-config-file)
                                  files))))))))
    (default-value (tailon-configuration))))
+
+
+;;;
+;;; Varnish
+;;;
+
+(define-record-type* <varnish-configuration>
+  varnish-configuration make-varnish-configuration
+  varnish-configuration?
+  (package             varnish-configuration-package          ;<package>
+                       (default varnish))
+  (name                varnish-configuration-name             ;string
+                       (default "default"))
+  (backend             varnish-configuration-backend          ;string
+                       (default "localhost:8080"))
+  (vcl                 varnish-configuration-vcl              ;#f | <file-like>
+                       (default #f))
+  (listen              varnish-configuration-listen           ;list of strings
+                       (default '("localhost:80")))
+  (storage             varnish-configuration-storage          ;list of strings
+                       (default '("malloc,128m")))
+  (parameters          varnish-configuration-parameters       ;list of string pairs
+                       (default '()))
+  (extra-options       varnish-configuration-extra-options    ;list of strings
+                       (default '())))
+
+(define %varnish-accounts
+  (list (user-group
+         (name "varnish")
+         (system? #t))
+        (user-account
+         (name "varnish")
+         (group "varnish")
+         (system? #t)
+         (comment "Varnish Cache User")
+         (home-directory "/var/varnish")
+         (shell (file-append shadow "/sbin/nologin")))))
+
+(define varnish-shepherd-service
+  (match-lambda
+    (($ <varnish-configuration> package name backend vcl listen storage
+                                parameters extra-options)
+     (list (shepherd-service
+            (provision (list (symbol-append 'varnish- (string->symbol name))))
+            (documentation (string-append "The Varnish Web Accelerator"
+                                          " (" name ")"))
+            (requirement '(networking))
+            (start #~(make-forkexec-constructor
+                      (list #$(file-append package "/sbin/varnishd")
+                            "-n" #$name
+                            #$@(if vcl
+                                   #~("-f" #$vcl)
+                                   #~("-b" #$backend))
+                            #$@(append-map (lambda (a) (list "-a" a)) listen)
+                            #$@(append-map (lambda (s) (list "-s" s)) storage)
+                            #$@(append-map (lambda (p)
+                                             (list "-p" (format #f "~a=~a"
+                                                                (car p) (cdr p))))
+                                           parameters)
+                            #$@extra-options)
+                      ;; Varnish will drop privileges to the "varnish" user when
+                      ;; it exists.  Not passing #:user here allows the service
+                      ;; to bind to ports < 1024.
+                      #:pid-file (if (string-prefix? "/" #$name)
+                                     (string-append #$name "/_.pid")
+                                     (string-append "/var/varnish/" #$name "/_.pid"))))
+            (stop #~(make-kill-destructor)))))))
+
+(define varnish-service-type
+  (service-type
+   (name 'varnish)
+   (description "Run the Varnish cache server.")
+   (extensions
+    (list (service-extension account-service-type
+                             (const %varnish-accounts))
+          (service-extension shepherd-root-service-type
+                             varnish-shepherd-service)))
+   (default-value
+     (varnish-configuration))))
diff --git a/gnu/tests/web.scm b/gnu/tests/web.scm
index 45fcb668fb..bcc919137b 100644
--- a/gnu/tests/web.scm
+++ b/gnu/tests/web.scm
@@ -32,6 +32,7 @@
   #:use-module (guix store)
   #:export (%test-httpd
             %test-nginx
+            %test-varnish
             %test-php-fpm
             %test-hpcguix-web
             %test-tailon))
@@ -167,6 +168,46 @@ HTTP-PORT."
    (value (run-webserver-test name %nginx-os
                               #:log-file "/var/log/nginx/access.log"))))
 
+
+;;;
+;;; Varnish
+;;;
+
+(define %varnish-vcl
+  (mixed-text-file
+   "varnish-test.vcl"
+   "vcl 4.0;
+backend dummy { .host = \"127.1.1.1\"; }
+sub vcl_recv { return(synth(200, \"OK\")); }
+sub vcl_synth {
+  synthetic(\"" %index.html-contents "\");
+  set resp.http.Content-Type = \"text/plain\";
+  return(deliver);
+}"))
+
+(define %varnish-os
+  (simple-operating-system
+   (dhcp-client-service)
+   ;; Pretend to be a web server that serves %index.html-contents.
+   (service varnish-service-type
+            (varnish-configuration
+             (name "/tmp/server")
+             ;; Use a small VSL buffer to fit in the test VM.
+             (parameters '(("vsl_space" . "4M")))
+             (vcl %varnish-vcl)))
+   ;; Proxy the "server" using the builtin configuration.
+   (service varnish-service-type
+            (varnish-configuration
+             (parameters '(("vsl_space" . "4M")))
+             (backend "localhost:80")
+             (listen '(":8080"))))))
+
+(define %test-varnish
+  (system-test
+   (name "varnish")
+   (description "Test the Varnish Cache server.")
+   (value (run-webserver-test "varnish-default" %varnish-os))))
+
 
 ;;;
 ;;; PHP-FPM

From ffec356a29a58d97ec34e1152aa3136e78471dc6 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 23 Sep 2018 14:45:34 +0200
Subject: [PATCH 127/909] gnu: node: Build against libuv@1.19.

* gnu/packages/libevent.scm (libuv-1.19): New public variable.
* gnu/packages/node.scm (node)[inputs]: Change LIBUV to LIBUV-1.19.
---
 gnu/packages/libevent.scm | 13 +++++++++++++
 gnu/packages/node.scm     |  2 +-
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm
index bc7f6c670d..2de29707ca 100644
--- a/gnu/packages/libevent.scm
+++ b/gnu/packages/libevent.scm
@@ -152,6 +152,19 @@ resolution, asynchronous file system operations, and threading primitives.")
     ;; details.  Documentation is CC-BY 4.0 as of 1.12.0; see 'LICENSE-docs'.
     (license (list expat cc-by4.0))))
 
+;; This version is required for Node versions < 10.
+(define-public libuv-1.19
+  (package
+    (inherit libuv)
+    (version "1.19.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://dist.libuv.org/dist/v" version
+                                  "/libuv-v" version ".tar.gz"))
+              (sha256
+               (base32
+                "1msk9ac1z69whww88ibrwjqkd1apdla6l77cm2fwy5kigq0z5g3w"))))))
+
 (define-public perl-anyevent
   (package
     (name "perl-anyevent")
diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index b525804bdb..a0221601dd 100644
--- a/gnu/packages/node.scm
+++ b/gnu/packages/node.scm
@@ -184,7 +184,7 @@
      `(("c-ares" ,c-ares)
        ("http-parser" ,http-parser)
        ("icu4c" ,icu4c)
-       ("libuv" ,libuv)
+       ("libuv" ,libuv-1.19)
        ("nghttp2" ,nghttp2 "lib")
        ("openssl" ,openssl)
        ("zlib" ,zlib)))

From 257e3247910610fe24ae1b86f38e85552d53e48c Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 23 Sep 2018 04:46:59 -0400
Subject: [PATCH 128/909] gnu: icecat: Unbundle graphite2 and harfbuzz.

* gnu/packages/patches/icecat-use-system-graphite2+harfbuzz.patch: New file.
* gnu/packages/patches/icecat-use-system-graphite2.patch,
gnu/packages/patches/icecat-use-system-harfbuzz.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add new patch.  Delete
bundled graphite2 and harfbuzz in snippet.
[inputs]: Add graphite2 and harfbuzz.
[arguments]: Add --with-system-{graphite2,harfbuzz} to configure flags.
---
 gnu/local.mk                                  |   3 +-
 gnu/packages/gnuzilla.scm                     |  19 +-
 ...icecat-use-system-graphite2+harfbuzz.patch | 226 ++++++++++++++
 .../patches/icecat-use-system-graphite2.patch | 248 ----------------
 .../patches/icecat-use-system-harfbuzz.patch  | 279 ------------------
 5 files changed, 236 insertions(+), 539 deletions(-)
 create mode 100644 gnu/packages/patches/icecat-use-system-graphite2+harfbuzz.patch
 delete mode 100644 gnu/packages/patches/icecat-use-system-graphite2.patch
 delete mode 100644 gnu/packages/patches/icecat-use-system-harfbuzz.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index fe2b573dd5..35e78e7816 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -811,8 +811,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/hydra-disable-darcs-test.patch		\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
   %D%/packages/patches/icecat-CVE-2018-12383.patch		\
-  %D%/packages/patches/icecat-use-system-graphite2.patch	\
-  %D%/packages/patches/icecat-use-system-harfbuzz.patch		\
+  %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch	\
   %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
   %D%/packages/patches/icedtea-7-hotspot-gcc-segfault-workaround.patch  \
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 653cee93d5..ad83444e3c 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -495,9 +495,8 @@ security standards.")
         "0lqx7g79x15941rhjr3qsfwsny6vzc7d7abdmvjy6jjbqkqlc1zl"))
       (patches
        (list
-        (search-patch "icecat-avoid-bundled-libraries.patch")
-        ;; FIXME (search-patch "icecat-use-system-harfbuzz.patch")
-        ;; FIXME (search-patch "icecat-use-system-graphite2.patch")
+        (search-patch  "icecat-avoid-bundled-libraries.patch")
+        (search-patch  "icecat-use-system-graphite2+harfbuzz.patch")
         (mozilla-patch "icecat-CVE-2018-12385.patch"      "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5")
         (search-patch  "icecat-CVE-2018-12383.patch")
         (mozilla-patch "icecat-bug-1489744.patch"         "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")))
@@ -535,8 +534,8 @@ security standards.")
                       "media/libvpx"
                       "security/nss"
                       ;; UNBUNDLE-ME "gfx/cairo"
-                      ;; UNBUNDLE-ME "gfx/harfbuzz"
-                      ;; UNBUNDLE-ME "gfx/graphite2"
+                      "gfx/harfbuzz"
+                      "gfx/graphite2"
                       "js/src/ctypes/libffi"
                       "db/sqlite3"))
           ;; Delete .pyc files, typically present in icecat source tarballs
@@ -557,10 +556,10 @@ security standards.")
        ("glib" ,glib)
        ("gtk+" ,gtk+)
        ("gtk+-2" ,gtk+-2)
-       ;; UNBUNDLE-ME ("graphite2" ,graphite2)
+       ("graphite2" ,graphite2)
        ("pango" ,pango)
        ("freetype" ,freetype)
-       ;; UNBUNDLE-ME ("harfbuzz" ,harfbuzz)
+       ("harfbuzz" ,harfbuzz)
        ("hunspell" ,hunspell)
        ("libcanberra" ,libcanberra)
        ("libgnome" ,libgnome)
@@ -643,8 +642,8 @@ security standards.")
                            "--with-system-icu"
                            "--with-system-nspr"
                            "--with-system-nss"
-                           ;; UNBUNDLE-ME "--with-system-harfbuzz"
-                           ;; UNBUNDLE-ME "--with-system-graphite2"
+                           "--with-system-harfbuzz"
+                           "--with-system-graphite2"
                            "--enable-system-pixman"
                            ;; UNBUNDLE-ME "--enable-system-cairo"
                            "--enable-system-ffi"
@@ -697,7 +696,7 @@ security standards.")
                               all)))
             #t))
          (add-after 'patch-source-shebangs 'patch-cargo-checksums
-           (lambda* _
+           (lambda _
              (use-modules (guix build cargo-build-system))
              (let ((null-file "/dev/null")
                    (null-hash "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"))
diff --git a/gnu/packages/patches/icecat-use-system-graphite2+harfbuzz.patch b/gnu/packages/patches/icecat-use-system-graphite2+harfbuzz.patch
new file mode 100644
index 0000000000..94c211b797
--- /dev/null
+++ b/gnu/packages/patches/icecat-use-system-graphite2+harfbuzz.patch
@@ -0,0 +1,226 @@
+Allow building against system-wide graphite2/harfbuzz.
+See <https://bugzilla.mozilla.org/show_bug.cgi?id=847568>
+Based on:
+  https://svnweb.freebsd.org/ports/head/www/firefox-esr/files/patch-bug847568?revision=472833&view=co
+Modified for use with patch -p1, and to apply cleanly to GNU IceCat.
+
+--- icecat-60.2.0/config/system-headers.mozbuild
++++ icecat-60.2.0/config/system-headers.mozbuild
+@@ -1311,6 +1311,19 @@
+         'pixman.h',
+     ]
+ 
++if CONFIG['MOZ_SYSTEM_GRAPHITE2']:
++    system_headers += [
++        'graphite2/Font.h',
++        'graphite2/Segment.h',
++    ]
++
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    system_headers += [
++        'harfbuzz/hb-glib.h',
++        'harfbuzz/hb-ot.h',
++        'harfbuzz/hb.h',
++    ]
++
+ if CONFIG['MOZ_SYSTEM_LIBVPX']:
+     system_headers += [
+         'vpx_mem/vpx_mem.h',
+--- icecat-60.2.0/dom/base/moz.build
++++ icecat-60.2.0/dom/base/moz.build
+@@ -474,6 +474,9 @@
+ if CONFIG['MOZ_X11']:
+     CXXFLAGS += CONFIG['TK_CFLAGS']
+ 
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
++
+ GENERATED_FILES += [
+     'PropertyUseCounterMap.inc',
+     'UseCounterList.h',
+--- icecat-60.2.0/gfx/graphite2/moz-gr-update.sh
++++ icecat-60.2.0/gfx/graphite2/moz-gr-update.sh
+@@ -1,6 +1,7 @@
+ #!/bin/bash
+ 
+ # Script used to update the Graphite2 library in the mozilla source tree
++# and bump version for --with-system-graphite2
+ 
+ # This script lives in gfx/graphite2, along with the library source,
+ # but must be run from the top level of the mozilla-central tree.
+@@ -37,12 +38,16 @@ echo "See" $0 "for update procedure." >> gfx/graphite2/README.mozilla
+ #find gfx/graphite2/ -name "*.cpp" -exec perl -p -i -e "s/<cstdio>/<stdio.h>/;s/Windows.h/windows.h/;" {} \;
+ #find gfx/graphite2/ -name "*.h" -exec perl -p -i -e "s/<cstdio>/<stdio.h>/;s/Windows.h/windows.h/;" {} \;
+ 
++# chase version for --with-system-graphite2
++perl -p -i -e "s/[0-9]+\,[0-9]+\,[0-9]+/$RELEASE/ and tr/./,/ \
++  if /GR2_VERSION_REQUIRE/" old-configure.in
++
+ # summarize what's been touched
+ echo Updated to $RELEASE.
+ echo Here is what changed in the gfx/graphite2 directory:
+ echo
+ 
+-hg stat gfx/graphite2
++hg stat old-configure.in gfx/graphite2
+ 
+ echo
+ echo If gfx/graphite2/src/files.mk has changed, please make corresponding
+--- icecat-60.2.0/gfx/moz.build
++++ icecat-60.2.0/gfx/moz.build
+@@ -10,6 +10,12 @@ with Files('**'):
+ if CONFIG['MOZ_TREE_CAIRO']:
+     DIRS += ['cairo']
+ 
++if not CONFIG['MOZ_SYSTEM_GRAPHITE2']:
++    DIRS += ['graphite2/src' ]
++
++if not CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    DIRS += ['harfbuzz/src']
++
+ DIRS += [
+     '2d',
+     'ycbcr',
+@@ -18,8 +24,6 @@ DIRS += [
+     'qcms',
+     'gl',
+     'layers',
+-    'graphite2/src',
+-    'harfbuzz/src',
+     'ots/src',
+     'thebes',
+     'ipc',
+--- icecat-60.2.0/gfx/skia/generate_mozbuild.py
++++ icecat-60.2.0/gfx/skia/generate_mozbuild.py
+@@ -148,6 +148,9 @@
+         '-Wno-unused-private-field',
+     ]
+ 
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
++
+ if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk3', 'android'):
+     CXXFLAGS += CONFIG['MOZ_CAIRO_CFLAGS']
+     CXXFLAGS += CONFIG['CAIRO_FT_CFLAGS']
+--- icecat-60.2.0/gfx/skia/moz.build
++++ icecat-60.2.0/gfx/skia/moz.build
+@@ -822,6 +822,9 @@
+         '-Wno-unused-private-field',
+     ]
+ 
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
++
+ if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk3', 'android'):
+     CXXFLAGS += CONFIG['MOZ_CAIRO_CFLAGS']
+     CXXFLAGS += CONFIG['CAIRO_FT_CFLAGS']
+--- icecat-60.2.0/gfx/thebes/moz.build
++++ icecat-60.2.0/gfx/thebes/moz.build
+@@ -272,7 +272,13 @@
+ 
+ LOCAL_INCLUDES += CONFIG['SKIA_INCLUDES']
+ 
+-DEFINES['GRAPHITE2_STATIC'] = True
++if CONFIG['MOZ_SYSTEM_GRAPHITE2']:
++    CXXFLAGS += CONFIG['MOZ_GRAPHITE2_CFLAGS']
++else:
++    DEFINES['GRAPHITE2_STATIC'] = True
++
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
+ 
+ if CONFIG['CC_TYPE'] == 'clang':
+     # Suppress warnings from Skia header files.
+--- icecat-60.2.0/intl/unicharutil/util/moz.build
++++ icecat-60.2.0/intl/unicharutil/util/moz.build
+@@ -25,4 +25,7 @@ UNIFIED_SOURCES += [
+     'nsUnicodeProperties.cpp',
+ ]
+ 
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
++
+ FINAL_LIBRARY = 'xul'
+--- icecat-60.2.0/netwerk/dns/moz.build
++++ icecat-60.2.0/netwerk/dns/moz.build
+@@ -76,3 +76,6 @@
+ 
+ if CONFIG['CC_TYPE'] in ('clang', 'gcc'):
+     CXXFLAGS += ['-Wno-error=shadow']
++
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
+--- icecat-60.2.0/old-configure.in
++++ icecat-60.2.0/old-configure.in
+@@ -3995,6 +3995,27 @@
+ AC_SUBST(MOZ_LINUX_32_SSE2_STARTUP_ERROR)
+ 
+ dnl ========================================================
++dnl Check for graphite2
++dnl ========================================================
++if test -n "$MOZ_SYSTEM_GRAPHITE2"; then
++    dnl graphite2.pc has bogus version, check manually
++    _SAVE_CFLAGS=$CFLAGS
++    CFLAGS="$CFLAGS $MOZ_GRAPHITE2_CFLAGS"
++    AC_TRY_COMPILE([ #include <graphite2/Font.h>
++                     #define GR2_VERSION_REQUIRE(major,minor,bugfix)  \
++                             ( GR2_VERSION_MAJOR * 10000 + GR2_VERSION_MINOR \
++                               * 100 + GR2_VERSION_BUGFIX >= \
++                               (major) * 10000 + (minor) * 100 + (bugfix) )
++                   ], [
++                     #if !GR2_VERSION_REQUIRE(1,3,10)
++                     #error "Insufficient graphite2 version."
++                     #endif
++                   ], [],
++                   [AC_MSG_ERROR([--with-system-graphite2 requested but no working libgraphite2 found])])
++    CFLAGS=$_SAVE_CFLAGS
++fi
++
++dnl ========================================================
+ dnl Check for pixman and cairo
+ dnl ========================================================
+ 
+--- icecat-60.2.0/toolkit/library/moz.build
++++ icecat-60.2.0/toolkit/library/moz.build
+@@ -235,6 +235,12 @@
+ if CONFIG['MOZ_SYSTEM_PNG']:
+     OS_LIBS += CONFIG['MOZ_PNG_LIBS']
+ 
++if CONFIG['MOZ_SYSTEM_GRAPHITE2']:
++    OS_LIBS += CONFIG['MOZ_GRAPHITE2_LIBS']
++
++if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
++    OS_LIBS += CONFIG['MOZ_HARFBUZZ_LIBS']
++
+ if CONFIG['MOZ_SYSTEM_HUNSPELL']:
+     OS_LIBS += CONFIG['MOZ_HUNSPELL_LIBS']
+ 
+--- icecat-60.2.0/toolkit/moz.configure
++++ icecat-60.2.0/toolkit/moz.configure
+@@ -1051,6 +1051,26 @@
+ add_old_configure_assignment('FT2_CFLAGS',
+                              ft2_info.cflags)
+ 
++# Graphite2
++# ==============================================================
++option('--with-system-graphite2',
++       help="Use system graphite2 (located with pkgconfig)")
++
++system_graphite2 = pkg_check_modules('MOZ_GRAPHITE2', 'graphite2',
++                                     when='--with-system-graphite2')
++
++set_config('MOZ_SYSTEM_GRAPHITE2', depends_if(system_graphite2)(lambda _: True))
++
++# HarfBuzz
++# ==============================================================
++option('--with-system-harfbuzz',
++       help="Use system harfbuzz (located with pkgconfig)")
++
++system_harfbuzz = pkg_check_modules('MOZ_HARFBUZZ', 'harfbuzz >= 1.7.4',
++                                    when='--with-system-harfbuzz')
++
++set_config('MOZ_SYSTEM_HARFBUZZ', depends_if(system_harfbuzz)(lambda _: True))
++
+ # Mortar
+ # ==============================================================
+ option('--enable-mortar', help='Enable mortar extension')
diff --git a/gnu/packages/patches/icecat-use-system-graphite2.patch b/gnu/packages/patches/icecat-use-system-graphite2.patch
deleted file mode 100644
index 188fba2bc9..0000000000
--- a/gnu/packages/patches/icecat-use-system-graphite2.patch
+++ /dev/null
@@ -1,248 +0,0 @@
-Copied from <https://reviewboard.mozilla.org/r/90218/diff/4>
-See <https://bugzilla.mozilla.org/show_bug.cgi?id=847568>
-
-diff --git a/config/Makefile.in b/config/Makefile.in
---- a/config/Makefile.in
-+++ b/config/Makefile.in
-@@ -36,16 +36,17 @@ ifdef WRAP_SYSTEM_INCLUDES
- export-preqs = \
-   $(call mkdir_deps,system_wrappers) \
-   $(NULL)
- 
- export:: $(export-preqs)
- 	$(PYTHON) -m mozbuild.action.preprocessor $(DEFINES) $(ACDEFINES) \
- 		-DMOZ_TREE_CAIRO=$(MOZ_TREE_CAIRO) \
- 		-DMOZ_TREE_PIXMAN=$(MOZ_TREE_PIXMAN) \
-+		-DMOZ_SYSTEM_GRAPHITE2=$(MOZ_SYSTEM_GRAPHITE2) \
- 		-DMOZ_SYSTEM_HARFBUZZ=$(MOZ_SYSTEM_HARFBUZZ) \
- 		-DMOZ_SYSTEM_HUNSPELL=$(MOZ_SYSTEM_HUNSPELL) \
- 		-DMOZ_SYSTEM_BZ2=$(MOZ_SYSTEM_BZ2) \
- 		-DMOZ_SYSTEM_ZLIB=$(MOZ_SYSTEM_ZLIB) \
- 		-DMOZ_SYSTEM_PNG=$(MOZ_SYSTEM_PNG) \
- 		-DMOZ_SYSTEM_JPEG=$(MOZ_SYSTEM_JPEG) \
- 		-DMOZ_SYSTEM_LIBEVENT=$(MOZ_SYSTEM_LIBEVENT) \
- 		-DMOZ_SYSTEM_LIBVPX=$(MOZ_SYSTEM_LIBVPX) \
-diff --git a/config/system-headers b/config/system-headers
---- a/config/system-headers
-+++ b/config/system-headers
-@@ -1260,16 +1260,20 @@ zlib.h
- #ifdef MOZ_ENABLE_STARTUP_NOTIFICATION
- libsn/sn.h
- libsn/sn-common.h
- libsn/sn-launchee.h
- libsn/sn-launcher.h
- libsn/sn-monitor.h
- libsn/sn-util.h
- #endif
-+#if MOZ_SYSTEM_GRAPHITE2==1
-+graphite2/Font.h
-+graphite2/Segment.h
-+#endif
- #if MOZ_SYSTEM_HARFBUZZ==1
- harfbuzz/hb-glib.h
- harfbuzz/hb-ot.h
- harfbuzz/hb.h
- #endif
- #if MOZ_SYSTEM_HUNSPELL==1
- hunspell.hxx
- #endif
-diff --git a/gfx/graphite2/moz-gr-update.sh b/gfx/graphite2/moz-gr-update.sh
---- a/gfx/graphite2/moz-gr-update.sh
-+++ b/gfx/graphite2/moz-gr-update.sh
-@@ -1,11 +1,12 @@
- #!/bin/bash
- 
- # Script used to update the Graphite2 library in the mozilla source tree
-+# and bump version for --with-system-graphite2
- 
- # This script lives in gfx/graphite2, along with the library source,
- # but must be run from the top level of the mozilla-central tree.
- 
- # Run as
- #
- #    ./gfx/graphite2/moz-gr-update.sh RELEASE
- #
-@@ -32,22 +33,26 @@ echo "This directory contains the Graphi
- echo "$TARBALL" >> gfx/graphite2/README.mozilla
- echo ""
- echo "See" $0 "for update procedure." >> gfx/graphite2/README.mozilla
- 
- # fix up includes because of bug 721839 (cstdio) and bug 803066 (Windows.h)
- #find gfx/graphite2/ -name "*.cpp" -exec perl -p -i -e "s/<cstdio>/<stdio.h>/;s/Windows.h/windows.h/;" {} \;
- #find gfx/graphite2/ -name "*.h" -exec perl -p -i -e "s/<cstdio>/<stdio.h>/;s/Windows.h/windows.h/;" {} \;
- 
-+# chase version for --with-system-graphite2
-+perl -p -i -e "s/[0-9]+\,[0-9]+\,[0-9]+/$RELEASE/ and tr/./,/ \
-+  if /GR2_VERSION_REQUIRE/" old-configure.in
-+
- # summarize what's been touched
- echo Updated to $RELEASE.
- echo Here is what changed in the gfx/graphite2 directory:
- echo
- 
--hg stat gfx/graphite2
-+hg stat old-configure.in gfx/graphite2
- 
- echo
- echo If gfx/graphite2/src/files.mk has changed, please make corresponding
- echo changes to gfx/graphite2/src/moz.build
- echo
- 
- echo
- echo Now use hg commands to create a patch for the mozilla tree.
-diff --git a/gfx/moz.build b/gfx/moz.build
---- a/gfx/moz.build
-+++ b/gfx/moz.build
-@@ -2,28 +2,30 @@
- # vim: set filetype=python:
- # This Source Code Form is subject to the terms of the Mozilla Public
- # License, v. 2.0. If a copy of the MPL was not distributed with this
- # file, You can obtain one at http://mozilla.org/MPL/2.0/.
- 
- if CONFIG['MOZ_TREE_CAIRO']:
-     DIRS += ['cairo']
- 
-+if not CONFIG['MOZ_SYSTEM_GRAPHITE2']:
-+    DIRS += ['graphite2/src' ]
-+
- if not CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-     DIRS += ['harfbuzz/src']
- 
- DIRS += [
-     '2d',
-     'ycbcr',
-     'angle',
-     'src',
-     'qcms',
-     'gl',
-     'layers',
--    'graphite2/src',
-     'ots/src',
-     'thebes',
-     'ipc',
-     'vr',
-     'config',
- ]
- 
- if CONFIG['MOZ_ENABLE_SKIA']:
-diff --git a/gfx/thebes/moz.build b/gfx/thebes/moz.build
---- a/gfx/thebes/moz.build
-+++ b/gfx/thebes/moz.build
-@@ -261,16 +261,19 @@ if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('and
-     CXXFLAGS += CONFIG['CAIRO_FT_CFLAGS']
- 
- if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk2', 'gtk3'):
-     CXXFLAGS += CONFIG['MOZ_PANGO_CFLAGS']
- 
- LOCAL_INCLUDES += CONFIG['SKIA_INCLUDES']
- LOCAL_INCLUDES += ['/media/libyuv/include']
- 
--DEFINES['GRAPHITE2_STATIC'] = True
-+if CONFIG['MOZ_SYSTEM_GRAPHITE2']:
-+    CXXFLAGS += CONFIG['MOZ_GRAPHITE2_CFLAGS']
-+else:
-+    DEFINES['GRAPHITE2_STATIC'] = True
- 
- if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-     CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
- 
- if CONFIG['CLANG_CXX']:
-     # Suppress warnings from Skia header files.
-     SOURCES['gfxPlatform.cpp'].flags += ['-Wno-implicit-fallthrough']
-diff --git a/moz.configure b/moz.configure
---- a/moz.configure
-+++ b/moz.configure
-@@ -260,16 +260,28 @@ def extra_programs(target):
- 
- check_prog('DSYMUTIL', delayed_getattr(extra_programs, 'DSYMUTIL'),
-            allow_missing=True)
- check_prog('GENISOIMAGE', delayed_getattr(extra_programs, 'GENISOIMAGE'),
-            allow_missing=True)
- check_prog('RPMBUILD', delayed_getattr(extra_programs, 'RPMBUILD'),
-            allow_missing=True)
- 
-+option('--with-system-graphite2',
-+       help="Use system graphite2 (located with pkgconfig)")
-+
-+@depends('--with-system-graphite2', compile_environment)
-+def check_for_graphite2(value, compile_env):
-+    return value and compile_env
-+
-+system_graphite2 = pkg_check_modules('MOZ_GRAPHITE2', 'graphite2',
-+                                    check_for_graphite2)
-+
-+set_config('MOZ_SYSTEM_GRAPHITE2', depends_if(system_graphite2)(lambda _: True))
-+
- option('--with-system-harfbuzz',
-        help="Use system harfbuzz (located with pkgconfig)")
- 
- @depends('--with-system-harfbuzz', compile_environment)
- def check_for_harfbuzz(value, compile_env):
-     return value and compile_env
- 
- system_harfbuzz = pkg_check_modules('MOZ_HARFBUZZ', 'harfbuzz >= 1.3.3',
-diff --git a/old-configure.in b/old-configure.in
---- a/old-configure.in
-+++ b/old-configure.in
-@@ -5060,16 +5060,37 @@ if test "$USE_FC_FREETYPE"; then
-         CPPFLAGS="$CPPFLAGS $FT2_CFLAGS $XCFLAGS"
-         MOZ_CHECK_HEADERS([fontconfig/fcfreetype.h], ,
-             [AC_MSG_ERROR(Can't find header fontconfig/fcfreetype.h.)], [#include <fontconfig/fontconfig.h>])
-         CPPFLAGS="$_SAVE_CPPFLAGS"
-     fi
- fi
- 
- dnl ========================================================
-+dnl Check for graphite2
-+dnl ========================================================
-+if test -n "$MOZ_SYSTEM_GRAPHITE2"; then
-+    dnl graphite2.pc has bogus version, check manually
-+    _SAVE_CFLAGS=$CFLAGS
-+    CFLAGS="$CFLAGS $MOZ_GRAPHITE2_CFLAGS"
-+    AC_TRY_COMPILE([ #include <graphite2/Font.h>
-+                     #define GR2_VERSION_REQUIRE(major,minor,bugfix)  \
-+                             ( GR2_VERSION_MAJOR * 10000 + GR2_VERSION_MINOR \
-+                               * 100 + GR2_VERSION_BUGFIX >= \
-+                               (major) * 10000 + (minor) * 100 + (bugfix) )
-+                   ], [
-+                     #if !GR2_VERSION_REQUIRE(1,3,8)
-+                     #error "Insufficient graphite2 version."
-+                     #endif
-+                   ], [],
-+                   [AC_MSG_ERROR([--with-system-graphite2 requested but no working libgraphite2 found])])
-+    CFLAGS=$_SAVE_CFLAGS
-+fi
-+
-+dnl ========================================================
- dnl Check for pixman and cairo
- dnl ========================================================
- 
- MOZ_TREE_CAIRO=1
- MOZ_ARG_ENABLE_BOOL(system-cairo,
- [  --enable-system-cairo   Use system cairo (located with pkgconfig)],
- MOZ_TREE_CAIRO=,
- MOZ_TREE_CAIRO=1 )
-diff --git a/toolkit/library/moz.build b/toolkit/library/moz.build
---- a/toolkit/library/moz.build
-+++ b/toolkit/library/moz.build
-@@ -221,16 +221,19 @@ if CONFIG['SERVO_TARGET_DIR']:
-         OS_LIBS += ['-L%s' % CONFIG['SERVO_TARGET_DIR'], '-lgeckoservo']
- 
- if CONFIG['MOZ_SYSTEM_JPEG']:
-     OS_LIBS += CONFIG['MOZ_JPEG_LIBS']
- 
- if CONFIG['MOZ_SYSTEM_PNG']:
-     OS_LIBS += CONFIG['MOZ_PNG_LIBS']
- 
-+if CONFIG['MOZ_SYSTEM_GRAPHITE2']:
-+    OS_LIBS += CONFIG['MOZ_GRAPHITE2_LIBS']
-+
- if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-     OS_LIBS += CONFIG['MOZ_HARFBUZZ_LIBS']
- 
- if CONFIG['MOZ_SYSTEM_HUNSPELL']:
-     OS_LIBS += CONFIG['MOZ_HUNSPELL_LIBS']
- 
- if CONFIG['MOZ_SYSTEM_LIBEVENT']:
-     OS_LIBS += CONFIG['MOZ_LIBEVENT_LIBS']
-
diff --git a/gnu/packages/patches/icecat-use-system-harfbuzz.patch b/gnu/packages/patches/icecat-use-system-harfbuzz.patch
deleted file mode 100644
index 083d404c13..0000000000
--- a/gnu/packages/patches/icecat-use-system-harfbuzz.patch
+++ /dev/null
@@ -1,279 +0,0 @@
-Copied from <https://reviewboard.mozilla.org/r/35763/diff/9>
-See <https://bugzilla.mozilla.org/show_bug.cgi?id=847568>
-
-diff --git a/config/Makefile.in b/config/Makefile.in
---- a/config/Makefile.in
-+++ b/config/Makefile.in
-@@ -36,16 +36,17 @@ ifdef WRAP_SYSTEM_INCLUDES
- export-preqs = \
-   $(call mkdir_deps,system_wrappers) \
-   $(NULL)
- 
- export:: $(export-preqs)
- 	$(PYTHON) -m mozbuild.action.preprocessor $(DEFINES) $(ACDEFINES) \
- 		-DMOZ_TREE_CAIRO=$(MOZ_TREE_CAIRO) \
- 		-DMOZ_TREE_PIXMAN=$(MOZ_TREE_PIXMAN) \
-+		-DMOZ_SYSTEM_HARFBUZZ=$(MOZ_SYSTEM_HARFBUZZ) \
- 		-DMOZ_SYSTEM_HUNSPELL=$(MOZ_SYSTEM_HUNSPELL) \
- 		-DMOZ_SYSTEM_BZ2=$(MOZ_SYSTEM_BZ2) \
- 		-DMOZ_SYSTEM_ZLIB=$(MOZ_SYSTEM_ZLIB) \
- 		-DMOZ_SYSTEM_PNG=$(MOZ_SYSTEM_PNG) \
- 		-DMOZ_SYSTEM_JPEG=$(MOZ_SYSTEM_JPEG) \
- 		-DMOZ_SYSTEM_LIBEVENT=$(MOZ_SYSTEM_LIBEVENT) \
- 		-DMOZ_SYSTEM_LIBVPX=$(MOZ_SYSTEM_LIBVPX) \
- 		-DMOZ_SYSTEM_ICU=$(MOZ_SYSTEM_ICU) \
-diff --git a/config/system-headers b/config/system-headers
---- a/config/system-headers
-+++ b/config/system-headers
-@@ -1260,16 +1260,21 @@ zlib.h
- #ifdef MOZ_ENABLE_STARTUP_NOTIFICATION
- libsn/sn.h
- libsn/sn-common.h
- libsn/sn-launchee.h
- libsn/sn-launcher.h
- libsn/sn-monitor.h
- libsn/sn-util.h
- #endif
-+#if MOZ_SYSTEM_HARFBUZZ==1
-+harfbuzz/hb-glib.h
-+harfbuzz/hb-ot.h
-+harfbuzz/hb.h
-+#endif
- #if MOZ_SYSTEM_HUNSPELL==1
- hunspell.hxx
- #endif
- #if MOZ_SYSTEM_BZ2==1
- bzlib.h
- #endif
- #ifdef MOZ_ENABLE_GIO
- gio/gio.h
-diff --git a/dom/base/moz.build b/dom/base/moz.build
---- a/dom/base/moz.build
-+++ b/dom/base/moz.build
-@@ -474,16 +474,19 @@ for var in ('MOZ_B2G_RIL'):
-         DEFINES[var] = True
- 
- if CONFIG['MOZ_BUILD_APP'] in ['browser', 'mobile/android', 'xulrunner']:
-     DEFINES['HAVE_SIDEBAR'] = True
- 
- if CONFIG['MOZ_X11']:
-     CXXFLAGS += CONFIG['TK_CFLAGS']
- 
-+if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
-+
- GENERATED_FILES += [
-     'PropertyUseCounterMap.inc',
-     'UseCounterList.h',
- ]
- 
- countermap = GENERATED_FILES['PropertyUseCounterMap.inc']
- countermap.script = 'gen-usecounters.py:property_map'
- countermap.inputs = ['UseCounters.conf']
-diff --git a/gfx/harfbuzz/README-mozilla b/gfx/harfbuzz/README-mozilla
---- a/gfx/harfbuzz/README-mozilla
-+++ b/gfx/harfbuzz/README-mozilla
-@@ -14,8 +14,13 @@ this file when updating harfbuzz, and ch
- 
- The normal approach to updating harfbuzz, therefore, is to pull the latest HB
- source into a scratch directory and do a local build; then copy the original
- sources AND the generated header mentioned above from the build directory into
- the mozilla tree.
- 
- If the collection of source files changes, manual updates to moz.build may be
- needed, as we don't use the upstream makefiles.
-+
-+The in-tree copy may be omitted during build by --with-system-harfbuzz.
-+Make sure to keep pkg-config version check within old-configure.in in sync
-+with checkout version or increment latest tag by one if it's not based
-+on upstream release.
-diff --git a/gfx/moz.build b/gfx/moz.build
---- a/gfx/moz.build
-+++ b/gfx/moz.build
-@@ -2,26 +2,28 @@
- # vim: set filetype=python:
- # This Source Code Form is subject to the terms of the Mozilla Public
- # License, v. 2.0. If a copy of the MPL was not distributed with this
- # file, You can obtain one at http://mozilla.org/MPL/2.0/.
- 
- if CONFIG['MOZ_TREE_CAIRO']:
-     DIRS += ['cairo']
- 
-+if not CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    DIRS += ['harfbuzz/src']
-+
- DIRS += [
-     '2d',
-     'ycbcr',
-     'angle',
-     'src',
-     'qcms',
-     'gl',
-     'layers',
-     'graphite2/src',
--    'harfbuzz/src',
-     'ots/src',
-     'thebes',
-     'ipc',
-     'vr',
-     'config',
- ]
- 
- if CONFIG['MOZ_ENABLE_SKIA']:
-diff --git a/gfx/skia/generate_mozbuild.py b/gfx/skia/generate_mozbuild.py
---- a/gfx/skia/generate_mozbuild.py
-+++ b/gfx/skia/generate_mozbuild.py
-@@ -138,16 +138,19 @@ if CONFIG['GNU_CXX'] and not CONFIG['CLA
- if CONFIG['CLANG_CXX'] or CONFIG['CLANG_CL']:
-     CXXFLAGS += [
-         '-Wno-implicit-fallthrough',
-         '-Wno-inconsistent-missing-override',
-         '-Wno-macro-redefined',
-         '-Wno-unused-private-field',
-     ]
- 
-+if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
-+
- if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk2', 'gtk3', 'android'):
-     CXXFLAGS += CONFIG['MOZ_CAIRO_CFLAGS']
-     CXXFLAGS += CONFIG['CAIRO_FT_CFLAGS']
- 
- if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk2', 'gtk3'):
-     CXXFLAGS += CONFIG['MOZ_PANGO_CFLAGS']
- """
- 
-diff --git a/gfx/skia/moz.build b/gfx/skia/moz.build
---- a/gfx/skia/moz.build
-+++ b/gfx/skia/moz.build
-@@ -748,14 +748,17 @@ if CONFIG['GNU_CXX'] and not CONFIG['CLA
- if CONFIG['CLANG_CXX'] or CONFIG['CLANG_CL']:
-     CXXFLAGS += [
-         '-Wno-implicit-fallthrough',
-         '-Wno-inconsistent-missing-override',
-         '-Wno-macro-redefined',
-         '-Wno-unused-private-field',
-     ]
- 
-+if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
-+
- if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk2', 'gtk3', 'android'):
-     CXXFLAGS += CONFIG['MOZ_CAIRO_CFLAGS']
-     CXXFLAGS += CONFIG['CAIRO_FT_CFLAGS']
- 
- if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk2', 'gtk3'):
-     CXXFLAGS += CONFIG['MOZ_PANGO_CFLAGS']
-diff --git a/gfx/thebes/moz.build b/gfx/thebes/moz.build
---- a/gfx/thebes/moz.build
-+++ b/gfx/thebes/moz.build
-@@ -263,11 +263,14 @@ if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('and
- if CONFIG['MOZ_WIDGET_TOOLKIT'] in ('gtk2', 'gtk3'):
-     CXXFLAGS += CONFIG['MOZ_PANGO_CFLAGS']
- 
- LOCAL_INCLUDES += CONFIG['SKIA_INCLUDES']
- LOCAL_INCLUDES += ['/media/libyuv/include']
- 
- DEFINES['GRAPHITE2_STATIC'] = True
- 
-+if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
-+
- if CONFIG['CLANG_CXX']:
-     # Suppress warnings from Skia header files.
-     SOURCES['gfxPlatform.cpp'].flags += ['-Wno-implicit-fallthrough']
-diff --git a/intl/unicharutil/util/moz.build b/intl/unicharutil/util/moz.build
---- a/intl/unicharutil/util/moz.build
-+++ b/intl/unicharutil/util/moz.build
-@@ -37,9 +37,12 @@ if CONFIG['_MSC_VER']:
-     DEFINES['_USE_ANSI_CPP'] = True
-     # Don't include directives about which CRT to use
-     CFLAGS += ['-Zl']
-     CXXFLAGS += ['-Zl']
- 
- if CONFIG['ENABLE_INTL_API']:
-     USE_LIBS += ['icu']
- 
-+if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
-+
- DIST_INSTALL = True
-diff --git a/moz.configure b/moz.configure
---- a/moz.configure
-+++ b/moz.configure
-@@ -260,16 +260,28 @@ def extra_programs(target):
- 
- check_prog('DSYMUTIL', delayed_getattr(extra_programs, 'DSYMUTIL'),
-            allow_missing=True)
- check_prog('GENISOIMAGE', delayed_getattr(extra_programs, 'GENISOIMAGE'),
-            allow_missing=True)
- check_prog('RPMBUILD', delayed_getattr(extra_programs, 'RPMBUILD'),
-            allow_missing=True)
- 
-+option('--with-system-harfbuzz',
-+       help="Use system harfbuzz (located with pkgconfig)")
-+
-+@depends('--with-system-harfbuzz', compile_environment)
-+def check_for_harfbuzz(value, compile_env):
-+    return value and compile_env
-+
-+system_harfbuzz = pkg_check_modules('MOZ_HARFBUZZ', 'harfbuzz >= 1.3.3',
-+                                    check_for_harfbuzz)
-+
-+set_config('MOZ_SYSTEM_HARFBUZZ', depends_if(system_harfbuzz)(lambda _: True))
-+
- option('--enable-system-hunspell',
-        help="Use system hunspell (located with pkgconfig)")
- 
- @depends('--enable-system-hunspell', compile_environment)
- def check_for_hunspell(value, compile_env):
-     return value and compile_env
- 
- system_hunspell = pkg_check_modules('MOZ_HUNSPELL', 'hunspell',
-diff --git a/netwerk/dns/moz.build b/netwerk/dns/moz.build
---- a/netwerk/dns/moz.build
-+++ b/netwerk/dns/moz.build
-@@ -61,16 +61,19 @@ etld_data = GENERATED_FILES['etld_data.i
- etld_data.script = 'prepare_tlds.py'
- etld_data.inputs = ['effective_tld_names.dat']
- 
- # need to include etld_data.inc
- LOCAL_INCLUDES += [
-     '/netwerk/base',
- ]
- 
-+if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    CXXFLAGS += CONFIG['MOZ_HARFBUZZ_CFLAGS']
-+
- if CONFIG['ENABLE_INTL_API']:
-     DEFINES['IDNA2008'] = True
-     USE_LIBS += ['icu']
- else:
-     UNIFIED_SOURCES += [
-         'nameprep.c',
-     ]
- 
-diff --git a/toolkit/library/moz.build b/toolkit/library/moz.build
---- a/toolkit/library/moz.build
-+++ b/toolkit/library/moz.build
-@@ -221,16 +221,19 @@ if CONFIG['SERVO_TARGET_DIR']:
-         OS_LIBS += ['-L%s' % CONFIG['SERVO_TARGET_DIR'], '-lgeckoservo']
- 
- if CONFIG['MOZ_SYSTEM_JPEG']:
-     OS_LIBS += CONFIG['MOZ_JPEG_LIBS']
- 
- if CONFIG['MOZ_SYSTEM_PNG']:
-     OS_LIBS += CONFIG['MOZ_PNG_LIBS']
- 
-+if CONFIG['MOZ_SYSTEM_HARFBUZZ']:
-+    OS_LIBS += CONFIG['MOZ_HARFBUZZ_LIBS']
-+
- if CONFIG['MOZ_SYSTEM_HUNSPELL']:
-     OS_LIBS += CONFIG['MOZ_HUNSPELL_LIBS']
- 
- if CONFIG['MOZ_SYSTEM_LIBEVENT']:
-     OS_LIBS += CONFIG['MOZ_LIBEVENT_LIBS']
- 
- if CONFIG['MOZ_SYSTEM_LIBVPX']:
-     OS_LIBS += CONFIG['MOZ_LIBVPX_LIBS']
-

From 94e96f7f68c3b9053fdb5dee5b0ab614163aaa08 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Mon, 24 Sep 2018 00:10:37 -0400
Subject: [PATCH 129/909] gnu: icecat: Unbundle libevent, libogg, and
 libvorbis.

* gnu/packages/patches/icecat-use-system-media-libs.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/patches/icecat-avoid-bundled-libraries.patch: Add
another hunk to enable removal of libevent.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add patch.  In the snippet, add
libevent, libogg, libvorbis, and libtremor to the list of bundled libraries to
remove.  Add a comment regarding theora.  Remove comments regarding unbundling
cairo, which is no longer supported.
[inputs]: Add libevent, libogg, and libvorbis.
[arguments]: Add --with-system-{libevent,ogg,vorbis} to configure flags.
Add custom bootstrap phase.  Add comments.
---
 gnu/local.mk                                  |   1 +
 gnu/packages/gnuzilla.scm                     |  39 +-
 .../icecat-avoid-bundled-libraries.patch      |  14 +
 .../icecat-use-system-media-libs.patch        | 381 ++++++++++++++++++
 4 files changed, 423 insertions(+), 12 deletions(-)
 create mode 100644 gnu/packages/patches/icecat-use-system-media-libs.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 35e78e7816..244c79d221 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -812,6 +812,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/icecat-avoid-bundled-libraries.patch	\
   %D%/packages/patches/icecat-CVE-2018-12383.patch		\
   %D%/packages/patches/icecat-use-system-graphite2+harfbuzz.patch	\
+  %D%/packages/patches/icecat-use-system-media-libs.patch	\
   %D%/packages/patches/icedtea-6-hotspot-gcc-segfault-workaround.patch  \
   %D%/packages/patches/icedtea-7-hotspot-gcc-segfault-workaround.patch  \
   %D%/packages/patches/id3lib-CVE-2007-4460.patch			\
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index ad83444e3c..6834d82426 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -36,6 +36,7 @@
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cargo)
+  #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages databases)
@@ -62,6 +63,7 @@
   #:use-module (gnu packages rust)
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages video)
+  #:use-module (gnu packages xiph)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages readline))
 
@@ -497,6 +499,7 @@ security standards.")
        (list
         (search-patch  "icecat-avoid-bundled-libraries.patch")
         (search-patch  "icecat-use-system-graphite2+harfbuzz.patch")
+        (search-patch  "icecat-use-system-media-libs.patch")
         (mozilla-patch "icecat-CVE-2018-12385.patch"      "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5")
         (search-patch  "icecat-CVE-2018-12383.patch")
         (mozilla-patch "icecat-bug-1489744.patch"         "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")))
@@ -516,24 +519,29 @@ security standards.")
                       ;; FIXME: A script from the bundled nspr is used.
                       ;;"nsprpub"
                       ;;
-                      ;; TODO: Use system media libraries.  Waiting for:
+                      ;; TODO: Use more system media libraries.  See:
                       ;; <https://bugzilla.mozilla.org/show_bug.cgi?id=517422>
-                      ;;   * libogg
-                      ;;   * libtheora
-                      ;;   * libvorbis
-                      ;;   * libtremor (not yet in guix)
+                      ;;   * libtheora: esr60 wants v1.2, not yet released.
+                      ;;   * soundtouch: avoiding the bundled library would
+                      ;;     result in some loss of functionality.  There's
+                      ;;     also an issue with exception handling
+                      ;;     configuration.  It seems that this is needed in
+                      ;;     some moz.build:
+                      ;;       DEFINES['ST_NO_EXCEPTION_HANDLING'] = 1
                       ;;   * libopus
                       ;;   * speex
-                      ;;   * soundtouch (not yet in guix)
                       ;;
                       "modules/freetype2"
                       "modules/zlib"
                       "modules/libbz2"
-                      ;; UNBUNDLE-ME "ipc/chromium/src/third_party/libevent"
+                      "ipc/chromium/src/third_party/libevent"
                       "media/libjpeg"
                       "media/libvpx"
+                      "media/libogg"
+                      "media/libvorbis"
+                      ;; "media/libtheora" ; wants theora-1.2, not yet released
+                      "media/libtremor"
                       "security/nss"
-                      ;; UNBUNDLE-ME "gfx/cairo"
                       "gfx/harfbuzz"
                       "gfx/graphite2"
                       "js/src/ctypes/libffi"
@@ -549,7 +557,6 @@ security standards.")
     (inputs
      `(("alsa-lib" ,alsa-lib)
        ("bzip2" ,bzip2)
-       ;; UNBUNDLE-ME ("cairo" ,cairo)
        ("cups" ,cups)
        ("dbus-glib" ,dbus-glib)
        ("gdk-pixbuf" ,gdk-pixbuf)
@@ -564,8 +571,11 @@ security standards.")
        ("libcanberra" ,libcanberra)
        ("libgnome" ,libgnome)
        ("libjpeg-turbo" ,libjpeg-turbo)
+       ("libogg" ,libogg)
+       ;; ("libtheora" ,libtheora) ; wants theora-1.2, not yet released
+       ("libvorbis" ,libvorbis)
        ("libxft" ,libxft)
-       ;; UNBUNDLE-ME ("libevent" ,libevent-2.0)
+       ("libevent" ,libevent)
        ("libxinerama" ,libxinerama)
        ("libxscrnsaver" ,libxscrnsaver)
        ("libxcomposite" ,libxcomposite)
@@ -637,7 +647,10 @@ security standards.")
                            "--with-system-zlib"
                            "--with-system-bz2"
                            "--with-system-jpeg"        ; must be libjpeg-turbo
-                           ;; UNBUNDLE-ME "--with-system-libevent"
+                           "--with-system-libevent"
+                           "--with-system-ogg"
+                           "--with-system-vorbis"
+                           ;; "--with-system-theora" ; wants theora-1.2, not yet released
                            "--with-system-libvpx"
                            "--with-system-icu"
                            "--with-system-nspr"
@@ -645,7 +658,6 @@ security standards.")
                            "--with-system-harfbuzz"
                            "--with-system-graphite2"
                            "--enable-system-pixman"
-                           ;; UNBUNDLE-ME "--enable-system-cairo"
                            "--enable-system-ffi"
                            "--enable-system-hunspell"
                            "--enable-system-sqlite"
@@ -695,6 +707,9 @@ security standards.")
     'avcodec', 'avutil', 'pulse' ]\n\n"
                               all)))
             #t))
+         (replace 'bootstrap
+           (lambda _
+             (invoke "sh" "-c" "autoconf old-configure.in > old-configure")))
          (add-after 'patch-source-shebangs 'patch-cargo-checksums
            (lambda _
              (use-modules (guix build cargo-build-system))
diff --git a/gnu/packages/patches/icecat-avoid-bundled-libraries.patch b/gnu/packages/patches/icecat-avoid-bundled-libraries.patch
index b5e9fb887e..33203b1a33 100644
--- a/gnu/packages/patches/icecat-avoid-bundled-libraries.patch
+++ b/gnu/packages/patches/icecat-avoid-bundled-libraries.patch
@@ -33,3 +33,17 @@ Fixes needed when avoiding bundled libraries.
      '/dom/base',
      '/dom/storage',
      '/ipc/glue',
+--- icecat-60.2.0/media/webrtc/trunk/webrtc/base/rtc_task_queue_gn/moz.build.orig	2018-09-13 17:40:54.000000000 -0400
++++ icecat-60.2.0/media/webrtc/trunk/webrtc/base/rtc_task_queue_gn/moz.build	2018-09-23 21:33:12.319975105 -0400
+@@ -130,11 +130,6 @@
+     DEFINES["WEBRTC_POSIX"] = True
+     DEFINES["_FILE_OFFSET_BITS"] = "64"
+ 
+-    LOCAL_INCLUDES += [
+-        "/ipc/chromium/src/third_party/libevent/include/",
+-        "/ipc/chromium/src/third_party/libevent/linux/"
+-    ]
+-
+     UNIFIED_SOURCES += [
+         "/media/webrtc/trunk/webrtc/base/task_queue_libevent.cc",
+         "/media/webrtc/trunk/webrtc/base/task_queue_posix.cc"
diff --git a/gnu/packages/patches/icecat-use-system-media-libs.patch b/gnu/packages/patches/icecat-use-system-media-libs.patch
new file mode 100644
index 0000000000..648585a6f0
--- /dev/null
+++ b/gnu/packages/patches/icecat-use-system-media-libs.patch
@@ -0,0 +1,381 @@
+Support building with system media libraries.
+See <https://bugzilla.mozilla.org/show_bug.cgi?id=517422>
+
+Based on:
+  https://svnweb.freebsd.org/ports/head/www/firefox-esr/files/patch-z-bug517422?revision=472833&view=markup
+
+Changes to files within the bundled libraries are omitted, since those files
+are removed from Guix sources.  Modified for use with patch -p1, and to apply
+cleanly to GNU IceCat.
+
+--- icecat-60.2.0/build/moz.configure/old.configure
++++ icecat-60.2.0/build/moz.configure/old.configure
+@@ -273,7 +273,12 @@
+     '--with-system-libvpx',
+     '--with-system-nspr',
+     '--with-system-nss',
++    '--with-system-ogg',
+     '--with-system-png',
++    '--with-system-soundtouch',
++    '--with-system-theora',
++    '--with-system-tremor',
++    '--with-system-vorbis',
+     '--with-system-zlib',
+     '--with-thumb',
+     '--with-thumb-interwork',
+--- icecat-60.2.0/config/external/moz.build
++++ icecat-60.2.0/config/external/moz.build
+@@ -23,12 +23,21 @@
+ 
+ external_dirs += ['modules/xz-embedded']
+ 
+-if CONFIG['MOZ_VORBIS']:
++if not CONFIG['MOZ_SYSTEM_OGG']:
++    external_dirs += ['media/libogg']
++
++if CONFIG['MOZ_VORBIS'] and not CONFIG['MOZ_SYSTEM_VORBIS']:
+     external_dirs += ['media/libvorbis']
+ 
+-if CONFIG['MOZ_TREMOR']:
++if CONFIG['MOZ_TREMOR'] and not CONFIG['MOZ_SYSTEM_TREMOR']:
+     external_dirs += ['media/libtremor']
+ 
++if not CONFIG['MOZ_SYSTEM_THEORA']:
++    external_dirs += ['media/libtheora']
++
++if not CONFIG['MOZ_SYSTEM_SOUNDTOUCH']:
++    external_dirs += ['media/libsoundtouch']
++
+ if CONFIG['MOZ_WEBM_ENCODER']:
+     external_dirs += ['media/libmkv']
+ 
+@@ -51,11 +60,8 @@
+     'media/kiss_fft',
+     'media/libcubeb',
+     'media/libnestegg',
+-    'media/libogg',
+     'media/libopus',
+-    'media/libtheora',
+     'media/libspeex_resampler',
+-    'media/libsoundtouch',
+     'media/mp4parse-rust',
+     'media/psshparser'
+ ]
+--- icecat-60.2.0/config/system-headers.mozbuild
++++ icecat-60.2.0/config/system-headers.mozbuild
+@@ -1324,6 +1324,28 @@
+         'harfbuzz/hb.h',
+     ]
+ 
++if CONFIG['MOZ_SYSTEM_OGG']:
++    system_headers += [
++        'ogg/ogg.h',
++        'ogg/os_types.h',
++    ]
++
++if CONFIG['MOZ_SYSTEM_THEORA']:
++    system_headers += [
++        'theora/theoradec.h',
++    ]
++
++if CONFIG['MOZ_SYSTEM_VORBIS']:
++    system_headers += [
++        'vorbis/codec.h',
++        'vorbis/vorbisenc.h',
++    ]
++
++if CONFIG['MOZ_SYSTEM_TREMOR']:
++    system_headers += [
++        'tremor/ivorbiscodec.h',
++    ]
++
+ if CONFIG['MOZ_SYSTEM_LIBVPX']:
+     system_headers += [
+         'vpx_mem/vpx_mem.h',
+--- icecat-60.2.0/dom/media/AudioStream.cpp
++++ icecat-60.2.0/dom/media/AudioStream.cpp
+@@ -121,7 +121,9 @@
+   : mMonitor("AudioStream")
+   , mChannels(0)
+   , mOutChannels(0)
++#ifndef MOZ_SYSTEM_SOUNDTOUCH
+   , mTimeStretcher(nullptr)
++#endif
+   , mDumpFile(nullptr)
+   , mState(INITIALIZED)
+   , mDataSource(aSource)
+@@ -142,9 +144,11 @@
+   if (mDumpFile) {
+     fclose(mDumpFile);
+   }
++#ifndef MOZ_SYSTEM_SOUNDTOUCH
+   if (mTimeStretcher) {
+     soundtouch::destroySoundTouchObj(mTimeStretcher);
+   }
++#endif
+ #if defined(XP_WIN)
+   if (XRE_IsContentProcess()) {
+     audio::AudioNotificationReceiver::Unregister(this);
+@@ -168,7 +172,11 @@
+ {
+   mMonitor.AssertCurrentThreadOwns();
+   if (!mTimeStretcher) {
++#ifdef MOZ_SYSTEM_SOUNDTOUCH
++    mTimeStretcher = new soundtouch::SoundTouch();
++#else
+     mTimeStretcher = soundtouch::createSoundTouchObj();
++#endif
+     mTimeStretcher->setSampleRate(mAudioClock.GetInputRate());
+     mTimeStretcher->setChannels(mOutChannels);
+     mTimeStretcher->setPitch(1.0);
+--- icecat-60.2.0/dom/media/AudioStream.h
++++ icecat-60.2.0/dom/media/AudioStream.h
+@@ -15,7 +15,11 @@
+ #include "mozilla/TimeStamp.h"
+ #include "mozilla/UniquePtr.h"
+ #include "CubebUtils.h"
++#ifdef MOZ_SYSTEM_SOUNDTOUCH
++#include "soundtouch/SoundTouch.h"
++#else
+ #include "soundtouch/SoundTouchFactory.h"
++#endif
+ 
+ #if defined(XP_WIN)
+ #include "mozilla/audio/AudioNotificationReceiver.h"
+@@ -297,7 +301,11 @@
+   uint32_t mChannels;
+   uint32_t mOutChannels;
+   AudioClock mAudioClock;
++#ifdef MOZ_SYSTEM_SOUNDTOUCH
++  nsAutoPtr<soundtouch::SoundTouch> mTimeStretcher;
++#else
+   soundtouch::SoundTouch* mTimeStretcher;
++#endif
+ 
+   // Output file for dumping audio
+   FILE* mDumpFile;
+--- icecat-60.2.0/dom/media/moz.build
++++ icecat-60.2.0/dom/media/moz.build
+@@ -327,6 +327,21 @@
+ 
+ DEFINES['MOZILLA_INTERNAL_API'] = True
+ 
++if CONFIG['MOZ_SYSTEM_OGG']:
++    CXXFLAGS += CONFIG['MOZ_OGG_CFLAGS']
++
++if CONFIG['MOZ_SYSTEM_THEORA']:
++    CXXFLAGS += CONFIG['MOZ_THEORA_CFLAGS']
++
++if CONFIG['MOZ_SYSTEM_VORBIS']:
++    CXXFLAGS += CONFIG['MOZ_VORBIS_CFLAGS']
++
++if CONFIG['MOZ_SYSTEM_TREMOR']:
++    CXXFLAGS += CONFIG['MOZ_TREMOR_CFLAGS']
++
++if CONFIG['MOZ_SYSTEM_SOUNDTOUCH']:
++    CXXFLAGS += CONFIG['MOZ_SOUNDTOUCH_CFLAGS']
++
+ if CONFIG['MOZ_ANDROID_HLS_SUPPORT']:
+     DEFINES['MOZ_ANDROID_HLS_SUPPORT'] = True
+ 
+--- icecat-60.2.0/dom/media/platforms/ffmpeg/ffvpx/FFVPXRuntimeLinker.cpp
++++ icecat-60.2.0/dom/media/platforms/ffmpeg/ffvpx/FFVPXRuntimeLinker.cpp
+@@ -15,9 +15,13 @@
+ #include <windows.h>
+ #endif
+ 
++#ifdef MOZ_SYSTEM_SOUNDTOUCH
++#include "nsXPCOMPrivate.h" // for XUL_DLL
++#else
+ // We use a known symbol located in lgpllibs to determine its location.
+ // soundtouch happens to be always included in lgpllibs
+ #include "soundtouch/SoundTouch.h"
++#endif
+ 
+ namespace mozilla {
+ 
+@@ -64,6 +68,12 @@
+ 
+   sLinkStatus = LinkStatus_FAILED;
+ 
++#ifdef MOZ_SYSTEM_SOUNDTOUCH
++  // We retrieve the path of the XUL library as this is where mozavcodec and
++  // mozavutil libs are located.
++  char* path =
++    PR_GetLibraryFilePathname(XUL_DLL, (PRFuncPtr)&FFVPXRuntimeLinker::Init);
++#else
+   // We retrieve the path of the lgpllibs library as this is where mozavcodec
+   // and mozavutil libs are located.
+   PathString lgpllibsname = GetLibraryName(nullptr, "lgpllibs");
+@@ -73,6 +83,7 @@
+   PathString path =
+     GetLibraryFilePathname(lgpllibsname.get(),
+                            (PRFuncPtr)&soundtouch::SoundTouch::getVersionId);
++#endif
+   if (path.IsEmpty()) {
+     return false;
+   }
+--- icecat-60.2.0/old-configure.in
++++ icecat-60.2.0/old-configure.in
+@@ -2451,6 +2451,111 @@
+ fi
+ fi # COMPILE_ENVIRONMENT
+ 
++dnl ========================================================
++dnl Check for libogg
++dnl ========================================================
++
++MOZ_ARG_WITH_BOOL(system-ogg,
++[  --with-system-ogg       Use system libogg (located with pkgconfig)],
++MOZ_SYSTEM_OGG=1,
++MOZ_SYSTEM_OGG=)
++
++if test -n "$MOZ_SYSTEM_OGG"; then
++    PKG_CHECK_MODULES(MOZ_OGG, ogg >= 1.3.3)
++
++    _SAVE_LIBS=$LIBS
++    LIBS="$LIBS $MOZ_OGG_LIBS"
++    AC_CHECK_FUNC(ogg_set_mem_functions, [],
++      [AC_DEFINE(MOZ_OGG_NO_MEM_REPORTING)])
++    LIBS=$_SAVE_LIBS
++fi
++
++AC_SUBST(MOZ_SYSTEM_OGG)
++
++dnl ========================================================
++dnl Check for libvorbis
++dnl ========================================================
++
++MOZ_ARG_WITH_BOOL(system-vorbis,
++[  --with-system-vorbis    Use system libvorbis (located with pkgconfig)],
++MOZ_SYSTEM_VORBIS=1,
++MOZ_SYSTEM_VORBIS=)
++
++if test -n "$MOZ_SYSTEM_VORBIS"; then
++    PKG_CHECK_MODULES(MOZ_VORBIS, vorbis vorbisenc >= 1.3.6)
++fi
++
++AC_SUBST(MOZ_SYSTEM_VORBIS)
++
++dnl ========================================================
++dnl Check for integer-only libvorbis aka tremor
++dnl ========================================================
++
++MOZ_ARG_WITH_BOOL(system-tremor,
++[  --with-system-tremor    Use system libtremor (located with pkgconfig)],
++MOZ_SYSTEM_TREMOR=1,
++MOZ_SYSTEM_TREMOR=)
++
++if test -n "$MOZ_SYSTEM_TREMOR"; then
++    PKG_CHECK_MODULES(MOZ_TREMOR, vorbisidec >= 1.2.1)
++fi
++
++AC_SUBST(MOZ_SYSTEM_TREMOR)
++
++dnl ========================================================
++dnl Check for libtheora
++dnl ========================================================
++
++MOZ_ARG_WITH_BOOL(system-theora,
++[  --with-system-theora    Use system libtheora (located with pkgconfig)],
++MOZ_SYSTEM_THEORA=1,
++MOZ_SYSTEM_THEORA=)
++
++if test -n "$MOZ_SYSTEM_THEORA"; then
++    PKG_CHECK_MODULES(MOZ_THEORA, theora >= 1.2)
++fi
++
++AC_SUBST(MOZ_SYSTEM_THEORA)
++
++dnl ========================================================
++dnl Check for libSoundTouch
++dnl ========================================================
++
++MOZ_ARG_WITH_BOOL(system-soundtouch,
++[  --with-system-soundtouch Use system libSoundTouch (located with pkgconfig)],
++MOZ_SYSTEM_SOUNDTOUCH=1,
++MOZ_SYSTEM_SOUNDTOUCH=)
++
++if test -n "$MOZ_SYSTEM_SOUNDTOUCH"; then
++    PKG_CHECK_MODULES(MOZ_SOUNDTOUCH, soundtouch >= 1.9.0)
++
++    AC_LANG_SAVE
++    AC_LANG_CPLUSPLUS
++    _SAVE_CXXFLAGS=$CXXFLAGS
++    CXXFLAGS="$CXXFLAGS $MOZ_SOUNDTOUCH_CFLAGS"
++    AC_CACHE_CHECK(for soundtouch sample type,
++                   ac_cv_soundtouch_sample_type,
++                   [AC_TRY_COMPILE([#include <SoundTouch.h>
++                                    #ifndef SOUNDTOUCH_INTEGER_SAMPLES
++                                    #error soundtouch expects float samples
++                                    #endif],
++                                   [],
++                                   [ac_cv_soundtouch_sample_type=short],
++                                   [ac_cv_soundtouch_sample_type=float])])
++    CXXFLAGS=$_SAVE_CXXFLAGS
++    AC_LANG_RESTORE
++
++    if test \( -n "$MOZ_SAMPLE_TYPE_S16" -a "$ac_cv_soundtouch_sample_type" != short \) \
++         -o \( -n "$MOZ_SAMPLE_TYPE_FLOAT32" -a "$ac_cv_soundtouch_sample_type" != float \) ; then
++        AC_MSG_ERROR([SoundTouch library is built with incompatible sample type. Either rebuild the library with/without --enable-integer-samples, chase default Mozilla sample type or remove --with-system-soundtouch.])
++    fi
++fi
++
++if test -n "$MOZ_SYSTEM_SOUNDTOUCH"; then
++    AC_DEFINE(MOZ_SYSTEM_SOUNDTOUCH)
++fi
++AC_SUBST(MOZ_SYSTEM_SOUNDTOUCH)
++
+ dnl system libvpx Support
+ dnl ========================================================
+ MOZ_ARG_WITH_BOOL(system-libvpx,
+--- icecat-60.2.0/toolkit/library/moz.build
++++ icecat-60.2.0/toolkit/library/moz.build
+@@ -244,6 +244,21 @@
+ if CONFIG['MOZ_SYSTEM_HUNSPELL']:
+     OS_LIBS += CONFIG['MOZ_HUNSPELL_LIBS']
+ 
++if CONFIG['MOZ_SYSTEM_OGG']:
++    OS_LIBS += CONFIG['MOZ_OGG_LIBS']
++
++if CONFIG['MOZ_SYSTEM_THEORA']:
++    OS_LIBS += CONFIG['MOZ_THEORA_LIBS']
++
++if CONFIG['MOZ_SYSTEM_VORBIS']:
++    OS_LIBS += CONFIG['MOZ_VORBIS_LIBS']
++
++if CONFIG['MOZ_SYSTEM_TREMOR']:
++    OS_LIBS += CONFIG['MOZ_TREMOR_LIBS']
++
++if CONFIG['MOZ_SYSTEM_SOUNDTOUCH']:
++    OS_LIBS += CONFIG['MOZ_SOUNDTOUCH_LIBS']
++
+ if CONFIG['MOZ_SYSTEM_LIBEVENT']:
+     OS_LIBS += CONFIG['MOZ_LIBEVENT_LIBS']
+ 
+--- icecat-60.2.0/xpcom/build/XPCOMInit.cpp
++++ icecat-60.2.0/xpcom/build/XPCOMInit.cpp
+@@ -138,7 +138,9 @@
+ 
+ #include "mozilla/ipc/GeckoChildProcessHost.h"
+ 
++#ifndef MOZ_OGG_NO_MEM_REPORTING
+ #include "ogg/ogg.h"
++#endif
+ #if defined(MOZ_VPX) && !defined(MOZ_VPX_NO_MEM_REPORTING)
+ #if defined(HAVE_STDINT_H)
+ // mozilla-config.h defines HAVE_STDINT_H, and then it's defined *again* in
+@@ -639,11 +641,13 @@
+   // this oddness.
+   mozilla::SetICUMemoryFunctions();
+ 
++#ifndef MOZ_OGG_NO_MEM_REPORTING
+   // Do the same for libogg.
+   ogg_set_mem_functions(OggReporter::CountingMalloc,
+                         OggReporter::CountingCalloc,
+                         OggReporter::CountingRealloc,
+                         OggReporter::CountingFree);
++#endif
+ 
+ #if defined(MOZ_VPX) && !defined(MOZ_VPX_NO_MEM_REPORTING)
+   // And for VPX.

From 6d328879378fac95240005233331f596fb5c68ed Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Tue, 25 Sep 2018 17:13:59 -0400
Subject: [PATCH 130/909] gnu: icecat: Rebundle NSPR and NSS [security fix].

Works around <https://bugs.gnu.org/32833>.

* gnu/packages/gnuzilla.scm (icecat)[source]: In snippet, don't remove NSS.
[inputs]: Remove 'nspr' and 'nss'.
[arguments]: Remove --with-system-{nspr,nss} from configure flags.
---
 gnu/packages/gnuzilla.scm | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index 6834d82426..ea3b61c231 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -519,6 +519,13 @@ security standards.")
                       ;; FIXME: A script from the bundled nspr is used.
                       ;;"nsprpub"
                       ;;
+                      ;; FIXME: With the update to IceCat 60, using system NSS
+                      ;;        broke certificate validation.  See
+                      ;;        <https://bugs.gnu.org/32833>.  For now, we use
+                      ;;        the bundled NSPR and NSS.  TODO: Investigate,
+                      ;;        and try to unbundle these libraries again.
+                      ;; UNBUNDLE-ME! "security/nss"
+                      ;;
                       ;; TODO: Use more system media libraries.  See:
                       ;; <https://bugzilla.mozilla.org/show_bug.cgi?id=517422>
                       ;;   * libtheora: esr60 wants v1.2, not yet released.
@@ -541,7 +548,6 @@ security standards.")
                       "media/libvorbis"
                       ;; "media/libtheora" ; wants theora-1.2, not yet released
                       "media/libtremor"
-                      "security/nss"
                       "gfx/harfbuzz"
                       "gfx/graphite2"
                       "js/src/ctypes/libffi"
@@ -588,8 +594,10 @@ security standards.")
        ("pulseaudio" ,pulseaudio)
        ("mesa" ,mesa)
        ("mit-krb5" ,mit-krb5)
-       ("nspr" ,nspr)
-       ("nss" ,nss)
+       ;; See <https://bugs.gnu.org/32833>
+       ;;   and related comments in the 'snippet' above.
+       ;; UNBUNDLE-ME! ("nspr" ,nspr)
+       ;; UNBUNDLE-ME! ("nss" ,nss)
        ("sqlite" ,sqlite)
        ("startup-notification" ,startup-notification)
        ("unzip" ,unzip)
@@ -653,8 +661,12 @@ security standards.")
                            ;; "--with-system-theora" ; wants theora-1.2, not yet released
                            "--with-system-libvpx"
                            "--with-system-icu"
-                           "--with-system-nspr"
-                           "--with-system-nss"
+                           
+                           ;; See <https://bugs.gnu.org/32833>
+                           ;;   and related comments in the 'snippet' above.
+                           ;; UNBUNDLE-ME! "--with-system-nspr"
+                           ;; UNBUNDLE-ME! "--with-system-nss"
+                           
                            "--with-system-harfbuzz"
                            "--with-system-graphite2"
                            "--enable-system-pixman"

From fe73352e8073ea0a0e6f6b5591f24395671998ab Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Tue, 25 Sep 2018 19:31:50 -0400
Subject: [PATCH 131/909] gnu: linux-libre: Enable SHPC PCI Hotplug driver, now
 built-in only.

Fixes <https://bugs.gnu.org/32840>.

* gnu/packages/aux-files/linux-libre/4.18-x86_64.conf,
gnu/packages/aux-files/linux-libre/4.18-i686.conf: Add
CONFIG_HOTPLUG_PCI_SHPC=y, plus updates made by 'make oldconfig'.
---
 gnu/packages/aux-files/linux-libre/4.18-i686.conf   | 6 ++++--
 gnu/packages/aux-files/linux-libre/4.18-x86_64.conf | 6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/aux-files/linux-libre/4.18-i686.conf b/gnu/packages/aux-files/linux-libre/4.18-i686.conf
index 606616b9fa..859b8b10b6 100644
--- a/gnu/packages/aux-files/linux-libre/4.18-i686.conf
+++ b/gnu/packages/aux-files/linux-libre/4.18-i686.conf
@@ -1,6 +1,6 @@
 #
 # Automatically generated file; DO NOT EDIT.
-# Linux/x86 4.18.0-gnu Kernel Configuration
+# Linux/x86 4.18.9-gnu Kernel Configuration
 #
 
 #
@@ -255,6 +255,7 @@ CONFIG_PROFILING=y
 CONFIG_TRACEPOINTS=y
 CONFIG_CRASH_CORE=y
 CONFIG_KEXEC_CORE=y
+CONFIG_HOTPLUG_SMT=y
 CONFIG_OPROFILE=m
 # CONFIG_OPROFILE_EVENT_MULTIPLEX is not set
 CONFIG_HAVE_OPROFILE=y
@@ -294,6 +295,7 @@ CONFIG_HAVE_PERF_REGS=y
 CONFIG_HAVE_PERF_USER_STACK_DUMP=y
 CONFIG_HAVE_ARCH_JUMP_LABEL=y
 CONFIG_HAVE_RCU_TABLE_FREE=y
+CONFIG_HAVE_RCU_TABLE_INVALIDATE=y
 CONFIG_ARCH_HAVE_NMI_SAFE_CMPXCHG=y
 CONFIG_HAVE_ALIGNED_STRUCT_PAGE=y
 CONFIG_HAVE_CMPXCHG_LOCAL=y
@@ -853,7 +855,7 @@ CONFIG_HOTPLUG_PCI_ACPI_IBM=m
 CONFIG_HOTPLUG_PCI_CPCI=y
 CONFIG_HOTPLUG_PCI_CPCI_ZT5550=m
 CONFIG_HOTPLUG_PCI_CPCI_GENERIC=m
-# CONFIG_HOTPLUG_PCI_SHPC is not set
+CONFIG_HOTPLUG_PCI_SHPC=y
 
 #
 # PCI controller drivers
diff --git a/gnu/packages/aux-files/linux-libre/4.18-x86_64.conf b/gnu/packages/aux-files/linux-libre/4.18-x86_64.conf
index 81fd822756..2a66c483d6 100644
--- a/gnu/packages/aux-files/linux-libre/4.18-x86_64.conf
+++ b/gnu/packages/aux-files/linux-libre/4.18-x86_64.conf
@@ -1,6 +1,6 @@
 #
 # Automatically generated file; DO NOT EDIT.
-# Linux/x86 4.18.0-gnu Kernel Configuration
+# Linux/x86 4.18.9-gnu Kernel Configuration
 #
 
 #
@@ -265,6 +265,7 @@ CONFIG_PROFILING=y
 CONFIG_TRACEPOINTS=y
 CONFIG_CRASH_CORE=y
 CONFIG_KEXEC_CORE=y
+CONFIG_HOTPLUG_SMT=y
 CONFIG_OPROFILE=m
 # CONFIG_OPROFILE_EVENT_MULTIPLEX is not set
 CONFIG_HAVE_OPROFILE=y
@@ -304,6 +305,7 @@ CONFIG_HAVE_PERF_REGS=y
 CONFIG_HAVE_PERF_USER_STACK_DUMP=y
 CONFIG_HAVE_ARCH_JUMP_LABEL=y
 CONFIG_HAVE_RCU_TABLE_FREE=y
+CONFIG_HAVE_RCU_TABLE_INVALIDATE=y
 CONFIG_ARCH_HAVE_NMI_SAFE_CMPXCHG=y
 CONFIG_HAVE_ALIGNED_STRUCT_PAGE=y
 CONFIG_HAVE_CMPXCHG_LOCAL=y
@@ -869,7 +871,7 @@ CONFIG_HOTPLUG_PCI_ACPI_IBM=m
 CONFIG_HOTPLUG_PCI_CPCI=y
 CONFIG_HOTPLUG_PCI_CPCI_ZT5550=m
 CONFIG_HOTPLUG_PCI_CPCI_GENERIC=m
-# CONFIG_HOTPLUG_PCI_SHPC is not set
+CONFIG_HOTPLUG_PCI_SHPC=y
 
 #
 # PCI controller drivers

From 06619128274c0f7e3ebfefab03db337e886fec51 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 25 Sep 2018 17:57:59 +0200
Subject: [PATCH 132/909] Fix URL in emacs-magit and emacs-groovy-modes.

* gnu/packages/emacs.scm (emacs-magit)[source]: Fix URL.
* gnu/packages/emacs.scm (emacs-groovy-modes)[source]: Fix URL.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index f29040c372..c541c51483 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -458,7 +458,7 @@ on stdout instead of using a socket as the Emacsclient does.")
              (method url-fetch)
              (uri (string-append
                    "https://github.com/magit/magit/releases/download/"
-                   version "/" name "-" version ".tar.gz"))
+                   version "/magit-" version ".tar.gz"))
              (sha256
               (base32
                "1ygaah3dd3nxpyd17297xgvdcgr7pgzzwlmpnmchki0kiwgg3sbc"))))
@@ -8019,7 +8019,7 @@ supports multiple backends such as @code{vlc}, @code{mpg123},
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "https://github.com/Groovy-Emacs-Modes/" name
+                    "https://github.com/Groovy-Emacs-Modes/groovy-emacs-modes"
                     "/archive/" version ".tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256

From 9bd85a785f47d039b027de854b78b9ded0892e02 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Sep 2018 15:42:15 +0200
Subject: [PATCH 133/909] gnu: shepherd: Update to 0.5.0.

* gnu/packages/admin.scm (shepherd): Update to 0.5.0.
---
 gnu/packages/admin.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 8f504cafef..ded7ce3b97 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -173,14 +173,14 @@ and provides a \"top-like\" mode (monitoring).")
 (define-public shepherd
   (package
     (name "shepherd")
-    (version "0.4.0")
+    (version "0.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://alpha.gnu.org/gnu/shepherd/shepherd-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1lgmsbxn8i8xdasxzkdp2cml75n128pplw6icvmspl6s0n9xmw8n"))))
+                "1wmciqml9yplnx1s4ynn00giqyk06rbrcsgvpjj2df47sawk2jp8"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--localstatedir=/var")))

From 4245ddcbc9f935804c17c97872b90ec1050c2d75 Mon Sep 17 00:00:00 2001
From: Carlo Zancanaro <carlo@zancanaro.id.au>
Date: Sun, 26 Aug 2018 21:54:14 +1000
Subject: [PATCH 134/909] guix system: Load all services on reconfigure, not
 just stopped ones.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This uses the 'replacement' service slot introduced in the Shepherd
version 0.5.0.

* gnu/services/shepherd.scm (shepherd-service-upgrade): Return a list of
  services that need to be restarted to complete their upgrade.
* guix/scripts/system.scm (call-with-service-upgrade-info): Rename an internal
  variable to reflect the change to shepherd-service-upgrade.
  (upgrade-shepherd-services): Call 'load-services/safe' instead of
  'load-services'.  Print a message about services that need to be
  manually restarted.
* gnu/services/herd.scm (load-services/safe): New procedure.
* doc/guix.texi (Invoking guix system): Document the new behaviour.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
---
 doc/guix.texi             |  8 ++++----
 gnu/services/herd.scm     | 20 ++++++++++++++++++++
 gnu/services/shepherd.scm | 23 ++++++++---------------
 guix/scripts/system.scm   | 25 ++++++++++++++++---------
 4 files changed, 48 insertions(+), 28 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 6b4b06f46d..e1046eb512 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -33,7 +33,7 @@ Copyright @copyright{} 2016 Alex ter Weele@*
 Copyright @copyright{} 2017, 2018 Clément Lassieur@*
 Copyright @copyright{} 2017 Mathieu Othacehe@*
 Copyright @copyright{} 2017 Federico Beffa@*
-Copyright @copyright{} 2017 Carlo Zancanaro@*
+Copyright @copyright{} 2017, 2018 Carlo Zancanaro@*
 Copyright @copyright{} 2017 Thomas Danckaert@*
 Copyright @copyright{} 2017 humanitiesNerd@*
 Copyright @copyright{} 2017 Christopher Allan Webber@*
@@ -21920,9 +21920,9 @@ systems already running GuixSD.}.
 This effects all the configuration specified in @var{file}: user
 accounts, system services, global package list, setuid programs, etc.
 The command starts system services specified in @var{file} that are not
-currently running; if a service is currently running, it does not
-attempt to upgrade it since this would not be possible without stopping it
-first.
+currently running; if a service is currently running this command will
+arrange for it to be upgraded the next time it is stopped (eg. by
+@code{herd stop X} or @code{herd restart X}).
 
 This command creates a new generation whose number is one greater than
 the current generation (as reported by @command{guix system
diff --git a/gnu/services/herd.scm b/gnu/services/herd.scm
index 8c96b70731..8ff817759d 100644
--- a/gnu/services/herd.scm
+++ b/gnu/services/herd.scm
@@ -50,6 +50,7 @@
             unload-services
             unload-service
             load-services
+            load-services/safe
             start-service
             stop-service))
 
@@ -232,6 +233,25 @@ returns a shepherd <service> object."
                          `(primitive-load ,file))
                        files))))
 
+(define (load-services/safe files)
+  "This is like 'load-services', but make sure only the subset of FILES that
+can be safely reloaded is actually reloaded.
+
+This is done to accommodate the Shepherd < 0.15.0 where services lacked the
+'replacement' slot, and where 'register-services' would throw an exception
+when passed a service with an already-registered name."
+  (eval-there `(let* ((services     (map primitive-load ',files))
+                      (slots        (map slot-definition-name
+                                         (class-slots <service>)))
+                      (can-replace? (memq 'replacement slots)))
+                 (define (registered? service)
+                   (not (null? (lookup-services (canonical-name service)))))
+
+                 (apply register-services
+                        (if can-replace?
+                            services
+                            (remove registered? services))))))
+
 (define (start-service name)
   (with-shepherd-action name ('start) result
     result))
diff --git a/gnu/services/shepherd.scm b/gnu/services/shepherd.scm
index 4cd2249841..4c7e72049f 100644
--- a/gnu/services/shepherd.scm
+++ b/gnu/services/shepherd.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Carlo Zancanaro <carlo@zancanaro.id.au>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -329,7 +330,7 @@ symbols provided/required by a service."
 (define (shepherd-service-upgrade live target)
   "Return two values: the subset of LIVE (a list of <live-service>) that needs
 to be unloaded, and the subset of TARGET (a list of <shepherd-service>) that
-needs to be loaded."
+need to be restarted to complete their upgrade."
   (define (essential? service)
     (memq (first (live-service-provision service))
           '(root shepherd)))
@@ -346,12 +347,6 @@ needs to be loaded."
     (and=> (lookup-live (shepherd-service-canonical-name service))
            live-service-running))
 
-  (define (stopped service)
-    (match (lookup-live (shepherd-service-canonical-name service))
-      (#f #f)
-      (service (and (not (live-service-running service))
-                    service))))
-
   (define live-service-dependents
     (shepherd-service-back-edges live
                                  #:provision live-service-provision
@@ -362,16 +357,14 @@ needs to be loaded."
       (#f (every obsolete? (live-service-dependents service)))
       (_  #f)))
 
-  (define to-load
-    ;; Only load services that are either new or currently stopped.
-    (remove running? target))
+  (define to-restart
+    ;; Restart services that are currently running.
+    (filter running? target))
 
   (define to-unload
-    ;; Unload services that are (1) no longer required, or (2) are in TO-LOAD.
-    (remove essential?
-            (append (filter obsolete? live)
-                    (filter-map stopped to-load))))
+    ;; Unload services that are no longer required.
+    (remove essential? (filter obsolete? live)))
 
-  (values to-unload to-load))
+  (values to-unload to-restart))
 
 ;;; shepherd.scm ends here
diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm
index 69bd05b516..1e7620f147 100644
--- a/guix/scripts/system.scm
+++ b/guix/scripts/system.scm
@@ -310,9 +310,9 @@ names of services to load (upgrade), and the list of names of services to
 unload."
   (match (current-services)
     ((services ...)
-     (let-values (((to-unload to-load)
+     (let-values (((to-unload to-restart)
                    (shepherd-service-upgrade services new-services)))
-       (mproc to-load
+       (mproc to-restart
               (map (compose first live-service-provision)
                    to-unload))))
     (#f
@@ -335,25 +335,32 @@ bring the system down."
   ;; Arrange to simply emit a warning if the service upgrade fails.
   (with-shepherd-error-handling
    (call-with-service-upgrade-info new-services
-     (lambda (to-load to-unload)
+     (lambda (to-restart to-unload)
         (for-each (lambda (unload)
                     (info (G_ "unloading service '~a'...~%") unload)
                     (unload-service unload))
                   to-unload)
 
         (with-monad %store-monad
-          (munless (null? to-load)
-            (let ((to-load-names  (map shepherd-service-canonical-name to-load))
-                  (to-start       (filter shepherd-service-auto-start? to-load)))
-              (info (G_ "loading new services:~{ ~a~}...~%") to-load-names)
+          (munless (null? new-services)
+            (let ((new-service-names  (map shepherd-service-canonical-name new-services))
+                  (to-restart-names   (map shepherd-service-canonical-name to-restart))
+                  (to-start           (filter shepherd-service-auto-start? new-services)))
+              (info (G_ "loading new services:~{ ~a~}...~%") new-service-names)
+              (unless (null? to-restart-names)
+                ;; Listing TO-RESTART-NAMES in the message below wouldn't help
+                ;; because many essential services cannot be meaningfully
+                ;; restarted.  See <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=22039#30>.
+                (format #t (G_ "To complete the upgrade, run 'herd restart SERVICE' to stop,
+upgrade, and restart each service that was not automatically restarted.\n")))
               (mlet %store-monad ((files (mapm %store-monad
                                                (compose lower-object
                                                         shepherd-service-file)
-                                               to-load)))
+                                               new-services)))
                 ;; Here we assume that FILES are exactly those that were computed
                 ;; as part of the derivation that built OS, which is normally the
                 ;; case.
-                (load-services (map derivation->output-path files))
+                (load-services/safe (map derivation->output-path files))
 
                 (for-each start-service
                           (map shepherd-service-canonical-name to-start))

From 2a5f2b1f7550db701172a338e98179e1cac55a1c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Sep 2018 16:35:37 +0200
Subject: [PATCH 135/909] gnu: Remove incorrect Emacs package deprecations.

This is a followup to 5c8031ff7382ec9079040d08ae5a05b4dd2352b7.  An
upgrade would wrongfully report things like:

  guix package: package 'emacs-typo' has been superseded by 'emacs-typo'
  guix package: package 'emacs-org-tree-slide' has been superseded by 'emacs-org-tree-slide'
  guix package: package 'emacs-emms' has been superseded by 'emacs-emms'

* gnu/packages/emacs.scm (flycheck, emms, typo, org-tree-slide)
(butler): Remove.
(emacs-emms-mode-line-cycle)[propagated-inputs]: Use EMACS-EMMS instead
of EMMS.
---
 gnu/packages/emacs.scm | 17 +----------------
 1 file changed, 1 insertion(+), 16 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index c541c51483..9dc11c59fc 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -782,9 +782,6 @@ different tools.  It highlights errors and warnings inline in the buffer, and
 provides an optional IDE-like error list.")
     (license license:gpl3+)))                     ;+GFDLv1.3+ for the manual
 
-(define-public flycheck
-  (deprecated-package "flycheck" emacs-flycheck))
-
 
 ;;;
 ;;; Web browsing.
@@ -1066,9 +1063,6 @@ light user interface.")
     (home-page "https://www.gnu.org/software/emms/")
     (license license:gpl3+)))
 
-(define-public emms
-  (deprecated-package "emacs-emms" emacs-emms))
-
 (define-public emacs-emms-player-mpv
   ;; A new mpv backend is included in Emms from 5.0.
   (deprecated-package "emacs-emms-player-mpv" emacs-emms))
@@ -1088,7 +1082,7 @@ light user interface.")
          "0ifszi930pnaxk1x8pcydmvnp06868gc7nfx14q17zbajbx735k6"))))
     (build-system emacs-build-system)
     (propagated-inputs
-     `(("emms" ,emms)))
+     `(("emms" ,emacs-emms)))
     (home-page "https://github.com/momomo5717/emms-mode-line-cycle")
     (synopsis "Display the EMMS mode line as a ticker")
     (description
@@ -2722,9 +2716,6 @@ view the build status of those servers' build jobs, and possibly to trigger
 build jobs.")
     (license license:gpl3+)))
 
-(define-public butler
-  (deprecated-package "emacs-butler" emacs-butler))
-
 (define-public emacs-company
   (package
     (name "emacs-company")
@@ -2874,9 +2865,6 @@ automatically inserts a Unicode opening or closing quotation mark, depending
 on context.")
     (license license:gpl3+)))
 
-(define-public typo
-  (deprecated-package "emacs-typo" emacs-typo))
-
 (define-public emacs-scheme-complete
   (let ((commit "9b5cf224bf2a5994bc6d5b152ff487517f1a9bb5"))
     (package
@@ -8061,9 +8049,6 @@ navigation with the grails mode.")
 @kbd{C-<} to jump to the next and previous slide.")
       (license license:gpl3+))))
 
-(define-public org-tree-slide
-  (deprecated-package "emacs-org-tree-slide" emacs-org-tree-slide))
-
 (define-public emacs-scratch-el
   (let ((commit "2cdf2b841ce7a0987093f65b0cc431947549f897")
         (revision "1"))

From 6f03b08089167ec863361352ab200830bffeb0b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Sep 2018 22:30:16 +0200
Subject: [PATCH 136/909] services: dhcp-client: Use 'read-pid-file'.

* gnu/services/networking.scm (dhcp-client-service-type)[start]: Use
'read-pid-file' instead of the custom and possibly infinite loop.
---
 gnu/services/networking.scm | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index bd1d5a2706..3fdb2bb9f7 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
@@ -191,19 +191,7 @@ fe80::1%lo0 apps.facebook.com\n")
                              (cons* #$dhclient "-nw"
                                     "-pf" #$pid-file ifaces))))
                    (and (zero? (cdr (waitpid pid)))
-                        (let loop ()
-                          (catch 'system-error
-                            (lambda ()
-                              (call-with-input-file #$pid-file read))
-                            (lambda args
-                              ;; 'dhclient' returned before PID-FILE was created,
-                              ;; so try again.
-                              (let ((errno (system-error-errno args)))
-                                (if (= ENOENT errno)
-                                    (begin
-                                      (sleep 1)
-                                      (loop))
-                                    (apply throw args))))))))))
+                        (read-pid-file #$pid-file)))))
       (stop #~(make-kill-destructor))))))
 
 (define* (dhcp-client-service #:key (dhcp isc-dhcp))

From a56c4eb8f43ae5555985d8a84308d150c0763c5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Sep 2018 22:52:38 +0200
Subject: [PATCH 137/909] services: shepherd: Add workaround for 0.5.0 in
 containers.

* gnu/services/shepherd.scm (%containerized-shepherd-service): New service.
* gnu/system.scm (essential-services): Use it when CONTAINER? is true.
---
 gnu/services/shepherd.scm | 16 ++++++++++++++++
 gnu/system.scm            |  2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/gnu/services/shepherd.scm b/gnu/services/shepherd.scm
index 4c7e72049f..49d08cc30f 100644
--- a/gnu/services/shepherd.scm
+++ b/gnu/services/shepherd.scm
@@ -59,6 +59,7 @@
             %default-modules
 
             shepherd-service-file
+            %containerized-shepherd-service
 
             shepherd-service-lookup-procedure
             shepherd-service-back-edges
@@ -327,6 +328,21 @@ symbols provided/required by a service."
   (lambda (service)
     (vhash-foldq* cons '() service edges)))
 
+(define %containerized-shepherd-service
+  ;; XXX: This service works around a bug in the Shepherd 0.5.0: shepherd
+  ;; calls reboot(2) (via 'disable-reboot-on-ctrl-alt-del') when it starts,
+  ;; but in a container that fails with EINVAL.  This was fixed in Shepherd
+  ;; commit 92e806bac1abaeeaf5d60f0ab50d1ae85ba6a62f.
+  (simple-service 'containerized-shepherd
+                  shepherd-root-service-type
+                  (list (shepherd-service
+                         (provision '(containerized-shepherd))
+                         (start #~(lambda ()
+                                    (set! (@@ (shepherd)
+                                              disable-reboot-on-ctrl-alt-del)
+                                      (const #t))
+                                    #t))))))
+
 (define (shepherd-service-upgrade live target)
   "Return two values: the subset of LIVE (a list of <live-service>) that needs
 to be unloaded, and the subset of TARGET (a list of <shepherd-service>) that
diff --git a/gnu/system.scm b/gnu/system.scm
index e4a57475a9..99bc09873d 100644
--- a/gnu/system.scm
+++ b/gnu/system.scm
@@ -501,7 +501,7 @@ a container or that of a \"bare metal\" system."
                    ;; Add the firmware service, unless we are building for a
                    ;; container.
                    (if container?
-                       '()
+                       (list %containerized-shepherd-service)
                        (list %linux-bare-metal-service
                              (service firmware-service-type
                                       (operating-system-firmware os))))))))

From 23784f0c3342a0fab5bf2a1c15c300b9f0856872 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Sep 2018 22:58:23 +0200
Subject: [PATCH 138/909] services: udev: Don't attempt to read
 "modules.devname" from a container.

Fixes <https://bugs.gnu.org/32814>.
Reported by Julien Lepiller <julien@lepiller.eu>.

* gnu/services/base.scm (udev-shepherd-service)[start]: Check whether
DIRECTORY exists and skip 'make-static-device-nodes' call if it doesn't.
---
 gnu/services/base.scm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 5ba2c6b86d..9dfabd9807 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -1881,7 +1881,12 @@ item of @var{packages}."
                             (string-append linux-module-directory "/"
                                            kernel-release))
                            (old-umask (umask #o022)))
-                      (make-static-device-nodes directory)
+                      ;; If we're in a container, DIRECTORY might not exist,
+                      ;; for instance because the host runs a different
+                      ;; kernel.  In that case, skip it; we'll just miss a few
+                      ;; nodes like /dev/fuse.
+                      (when (file-exists? directory)
+                        (make-static-device-nodes directory))
                       (umask old-umask))
 
                     (let ((pid (fork+exec-command (list udevd))))

From 09b7300c01a8e7100467c6caae9b2c8d8e673971 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 26 Sep 2018 23:01:33 +0200
Subject: [PATCH 139/909] services: virtual-terminal: Write to "default_utf8"
 only if necessary.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes a bug in containers whereby 'virtual-terminal' would always fail
to start because writing to /sys/…/default_utf8 would fail with EROFS.

* gnu/services/base.scm (virtual-terminal-service-type): Read from
"default_utf8" before attempting to write to it.
---
 gnu/services/base.scm | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/gnu/services/base.scm b/gnu/services/base.scm
index 9dfabd9807..47c7d8bb27 100644
--- a/gnu/services/base.scm
+++ b/gnu/services/base.scm
@@ -685,17 +685,20 @@ to add @var{device} to the kernel's entropy pool.  The service will fail if
   (shepherd-service-type
    'virtual-terminal
    (lambda (utf8?)
-     (shepherd-service
-      (documentation "Set virtual terminals in UTF-8 module.")
-      (provision '(virtual-terminal))
-      (requirement '(root-file-system))
-      (start #~(lambda _
-                 (call-with-output-file
-                     "/sys/module/vt/parameters/default_utf8"
-                   (lambda (port)
-                     (display 1 port)))
-                 #t))
-      (stop #~(const #f))))
+     (let ((knob "/sys/module/vt/parameters/default_utf8"))
+       (shepherd-service
+        (documentation "Set virtual terminals in UTF-8 module.")
+        (provision '(virtual-terminal))
+        (requirement '(root-file-system))
+        (start #~(lambda _
+                   ;; In containers /sys is read-only so don't insist on
+                   ;; writing to this file.
+                   (unless (= 1 (call-with-input-file #$knob read))
+                     (call-with-output-file #$knob
+                       (lambda (port)
+                         (display 1 port))))
+                   #t))
+        (stop #~(const #f)))))
    #t))                                           ;default to UTF-8
 
 (define console-keymap-service-type

From e15ede6e28cfaf5fe951faf88d7c1e3213a476a4 Mon Sep 17 00:00:00 2001
From: Timo Eisenmann <eisenmann@fn.de>
Date: Wed, 26 Sep 2018 17:01:33 +0200
Subject: [PATCH 140/909] gnu: enlightenment: Fix initial locale and keyboard
 selection.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/enlightenment.scm (enlightenment)[arguments]: In
'set-system-actions', set absolute file name to 'locale' and 'xorg.lst'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/enlightenment.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 45dc1dbbeb..c7812e8874 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Timo Eisenmann <eisenmann@fn.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -268,13 +269,19 @@ Libraries with some extra bells and whistles.")
          (add-before 'configure 'set-system-actions
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((xkeyboard (assoc-ref inputs "xkeyboard-config"))
-                   (utils     (assoc-ref inputs "util-linux")))
+                   (utils     (assoc-ref inputs "util-linux"))
+                   (libc      (assoc-ref inputs "libc")))
                ;; We need to patch the path to 'base.lst' to be able
                ;; to switch the keyboard layout in E.
-               (substitute* "src/modules/xkbswitch/e_mod_parse.c"
+               (substitute* (list "src/modules/xkbswitch/e_mod_parse.c"
+                                  "src/modules/wizard/page_011.c")
                  (("/usr/share/X11/xkb/rules/xorg.lst")
                   (string-append xkeyboard
                                  "/share/X11/xkb/rules/base.lst")))
+               (substitute* (list "src/bin/e_intl.c"
+                                  "src/modules/conf_intl/e_int_config_intl.c"
+                                  "src/modules/wizard/page_010.c")
+                 (("locale -a") (string-append libc "/bin/locale -a")))
                (substitute* "src/modules/everything/evry_plug_apps.c"
                  (("/usr/bin/") ""))
                (substitute* "configure"

From a9994b273585914a273f5c50bf2d39af1f657fd0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 20:58:07 +0200
Subject: [PATCH 141/909] gnu: perl-crypt-openssl-rsa: Update to 0.31.

* gnu/packages/tls.scm (perl-crypt-openssl-rsa): Update to 0.31.
---
 gnu/packages/tls.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 0cdb02b0aa..bdb63c0dbf 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -681,7 +681,7 @@ servers or clients for more complicated applications.")
 (define-public perl-crypt-openssl-rsa
  (package
   (name "perl-crypt-openssl-rsa")
-  (version "0.30")
+  (version "0.31")
   (source
     (origin
       (method url-fetch)
@@ -691,7 +691,7 @@ servers or clients for more complicated applications.")
              ".tar.gz"))
       (sha256
         (base32
-          "1b19kaaw4wda8dy6kjiwqa2prpbs2dqcyjyj9zdh5wbs74qkbq93"))))
+          "0djl5i6kibl7862b6ih29q8dhg5zpwzq77q9j8hp6xngshx40ws1"))))
   (build-system perl-build-system)
   (native-inputs
    `(("perl-crypt-openssl-guess" ,perl-crypt-openssl-guess)))

From 6f52db245564b5732577e4e40e0f3127d37fcaf0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 23:27:44 +0200
Subject: [PATCH 142/909] gnu: perl-catalyst-runtime: Update to 5.90119.

* gnu/packages/web.scm (perl-catalyst-runtime): Update to 5.90119.
---
 gnu/packages/web.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 26c2e9128a..2251daabf7 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -1862,15 +1862,15 @@ MIME type directly to the browser, without being processed through Catalyst.")
 (define-public perl-catalyst-runtime
   (package
     (name "perl-catalyst-runtime")
-    (version "5.90118")
+    (version "5.90119")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://cpan/authors/id/H/HA/HAARG/"
+       (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
                            "Catalyst-Runtime-" version ".tar.gz"))
        (sha256
         (base32
-         "0cws3szx3vvh0372qdx8fypgv6qphcc3v81rbq30sl1ghby7ksd3"))))
+         "1iw7x9rqk3sz2hm1bw01blz5vwm7zlljdf4xj3r8vz54f1yggzqr"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-test-fatal" ,perl-test-fatal)))

From af44f05af78e3187589c2c628c3d3436df7ceed0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 12:38:47 +0200
Subject: [PATCH 143/909] gnu: perl-net-dns: Update to 1.18.

* gnu/packages/networking.scm (perl-net-dns): Update to 1.18.
---
 gnu/packages/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 4800c2496b..0d6de040e5 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -902,7 +902,7 @@ private (reserved).")
 (define-public perl-net-dns
  (package
   (name "perl-net-dns")
-  (version "1.17")
+  (version "1.18")
   (source
     (origin
       (method url-fetch)
@@ -914,7 +914,7 @@ private (reserved).")
                        version ".tar.gz")))
       (sha256
         (base32
-          "1q62w9rf2w8kjzqagzr0rdn20ybl8gj3l6cdq4k8fw0sxa7zsycs"))))
+          "1lx902cbvlfl63bqfdrnyavmfwbjvrfdnwgdc1dgs1wpzja19kjj"))))
   (build-system perl-build-system)
   (inputs
     `(("perl-digest-hmac" ,perl-digest-hmac)))

From 3d190d6a219d03dc94c8d33614766df0fed1473f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 27 Sep 2018 03:47:24 +0200
Subject: [PATCH 144/909] gnu: dico: Update to 2.7.

* gnu/packages/dico.scm (dico): Update to 2.7.
[arguments]: Work around dodgy test in 'check' phase.
---
 gnu/packages/dico.scm | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/dico.scm b/gnu/packages/dico.scm
index a85987d9b1..d96dbb86d9 100644
--- a/gnu/packages/dico.scm
+++ b/gnu/packages/dico.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,14 +38,14 @@
 (define-public dico
   (package
     (name "dico")
-    (version "2.6")
+    (version "2.7")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/dico/dico-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0zmi041gv5nd5fmyzgdrgrsy2pvjaq9p8dvvhxwi842hiyng5b7i"))))
+               "0dg4aacnmlf3ljssd7dwh8z5644xzq8k1501mbsx8nz8p8a9mbsq"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags (list (string-append "--with-guile-site-dir=" %output
@@ -57,7 +58,11 @@
                       ;; infrastructure.  Gag it.
                       (setenv "GUILE_AUTO_COMPILE" "0")
                       (setenv "GUILE_WARN_DEPRECATED" "no")
-                      #t)))))
+                      #t))
+                  (replace 'check
+                    (lambda _
+                      ;; Test '71: append + dooffs + env' fails if $V is not 2.
+                      (invoke "make" "check" "V=2"))))))
     (inputs
      `(("m4" ,m4)                                 ;used at run time
        ("pcre" ,pcre)

From b733dbc0fb5bd1648f1fdce6471f048886e69e73 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 10:15:37 +0200
Subject: [PATCH 145/909] gnu: python-setproctitle: Use INVOKE.

* gnu/packages/python.scm (python-setproctitle)[arguments]: Substitute
INVOKE for SYSTEM*.
---
 gnu/packages/python.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5c6c79da88..4703d95a2d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -10482,7 +10482,7 @@ theme for the Sphinx documentation system.  It's the default theme of Sphinx.")
              (setenv "CC" "gcc")
              ;; No need to extend PYTHONPATH to find the built package, since
              ;; the Makefile will build anyway
-             (zero? (system* "make" "check")))))))
+             (invoke "make" "check"))))))
   (native-inputs
    `(("procps" ,procps))) ; required for tests
   (home-page

From 428d2ca2ecc57780fb4be90ca6009ea1d00eeade Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 20:33:00 +0200
Subject: [PATCH 146/909] gnu: youtube-dl: Update to 2018.09.18.

* gnu/packages/video.scm (youtube-dl): Update to 2018.09.18.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 448773e0d9..54ffef86de 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1271,7 +1271,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.09.08")
+    (version "2018.09.18")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1279,7 +1279,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0vwc4faqdddrb3nm4fzmkr60n5rc2zwyy8jwrrjad60kcp8isf05"))))
+                "0mlsdmddmyy3xaqy366k48xds14g17l81al3kglndjkbrrji63sb"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion

From c4a3ea38850e97cdc12252440c7fa9cdefd5790f Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Thu, 27 Sep 2018 09:50:01 +0200
Subject: [PATCH 147/909] gnu: mame: Update to 0.202.

* gnu/packages/emulators.scm (mame): Update to 0.202.
---
 gnu/packages/emulators.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 782bff5b18..443137f141 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -1184,7 +1184,7 @@ play them on systems for which they were never designed!")
 (define-public mame
   (package
     (name "mame")
-    (version "0.201")
+    (version "0.202")
     (source
      (origin
        (method git-fetch)
@@ -1194,7 +1194,7 @@ play them on systems for which they were never designed!")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "00whiig4ld3d4fkl34q48vlf28ygvvp5g7fp0rb5n31ymhl4kajk"))
+         "1v9gm124p65nbj678gfkcvwphp9qc15ky2p12ca6g3rllma94di5"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove bundled libraries.

From e07cb04d40eaea8aa792e2375f7f127ef54a79f3 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 27 Sep 2018 05:51:20 -0400
Subject: [PATCH 148/909] gnu: linux-libre@4.4: Update to 4.4.158.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.158.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 170c77374d..95a5234c76 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -452,8 +452,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.157"
-                    "00bnfqwkr0jfdabmwx5qk5bqxn5vwnnzwqbm5rfg7lggii74kk54"
+  (make-linux-libre "4.4.158"
+                    "1l3blfaw50a8l9bp735vzsmk1naq4l40qidza10dwkkrd2ip3n41"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 202190ec392d3284b0dae753b356cb74f4962682 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 27 Sep 2018 05:52:00 -0400
Subject: [PATCH 149/909] gnu: linux-libre@4.9: Update to 4.9.129.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.129.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 95a5234c76..b3ccaef89f 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.128"
-                    "0lww23xcyyg0dwzrap5x9d700gy3lbxln55n6sqqkm7m89dkqwha"
+  (make-linux-libre "4.9.129"
+                    "0y7p1xgbpn4nmr5pmqb58shr54lvryr5rxwm9m66knwzj332f3rh"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From e0b6085a7f69a8b2a8ff4fe90d8ef28f9ef50769 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 27 Sep 2018 05:52:52 -0400
Subject: [PATCH 150/909] gnu: linux-libre@4.14: Update to 4.14.72.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.72.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b3ccaef89f..93005e16da 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.71")
-(define %linux-libre-4.14-hash "1akvykaccy7ikl8v04grwxvgs4z2rrs7drf2s85ysqwq79mdh3gq")
+(define %linux-libre-4.14-version "4.14.72")
+(define %linux-libre-4.14-hash "1ngz5p8mvga45y1n6hbw6niy0ji5mfl4vc3bxlckjg42dcp5qf64")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From 1d1e4f8f9c46b13ed2c4a61bc4c5f25c6748649b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 27 Sep 2018 05:53:46 -0400
Subject: [PATCH 151/909] gnu: linux-libre: Update to 4.18.10.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.10.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 93005e16da..2503676396 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.9")
-(define %linux-libre-hash "0wwmhnfvcsdlqhzwwwyz1x5a3ldjky6l0xir1pi6pysr0lak402x")
+(define %linux-libre-version "4.18.10")
+(define %linux-libre-hash "1znc6kh3j8plmxail6hn2ss0r0fvbcp50s3xv5gxys7jc7k42znj")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch

From de1158d53fd106103214e79f8523a91b9cfa89d7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 27 Sep 2018 19:55:49 +0200
Subject: [PATCH 152/909] gnu: eolie: Update to 0.9.38.

* gnu/packages/gnome.scm (eolie): Update to 0.9.38.
---
 gnu/packages/gnome.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 1e8522c500..de938e4b14 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -4090,15 +4090,15 @@ work and the interface is well tested.")
 (define-public eolie
   (package
     (name "eolie")
-    (version "0.9.37")
+    (version "0.9.38")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gitlab.gnome.org/World/eolie/"
-                                  "uploads/4341cb428b7a45670308ee3fb3fa07dd/"
+                                  "uploads/9814c06a1bc83ea09c3da8719a9ed11b/"
                                   "eolie-" version ".tar.xz"))
               (sha256
                (base32
-                "126m0nwwy3lqv7z8aj9hiwangih03b1nlkg3xja9p7wbf7zcvp2n"))))
+                "10vrh91rapgfmqwc6jkcybpmlvn4q0y8bnklw3rddzigf9kvqsff"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t

From ea1a3601999887a0762a942460317145f3f53b30 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 27 Sep 2018 20:02:55 +0200
Subject: [PATCH 153/909] gnu: emacs-ert-runner: Do not use package name in
 directory.

* gnu/packages/emacs.scm (emacs-ert-runner)[arguments]: Use the upstream name
instead of the Guix package name in the "install-executable" phase.

This is a follow-up to commit 5c8031ff7382ec9079040d08ae5a05b4dd2352b7.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 9dc11c59fc..8da5add886 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -6982,8 +6982,8 @@ Emacs.")
                (substitute* "bin/ert-runner"
                  (("ERT_RUNNER=\"\\$\\(dirname \\$\\(dirname \\$0\\)\\)")
                   (string-append "ERT_RUNNER=\"" out
-                                 "/share/emacs/site-lisp/guix.d/"
-                                 ,name "-" ,version)))
+                                 "/share/emacs/site-lisp/guix.d/ert-runner-"
+                                 ,version)))
                (install-file "bin/ert-runner" (string-append out "/bin"))
                (wrap-program (string-append out "/bin/ert-runner")
                  (list "EMACSLOADPATH" ":" 'prefix

From 363d7d6608d599776f78525e50a920b1d641805b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 27 Sep 2018 21:52:07 +0200
Subject: [PATCH 154/909] gnu: yoshimi: Update to 1.5.9.

* gnu/packages/music.scm (yoshimi): Update to 1.5.9.
---
 gnu/packages/music.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index e563062018..2d834d8c1f 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1996,7 +1996,7 @@ capabilities, custom envelopes, effects, etc.")
 (define-public yoshimi
   (package
     (name "yoshimi")
-    (version "1.5.8.2")
+    (version "1.5.9")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/yoshimi/"
@@ -2004,7 +2004,7 @@ capabilities, custom envelopes, effects, etc.")
                                   "/yoshimi-" version ".tar.bz2"))
               (sha256
                (base32
-                "1kg7d6mnzdwzsqhrf7pmrf1hzgfpbpm5lv8xkaz32wiv391qrnxc"))))
+                "1nqwxwq6814m860zrh33r85vdyi2bgkvjg5372h3ngcdmxnb7wr0"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; there are no tests

From fe65b559a671390ed5034d2d0b2c58c276e5abff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 25 Sep 2018 10:30:21 +0200
Subject: [PATCH 155/909] progress: Add 'display-download-progress'.

* guix/progress.scm (display-download-progress): New procedure.
(progress-reporter/file)[render]: Rewrite in terms of
'display-download-progress'.
---
 guix/progress.scm | 72 +++++++++++++++++++++++++++--------------------
 1 file changed, 41 insertions(+), 31 deletions(-)

diff --git a/guix/progress.scm b/guix/progress.scm
index 53aea1c56d..d4ebb32991 100644
--- a/guix/progress.scm
+++ b/guix/progress.scm
@@ -39,6 +39,7 @@
             progress-reporter/file
             progress-reporter/bar
 
+            display-download-progress
             byte-count->string
             current-terminal-columns
 
@@ -183,6 +184,42 @@ width of the bar is BAR-WIDTH."
 move the cursor to the beginning of the line."
   (display "\r\x1b[K" port))
 
+(define* (display-download-progress file size
+                                    #:key
+                                    start-time (transferred 0)
+                                    (log-port (current-error-port)))
+  "Write the progress report to LOG-PORT.  Use START-TIME (a SRFI-19 time
+object) and TRANSFERRED (a total number of bytes) to determine the
+throughput."
+  (define elapsed
+    (duration->seconds
+     (time-difference (current-time time-monotonic) start-time)))
+  (if (number? size)
+      (let* ((%  (* 100.0 (/ transferred size)))
+             (throughput (/ transferred elapsed))
+             (left       (format #f " ~a  ~a" file
+                                 (byte-count->string size)))
+             (right      (format #f "~a/s ~a ~a~6,1f%"
+                                 (byte-count->string throughput)
+                                 (seconds->string elapsed)
+                                 (progress-bar %) %)))
+        (erase-current-line log-port)
+        (display (string-pad-middle left right
+                                    (current-terminal-columns))
+                 log-port)
+        (force-output log-port))
+      (let* ((throughput (/ transferred elapsed))
+             (left       (format #f " ~a" file))
+             (right      (format #f "~a/s ~a | ~a transferred"
+                                 (byte-count->string throughput)
+                                 (seconds->string elapsed)
+                                 (byte-count->string transferred))))
+        (erase-current-line log-port)
+        (display (string-pad-middle left right
+                                    (current-terminal-columns))
+                 log-port)
+        (force-output log-port))))
+
 (define* (progress-reporter/file file size
                                  #:optional (log-port (current-output-port))
                                  #:key (abbreviation basename))
@@ -192,37 +229,10 @@ ABBREVIATION used to shorten FILE for display."
   (let ((start-time (current-time time-monotonic))
         (transferred 0))
     (define (render)
-      "Write the progress report to LOG-PORT."
-      (define elapsed
-        (duration->seconds
-         (time-difference (current-time time-monotonic) start-time)))
-      (if (number? size)
-          (let* ((%  (* 100.0 (/ transferred size)))
-                 (throughput (/ transferred elapsed))
-                 (left       (format #f " ~a  ~a"
-                                     (abbreviation file)
-                                     (byte-count->string size)))
-                 (right      (format #f "~a/s ~a ~a~6,1f%"
-                                     (byte-count->string throughput)
-                                     (seconds->string elapsed)
-                                     (progress-bar %) %)))
-            (erase-current-line log-port)
-            (display (string-pad-middle left right
-                                        (current-terminal-columns))
-                     log-port)
-            (force-output log-port))
-          (let* ((throughput (/ transferred elapsed))
-                 (left       (format #f " ~a"
-                                     (abbreviation file)))
-                 (right      (format #f "~a/s ~a | ~a transferred"
-                                     (byte-count->string throughput)
-                                     (seconds->string elapsed)
-                                     (byte-count->string transferred))))
-            (erase-current-line log-port)
-            (display (string-pad-middle left right
-                                        (current-terminal-columns))
-                     log-port)
-            (force-output log-port))))
+      (display-download-progress (abbreviation file) size
+                                 #:start-time start-time
+                                 #:transferred transferred
+                                 #:log-port log-port))
 
     (progress-reporter
      (start render)

From dc0f74e5fc26977a3ee6c4f2aa74a141f4359982 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 18 Jan 2017 23:21:29 +0100
Subject: [PATCH 156/909] Add (guix status) and use it for pretty colored
 output.

* guix/progress.scm (progress-reporter/trace): New procedure.
(%progress-interval): New variable.
(progress-reporter/file): Use it.
* guix/scripts/build.scm (set-build-options-from-command-line): Pass
 #:print-extended-build-trace?.
(%default-options): Add 'print-extended-build-trace?'.
(guix-build): Parameterize CURRENT-TERMINAL-COLUMNS.  Use
'build-status-updater'.
* guix/scripts/environment.scm (%default-options): Add
'print-extended-build-trace?'.
(guix-environment): Wrap body in 'with-status-report'.
* guix/scripts/pack.scm (%default-options): Add 'print-build-trace?' and
'print-extended-build-trace?'.
(guix-pack): Wrap body in 'with-status-report'.
* guix/scripts/package.scm (%default-options, guix-package): Likewise.
* guix/scripts/system.scm (%default-options, guix-system): Likewise.
* guix/scripts/pull.scm (%default-options, guix-pull): Likewise.
* guix/scripts/substitute.scm (progress-report-port): Don't call STOP
when TOTAL is zero.
(process-substitution): Add #:print-build-trace? and honor it.
(guix-substitute)[print-build-trace?]: New variable.
Pass #:print-build-trace? to 'process-substitution'.
* guix/status.scm: New file.
* guix/store.scm (set-build-options): Add #:print-extended-build-trace?;
pass it into PAIRS.
(%protocol-version): Bump.
(protocol-version, nix-server-version): New procedures.
(current-store-protocol-version): New variable.
(with-store, build-things): Parameterize it.
* guix/ui.scm (build-output-port): Remove.
(colorize-string): Export.
* po/guix/POTFILES.in: Add guix/status.scm.
* tests/status.scm: New file.
* Makefile.am (SCM_TESTS): Add it.
* nix/libstore/worker-protocol.hh (PROTOCOL_VERSION): Bump to 0x162.
* nix/libstore/build.cc (DerivationGoal::registerOutputs)
(SubstitutionGoal::finished): Print a "@ hash-mismatch" trace before
throwing.
---
 .dir-locals.el                    |   1 +
 Makefile.am                       |   2 +
 guix/progress.scm                 |  38 ++-
 guix/scripts/build.scm            |  13 +-
 guix/scripts/environment.scm      | 110 +++----
 guix/scripts/pack.scm             | 140 ++++-----
 guix/scripts/package.scm          |  25 +-
 guix/scripts/perform-download.scm |   1 +
 guix/scripts/pull.scm             |  64 ++--
 guix/scripts/substitute.scm       |  42 ++-
 guix/scripts/system.scm           |  11 +-
 guix/status.scm                   | 493 ++++++++++++++++++++++++++++++
 guix/store.scm                    |  53 +++-
 guix/ui.scm                       | 122 +-------
 nix/libstore/build.cc             |  27 +-
 nix/libstore/worker-protocol.hh   |   2 +-
 po/guix/POTFILES.in               |   1 +
 tests/status.scm                  | 115 +++++++
 18 files changed, 934 insertions(+), 326 deletions(-)
 create mode 100644 guix/status.scm
 create mode 100644 tests/status.scm

diff --git a/.dir-locals.el b/.dir-locals.el
index eb99a5bcc1..793117c0ae 100644
--- a/.dir-locals.el
+++ b/.dir-locals.el
@@ -59,6 +59,7 @@
    (eval . (put 'emacs-substitute-variables 'scheme-indent-function 1))
    (eval . (put 'with-derivation-narinfo 'scheme-indent-function 1))
    (eval . (put 'with-derivation-substitute 'scheme-indent-function 2))
+   (eval . (put 'with-status-report 'scheme-indent-function 1))
 
    (eval . (put 'mlambda 'scheme-indent-function 1))
    (eval . (put 'mlambdaq 'scheme-indent-function 1))
diff --git a/Makefile.am b/Makefile.am
index 5c8639d665..7fd29b90a8 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -131,6 +131,7 @@ MODULES =					\
   guix/svn-download.scm				\
   guix/i18n.scm					\
   guix/ui.scm					\
+  guix/status.scm				\
   guix/build/android-ndk-build-system.scm	\
   guix/build/ant-build-system.scm		\
   guix/build/download.scm			\
@@ -340,6 +341,7 @@ SCM_TESTS =					\
   tests/glob.scm				\
   tests/grafts.scm				\
   tests/ui.scm					\
+  tests/status.scm				\
   tests/records.scm				\
   tests/upstream.scm				\
   tests/combinators.scm				\
diff --git a/guix/progress.scm b/guix/progress.scm
index d4ebb32991..3b9ff408cd 100644
--- a/guix/progress.scm
+++ b/guix/progress.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2015 Steve Sprang <scs@stevesprang.com>
-;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,8 +38,11 @@
             progress-reporter/silent
             progress-reporter/file
             progress-reporter/bar
+            progress-reporter/trace
 
             display-download-progress
+            erase-current-line
+            progress-bar
             byte-count->string
             current-terminal-columns
 
@@ -220,6 +223,10 @@ throughput."
                  log-port)
         (force-output log-port))))
 
+(define %progress-interval
+  ;; Default interval between subsequent outputs for rate-limited displays.
+  (make-time time-monotonic 200000000 0))
+
 (define* (progress-reporter/file file size
                                  #:optional (log-port (current-output-port))
                                  #:key (abbreviation basename))
@@ -238,8 +245,7 @@ ABBREVIATION used to shorten FILE for display."
      (start render)
      ;; Report the progress every 300ms or longer.
      (report
-      (let ((rate-limited-render
-             (rate-limited render (make-time time-monotonic 300000000 0))))
+      (let ((rate-limited-render (rate-limited render %progress-interval)))
         (lambda (value)
           (set! transferred value)
           (rate-limited-render))))
@@ -279,6 +285,32 @@ tasks is performed.  Write PREFIX at the beginning of the line."
              (newline port))
            (force-output port)))))
 
+(define* (progress-reporter/trace file url size
+                                  #:optional (log-port (current-output-port)))
+  "Like 'progress-reporter/file', but instead of returning human-readable
+progress reports, write \"build trace\" lines to be processed elsewhere."
+  (define (report-progress transferred)
+    (define message
+      (format #f "@ download-progress ~a ~a ~a ~a~%"
+              file url (or size "-") transferred))
+
+    (display message log-port)                    ;should be atomic
+    (flush-output-port log-port))
+
+  (progress-reporter
+   (start (lambda ()
+            (display (format #f "@ download-started ~a ~a ~a~%"
+                             file url (or size "-"))
+                     log-port)))
+   (report (rate-limited report-progress %progress-interval))
+   (stop (lambda ()
+           (report-progress size)
+           (display (format #f "@ download-succeeded ~a ~a ~a~%"
+                            file url
+                            (or (and=> (stat file #f) stat:size)
+                                size))
+                    log-port)))))
+
 ;; TODO: replace '(@ (guix build utils) dump-port))'.
 (define* (dump-port* in out
                      #:key (buffer-size 16384)
diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index 9d38610633..5a6ba62bc3 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -45,6 +45,9 @@
   #:use-module (srfi srfi-37)
   #:autoload   (gnu packages) (specification->package %package-module-path)
   #:autoload   (guix download) (download-to-store)
+  #:use-module (guix status)
+  #:use-module ((guix progress) #:select (current-terminal-columns))
+  #:use-module ((guix build syscalls) #:select (terminal-columns))
   #:export (%standard-build-options
             set-build-options-from-command-line
             set-build-options-from-command-line*
@@ -390,6 +393,8 @@ options handled by 'set-build-options-from-command-line', and listed in
                      #:max-silent-time (assoc-ref opts 'max-silent-time)
                      #:timeout (assoc-ref opts 'timeout)
                      #:print-build-trace (assoc-ref opts 'print-build-trace?)
+                     #:print-extended-build-trace?
+                     (assoc-ref opts 'print-extended-build-trace?)
                      #:verbosity (assoc-ref opts 'verbosity)))
 
 (define set-build-options-from-command-line*
@@ -499,6 +504,7 @@ options handled by 'set-build-options-from-command-line', and listed in
     (substitutes? . #t)
     (build-hook? . #t)
     (print-build-trace? . #t)
+    (print-extended-build-trace? . #t)
     (verbosity . 0)))
 
 (define (show-help)
@@ -733,11 +739,12 @@ needed."
         ;; Set the build options before we do anything else.
         (set-build-options-from-command-line store opts)
 
-        (parameterize ((current-build-output-port
+        (parameterize ((current-terminal-columns (terminal-columns))
+                       (current-build-output-port
                         (if quiet?
                             (%make-void-port "w")
-                            (build-output-port #:verbose? #t
-                                               #:port (duplicate-port (current-error-port) "w")))))
+                            (build-event-output-port
+                             (build-status-updater print-build-event)))))
           (let* ((mode  (assoc-ref opts 'build-mode))
                  (drv   (options->derivations store opts))
                  (urls  (map (cut string-append <> "/log")
diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm
index 1c04800e42..9fc7edcd36 100644
--- a/guix/scripts/environment.scm
+++ b/guix/scripts/environment.scm
@@ -21,6 +21,7 @@
 (define-module (guix scripts environment)
   #:use-module (guix ui)
   #:use-module (guix store)
+  #:use-module (guix status)
   #:use-module (guix grafts)
   #:use-module (guix derivations)
   #:use-module (guix packages)
@@ -173,6 +174,8 @@ COMMAND or an interactive shell in that environment.\n"))
     (substitutes? . #t)
     (build-hook? . #t)
     (graft? . #t)
+    (print-build-trace? . #t)
+    (print-extended-build-trace? . #t)
     (verbosity . 0)))
 
 (define (tag-package-arg opts arg)
@@ -661,59 +664,60 @@ message if any test fails."
         (leave (G_ "'--user' cannot be used without '--container'~%")))
 
       (with-store store
-        (set-build-options-from-command-line store opts)
+        (with-status-report print-build-event
+          (set-build-options-from-command-line store opts)
 
-        ;; Use the bootstrap Guile when requested.
-        (parameterize ((%graft? (assoc-ref opts 'graft?))
-                       (%guile-for-build
-                        (package-derivation
-                         store
-                         (if bootstrap?
-                             %bootstrap-guile
-                             (canonical-package guile-2.2)))))
-          (run-with-store store
-            ;; Containers need a Bourne shell at /bin/sh.
-            (mlet* %store-monad ((bash       (environment-bash container?
-                                                               bootstrap?
-                                                               system))
-                                 (prof-drv   (manifest->derivation
-                                              manifest system bootstrap?))
-                                 (profile -> (derivation->output-path prof-drv))
-                                 (gc-root -> (assoc-ref opts 'gc-root)))
+          ;; Use the bootstrap Guile when requested.
+          (parameterize ((%graft? (assoc-ref opts 'graft?))
+                         (%guile-for-build
+                          (package-derivation
+                           store
+                           (if bootstrap?
+                               %bootstrap-guile
+                               (canonical-package guile-2.2)))))
+            (run-with-store store
+              ;; Containers need a Bourne shell at /bin/sh.
+              (mlet* %store-monad ((bash       (environment-bash container?
+                                                                 bootstrap?
+                                                                 system))
+                                   (prof-drv   (manifest->derivation
+                                                manifest system bootstrap?))
+                                   (profile -> (derivation->output-path prof-drv))
+                                   (gc-root -> (assoc-ref opts 'gc-root)))
 
-              ;; First build the inputs.  This is necessary even for
-              ;; --search-paths.  Additionally, we might need to build bash for
-              ;; a container.
-              (mbegin %store-monad
-                (build-environment (if (derivation? bash)
-                                       (list prof-drv bash)
-                                       (list prof-drv))
-                                   opts)
-                (mwhen gc-root
-                  (register-gc-root profile gc-root))
+                ;; First build the inputs.  This is necessary even for
+                ;; --search-paths.  Additionally, we might need to build bash for
+                ;; a container.
+                (mbegin %store-monad
+                  (build-environment (if (derivation? bash)
+                                         (list prof-drv bash)
+                                         (list prof-drv))
+                                     opts)
+                  (mwhen gc-root
+                    (register-gc-root profile gc-root))
 
-                (cond
-                 ((assoc-ref opts 'dry-run?)
-                  (return #t))
-                 ((assoc-ref opts 'search-paths)
-                  (show-search-paths profile manifest #:pure? pure?)
-                  (return #t))
-                 (container?
-                  (let ((bash-binary
-                         (if bootstrap?
-                             bash
-                             (string-append (derivation->output-path bash)
-                                            "/bin/sh"))))
-                    (launch-environment/container #:command command
-                                                  #:bash bash-binary
-                                                  #:user user
-                                                  #:user-mappings mappings
-                                                  #:profile profile
-                                                  #:manifest manifest
-                                                  #:link-profile? link-prof?
-                                                  #:network? network?)))
-                 (else
-                  (return
-                   (exit/status
-                    (launch-environment/fork command profile manifest
-                                             #:pure? pure?)))))))))))))
+                  (cond
+                   ((assoc-ref opts 'dry-run?)
+                    (return #t))
+                   ((assoc-ref opts 'search-paths)
+                    (show-search-paths profile manifest #:pure? pure?)
+                    (return #t))
+                   (container?
+                    (let ((bash-binary
+                           (if bootstrap?
+                               bash
+                               (string-append (derivation->output-path bash)
+                                              "/bin/sh"))))
+                      (launch-environment/container #:command command
+                                                    #:bash bash-binary
+                                                    #:user user
+                                                    #:user-mappings mappings
+                                                    #:profile profile
+                                                    #:manifest manifest
+                                                    #:link-profile? link-prof?
+                                                    #:network? network?)))
+                   (else
+                    (return
+                     (exit/status
+                      (launch-environment/fork command profile manifest
+                                               #:pure? pure?))))))))))))))
diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm
index 1916f3b9d7..163f5b1dc1 100644
--- a/guix/scripts/pack.scm
+++ b/guix/scripts/pack.scm
@@ -25,6 +25,7 @@
   #:use-module (guix gexp)
   #:use-module (guix utils)
   #:use-module (guix store)
+  #:use-module (guix status)
   #:use-module (guix grafts)
   #:use-module (guix monads)
   #:use-module (guix modules)
@@ -538,6 +539,8 @@ please email '~a'~%")
     (substitutes? . #t)
     (build-hook? . #t)
     (graft? . #t)
+    (print-build-trace? . #t)
+    (print-extended-build-trace? . #t)
     (verbosity . 0)
     (symlinks . ())
     (compressor . ,(first %compressors))))
@@ -684,72 +687,73 @@ Create a bundle of PACKAGE.\n"))
 
   (with-error-handling
     (with-store store
-      ;; Set the build options before we do anything else.
-      (set-build-options-from-command-line store opts)
+      (with-status-report print-build-event
+        ;; Set the build options before we do anything else.
+        (set-build-options-from-command-line store opts)
 
-      (parameterize ((%graft? (assoc-ref opts 'graft?))
-                     (%guile-for-build (package-derivation
-                                        store
-                                        (if (assoc-ref opts 'bootstrap?)
-                                            %bootstrap-guile
-                                            (canonical-package guile-2.2))
-                                        (assoc-ref opts 'system)
-                                        #:graft? (assoc-ref opts 'graft?))))
-        (let* ((dry-run?    (assoc-ref opts 'dry-run?))
-               (relocatable? (assoc-ref opts 'relocatable?))
-               (manifest    (let ((manifest (manifest-from-args store opts)))
-                              ;; Note: We cannot honor '--bootstrap' here because
-                              ;; 'glibc-bootstrap' lacks 'libc.a'.
-                              (if relocatable?
-                                  (map-manifest-entries wrapped-package manifest)
-                                  manifest)))
-               (pack-format (assoc-ref opts 'format))
-               (name        (string-append (symbol->string pack-format)
-                                           "-pack"))
-               (target      (assoc-ref opts 'target))
-               (bootstrap?  (assoc-ref opts 'bootstrap?))
-               (compressor  (if bootstrap?
-                                bootstrap-xz
-                                (assoc-ref opts 'compressor)))
-               (archiver    (if (equal? pack-format 'squashfs)
-                                squashfs-tools-next
-                                (if bootstrap?
-                                    %bootstrap-coreutils&co
-                                    tar)))
-               (symlinks    (assoc-ref opts 'symlinks))
-               (build-image (match (assq-ref %formats pack-format)
-                              ((? procedure? proc) proc)
-                              (#f
-                               (leave (G_ "~a: unknown pack format~%")
-                                      pack-format))))
-               (localstatedir? (assoc-ref opts 'localstatedir?)))
-          (run-with-store store
-            (mlet* %store-monad ((profile (profile-derivation
-                                           manifest
-                                           #:relative-symlinks? relocatable?
-                                           #:hooks (if bootstrap?
-                                                       '()
-                                                       %default-profile-hooks)
-                                           #:locales? (not bootstrap?)
-                                           #:target target))
-                                 (drv (build-image name profile
-                                                   #:target
-                                                   target
-                                                   #:compressor
-                                                   compressor
-                                                   #:symlinks
-                                                   symlinks
-                                                   #:localstatedir?
-                                                   localstatedir?
-                                                   #:archiver
-                                                   archiver)))
-              (mbegin %store-monad
-                (show-what-to-build* (list drv)
-                                     #:use-substitutes?
-                                     (assoc-ref opts 'substitutes?)
-                                     #:dry-run? dry-run?)
-                (munless dry-run?
-                  (built-derivations (list drv))
-                  (return (format #t "~a~%"
-                                  (derivation->output-path drv))))))
-            #:system (assoc-ref opts 'system)))))))
+        (parameterize ((%graft? (assoc-ref opts 'graft?))
+                       (%guile-for-build (package-derivation
+                                          store
+                                          (if (assoc-ref opts 'bootstrap?)
+                                              %bootstrap-guile
+                                              (canonical-package guile-2.2))
+                                          (assoc-ref opts 'system)
+                                          #:graft? (assoc-ref opts 'graft?))))
+          (let* ((dry-run?    (assoc-ref opts 'dry-run?))
+                 (relocatable? (assoc-ref opts 'relocatable?))
+                 (manifest    (let ((manifest (manifest-from-args store opts)))
+                                ;; Note: We cannot honor '--bootstrap' here because
+                                ;; 'glibc-bootstrap' lacks 'libc.a'.
+                                (if relocatable?
+                                    (map-manifest-entries wrapped-package manifest)
+                                    manifest)))
+                 (pack-format (assoc-ref opts 'format))
+                 (name        (string-append (symbol->string pack-format)
+                                             "-pack"))
+                 (target      (assoc-ref opts 'target))
+                 (bootstrap?  (assoc-ref opts 'bootstrap?))
+                 (compressor  (if bootstrap?
+                                  bootstrap-xz
+                                  (assoc-ref opts 'compressor)))
+                 (archiver    (if (equal? pack-format 'squashfs)
+                                  squashfs-tools-next
+                                  (if bootstrap?
+                                      %bootstrap-coreutils&co
+                                      tar)))
+                 (symlinks    (assoc-ref opts 'symlinks))
+                 (build-image (match (assq-ref %formats pack-format)
+                                ((? procedure? proc) proc)
+                                (#f
+                                 (leave (G_ "~a: unknown pack format~%")
+                                        pack-format))))
+                 (localstatedir? (assoc-ref opts 'localstatedir?)))
+            (run-with-store store
+              (mlet* %store-monad ((profile (profile-derivation
+                                             manifest
+                                             #:relative-symlinks? relocatable?
+                                             #:hooks (if bootstrap?
+                                                         '()
+                                                         %default-profile-hooks)
+                                             #:locales? (not bootstrap?)
+                                             #:target target))
+                                   (drv (build-image name profile
+                                                     #:target
+                                                     target
+                                                     #:compressor
+                                                     compressor
+                                                     #:symlinks
+                                                     symlinks
+                                                     #:localstatedir?
+                                                     localstatedir?
+                                                     #:archiver
+                                                     archiver)))
+                (mbegin %store-monad
+                  (show-what-to-build* (list drv)
+                                       #:use-substitutes?
+                                       (assoc-ref opts 'substitutes?)
+                                       #:dry-run? dry-run?)
+                  (munless dry-run?
+                    (built-derivations (list drv))
+                    (return (format #t "~a~%"
+                                    (derivation->output-path drv))))))
+              #:system (assoc-ref opts 'system))))))))
diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index c3ed2ac935..93a77915fe 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -24,6 +24,7 @@
 
 (define-module (guix scripts package)
   #:use-module (guix ui)
+  #:use-module (guix status)
   #:use-module (guix store)
   #:use-module (guix grafts)
   #:use-module (guix derivations)
@@ -330,7 +331,8 @@ ENTRIES, a list of manifest entries, in the context of PROFILE."
     (graft? . #t)
     (substitutes? . #t)
     (build-hook? . #t)
-    (print-build-trace? . #t)))
+    (print-build-trace? . #t)
+    (print-extended-build-trace? . #t)))
 
 (define (show-help)
   (display (G_ "Usage: guix package [OPTION]...
@@ -941,15 +943,12 @@ processed, #f otherwise."
     (or (process-query opts)
         (parameterize ((%store  (open-connection))
                        (%graft? (assoc-ref opts 'graft?)))
-          (set-build-options-from-command-line (%store) opts)
-
-          (parameterize ((%guile-for-build
-                          (package-derivation
-                           (%store)
-                           (if (assoc-ref opts 'bootstrap?)
-                               %bootstrap-guile
-                               (canonical-package guile-2.2))))
-                         (current-build-output-port
-                          (build-output-port #:verbose? verbose?
-                                             #:port (duplicate-port (current-error-port) "w"))))
-            (process-actions (%store) opts))))))
+          (with-status-report print-build-event/quiet
+            (set-build-options-from-command-line (%store) opts)
+            (parameterize ((%guile-for-build
+                            (package-derivation
+                             (%store)
+                             (if (assoc-ref opts 'bootstrap?)
+                                 %bootstrap-guile
+                                 (canonical-package guile-2.2)))))
+              (process-actions (%store) opts)))))))
diff --git a/guix/scripts/perform-download.scm b/guix/scripts/perform-download.scm
index 18e2fc92f2..9f6ecc00d2 100644
--- a/guix/scripts/perform-download.scm
+++ b/guix/scripts/perform-download.scm
@@ -48,6 +48,7 @@ OUTPUT.
 Note: Unless OUTPUT is #f, we don't read the value of 'out' in DRV since the
 actual output is different from that when we're doing a 'bmCheck' or
 'bmRepair' build."
+  ;; TODO: Use 'trace-progress-proc' when possible.
   (derivation-let drv ((url "url")
                        (output* "out")
                        (executable "executable")
diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 39aebb18e2..803f7cf142 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -20,6 +20,7 @@
 (define-module (guix scripts pull)
   #:use-module (guix ui)
   #:use-module (guix utils)
+  #:use-module (guix status)
   #:use-module (guix scripts)
   #:use-module (guix store)
   #:use-module (guix config)
@@ -61,6 +62,8 @@
   `((system . ,(%current-system))
     (substitutes? . #t)
     (build-hook? . #t)
+    (print-build-trace? . #t)
+    (print-extended-build-trace? . #t)
     (graft? . #t)
     (verbosity . 0)))
 
@@ -447,36 +450,37 @@ Use '~/.config/guix/channels.scm' instead."))
               #t)                                 ;XXX: not very useful
              (else
               (with-store store
-                (parameterize ((%graft? (assoc-ref opts 'graft?))
-                               (%repository-cache-directory cache))
-                  (set-build-options-from-command-line store opts)
-                  (honor-x509-certificates store)
+                (with-status-report print-build-event
+                  (parameterize ((%graft? (assoc-ref opts 'graft?))
+                                 (%repository-cache-directory cache))
+                    (set-build-options-from-command-line store opts)
+                    (honor-x509-certificates store)
 
-                  (let ((instances (latest-channel-instances store channels)))
-                    (format (current-error-port)
-                            (N_ "Building from this channel:~%"
-                                "Building from these channels:~%"
-                                (length instances)))
-                    (for-each (lambda (instance)
-                                (let ((channel
-                                       (channel-instance-channel instance)))
-                                  (format (current-error-port)
-                                          "  ~10a~a\t~a~%"
-                                          (channel-name channel)
-                                          (channel-url channel)
-                                          (string-take
-                                           (channel-instance-commit instance)
-                                           7))))
-                              instances)
-                    (parameterize ((%guile-for-build
-                                    (package-derivation
-                                     store
-                                     (if (assoc-ref opts 'bootstrap?)
-                                         %bootstrap-guile
-                                         (canonical-package guile-2.2)))))
-                      (run-with-store store
-                        (build-and-install instances profile
-                                           #:verbose?
-                                           (assoc-ref opts 'verbose?)))))))))))))
+                    (let ((instances (latest-channel-instances store channels)))
+                      (format (current-error-port)
+                              (N_ "Building from this channel:~%"
+                                  "Building from these channels:~%"
+                                  (length instances)))
+                      (for-each (lambda (instance)
+                                  (let ((channel
+                                         (channel-instance-channel instance)))
+                                    (format (current-error-port)
+                                            "  ~10a~a\t~a~%"
+                                            (channel-name channel)
+                                            (channel-url channel)
+                                            (string-take
+                                             (channel-instance-commit instance)
+                                             7))))
+                                instances)
+                      (parameterize ((%guile-for-build
+                                      (package-derivation
+                                       store
+                                       (if (assoc-ref opts 'bootstrap?)
+                                           %bootstrap-guile
+                                           (canonical-package guile-2.2)))))
+                        (run-with-store store
+                          (build-and-install instances profile
+                                             #:verbose?
+                                             (assoc-ref opts 'verbose?))))))))))))))
 
 ;;; pull.scm ends here
diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm
index 50c6a22064..eb82224016 100755
--- a/guix/scripts/substitute.scm
+++ b/guix/scripts/substitute.scm
@@ -837,7 +837,16 @@ REPORTER, which should be a <progress-reporter> object."
        (make-custom-binary-input-port "progress-port-proc"
                                       read! #f #f
                                       (lambda ()
-                                        (stop)
+                                        ;; XXX: Kludge!  When used through
+                                        ;; 'decompressed-port', this port ends
+                                        ;; up being closed twice: once in a
+                                        ;; child process early on, and at the
+                                        ;; end in the parent process.  Ignore
+                                        ;; the early close so we don't output
+                                        ;; a spurious "download-succeeded"
+                                        ;; trace.
+                                        (unless (zero? total)
+                                          (stop))
                                         (close-port port)))))))
 
 (define-syntax with-networking
@@ -930,7 +939,7 @@ authorized substitutes."
      (error "unknown `--query' command" wtf))))
 
 (define* (process-substitution store-item destination
-                               #:key cache-urls acl)
+                               #:key cache-urls acl print-build-trace?)
   "Substitute STORE-ITEM (a store file name) from CACHE-URLS, and write it to
 DESTINATION as a nar file.  Verify the substitute against ACL."
   (let* ((narinfo (lookup-narinfo cache-urls store-item
@@ -943,8 +952,10 @@ DESTINATION as a nar file.  Verify the substitute against ACL."
     ;; Tell the daemon what the expected hash of the Nar itself is.
     (format #t "~a~%" (narinfo-hash narinfo))
 
-    (format (current-error-port)
-            (G_ "Downloading ~a...~%") (uri->string uri))
+    (unless print-build-trace?
+      (format (current-error-port)
+              (G_ "Downloading ~a...~%") (uri->string uri)))
+
     (let*-values (((raw download-size)
                    ;; Note that Hydra currently generates Nars on the fly
                    ;; and doesn't specify a Content-Length, so
@@ -955,10 +966,15 @@ DESTINATION as a nar file.  Verify the substitute against ACL."
                           (dl-size  (or download-size
                                         (and (equal? comp "none")
                                              (narinfo-size narinfo))))
-                          (reporter (progress-reporter/file
-                                     (uri->string uri) dl-size
-                                     (current-error-port)
-                                     #:abbreviation nar-uri-abbreviation)))
+                          (reporter (if print-build-trace?
+                                        (progress-reporter/trace
+                                         destination
+                                         (uri->string uri) dl-size
+                                         (current-error-port))
+                                        (progress-reporter/file
+                                         (uri->string uri) dl-size
+                                         (current-error-port)
+                                         #:abbreviation nar-uri-abbreviation))))
                      (progress-report-port reporter raw)))
                   ((input pids)
                    ;; NOTE: This 'progress' port of current process will be
@@ -1058,6 +1074,13 @@ default value."
 
 (define (guix-substitute . args)
   "Implement the build daemon's substituter protocol."
+  (define print-build-trace?
+    (match (or (find-daemon-option "untrusted-print-extended-build-trace")
+               (find-daemon-option "print-extended-build-trace"))
+      (#f #f)
+      ((= string->number number) (> number 0))
+      (_ #f)))
+
   (mkdir-p %narinfo-cache-directory)
   (maybe-remove-expired-cache-entries %narinfo-cache-directory
                                       cached-narinfo-files
@@ -1111,7 +1134,8 @@ default value."
         (parameterize ((current-terminal-columns (client-terminal-columns)))
           (process-substitution store-path destination
                                 #:cache-urls (substitute-urls)
-                                #:acl (current-acl))))
+                                #:acl (current-acl)
+                                #:print-build-trace? print-build-trace?)))
        ((or ("-V") ("--version"))
         (show-version-and-exit "guix substitute"))
        (("--help")
diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm
index 1e7620f147..f9d6b9e5b6 100644
--- a/guix/scripts/system.scm
+++ b/guix/scripts/system.scm
@@ -23,6 +23,7 @@
 (define-module (guix scripts system)
   #:use-module (guix config)
   #:use-module (guix ui)
+  #:use-module (guix status)
   #:use-module (guix store)
   #:autoload   (guix store database) (register-path)
   #:use-module (guix grafts)
@@ -1079,6 +1080,8 @@ Some ACTIONS support additional ARGS.\n"))
   `((system . ,(%current-system))
     (substitutes? . #t)
     (build-hook? . #t)
+    (print-build-trace? . #t)
+    (print-extended-build-trace? . #t)
     (graft? . #t)
     (verbosity . 0)
     (file-system-type . "ext4")
@@ -1253,9 +1256,11 @@ argument list and OPTS is the option alist."
                                          parse-sub-command))
            (args     (option-arguments opts))
            (command  (assoc-ref opts 'action)))
-      (parameterize ((%graft? (assoc-ref opts 'graft?))
-                     (current-terminal-columns (terminal-columns)))
-        (process-command command args opts)))))
+      (parameterize ((%graft? (assoc-ref opts 'graft?)))
+        (with-status-report (if (memq command '(init reconfigure))
+                                print-build-event/quiet
+                                print-build-event)
+          (process-command command args opts))))))
 
 ;;; Local Variables:
 ;;; eval: (put 'call-with-service-upgrade-info 'scheme-indent-function 1)
diff --git a/guix/status.scm b/guix/status.scm
new file mode 100644
index 0000000000..94d4748af5
--- /dev/null
+++ b/guix/status.scm
@@ -0,0 +1,493 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (guix status)
+  #:use-module (guix records)
+  #:use-module (guix i18n)
+  #:use-module ((guix ui) #:select (colorize-string))
+  #:use-module (guix progress)
+  #:autoload   (guix build syscalls) (terminal-columns)
+  #:use-module ((guix build download)
+                #:select (nar-uri-abbreviation))
+  #:use-module ((guix store)
+                #:select (current-build-output-port
+                          current-store-protocol-version
+                          log-file))
+  #:use-module (guix derivations)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-9)
+  #:use-module (srfi srfi-19)
+  #:use-module (srfi srfi-26)
+  #:use-module (ice-9 regex)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 format)
+  #:use-module (ice-9 binary-ports)
+  #:use-module (rnrs bytevectors)
+  #:use-module ((system foreign)
+                #:select (bytevector->pointer pointer->bytevector))
+  #:export (build-event-output-port
+            compute-status
+
+            build-status
+            build-status?
+            build-status-building
+            build-status-downloading
+            build-status-builds-completed
+            build-status-downloads-completed
+
+            download?
+            download
+            download-item
+            download-uri
+            download-size
+            download-start
+            download-end
+            download-transferred
+
+            build-status-updater
+            print-build-event
+            print-build-event/quiet
+            print-build-status
+
+            with-status-report))
+
+;;; Commentary:
+;;;
+;;; This module provides facilities to track the status of ongoing builds and
+;;; downloads in a given session, as well as tools to report about the current
+;;; status to user interfaces.  It does so by analyzing the output of
+;;; 'current-build-output-port'.  The build status is maintained in a
+;;; <build-status> record.
+;;;
+;;; Code:
+
+
+;;;
+;;; Build status tracking.
+;;;
+
+;; Builds and substitutions performed by the daemon.
+(define-record-type* <build-status> build-status make-build-status
+  build-status?
+  (building     build-status-building             ;list of drv
+                (default '()))
+  (downloading  build-status-downloading          ;list of <download>
+                (default '()))
+  (builds-completed build-status-builds-completed ;list of drv
+                    (default '()))
+  (downloads-completed build-status-downloads-completed ;list of store items
+                       (default '())))
+
+;; On-going or completed downloads.  Downloads can be stem from substitutes
+;; and from "builtin:download" fixed-output derivations.
+(define-record-type <download>
+  (%download item uri size start end transferred)
+  download?
+  (item         download-item)            ;store item
+  (uri          download-uri)             ;string | #f
+  (size         download-size)            ;integer | #f
+  (start        download-start)           ;<time>
+  (end          download-end)             ;#f | <time>
+  (transferred  download-transferred))    ;integer
+
+(define* (download item uri
+                   #:key size
+                   (start (current-time time-monotonic)) end
+                   (transferred 0))
+  "Return a new download."
+  (%download item uri size start end transferred))
+
+(define (matching-download item)
+  "Return a predicate that matches downloads of ITEM."
+  (lambda (download)
+    (string=? item (download-item download))))
+
+(define* (compute-status event status
+                         #:key (current-time current-time))
+  "Given EVENT, a tuple like (build-started \"/gnu/store/...-foo.drv\" ...),
+compute a new status based on STATUS."
+  (match event
+    (('build-started drv _ ...)
+     (build-status
+      (inherit status)
+      (building (cons drv (build-status-building status)))))
+    (((or 'build-succeeded 'build-failed) drv _ ...)
+     (build-status
+      (inherit status)
+      (building (delete drv (build-status-building status)))
+      (builds-completed (cons drv (build-status-builds-completed status)))))
+
+    ;; Note: Ignore 'substituter-started' and 'substituter-succeeded' because
+    ;; they're not as informative as 'download-started' and
+    ;; 'download-succeeded'.
+
+    (('download-started item uri (= string->number size))
+     ;; This is presumably a fixed-output derivation so move it from
+     ;; 'building' to 'downloading'.  XXX: This doesn't work in 'check' mode
+     ;; because ITEM is different from DRV's output.
+     (build-status
+      (inherit status)
+      (building (remove (lambda (drv)
+                          (equal? (false-if-exception
+                                   (derivation->output-path
+                                    (read-derivation-from-file drv)))
+                                  item))
+                        (build-status-building status)))
+      (downloading (cons (download item uri #:size size
+                                   #:start (current-time time-monotonic))
+                         (build-status-downloading status)))))
+    (('download-succeeded item uri (= string->number size))
+     (let ((current (find (matching-download item)
+                          (build-status-downloading status))))
+       (build-status
+        (inherit status)
+        (downloading (delq current (build-status-downloading status)))
+        (downloads-completed
+         (cons (download item uri
+                         #:size size
+                         #:start (download-start current)
+                         #:transferred size
+                         #:end (current-time time-monotonic))
+               (build-status-downloads-completed status))))))
+    (('substituter-succeeded item _ ...)
+     (match (find (matching-download item)
+                  (build-status-downloading status))
+       (#f
+        ;; Presumably we already got a 'download-succeeded' event for ITEM,
+        ;; everything is fine.
+        status)
+       (current
+        ;; Maybe the build process didn't emit a 'download-succeeded' event
+        ;; for ITEM, so remove CURRENT from the queue now.
+        (build-status
+         (inherit status)
+         (downloading (delq current (build-status-downloading status)))
+         (downloads-completed
+          (cons (download item (download-uri current)
+                          #:size (download-size current)
+                          #:start (download-start current)
+                          #:transferred (download-size current)
+                          #:end (current-time time-monotonic))
+                (build-status-downloads-completed status)))))))
+    (('download-progress item uri
+                         (= string->number size)
+                         (= string->number transferred))
+     (let ((downloads (remove (matching-download item)
+                              (build-status-downloading status)))
+           (current   (find (matching-download item)
+                            (build-status-downloading status))))
+       (build-status
+        (inherit status)
+        (downloading (cons (download item uri
+                                     #:size size
+                                     #:start
+                                     (or (and current
+                                              (download-start current))
+                                         (current-time time-monotonic))
+                                     #:transferred transferred)
+                           downloads)))))
+    (_
+     status)))
+
+(define (simultaneous-jobs status)
+  "Return the number of on-going builds and downloads for STATUS."
+  (+ (length (build-status-building status))
+     (length (build-status-downloading status))))
+
+
+;;;
+;;; Rendering.
+;;;
+
+(define (extended-build-trace-supported?)
+  "Return true if the currently used store is known to support \"extended
+build traces\" such as \"@ download-progress\" traces."
+  ;; Support for extended build traces was added in protocol version #x162.
+  (and (current-store-protocol-version)
+       (>= (current-store-protocol-version) #x162)))
+
+(define spin!
+  (let ((steps (circular-list "\\" "|" "/" "-")))
+    (lambda (port)
+      "Display a spinner on PORT."
+      (match steps
+        ((first . rest)
+         (set! steps rest)
+         (display "\r\x1b[K" port)
+         (display first port)
+         (force-output port))))))
+
+(define (color-output? port)
+  "Return true if we should write colored output to PORT."
+  (and (not (getenv "INSIDE_EMACS"))
+       (not (getenv "NO_COLOR"))
+       (isatty? port)))
+
+(define-syntax color-rules
+  (syntax-rules ()
+    "Return a procedure that colorizes the string it is passed according to
+the given rules.  Each rule has the form:
+
+  (REGEXP COLOR1 COLOR2 ...)
+
+where COLOR1 specifies how to colorize the first submatch of REGEXP, and so
+on."
+    ((_ (regexp colors ...) rest ...)
+     (let ((next (color-rules rest ...))
+           (rx   (make-regexp regexp)))
+       (lambda (str)
+         (if (string-index str #\nul)
+             str
+             (match (regexp-exec rx str)
+               (#f (next str))
+               (m  (let loop ((n 1)
+                              (c '(colors ...))
+                              (result '()))
+                     (match c
+                       (()
+                        (string-concatenate-reverse result))
+                       ((first . tail)
+                        (loop (+ n 1) tail
+                              (cons (colorize-string (match:substring m n)
+                                                     first)
+                                    result)))))))))))
+    ((_)
+     (lambda (str)
+       str))))
+
+(define colorize-log-line
+  ;; Take a string and return a possibly colorized string according to the
+  ;; rules below.
+  (color-rules
+   ("^(phase)(.*)(succeeded after)(.*)(seconds)(.*)"
+    GREEN    BOLD GREEN          RESET  GREEN  BLUE)
+   ("^(phase)(.*)(failed after)(.*)(seconds)(.*)"
+    RED BLUE RED BLUE RED BLUE)
+   ("^(.*)(error|fail|failed|FAIL|FAILED)([[:blank:]]*)(:)(.*)"
+    RESET  RED                           BOLD         BOLD BOLD)
+   ("^(.*)(warning)([[:blank:]]*)(:)(.*)"
+    RESET  ORANGE   BOLD        BOLD BOLD)))
+
+(define* (print-build-event event old-status status
+                            #:optional (port (current-error-port))
+                            #:key
+                            (colorize? (color-output? port))
+                            (print-log? #t))
+  "Print information about EVENT and STATUS to PORT.  When COLORIZE? is true,
+produce colorful output.  When PRINT-LOG? is true, display the build log in
+addition to build events."
+  (define info
+    (if colorize?
+        (cut colorize-string <> 'BOLD)
+        identity))
+
+  (define success
+    (if colorize?
+        (cut colorize-string <> 'GREEN 'BOLD)
+        identity))
+
+  (define failure
+    (if colorize?
+        (cut colorize-string <> 'RED 'BOLD)
+        identity))
+
+  (define print-log-line
+    (if print-log?
+        (if colorize?
+            (lambda (line)
+              (display (colorize-log-line line) port))
+            (cut display <> port))
+        (lambda (line)
+          (spin! port))))
+
+  (display "\r" port)                             ;erase the spinner
+  (match event
+    (('build-started drv . _)
+     (format port (info (G_ "building ~a...")) drv)
+     (newline port))
+    (('build-succeeded drv . _)
+     (format port (success (G_ "successfully built ~a")) drv)
+     (newline port)
+     (match (build-status-building status)
+       (() #t)
+       (ongoing                                   ;when max-jobs > 1
+        (format port
+                (N_ "The following build is still in progress:~%~{  ~a~%~}~%"
+                    "The following builds are still in progress:~%~{  ~a~%~}~%"
+                    (length ongoing))
+                ongoing))))
+    (('build-failed drv . _)
+     (format port (failure (G_ "build of ~a failed")) drv)
+     (newline port)
+     (format port (info (G_ "View build log at '~a'.~%"))
+             (log-file #f drv)))
+    (('substituter-started item _ ...)
+     (when (or print-log? (not (extended-build-trace-supported?)))
+       (format port (info (G_ "substituting ~a...")) item)
+       (newline port)))
+    (('download-started item uri _ ...)
+     (format port (info (G_ "downloading from ~a...")) uri)
+     (newline port))
+    (('download-progress item uri
+                         (= string->number size)
+                         (= string->number transferred))
+     ;; Print a progress bar, but only if there's only one on-going
+     ;; job--otherwise the output would be intermingled.
+     (when (= 1 (simultaneous-jobs status))
+       (match (find (matching-download item)
+                    (build-status-downloading status))
+         (#f #f)                                  ;shouldn't happen!
+         (download
+          ;; XXX: It would be nice to memoize the abbreviation.
+          (let ((uri (if (string-contains uri "/nar/")
+                         (nar-uri-abbreviation uri)
+                         (basename uri))))
+            (display-download-progress uri size
+                                       #:start-time
+                                       (download-start download)
+                                       #:transferred transferred))))))
+    (('substituter-succeeded item _ ...)
+     ;; If there are no jobs running, we already reported download completion
+     ;; so there's nothing left to do.
+     (unless (and (zero? (simultaneous-jobs status))
+                  (extended-build-trace-supported?))
+       (format port (success (G_ "substitution of ~a complete")) item)
+       (newline port)))
+    (('substituter-failed item _ ...)
+     (format port (failure (G_ "substitution of ~a failed")) item)
+     (newline port))
+    (('hash-mismatch item algo expected actual _ ...)
+     ;; TRANSLATORS: The final string looks like "sha256 hash mismatch for
+     ;; /gnu/store/…-sth:", where "sha256" is the hash algorithm.
+     (format port (failure (G_ "~a hash mismatch for ~a:")) algo item)
+     (newline port)
+     (format port (info (G_ "\
+  expected hash: ~a
+  actual hash:   ~a~%"))
+             expected actual))
+    (('build-log line)
+     ;; The daemon prefixes early messages coming with 'guix substitute' with
+     ;; "substitute:".  These are useful ("updating substitutes from URL"), so
+     ;; let them through.
+     (if (string-prefix? "substitute: " line)
+         (begin
+           (format port line)
+           (force-output port))
+         (print-log-line line)))
+    (_
+     event)))
+
+(define* (print-build-event/quiet event old-status status
+                                  #:optional
+                                  (port (current-error-port))
+                                  #:key
+                                  (colorize? (color-output? port)))
+  (print-build-event event old-status status port
+                     #:colorize? colorize?
+                     #:print-log? #f))
+
+(define* (build-status-updater #:optional (on-change (const #t)))
+  "Return a procedure that can be passed to 'build-event-output-port'.  That
+procedure computes the new build status upon each event and calls ON-CHANGE:
+
+  (ON-CHANGE event status new-status)
+
+ON-CHANGE can display the build status, build events, etc."
+  (lambda (event status)
+    (let ((new (compute-status event status)))
+      (on-change event status new)
+      new)))
+
+
+;;;
+;;; Build port.
+;;;
+
+(define %newline
+  (char-set #\return #\newline))
+
+(define* (build-event-output-port proc #:optional (seed (build-status)))
+  "Return an output port for use as 'current-build-output-port' that calls
+PROC with its current state value, initialized with SEED, on every build
+event.  Build events passed to PROC are tuples corresponding to the \"build
+traces\" produced by the daemon:
+
+  (build-started \"/gnu/store/...-foo.drv\" ...)
+  (substituter-started \"/gnu/store/...-foo\" ...)
+
+and so on.
+
+The second return value is a thunk to retrieve the current state."
+  (define %fragments
+    ;; Line fragments received so far.
+    '())
+
+  (define %state
+    ;; Current state for PROC.
+    seed)
+
+  (define (process-line line)
+    (if (string-prefix? "@ " line)
+        (match (string-tokenize (string-drop line 2))
+          (((= string->symbol event-name) args ...)
+           (set! %state
+             (proc (cons event-name args)
+                   %state))))
+        (set! %state (proc (list 'build-log line)
+                           %state))))
+
+  (define (bytevector-range bv offset count)
+    (let ((ptr (bytevector->pointer bv offset)))
+      (pointer->bytevector ptr count)))
+
+  (define (write! bv offset count)
+    (let loop ((str (utf8->string (bytevector-range bv offset count))))
+      (match (string-index str %newline)
+        ((? integer? cr)
+         (let ((tail (string-take str (+ 1 cr))))
+           (process-line (string-concatenate-reverse
+                          (cons tail %fragments)))
+           (set! %fragments '())
+           (loop (string-drop str (+ 1 cr)))))
+        (#f
+         (unless (string-null? str)
+           (set! %fragments (cons str %fragments)))
+         count))))
+
+  (define port
+    (make-custom-binary-output-port "filtering-input-port"
+                                    write!
+                                    #f #f
+                                    #f))
+
+  ;; The build port actually receives Unicode strings.
+  (set-port-encoding! port "UTF-8")
+  (setvbuf port (cond-expand (guile-2.2 'line) (else _IOLBF)))
+
+  (values port (lambda () %state)))
+
+(define (call-with-status-report on-event thunk)
+  (parameterize ((current-terminal-columns (terminal-columns))
+                 (current-build-output-port
+                  (build-event-output-port (build-status-updater on-event))))
+    (thunk)))
+
+(define-syntax-rule (with-status-report on-event exp ...)
+  "Set up build status reporting to the user using the ON-EVENT procedure;
+evaluate EXP... in that context."
+  (call-with-status-report on-event (lambda () exp ...)))
diff --git a/guix/store.scm b/guix/store.scm
index f88cdefe87..7785a53aa1 100644
--- a/guix/store.scm
+++ b/guix/store.scm
@@ -50,9 +50,11 @@
             %default-substitute-urls
 
             nix-server?
+            nix-server-version
             nix-server-major-version
             nix-server-minor-version
             nix-server-socket
+            current-store-protocol-version        ;for internal use
 
             &nix-error nix-error?
             &nix-connection-error nix-connection-error?
@@ -152,7 +154,7 @@
             direct-store-path
             log-file))
 
-(define %protocol-version #x161)
+(define %protocol-version #x162)
 
 (define %worker-magic-1 #x6e697863)               ; "nixc"
 (define %worker-magic-2 #x6478696f)               ; "dxio"
@@ -161,6 +163,8 @@
   (logand magic #xff00))
 (define (protocol-minor magic)
   (logand magic #x00ff))
+(define (protocol-version major minor)
+  (logior major minor))
 
 (define-syntax define-enumerate-type
   (syntax-rules ()
@@ -540,6 +544,11 @@ connection.  Use with care."
                       (make-hash-table 100)
                       (make-hash-table 100))))
 
+(define (nix-server-version store)
+  "Return the protocol version of STORE as an integer."
+  (protocol-version (nix-server-major-version store)
+                    (nix-server-minor-version store)))
+
 (define (write-buffered-output server)
   "Flush SERVER's output port."
   (force-output (nix-server-output-port server))
@@ -556,10 +565,20 @@ automatically close the store when the dynamic extent of EXP is left."
     (dynamic-wind
       (const #f)
       (lambda ()
-        exp ...)
+        (parameterize ((current-store-protocol-version
+                        (nix-server-version store)))
+         exp) ...)
       (lambda ()
         (false-if-exception (close-connection store))))))
 
+(define current-store-protocol-version
+  ;; Protocol version of the store currently used.  XXX: This is a hack to
+  ;; communicate the protocol version to the build output port.  It's a hack
+  ;; because it could be inaccurrate, for instance if there's code that
+  ;; manipulates several store connections at once; it works well for the
+  ;; purposes of (guix status) though.
+  (make-parameter #f))
+
 (define current-build-output-port
   ;; The port where build output is sent.
   (make-parameter (current-error-port)))
@@ -682,6 +701,13 @@ encoding conversion errors."
                             (build-verbosity 0)
                             (log-type 0)
                             (print-build-trace #t)
+
+                            ;; When true, provide machine-readable "build
+                            ;; traces" for use by (guix status).  Old clients
+                            ;; are unable to make sense, which is why it's
+                            ;; disabled by default.
+                            print-extended-build-trace?
+
                             build-cores
                             (use-substitutes? #t)
 
@@ -725,7 +751,12 @@ encoding conversion errors."
     (when (>= (nix-server-minor-version server) 10)
       (send (boolean use-substitutes?)))
     (when (>= (nix-server-minor-version server) 12)
-      (let ((pairs `(,@(if timeout
+      (let ((pairs `(;; This option is honored by 'guix substitute' et al.
+                     ,@(if print-build-trace
+                           `(("print-extended-build-trace"
+                              . ,(if print-extended-build-trace? "1" "0")))
+                           '())
+                     ,@(if timeout
                            `(("build-timeout" . ,(number->string timeout)))
                            '())
                      ,@(if max-silent-time
@@ -1064,13 +1095,15 @@ an arbitrary directory layout in the store without creating a derivation."
 outputs, and return when the worker is done building them.  Elements of THINGS
 that are not derivations can only be substituted and not built locally.
 Return #t on success."
-      (if (>= (nix-server-minor-version store) 15)
-          (build store things mode)
-          (if (= mode (build-mode normal))
-              (build/old store things)
-              (raise (condition (&nix-protocol-error
-                                 (message "unsupported build mode")
-                                 (status  1)))))))))
+      (parameterize ((current-store-protocol-version
+                      (nix-server-version store)))
+        (if (>= (nix-server-minor-version store) 15)
+            (build store things mode)
+            (if (= mode (build-mode normal))
+                (build/old store things)
+                (raise (condition (&nix-protocol-error
+                                   (message "unsupported build mode")
+                                   (status  1))))))))))
 
 (define-operation (add-temp-root (store-path path))
   "Make PATH a temporary root for the duration of the current session.
diff --git a/guix/ui.scm b/guix/ui.scm
index c55ae7e2f8..96f403acf5 100644
--- a/guix/ui.scm
+++ b/guix/ui.scm
@@ -119,7 +119,7 @@
             warning
             info
             guix-main
-            build-output-port))
+            colorize-string))
 
 ;;; Commentary:
 ;;;
@@ -1676,124 +1676,4 @@ be reset such that subsequent output will not have any colors in effect."
    str
    (color 'RESET)))
 
-(define* (build-output-port #:key
-                            (colorize? #t)
-                            verbose?
-                            (port (current-error-port)))
-  "Return a soft port that processes build output.  By default it colorizes
-phase announcements and replaces any other output with a spinner."
-  (define spun? #f)
-  (define spin!
-    (let ((steps (circular-list "\\" "|" "/" "-")))
-      (lambda ()
-        (match steps
-          ((first . rest)
-           (set! steps rest)
-           (set! spun? #t) ; remember to erase spinner
-           first)))))
-
-  (define use-color?
-    (and colorize?
-         (not (or (getenv "NO_COLOR")
-                  (getenv "INSIDE_EMACS")
-                  (not (isatty? port))))))
-
-  (define handle-string
-    (let* ((proc (if use-color?
-                     colorize-string
-                     (lambda (s . _) s)))
-           (rules `(("^(@ build-started) (.*) (.*)"
-                     #:transform
-                     ,(lambda (m)
-                        (string-append
-                         (proc "Building " 'BLUE 'BOLD)
-                         (match:substring m 2) "\n")))
-                    ,(if verbose?
-                         ;; Err on the side of caution: show everything, even
-                         ;; if it might be redundant.
-                         `("^(@ build-failed)(.+)"
-                           #:transform
-                           ,(lambda (m)
-                              (string-append
-                               (proc "Build failed: " 'RED 'BOLD)
-                               (match:substring m 2))))
-                         ;; Show only that the build failed.
-                         `("^(@ build-failed)(.+) -.*"
-                           #:transform
-                           ,(lambda (m)
-                              (string-append
-                               (proc "Build failed: " 'RED 'BOLD)
-                               (match:substring m 2)
-                               "\n"))))
-                    ;; NOTE: this line contains "\n" characters.
-                    ("^(sha256 hash mismatch for output path)(.*)"
-                     RED BLACK)
-                    ("^(@ build-succeeded) (.*) (.*)"
-                     #:transform
-                     ,(lambda (m)
-                        (string-append
-                         (proc "Built " 'GREEN 'BOLD)
-                         (match:substring m 2) "\n")))
-                    ("^(@ substituter-started) (.*) (.*)"
-                     #:transform
-                     ,(lambda (m)
-                        (string-append
-                         (proc "Substituting " 'BLUE 'BOLD)
-                         (match:substring m 2) "\n")))
-                    ("^(@ substituter-failed) (.*) (.*) (.*)"
-                     #:transform
-                     ,(lambda (m)
-                        (string-append
-                         (proc "Substituter failed: " 'RED 'BOLD)
-                         (match:substring m 2) "\n"
-                         (match:substring m 3) ": "
-                         (match:substring m 4) "\n")))
-                    ("^(@ substituter-succeeded) (.*)"
-                     #:transform
-                     ,(lambda (m)
-                        (string-append
-                         (proc "Substituted " 'GREEN 'BOLD)
-                         (match:substring m 2) "\n")))
-                    ("^(starting phase )(.*)"
-                     BLUE GREEN)
-                    ("^(phase)(.*)(succeeded after)(.*)(seconds)(.*)"
-                     GREEN BLUE GREEN BLUE GREEN BLUE)
-                    ("^(phase)(.*)(failed after)(.*)(seconds)(.*)"
-                     RED BLUE RED BLUE RED BLUE))))
-      (lambda (str)
-        (let ((processed
-               (any (match-lambda
-                      ((pattern #:transform transform)
-                       (and=> (string-match pattern str)
-                              transform))
-                      ((pattern . colors)
-                       (and=> (string-match pattern str)
-                              (lambda (m)
-                                (let ((substrings
-                                       (map (cut match:substring m <>)
-                                            (iota (- (match:count m) 1) 1))))
-                                  (string-join (map proc substrings colors) ""))))))
-                    rules)))
-          (when spun?
-            (display (string #\backspace) port))
-          (if processed
-              (begin
-                (display processed port)
-                (set! spun? #f))
-              ;; Print unprocessed line, or replace with spinner
-              (display (if verbose? str (spin!)) port))))))
-  (make-soft-port
-   (vector
-    ;; procedure accepting one character for output
-    (cut write <> port)
-    ;; procedure accepting a string for output
-    handle-string
-    ;; thunk for flushing output
-    (lambda () (force-output port))
-    ;; thunk for getting one character
-    (const #t)
-    ;; thunk for closing port (not by garbage collection)
-    (lambda () (close port)))
-   "w"))
-
 ;;; ui.scm ends here
diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc
index c7f32494d0..b2c319f00b 100644
--- a/nix/libstore/build.cc
+++ b/nix/libstore/build.cc
@@ -2466,13 +2466,13 @@ void DerivationGoal::registerOutputs()
 
             /* Check the hash. */
             Hash h2 = recursive ? hashPath(ht, actualPath).first : hashFile(ht, actualPath);
-            if (h != h2)
-                throw BuildError(
-                    format("%1% hash mismatch for output path `%2%'\n"
-			   "  expected: %3%\n"
-			   "  actual:   %4%")
-                    % i->second.hashAlgo % path
-		    % printHash16or32(h) % printHash16or32(h2));
+            if (h != h2) {
+		if (settings.printBuildTrace)
+		    printMsg(lvlError, format("@ hash-mismatch %1% %2% %3% %4%")
+			     % path % i->second.hashAlgo
+			     % printHash16or32(h) % printHash16or32(h2));
+                throw BuildError(format("hash mismatch for store item '%1%'") % path);
+	    }
         }
 
         /* Get rid of all weird permissions.  This also checks that
@@ -3157,11 +3157,14 @@ void SubstitutionGoal::finished()
                 throw Error(format("unknown hash algorithm in `%1%'") % expectedHashStr);
             Hash expectedHash = parseHash16or32(hashType, string(expectedHashStr, n + 1));
             Hash actualHash = hashType == htSHA256 ? hash.first : hashPath(hashType, destPath).first;
-            if (expectedHash != actualHash)
-                throw SubstError(format("hash mismatch in downloaded path `%1%'\n"
-					"  expected: %2%\n"
-					"  actual:   %3%")
-                    % storePath % printHash(expectedHash) % printHash(actualHash));
+            if (expectedHash != actualHash) {
+		if (settings.printBuildTrace)
+		    printMsg(lvlError, format("@ hash-mismatch %1% %2% %3% %4%")
+			     % storePath % "sha256"
+			     % printHash16or32(expectedHash)
+			     % printHash16or32(actualHash));
+                throw SubstError(format("hash mismatch for substituted item `%1%'") % storePath);
+	    }
         }
 
     } catch (SubstError & e) {
diff --git a/nix/libstore/worker-protocol.hh b/nix/libstore/worker-protocol.hh
index efe9eadf23..103d60a8c2 100644
--- a/nix/libstore/worker-protocol.hh
+++ b/nix/libstore/worker-protocol.hh
@@ -6,7 +6,7 @@ namespace nix {
 #define WORKER_MAGIC_1 0x6e697863
 #define WORKER_MAGIC_2 0x6478696f
 
-#define PROTOCOL_VERSION 0x161
+#define PROTOCOL_VERSION 0x162
 #define GET_PROTOCOL_MAJOR(x) ((x) & 0xff00)
 #define GET_PROTOCOL_MINOR(x) ((x) & 0x00ff)
 
diff --git a/po/guix/POTFILES.in b/po/guix/POTFILES.in
index 2762ea078a..df2cf12de2 100644
--- a/po/guix/POTFILES.in
+++ b/po/guix/POTFILES.in
@@ -37,6 +37,7 @@ guix/scripts/container.scm
 guix/scripts/container/exec.scm
 guix/upstream.scm
 guix/ui.scm
+guix/status.scm
 guix/http-client.scm
 guix/nar.scm
 guix/channels.scm
diff --git a/tests/status.scm b/tests/status.scm
new file mode 100644
index 0000000000..04dedb702c
--- /dev/null
+++ b/tests/status.scm
@@ -0,0 +1,115 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (test-status)
+  #:use-module (guix status)
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-11)
+  #:use-module (srfi srfi-64))
+
+(test-begin "status")
+
+(test-equal "compute-status, no-op"
+  (build-status)
+  (let-values (((port get-status)
+                (build-event-output-port compute-status)))
+    (display "foo\nbar\n\baz\n" port)
+    (get-status)))
+
+(test-equal "compute-status, builds + substitutes"
+  (list (build-status
+         (building '("foo.drv"))
+         (downloading (list (download "bar" "http://example.org/bar"
+                                      #:size 500
+                                      #:start 'now))))
+        (build-status
+         (building '("foo.drv"))
+         (downloading (list (download "bar" "http://example.org/bar"
+                                      #:size 500
+                                      #:transferred 42
+                                      #:start 'now))))
+        (build-status
+         (builds-completed '("foo.drv"))
+         (downloads-completed (list (download "bar" "http://example.org/bar"
+                                              #:size 500
+                                              #:transferred 500
+                                              #:start 'now
+                                              #:end 'now)))))
+  (let-values (((port get-status)
+                (build-event-output-port (lambda (event status)
+                                           (compute-status event status
+                                                           #:current-time
+                                                           (const 'now))))))
+    (display "@ build-started foo.drv\n" port)
+    (display "@ substituter-started bar\n" port)
+    (display "@ download-started bar http://example.org/bar 500\n" port)
+    (display "various\nthings\nget\nwritten\n" port)
+    (let ((first (get-status)))
+      (display "@ download-progress bar http://example.org/bar 500 42\n"
+               port)
+      (let ((second (get-status)))
+        (display "@ download-progress bar http://example.org/bar 500 84\n"
+                 port)
+        (display "@ build-succeeded foo.drv\n" port)
+        (display "@ download-succeeded bar http://example.org/bar 500\n" port)
+        (display "Almost done!\n" port)
+        (display "@ substituter-succeeded bar\n" port)
+        (list first second (get-status))))))
+
+(test-equal "compute-status, missing events"
+  (list (build-status
+         (building '("foo.drv"))
+         (downloading (list (download "baz" "http://example.org/baz"
+                                      #:size 500
+                                      #:transferred 42
+                                      #:start 'now)
+                            (download "bar" "http://example.org/bar"
+                                      #:size 999
+                                      #:transferred 0
+                                      #:start 'now))))
+        (build-status
+         (builds-completed '("foo.drv"))
+         (downloads-completed (list (download "baz" "http://example.org/baz"
+                                              #:size 500
+                                              #:transferred 500
+                                              #:start 'now
+                                              #:end 'now)
+                                    (download "bar" "http://example.org/bar"
+                                              #:size 999
+                                              #:transferred 999
+                                              #:start 'now
+                                              #:end 'now)))))
+  ;; Below we omit 'substituter-started' events and the like.
+  (let-values (((port get-status)
+                (build-event-output-port (lambda (event status)
+                                           (compute-status event status
+                                                           #:current-time
+                                                           (const 'now))))))
+    (display "@ build-started foo.drv\n" port)
+    (display "@ download-started bar http://example.org/bar 999\n" port)
+    (display "various\nthings\nget\nwritten\n" port)
+    (display "@ download-progress baz http://example.org/baz 500 42\n"
+             port)
+    (let ((first (get-status)))
+      (display "@ build-succeeded foo.drv\n" port)
+      (display "@ download-succeeded bar http://example.org/bar 999\n" port)
+      (display "Almost done!\n" port)
+      (display "@ substituter-succeeded baz\n" port)
+      (list first (get-status)))))
+
+(test-end "status")

From 240a9c69a6064544a616acc521c993542c364948 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 12 Sep 2018 15:08:38 +0200
Subject: [PATCH 157/909] perform-download: Optionally report a
 "download-progress" trace.

* guix/scripts/perform-download.scm (perform-download): Add
 #:print-build-trace? and pass it to 'url-fetch'.
(guix-perform-download): Define 'print-build-trace?' and pass it to
'perform-download'.
* guix/build/download.scm (ftp-fetch): Add #:print-build-trace? and
honor it.
(url-fetch): Likewise.
* nix/libstore/builtins.cc (builtinDownload): Set _NIX_OPTIONS
environment variable.
---
 guix/build/download.scm           | 31 +++++++++++++++++++++----------
 guix/scripts/perform-download.scm | 18 +++++++++++++-----
 nix/libstore/builtins.cc          |  5 ++++-
 3 files changed, 38 insertions(+), 16 deletions(-)

diff --git a/guix/build/download.scm b/guix/build/download.scm
index 315a3554ec..54163849a2 100644
--- a/guix/build/download.scm
+++ b/guix/build/download.scm
@@ -115,7 +115,7 @@ and 'guix publish', something like
         (string-drop path 33)
         path)))
 
-(define* (ftp-fetch uri file #:key timeout)
+(define* (ftp-fetch uri file #:key timeout print-build-trace?)
   "Fetch data from URI and write it to FILE.  Return FILE on success.  Bail
 out if the connection could not be established in less than TIMEOUT seconds."
   (let* ((conn (match (and=> (uri-userinfo uri)
@@ -136,12 +136,17 @@ out if the connection could not be established in less than TIMEOUT seconds."
       (lambda (out)
         (dump-port* in out
                     #:buffer-size %http-receive-buffer-size
-                    #:reporter (progress-reporter/file
-                                (uri-abbreviation uri) size))))
+                    #:reporter
+                    (if print-build-trace?
+                        (progress-reporter/trace
+                         file (uri->string uri) size)
+                        (progress-reporter/file
+                         (uri-abbreviation uri) size)))))
 
-    (ftp-close conn))
-    (newline)
-  file)
+    (ftp-close conn)
+    (unless print-build-trace?
+      (newline))
+    file))
 
 ;; Autoload GnuTLS so that this module can be used even when GnuTLS is
 ;; not available.  At compile time, this yields "possibly unbound
@@ -723,7 +728,8 @@ Return a list of URIs."
                     #:key
                     (timeout 10) (verify-certificate? #t)
                     (mirrors '()) (content-addressed-mirrors '())
-                    (hashes '()))
+                    (hashes '())
+                    print-build-trace?)
   "Fetch FILE from URL; URL may be either a single string, or a list of
 string denoting alternate URLs for FILE.  Return #f on failure, and FILE
 on success.
@@ -759,13 +765,18 @@ otherwise simply ignore them."
             (lambda (output)
               (dump-port* port output
                           #:buffer-size %http-receive-buffer-size
-                          #:reporter (progress-reporter/file
-                                      (uri-abbreviation uri) size))
+                          #:reporter (if print-build-trace?
+                                         (progress-reporter/trace
+                                          file (uri->string uri) size)
+                                         (progress-reporter/file
+                                          (uri-abbreviation uri) size)))
               (newline)))
           file)))
       ((ftp)
        (false-if-exception* (ftp-fetch uri file
-                                       #:timeout timeout)))
+                                       #:timeout timeout
+                                       #:print-build-trace?
+                                       print-build-trace?)))
       (else
        (format #t "skipping URI with unsupported scheme: ~s~%"
                uri)
diff --git a/guix/scripts/perform-download.scm b/guix/scripts/perform-download.scm
index 9f6ecc00d2..df787a9940 100644
--- a/guix/scripts/perform-download.scm
+++ b/guix/scripts/perform-download.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,14 +41,14 @@
     (module-use! module (resolve-interface '(guix base32)))
     module))
 
-(define* (perform-download drv #:optional output)
+(define* (perform-download drv #:optional output
+                           #:key print-build-trace?)
   "Perform the download described by DRV, a fixed-output derivation, to
 OUTPUT.
 
 Note: Unless OUTPUT is #f, we don't read the value of 'out' in DRV since the
 actual output is different from that when we're doing a 'bmCheck' or
 'bmRepair' build."
-  ;; TODO: Use 'trace-progress-proc' when possible.
   (derivation-let drv ((url "url")
                        (output* "out")
                        (executable "executable")
@@ -68,6 +68,7 @@ actual output is different from that when we're doing a 'bmCheck' or
 
       ;; We're invoked by the daemon, which gives us write access to OUTPUT.
       (when (url-fetch url output
+                       #:print-build-trace? print-build-trace?
                        #:mirrors (if mirrors
                                      (call-with-input-file mirrors read)
                                      '())
@@ -99,6 +100,11 @@ allows us to sidestep bootstrapping problems, such downloading the source code
 of GnuTLS over HTTPS, before we have built GnuTLS.  See
 <http://bugs.gnu.org/22774>."
 
+  (define print-build-trace?
+    (match (getenv "_NIX_OPTIONS")
+      (#f #f)
+      (str (string-contains str "print-extended-build-trace=1"))))
+
   ;; This program must be invoked by guix-daemon under an unprivileged UID to
   ;; prevent things downloading from 'file:///etc/shadow' or arbitrary code
   ;; execution via the content-addressed mirror procedures.  (That means we
@@ -108,10 +114,12 @@ of GnuTLS over HTTPS, before we have built GnuTLS.  See
       (((? derivation-path? drv) (? store-path? output))
        (assert-low-privileges)
        (perform-download (read-derivation-from-file drv)
-                         output))
+                         output
+                         #:print-build-trace? print-build-trace?))
       (((? derivation-path? drv))                 ;backward compatibility
        (assert-low-privileges)
-       (perform-download (read-derivation-from-file drv)))
+       (perform-download (read-derivation-from-file drv)
+                         #:print-build-trace? print-build-trace?))
       (("--version")
        (show-version-and-exit))
       (x
diff --git a/nix/libstore/builtins.cc b/nix/libstore/builtins.cc
index a5ebb47737..1f52511c80 100644
--- a/nix/libstore/builtins.cc
+++ b/nix/libstore/builtins.cc
@@ -1,5 +1,5 @@
 /* GNU Guix --- Functional package management for GNU
-   Copyright (C) 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+   Copyright (C) 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 
    This file is part of GNU Guix.
 
@@ -47,6 +47,9 @@ static void builtinDownload(const Derivation &drv,
        content-addressed mirrors) works correctly.  */
     setenv("NIX_STORE", settings.nixStore.c_str(), 1);
 
+    /* Tell it about options such as "print-extended-build-trace".  */
+    setenv("_NIX_OPTIONS", settings.pack().c_str(), 1);
+
     /* XXX: Hack our way to use the 'download' script from 'LIBEXECDIR/guix'
        or just 'LIBEXECDIR', depending on whether we're running uninstalled or
        not.  */

From d4e9317b9de29f77eb8559bd99e0e2fe20d5f1fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 27 Sep 2018 23:46:44 +0200
Subject: [PATCH 158/909] tests: Update (guix build store-copy) tests.

This is a followup to a387b0bebb151a766ca6a454a891f2370c96703c.

* tests/gexp.scm ("gexp->derivation, store copy")
("gexp->derivation #:references-graphs"): Add (guix progress) and (guix
records) to the imported modules.
---
 tests/gexp.scm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/gexp.scm b/tests/gexp.scm
index 5d049cd5fc..813ea2ff6f 100644
--- a/tests/gexp.scm
+++ b/tests/gexp.scm
@@ -615,6 +615,8 @@
                                                 `(("graph" ,two))
                                                 #:modules
                                                 '((guix build store-copy)
+                                                  (guix progress)
+                                                  (guix records)
                                                   (guix sets)
                                                   (guix build utils))))
                          (ok? (built-derivations (list drv)))
@@ -817,6 +819,8 @@
        (two (gexp->derivation "two"
                               #~(symlink #$one #$output:chbouib)))
        (build -> (with-imported-modules '((guix build store-copy)
+                                          (guix progress)
+                                          (guix records)
                                           (guix sets)
                                           (guix build utils))
                    #~(begin

From 7fed9353ece5974ff431fa666a530da237a12085 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 27 Sep 2018 23:58:05 +0200
Subject: [PATCH 159/909] tests: Adjust services tests to new
 'shepherd-service-upgrade'.

This is a followup to 4245ddcbc9f935804c17c97872b90ec1050c2d75.

* tests/services.scm ("shepherd-service-upgrade: one unchanged, one upgraded, one new")
("shepherd-service-upgrade: service depended on is not unloaded")
("shepherd-service-upgrade: obsolete services that depend on each
other"): Adjust to changes in 'shepherd-service-upgrade'.
---
 tests/services.scm | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/tests/services.scm b/tests/services.scm
index 1ad577e601..5827dee80d 100644
--- a/tests/services.scm
+++ b/tests/services.scm
@@ -207,13 +207,14 @@
     list))
 
 (test-equal "shepherd-service-upgrade: one unchanged, one upgraded, one new"
-  '(((bar))                                       ;unload
-    ((bar) (baz)))                                ;load
+  '(()                                            ;unload
+    ((foo)))                                      ;restart
   (call-with-values
       (lambda ()
-        ;; Here 'foo' is not upgraded because it is still running, whereas
-        ;; 'bar' is upgraded because it is not currently running.  'baz' is
-        ;; loaded because it's a new service.
+        ;; Here 'foo' is replaced and must be explicitly restarted later
+        ;; because it is still running, whereas 'bar' is upgraded right away
+        ;; because it is not currently running.  'baz' is loaded because it's
+        ;; a new service.
         (shepherd-service-upgrade
          (list (live-service '(foo) '() #t)
                (live-service '(bar) '() #f)
@@ -224,30 +225,31 @@
                                  (start #t))
                (shepherd-service (provision '(baz))
                                  (start #t)))))
-    (lambda (unload load)
+    (lambda (unload restart)
       (list (map live-service-provision unload)
-            (map shepherd-service-provision load)))))
+            (map shepherd-service-provision restart)))))
 
 (test-equal "shepherd-service-upgrade: service depended on is not unloaded"
   '(((baz))                                       ;unload
-    ())                                           ;load
+    ((foo)))                                      ;restart
   (call-with-values
       (lambda ()
         ;; Service 'bar' is not among the target services; yet, it must not be
-        ;; unloaded because 'foo' depends on it.
+        ;; unloaded because 'foo' depends on it.  'foo' gets replaced but it
+        ;; must be restarted manually.
         (shepherd-service-upgrade
          (list (live-service '(foo) '(bar) #t)
                (live-service '(bar) '() #t)       ;still used!
                (live-service '(baz) '() #t))
          (list (shepherd-service (provision '(foo))
                                  (start #t)))))
-    (lambda (unload load)
+    (lambda (unload restart)
       (list (map live-service-provision unload)
-            (map shepherd-service-provision load)))))
+            (map shepherd-service-provision restart)))))
 
 (test-equal "shepherd-service-upgrade: obsolete services that depend on each other"
   '(((foo) (bar) (baz))                           ;unload
-    ((qux)))                                      ;load
+    ())                                           ;restart
   (call-with-values
       (lambda ()
         ;; 'foo', 'bar', and 'baz' depend on each other, but all of them are
@@ -258,9 +260,9 @@
                (live-service '(baz) '() #t))      ;obsolete
          (list (shepherd-service (provision '(qux))
                                  (start #t)))))
-    (lambda (unload load)
+    (lambda (unload restart)
       (list (map live-service-provision unload)
-            (map shepherd-service-provision load)))))
+            (map shepherd-service-provision restart)))))
 
 (test-eq "lookup-service-types"
   system-service-type

From c32863e094d3489d2e08ccb3188988d7c6410976 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 27 Sep 2018 23:38:36 +0200
Subject: [PATCH 160/909] gnu: sshuttle: Patch FHS assumptions.

Reported-By: Nam Nguyen <namn@berkeley.edu>

* gnu/packages/vpn.scm (sshuttle)[arguments]: Set correct paths to 'env'
and 'sh'.
---
 gnu/packages/vpn.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 85bbe7e9c6..de5df5039d 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -347,6 +347,17 @@ private network between hosts on the internet.")
         (base32
          "0pqk43kd7crqhg6qgnl8kapncwgw1xgaf02zarzypcw64kvdih9h"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-FHS-file-names
+           (lambda _
+             (substitute* "sshuttle/client.py"
+               (("/usr/bin/env") (which "env")))
+             (substitute* "sshuttle/ssh.py"
+               ;; Perhaps this is unreachable, but don't let's take risks.
+               (("/bin/sh") (which "sh")))
+             #t)))))
     (native-inputs
      `(("python-setuptools-scm" ,python-setuptools-scm)
        ;; For tests only.

From 697c5846651cbee20538d96446cc48adb8e2462a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 01:41:39 +0200
Subject: [PATCH 161/909] gnu: mbpfan: Update to 2.1.0.

* gnu/packages/linux.scm (mbpfan): Update to 2.1.0.
---
 gnu/packages/linux.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 2503676396..ba0022a8a6 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -4827,7 +4827,7 @@ interface to this kernel feature.")
 (define-public mbpfan
   (package
     (name "mbpfan")
-    (version "2.0.2")
+    (version "2.1.0")
     (source
      (origin
        (method url-fetch)
@@ -4836,10 +4836,10 @@ interface to this kernel feature.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0wifsws9icki95hhfh4zw1hmk07ddmkcz9mg5a9jr7q2kkrk01cx"))))
+         "1j44bpwv2zszih3cia9h7i7gb2gbfhzqh0s4kscbl7nplvyk3rlp"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f ; no tests
+     '(#:tests? #f                      ; tests ask to be run as root
        #:make-flags (let ((out (assoc-ref %outputs "out")))
                       (list (string-append "DESTDIR=" out)
                             "CC=gcc"))
@@ -4850,7 +4850,7 @@ interface to this kernel feature.")
              (substitute* "Makefile"
                (("/usr") ""))
              #t))
-         (delete 'configure)))) ; There's no configure phase.
+         (delete 'configure))))         ; there's no configure phase
     (home-page "https://github.com/dgraziotin/mbpfan")
     (synopsis "Control fan speed on Macbooks")
     (description

From 5478ab1ecea15b506c1c286af1aa8ec89f26aa10 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 01:44:50 +0200
Subject: [PATCH 162/909] gnu: mbpfan: Don't use unstable tarball.

* gnu/packages/linux.scm (mbpfan)[source]: Use GIT-FETCH and
GIT-FILE-NAME.
---
 gnu/packages/linux.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index ba0022a8a6..9e279b91e8 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -4830,13 +4830,14 @@ interface to this kernel feature.")
     (version "2.1.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/dgraziotin/mbpfan/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dgraziotin/mbpfan.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1j44bpwv2zszih3cia9h7i7gb2gbfhzqh0s4kscbl7nplvyk3rlp"))))
+         "1gysq778rkl6dvvj9a1swxcl15wvz0bng5bn4nwq118cl8p8pask"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f                      ; tests ask to be run as root

From a4764ff00afff0840fb7e92c73d5137281fbc4b9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 25 Sep 2018 10:55:40 +0200
Subject: [PATCH 163/909] gnu: python-fakeredis: Edit description.

* gnu/packages/databases.scm (python-fakeredis)[description]:
Fix (upstream) typo. Get carried away.
---
 gnu/packages/databases.scm | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 9e8c9d8f9e..9c966494ad 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2673,12 +2673,14 @@ parsing code in hiredis.  It primarily speeds up parsing of multi bulk replies."
      `(#:tests? #f))
     (home-page "https://github.com/jamesls/fakeredis")
     (synopsis "Fake implementation of redis API for testing purposes")
-    (description "Fakeredis is a pure python implementation of the redis-py
-python client that simulates talking to a redis server.  This was created for a
-single purpose: to write unittests.  Setting up redis is not hard, but many time
- you want to write unittests that do not talk to an external server (such as
-redis).  This module now allows tests to simply use this module as a reasonable
-substitute for redis.")
+    (description
+     "Fakeredis is a pure-Python implementation of the redis-py Python client
+that simulates talking to a redis server.  It was created for a single purpose:
+to write unit tests.
+
+Setting up redis is not hard, but one often wants to write unit tests that don't
+talk to an external server such as redis.  This module can be used as a
+reasonable substitute.")
     (license license:bsd-3)))
 
 (define-public python2-fakeredis

From 5abcb1b0e6fe849d206b3683444c76d91f21a3d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 28 Sep 2018 00:29:25 +0200
Subject: [PATCH 164/909] gnu: guix: Update to 7fed935.

* gnu/packages/package-management.scm (guix): Update to 7fed935.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 3bc8ac6073..69788c9463 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -101,8 +101,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "0.15.0")
-        (commit "3d43017026f9995ad128915db8ca5eafe061bf75")
-        (revision 3))
+        (commit "7fed9353ece5974ff431fa666a530da237a12085")
+        (revision 4))
     (package
       (name "guix")
 
@@ -118,7 +118,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "167rzz2h33xmmchkplwzfq94s5jwdn5nabsq2lb84s54ps0sm89m"))
+                  "11j13xszjcrf3barf38bixx3hbrfj5w81fskjp8gn6m42knx1yal"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

From 7edfcd61a1d42f8e1f21c8e7b46d5d61aaeb4598 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 28 Sep 2018 14:22:11 +0200
Subject: [PATCH 165/909] gnu: httpd: Update to 2.4.35.

* gnu/packages/web.scm (httpd): Update to 2.4.35.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 2251daabf7..8e776258b3 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -124,14 +124,14 @@
 (define-public httpd
   (package
     (name "httpd")
-    (version "2.4.34")
+    (version "2.4.35")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://apache/httpd/httpd-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "1w1q2smdgf6ln0x741lk5pv5r0gzrxj2iza1vslhifzy65bcjlzs"))))
+               "0mlvwsm7hmpc7db6lfc2nx3v4cll3qljjxhjhgsw6aniskywc1r6"))))
     (build-system gnu-build-system)
     (native-inputs `(("pcre" ,pcre "bin")))       ;for 'pcre-config'
     (inputs `(("apr" ,apr)

From 29bdfe1367af34a0b9cf33f7ab021a23206c4bd7 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 28 Sep 2018 10:06:32 -0400
Subject: [PATCH 166/909] gnu: Krita: Update to 4.1.3.

* gnu/packages/kde.scm (krita): Update to 4.1.3.
---
 gnu/packages/kde.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm
index aa5be6b515..a835f42749 100644
--- a/gnu/packages/kde.scm
+++ b/gnu/packages/kde.scm
@@ -236,7 +236,7 @@ plugins, as well as code to create plugins, or complete applications.")
 (define-public krita
   (package
     (name "krita")
-    (version "4.1.1")
+    (version "4.1.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -245,7 +245,7 @@ plugins, as well as code to create plugins, or complete applications.")
                     "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1qz9bjvnwa5gc2b0063i2p72jq6y1b6kgqdj39599acp7ws11asw"))))
+                "0d546dxs552z0pxnaka1jm7ksravw17f777wf593z0pl4ds8dgdx"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f

From 4353981eb095459c47a9e12950745ac0304162ae Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 26 Sep 2018 01:45:05 +0200
Subject: [PATCH 167/909] tests: Add missing copyright statement.

This is a follow-up to commit 3b97a1779f3b65d582b8edc8c154b6414314b946.

* gnu/tests/web.scm: Update copyright header.
---
 gnu/tests/web.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/tests/web.scm b/gnu/tests/web.scm
index bcc919137b..2e209fee97 100644
--- a/gnu/tests/web.scm
+++ b/gnu/tests/web.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;

From 87c39618719374f7f3cb0dc81c8ab587773c4c66 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 26 Sep 2018 19:06:38 +0200
Subject: [PATCH 168/909] gnu: newsboat: Update to 2.13.

* gnu/packages/syndication.scm (newsboat): Update to 2.13.
---
 gnu/packages/syndication.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index 6247d1f3b6..a7c685fdc1 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -35,7 +35,7 @@
 (define-public newsboat
   (package
     (name "newsboat")
-    (version "2.12")
+    (version "2.13")
     (source
      (origin
        (method url-fetch)
@@ -43,7 +43,7 @@
                            "/newsboat-" version ".tar.xz"))
        (sha256
         (base32
-         "1x23zlgljaqf46v7sp8wnkyf6wighvirvn48ankpa34yr8mvrgcv"))))
+         "0pik1d98ydzqi6055vdbkjg5krwifbk2hy2f5jp5p1wcy2s16dn7"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)

From c6b772a059da1f47a0561ca915f43c1399ee8c65 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 26 Sep 2018 19:09:45 +0200
Subject: [PATCH 169/909] gnu: rng-tools: Update home page.

* gnu/packages/linux.scm (rng-tools)[home-page]: Set to URL mentioned in
legacy wiki.
---
 gnu/packages/linux.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 9e279b91e8..a6efded72d 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3668,6 +3668,7 @@ The collection contains a set of bandwidth and latency benchmark such as:
 (define-public rng-tools
   (package
     (name "rng-tools")
+    (home-page "https://github.com/nhorman/rng-tools")
     (version "6.4")
     (source (origin
               (method url-fetch)
@@ -3691,7 +3692,6 @@ The collection contains a set of bandwidth and latency benchmark such as:
     (description
      "Monitor a hardware random number generator, and supply entropy
 from that to the system kernel's @file{/dev/random} machinery.")
-    (home-page "https://sourceforge.net/projects/gkernel")
     ;; The source package is offered under the GPL2+, but the files
     ;; 'rngd_rdrand.c' and 'rdrand_asm.S' are only available under the GPL2.
     (license (list license:gpl2 license:gpl2+))))

From f289820c31f0d493caaa6d1d9fac7750176ba492 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 26 Sep 2018 19:13:07 +0200
Subject: [PATCH 170/909] gnu: rng-tools: Don't use unstable tarball.

* gnu/packages/linux.scm (rng-tools)[source]: Use GIT-FETCH.
---
 gnu/packages/linux.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index a6efded72d..a3c2c4c946 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3671,13 +3671,13 @@ The collection contains a set of bandwidth and latency benchmark such as:
     (home-page "https://github.com/nhorman/rng-tools")
     (version "6.4")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/nhorman/rng-tools/"
-                                  "archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference (url home-page)
+                                  (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "005krksl8iz37l5p1nx8apl1yg7q78yrsb6inby31d2g5ck8nnwa"))))
+                "10r8vy240q04xx6j48qm063w0ssp0dkxchvq6x3fwd9bwp8m3sj7"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Avoid using OpenSSL, curl, and libxml2, reducing the closure by 166 MiB.

From 31f0fc612fe0baf949c647138cba7217b60cae26 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 26 Sep 2018 19:13:53 +0200
Subject: [PATCH 171/909] gnu: rng-tools: Update to 6.5.

* gnu/packages/linux.scm (rng-tools): Update to 6.5.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index a3c2c4c946..cb8203da0b 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3669,7 +3669,7 @@ The collection contains a set of bandwidth and latency benchmark such as:
   (package
     (name "rng-tools")
     (home-page "https://github.com/nhorman/rng-tools")
-    (version "6.4")
+    (version "6.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference (url home-page)
@@ -3677,7 +3677,7 @@ The collection contains a set of bandwidth and latency benchmark such as:
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "10r8vy240q04xx6j48qm063w0ssp0dkxchvq6x3fwd9bwp8m3sj7"))))
+                "11kw1rcgzmgzwk7g1w2g0nzjraqb0pf24gxpy50k4ls2qxslw3rk"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Avoid using OpenSSL, curl, and libxml2, reducing the closure by 166 MiB.

From 02817df07e965c3413e6986966b3e607de47709c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 27 Sep 2018 20:38:18 +0200
Subject: [PATCH 172/909] gnu: libreoffice: Update to 6.1.2.1.

* gnu/packages/libreoffice.scm (libreoffice): Update to 6.1.2.1.
---
 gnu/packages/libreoffice.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 35d49b0216..68b4e265f3 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -926,7 +926,7 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
 (define-public libreoffice
   (package
     (name "libreoffice")
-    (version "6.1.0.3")
+    (version "6.1.2.1")
     (source
      (origin
        (method url-fetch)
@@ -936,7 +936,7 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
          (version-prefix version 3) "/libreoffice-" version ".tar.xz"))
        (sha256
         (base32
-         "1n7b6abc0bp9x8lddx60w5br444wf62mdlkqmfk2zmkmiwkcvv2l"))
+         "149ziasibplihfxlzafzcm4737ns30hg9175967b43c81yv5f335"))
        (patches (search-patches "libreoffice-icu.patch"
                                 "libreoffice-glm.patch"))))
     (build-system gnu-build-system)

From 595af457aedb887c5fb4409f2fbaf4d23c059024 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Fri, 13 Jul 2018 20:39:34 +0100
Subject: [PATCH 173/909] gnu: Modify the gitolite package to support the Guix
 service.

Previously the gitolite package worked, but there were problems using it for
the service where you might have a minimal PATH. This commit patches the
source and scripts where possible to use store paths, and also wraps the
gitolite script to handle the harder dependencies.

* gnu/packages/version-control.scm (gitolite)[arguments]: Add more patching to
the patch-scripts phase, and add two new phases (patch-source and
wrap-scripts).
[inputs]: Add coreutils, findutils and inetutils.
---
 gnu/packages/version-control.scm | 53 +++++++++++++++++++++++++++++++-
 1 file changed, 52 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 204ec403f6..d06055de45 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1031,12 +1031,48 @@ also walk each side of a merge and test those changes individually.")
                           ((" perl -")
                            (string-append " " perl " -")))
 
+                        (substitute* (find-files "src/triggers" ".*")
+                          ((" sed ")
+                           (string-append " " (which "sed") " ")))
+
+                        (substitute*
+                            '("src/triggers/post-compile/update-gitweb-access-list"
+                              "src/triggers/post-compile/ssh-authkeys-split"
+                              "src/triggers/upstream")
+                          ((" grep ")
+                           (string-append " " (which "grep") " ")))
+
                         ;; Avoid references to the store in authorized_keys.
                         ;; This works because gitolite-shell is in the PATH.
                         (substitute* "src/triggers/post-compile/ssh-authkeys"
                           (("\\$glshell \\$user")
                            "gitolite-shell $user"))
                         #t)))
+                  (add-before 'install 'patch-source
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      ;; Gitolite uses cat to test the readability of the
+                      ;; pubkey
+                      (substitute* "src/lib/Gitolite/Setup.pm"
+                        (("\"cat ")
+                         (string-append "\"" (which "cat") " "))
+                        (("\"ssh-keygen")
+                         (string-append "\"" (which "ssh-keygen"))))
+
+                      (substitute* '("src/lib/Gitolite/Hooks/PostUpdate.pm"
+                                     "src/lib/Gitolite/Hooks/Update.pm")
+                        (("/usr/bin/perl")
+                         (string-append (assoc-ref inputs "perl")
+                                        "/bin/perl")))
+
+                      (substitute* "src/lib/Gitolite/Common.pm"
+                        (("\"ssh-keygen")
+                         (string-append "\"" (which "ssh-keygen")))
+                        (("\"logger\"")
+                         (string-append "\""
+                                        (assoc-ref inputs "inetutils")
+                                        "/bin/logger\"")))
+
+                      #t))
                   (replace 'install
                     (lambda* (#:key outputs #:allow-other-keys)
                       (let* ((output (assoc-ref outputs "out"))
@@ -1050,9 +1086,24 @@ also walk each side of a merge and test those changes individually.")
                                     (symlink (string-append sharedir "/" script)
                                              (string-append bindir "/" script)))
                                   '("gitolite" "gitolite-shell"))
+                        #t)))
+                  (add-after 'install 'wrap-scripts
+                    (lambda* (#:key inputs outputs #:allow-other-keys)
+                      (let ((out (assoc-ref outputs "out"))
+                            (coreutils (assoc-ref inputs "coreutils"))
+                            (findutils (assoc-ref inputs "findutils"))
+                            (git (assoc-ref inputs "git")))
+                        (wrap-program (string-append out "/bin/gitolite")
+                          `("PATH" ":" prefix
+                            ,(map (lambda (dir)
+                                    (string-append dir "/bin"))
+                                  (list out coreutils findutils git))))
                         #t))))))
     (inputs
-     `(("perl" ,perl)))
+     `(("perl" ,perl)
+       ("coreutils" ,coreutils)
+       ("findutils" ,findutils)
+       ("inetutils" ,inetutils)))
     ;; git and openssh are propagated because trying to patch the source via
     ;; regexp matching is too brittle and prone to false positives.
     (propagated-inputs

From 258a6d944ed891fa92fa87a16731e5dfe0bac477 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Fri, 13 Jul 2018 20:39:46 +0100
Subject: [PATCH 174/909] services: Add Gitolite.

* gnu/services/version-control.scm (<gitolite-configuration>,
<gitolite-rc-file>): New record types.
(gitolite-accounts, gitolite-activation): New procedures.
(gitolite-service-type): New variables.
* gnu/tests/version-control.scm (%gitolite-test-admin-keypair, %gitolite-os,
%test-gitolite): New variables.
(run-gitolite-test): New procedure.
* doc/guix.texi (Version Control): Document the gitolite service.
---
 doc/guix.texi                    |  94 ++++++++++++++++
 gnu/services/version-control.scm | 179 ++++++++++++++++++++++++++++++-
 gnu/tests/version-control.scm    | 114 +++++++++++++++++++-
 3 files changed, 385 insertions(+), 2 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index e1046eb512..94bb0ec4e1 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -21028,6 +21028,100 @@ could instantiate a cgit service like this:
           (cgitrc "")))
 @end example
 
+@subsubheading Gitolite Service
+
+@cindex Gitolite service
+@cindex Git, hosting
+@uref{http://gitolite.com/gitolite/, Gitolite} is a tool for hosting Git
+repositories on a central server.
+
+Gitolite can handle multiple repositories and users, and supports flexible
+configuration of the permissions for the users on the repositories.
+
+The following example will configure Gitolite using the default @code{git}
+user, and the provided SSH public key.
+
+@example
+(service gitolite-service-type
+         (gitolite-configuration
+           (admin-pubkey (plain-file
+                           "yourname.pub"
+                           "ssh-rsa AAAA... guix@@example.com"))))
+@end example
+
+Gitolite is configured through a special admin repository which you can clone,
+for example, if you setup Gitolite on @code{example.com}, you would run the
+following command to clone the admin repository.
+
+@example
+git clone git@@example.com:gitolite-admin
+@end example
+
+When the Gitolite service is activated, the provided @code{admin-pubkey} will
+be inserted in to the @file{keydir} directory in the gitolite-admin
+repository.  If this results in a change in the repository, it will be
+committed using the message ``gitolite setup by GNU Guix''.
+
+@deftp {Data Type} gitolite-configuration
+Data type representing the configuration for @code{gitolite-service-type}.
+
+@table @asis
+@item @code{package} (default: @var{gitolite})
+Gitolite package to use.
+
+@item @code{user} (default: @var{git})
+User to use for Gitolite.  This will be user that you use when accessing
+Gitolite over SSH.
+
+@item @code{group} (default: @var{git})
+Group to use for Gitolite.
+
+@item @code{home-directory} (default: @var{"/var/lib/gitolite"})
+Directory in which to store the Gitolite configuration and repositories.
+
+@item @code{rc-file} (default: @var{(gitolite-rc-file)})
+A ``file-like'' object (@pxref{G-Expressions, file-like objects}),
+representing the configuration for Gitolite.
+
+@item @code{admin-pubkey} (default: @var{#f})
+A ``file-like'' object (@pxref{G-Expressions, file-like objects}) used to
+setup Gitolite.  This will be inserted in to the @file{keydir} directory
+within the gitolite-admin repository.
+
+To specify the SSH key as a string, use the @code{plain-file} function.
+
+@example
+(plain-file "yourname.pub" "ssh-rsa AAAA... guix@@example.com")
+@end example
+
+@end table
+@end deftp
+
+@deftp {Data Type} gitolite-rc-file
+Data type representing the Gitolite RC file.
+
+@table @asis
+@item @code{umask} (default: @code{#o0077})
+This controls the permissions Gitolite sets on the repositories and their
+contents.
+
+A value like @code{#o0027} will give read access to the group used by Gitolite
+(by default: @code{git}). This is necessary when using Gitolite with software
+like cgit or gitweb.
+
+@item @code{git-config-keys} (default: @code{""})
+Gitolite allows you to set git config values using the "config" keyword. This
+setting allows control over the config keys to accept.
+
+@item @code{roles} (default: @code{'(("READERS" . 1) ("WRITERS" . ))})
+Set the role names allowed to be used by users running the perms command.
+
+@item @code{enable} (default: @code{'("help" "desc" "info" "perms" "writable" "ssh-authkeys" "git-config" "daemon" "gitweb")})
+This setting controls the commands and features to enable within Gitolite.
+
+@end table
+@end deftp
+
 
 @node Game Services
 @subsubsection Game Services
diff --git a/gnu/services/version-control.scm b/gnu/services/version-control.scm
index 58274c8bee..cc8cd22021 100644
--- a/gnu/services/version-control.scm
+++ b/gnu/services/version-control.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -40,7 +41,23 @@
 
             git-http-configuration
             git-http-configuration?
-            git-http-nginx-location-configuration))
+            git-http-nginx-location-configuration
+
+            <gitolite-configuration>
+            gitolite-configuration
+            gitolite-configuration-package
+            gitolite-configuration-user
+            gitolite-configuration-rc-file
+            gitolite-configuration-admin-pubkey
+
+            <gitolite-rc-file>
+            gitolite-rc-file
+            gitolite-rc-file-umask
+            gitolite-rc-file-git-config-keys
+            gitolite-rc-file-roles
+            gitolite-rc-file-enable
+
+            gitolite-service-type))
 
 ;;; Commentary:
 ;;;
@@ -197,3 +214,163 @@ access to exported repositories under @file{/srv/git}."
             "")
         (list "fastcgi_param GIT_PROJECT_ROOT " git-root ";")
         "fastcgi_param PATH_INFO $1;"))))))
+
+
+;;;
+;;; Gitolite
+;;;
+
+(define-record-type* <gitolite-rc-file>
+  gitolite-rc-file make-gitolite-rc-file
+  gitolite-rc-file?
+  (umask           gitolite-rc-file-umask
+                   (default #o0077))
+  (git-config-keys gitolite-rc-file-git-config-keys
+                   (default ""))
+  (roles           gitolite-rc-file-roles
+                   (default '(("READERS" . 1)
+                              ("WRITERS" . 1))))
+  (enable          gitolite-rc-file-enable
+                   (default '("help"
+                              "desc"
+                              "info"
+                              "perms"
+                              "writable"
+                              "ssh-authkeys"
+                              "git-config"
+                              "daemon"
+                              "gitweb"))))
+
+(define-gexp-compiler (gitolite-rc-file-compiler
+                       (file <gitolite-rc-file>) system target)
+  (match file
+    (($ <gitolite-rc-file> umask git-config-keys roles enable)
+     (apply text-file* "gitolite.rc"
+      `("%RC = (\n"
+        "    UMASK => " ,(format #f "~4,'0o" umask) ",\n"
+        "    GIT_CONFIG_KEYS => '" ,git-config-keys "',\n"
+        "    ROLES => {\n"
+        ,@(map (match-lambda
+                 ((role . value)
+                  (simple-format #f "        ~A => ~A,\n" role value)))
+               roles)
+        "    },\n"
+        "\n"
+        "    ENABLE => [\n"
+        ,@(map (lambda (value)
+                 (simple-format #f "        '~A',\n" value))
+               enable)
+        "    ],\n"
+        ");\n"
+        "\n"
+        "1;\n")))))
+
+(define-record-type* <gitolite-configuration>
+  gitolite-configuration make-gitolite-configuration
+  gitolite-configuration?
+  (package        gitolite-configuration-package
+                  (default gitolite))
+  (user           gitolite-configuration-user
+                  (default "git"))
+  (group          gitolite-configuration-group
+                  (default "git"))
+  (home-directory gitolite-configuration-home-directory
+                  (default "/var/lib/gitolite"))
+  (rc-file        gitolite-configuration-rc-file
+                  (default (gitolite-rc-file)))
+  (admin-pubkey   gitolite-configuration-admin-pubkey))
+
+(define gitolite-accounts
+  (match-lambda
+    (($ <gitolite-configuration> package user group home-directory
+                                 rc-file admin-pubkey)
+     ;; User group and account to run Gitolite.
+     (list (user-group (name user) (system? #t))
+           (user-account
+            (name user)
+            (group group)
+            (system? #t)
+            (comment "Gitolite user")
+            (home-directory home-directory))))))
+
+(define gitolite-activation
+  (match-lambda
+    (($ <gitolite-configuration> package user group home
+                                 rc-file admin-pubkey)
+     #~(begin
+         (use-modules (ice-9 match)
+                      (guix build utils))
+
+         (let* ((user-info (getpwnam #$user))
+                (admin-pubkey #$admin-pubkey)
+                (pubkey-file (string-append
+                              #$home "/"
+                              (basename
+                               (strip-store-file-name admin-pubkey)))))
+
+           (simple-format #t "guix: gitolite: installing ~A\n" #$rc-file)
+           (copy-file #$rc-file #$(string-append home "/.gitolite.rc"))
+
+           ;; The key must be writable, so copy it from the store
+           (copy-file admin-pubkey pubkey-file)
+
+           (chmod pubkey-file #o500)
+           (chown pubkey-file
+                  (passwd:uid user-info)
+                  (passwd:gid user-info))
+
+           ;; Set the git configuration, to avoid gitolite trying to use
+           ;; the hostname command, as the network might not be up yet
+           (with-output-to-file #$(string-append home "/.gitconfig")
+             (lambda ()
+               (display "[user]
+        name = GNU Guix
+        email = guix@localhost
+")))
+           ;; Run Gitolite setup, as this updates the hooks and include the
+           ;; admin pubkey if specified. The admin pubkey is required for
+           ;; initial setup, and will replace the previous key if run after
+           ;; initial setup
+           (match (primitive-fork)
+             (0
+              ;; Exit with a non-zero status code if an exception is thrown.
+              (dynamic-wind
+                (const #t)
+                (lambda ()
+                  (setenv "HOME" (passwd:dir user-info))
+                  (setenv "USER" #$user)
+                  (setgid (passwd:gid user-info))
+                  (setuid (passwd:uid user-info))
+                  (primitive-exit
+                   (system* #$(file-append package "/bin/gitolite")
+                            "setup"
+                            "-m" "gitolite setup by GNU Guix"
+                            "-pk" pubkey-file)))
+                (lambda ()
+                  (primitive-exit 1))))
+             (pid (waitpid pid)))
+
+           (when (file-exists? pubkey-file)
+             (delete-file pubkey-file)))))))
+
+(define gitolite-service-type
+  (service-type
+   (name 'gitolite)
+   (extensions
+    (list (service-extension activation-service-type
+                             gitolite-activation)
+          (service-extension account-service-type
+                             gitolite-accounts)
+          (service-extension profile-service-type
+                             ;; The Gitolite package in Guix uses
+                             ;; gitolite-shell in the authorized_keys file, so
+                             ;; gitolite-shell needs to be on the PATH for
+                             ;; gitolite to work.
+                             (lambda (config)
+                               (list
+                                (gitolite-configuration-package config))))))
+   (description
+    "Setup @command{gitolite}, a Git hosting tool providing access over SSH..
+By default, the @code{git} user is used, but this is configurable.
+Additionally, Gitolite can integrate with with tools like gitweb or cgit to
+provide a web interface to view selected repositories.")))
diff --git a/gnu/tests/version-control.scm b/gnu/tests/version-control.scm
index 3b935a1b48..4409b8a12b 100644
--- a/gnu/tests/version-control.scm
+++ b/gnu/tests/version-control.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2017, 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,14 +28,17 @@
   #:use-module (gnu services)
   #:use-module (gnu services version-control)
   #:use-module (gnu services cgit)
+  #:use-module (gnu services ssh)
   #:use-module (gnu services web)
   #:use-module (gnu services networking)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages ssh)
   #:use-module (guix gexp)
   #:use-module (guix store)
   #:use-module (guix modules)
   #:export (%test-cgit
-            %test-git-http))
+            %test-git-http
+            %test-gitolite))
 
 (define README-contents
   "Hello!  This is what goes inside the 'README' file.")
@@ -300,3 +304,111 @@ HTTP-PORT."
    (name "git-http")
    (description "Connect to a running Git HTTP server.")
    (value (run-git-http-test))))
+
+
+;;;
+;;; Gitolite.
+;;;
+
+(define %gitolite-test-admin-keypair
+  (computed-file
+   "gitolite-test-admin-keypair"
+   (with-imported-modules (source-module-closure
+                           '((guix build utils)))
+     #~(begin
+         (use-modules (ice-9 match) (srfi srfi-26)
+                      (guix build utils))
+
+         (mkdir #$output)
+         (invoke #$(file-append openssh "/bin/ssh-keygen")
+                 "-f" (string-append #$output "/test-admin")
+                 "-t" "rsa"
+                 "-q"
+                 "-N" "")))))
+
+(define %gitolite-os
+  (simple-operating-system
+   (dhcp-client-service)
+   (service openssh-service-type)
+   (service gitolite-service-type
+            (gitolite-configuration
+             (admin-pubkey
+              (file-append %gitolite-test-admin-keypair "/test-admin.pub"))))))
+
+(define (run-gitolite-test)
+  (define os
+    (marionette-operating-system
+     %gitolite-os
+     #:imported-modules '((gnu services herd)
+                          (guix combinators))))
+
+  (define vm
+    (virtual-machine
+     (operating-system os)
+     (port-forwardings `((2222 . 22)))))
+
+  (define test
+    (with-imported-modules '((gnu build marionette)
+                             (guix build utils))
+      #~(begin
+          (use-modules (srfi srfi-64)
+                       (rnrs io ports)
+                       (gnu build marionette)
+                       (guix build utils))
+
+          (define marionette
+            (make-marionette (list #$vm)))
+
+          (mkdir #$output)
+          (chdir #$output)
+
+          (test-begin "gitolite")
+
+          ;; Wait for sshd to be up and running.
+          (test-assert "service running"
+            (marionette-eval
+             '(begin
+                (use-modules (gnu services herd))
+                (start-service 'ssh-daemon))
+             marionette))
+
+          (display #$%gitolite-test-admin-keypair)
+
+          (setenv "GIT_SSH_VARIANT" "ssh")
+          (setenv "GIT_SSH_COMMAND"
+                  (string-join
+                   '(#$(file-append openssh "/bin/ssh")
+                     "-i" #$(file-append %gitolite-test-admin-keypair
+                                         "/test-admin")
+                     "-o" "UserKnownHostsFile=/dev/null"
+                     "-o" "StrictHostKeyChecking=no")))
+
+          (test-assert "cloning the admin repository"
+            (invoke #$(file-append git "/bin/git")
+                    "clone" "-v"
+                    "ssh://git@localhost:2222/gitolite-admin"
+                    "/tmp/clone"))
+
+          (test-assert "admin key exists"
+            (file-exists? "/tmp/clone/keydir/test-admin.pub"))
+
+          (with-directory-excursion "/tmp/clone"
+            (invoke #$(file-append git "/bin/git")
+                    "-c" "user.name=Guix" "-c" "user.email=guix"
+                    "commit"
+                    "-m" "Test commit"
+                    "--allow-empty")
+
+            (test-assert "pushing, and the associated hooks"
+              (invoke #$(file-append git "/bin/git") "push")))
+
+          (test-end)
+          (exit (= (test-runner-fail-count (test-runner-current)) 0)))))
+
+  (gexp->derivation "gitolite" test))
+
+(define %test-gitolite
+  (system-test
+   (name "gitolite")
+   (description "Clone the Gitolite admin repository.")
+   (value (run-gitolite-test))))

From fb94d82bc2dc8eec35520bc2b6101ab8aaf0a4a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 28 Sep 2018 23:19:13 +0200
Subject: [PATCH 175/909] status: Be more defensive when looking for a log
 file.

* guix/store.scm (derivation-log-file): New procedure.o
(log-file): Use it.
* guix/status.scm (print-build-event): Use 'derivation-log-file' instead
of 'log-file'.  Check wheter the return value is #f.
---
 guix/status.scm | 14 ++++++++------
 guix/store.scm  | 28 +++++++++++++++++-----------
 2 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/guix/status.scm b/guix/status.scm
index 94d4748af5..afa3c656a8 100644
--- a/guix/status.scm
+++ b/guix/status.scm
@@ -24,10 +24,7 @@
   #:autoload   (guix build syscalls) (terminal-columns)
   #:use-module ((guix build download)
                 #:select (nar-uri-abbreviation))
-  #:use-module ((guix store)
-                #:select (current-build-output-port
-                          current-store-protocol-version
-                          log-file))
+  #:use-module (guix store)
   #:use-module (guix derivations)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-9)
@@ -334,8 +331,13 @@ addition to build events."
     (('build-failed drv . _)
      (format port (failure (G_ "build of ~a failed")) drv)
      (newline port)
-     (format port (info (G_ "View build log at '~a'.~%"))
-             (log-file #f drv)))
+     (match (derivation-log-file drv)
+       (#f
+        (format port (failure (G_ "Could not find build log for '~a'."))
+                drv))
+       (log
+        (format port (info (G_ "View build log at '~a'.")) log)))
+     (newline port))
     (('substituter-started item _ ...)
      (when (or print-log? (not (extended-build-trace-supported?)))
        (format port (info (G_ "substituting ~a...")) item)
diff --git a/guix/store.scm b/guix/store.scm
index 7785a53aa1..8b35fc8d7a 100644
--- a/guix/store.scm
+++ b/guix/store.scm
@@ -152,6 +152,7 @@
             store-path-package-name
             store-path-hash-part
             direct-store-path
+            derivation-log-file
             log-file))
 
 (define %protocol-version #x162)
@@ -1706,21 +1707,26 @@ syntactically valid store path."
                 (and (string-every %nix-base32-charset hash)
                      hash))))))
 
+(define (derivation-log-file drv)
+  "Return the build log file for DRV, a derivation file name, or #f if it
+could not be found."
+  (let* ((base    (basename drv))
+         (log     (string-append (dirname %state-directory) ; XXX
+                                 "/log/guix/drvs/"
+                                 (string-take base 2) "/"
+                                 (string-drop base 2)))
+         (log.gz  (string-append log ".gz"))
+         (log.bz2 (string-append log ".bz2")))
+    (cond ((file-exists? log.gz) log.gz)
+          ((file-exists? log.bz2) log.bz2)
+          ((file-exists? log) log)
+          (else #f))))
+
 (define (log-file store file)
   "Return the build log file for FILE, or #f if none could be found.  FILE
 must be an absolute store file name, or a derivation file name."
   (cond ((derivation-path? file)
-         (let* ((base    (basename file))
-                (log     (string-append (dirname %state-directory) ; XXX
-                                        "/log/guix/drvs/"
-                                        (string-take base 2) "/"
-                                        (string-drop base 2)))
-                (log.gz  (string-append log ".gz"))
-                (log.bz2 (string-append log ".bz2")))
-           (cond ((file-exists? log.gz) log.gz)
-                 ((file-exists? log.bz2) log.bz2)
-                 ((file-exists? log) log)
-                 (else #f))))
+         (derivation-log-file file))
         (else
          (match (valid-derivers store file)
            ((derivers ...)

From ccccb467fb5dec58023717c7ec2699f2955f0d62 Mon Sep 17 00:00:00 2001
From: Jack Hill <jackhill@jackhill.us>
Date: Fri, 28 Sep 2018 11:18:01 -0400
Subject: [PATCH 176/909] gnu: mcabber: Update to 1.1.0
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/messaging.scm (mcabber): Update to 1.1.0

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/messaging.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 9b1aea788c..af67c922b4 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -1385,7 +1385,7 @@ protocol allows.")
 (define-public mcabber
   (package
     (name "mcabber")
-    (version "1.0.5")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
@@ -1393,7 +1393,7 @@ protocol allows.")
                            name "-" version ".tar.bz2"))
        (sha256
         (base32
-         "0ixdzk5b3s31a4bdfqgqrsiq7vbgdzhqr49p9pz9cq9bgn0h1wm0"))))
+         "1ggh865p1rf10ffsnf4g6qv9i8bls36dxdb1nzs5r9vdqci2rz04"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags (list "--enable-otr"

From 1dc876a39f39b963fbad7af9e38f62d45256432a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 28 Sep 2018 23:34:09 +0200
Subject: [PATCH 177/909] status: Tweak colorization.

* guix/status.scm (colorize-log-line): Add "\<" before "FAIL" (to
distinguish from "XFAIL".
Use MAGENTA instead of ORANGE, which doesn't exist.
---
 guix/status.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/guix/status.scm b/guix/status.scm
index afa3c656a8..b19f0199d1 100644
--- a/guix/status.scm
+++ b/guix/status.scm
@@ -275,10 +275,10 @@ on."
     GREEN    BOLD GREEN          RESET  GREEN  BLUE)
    ("^(phase)(.*)(failed after)(.*)(seconds)(.*)"
     RED BLUE RED BLUE RED BLUE)
-   ("^(.*)(error|fail|failed|FAIL|FAILED)([[:blank:]]*)(:)(.*)"
+   ("^(.*)(error|fail|failed|\\<FAIL|FAILED)([[:blank:]]*)(:)(.*)"
     RESET  RED                           BOLD         BOLD BOLD)
    ("^(.*)(warning)([[:blank:]]*)(:)(.*)"
-    RESET  ORANGE   BOLD        BOLD BOLD)))
+    RESET  MAGENTA   BOLD        BOLD BOLD)))
 
 (define* (print-build-event event old-status status
                             #:optional (port (current-error-port))

From be7c64ba2d82f6d800ad6577ff8e9e6306071977 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 23 Sep 2018 22:36:15 +0200
Subject: [PATCH 178/909] gnu: Add tegola.

* gnu/packages/geo.scm (tegola): New variable.
---
 gnu/packages/geo.scm | 46 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index ae6ba024e0..5641c742b4 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -26,6 +26,7 @@
 (define-module (gnu packages geo)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix build-system scons)
   #:use-module (guix build-system r)
@@ -760,3 +761,48 @@ location queries to be run in SQL.")
                license:bsd-3 ; files only say "BSD"
                ;; doc
                license:cc-by-sa3.0))))
+
+(define-public tegola
+  (package
+    (name "tegola")
+    (version "0.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                     "https://github.com/go-spatial/tegola/archive/v"
+                     version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "09vnzxfn0r70kmd776kcdfqxhzdj11syxa0b27z4ci1k367v7viw"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/go-spatial/tegola/cmd/tegola"
+       #:unpack-path "github.com/go-spatial"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'set-version
+           (lambda _
+             (with-directory-excursion
+               (string-append "src/github.com/go-spatial/tegola-" ,version)
+               (substitute* '("cmd/tegola/cmd/root.go"
+                              "cmd/tegola_lambda/main.go")
+                 (("version not set") ,version)))
+             #t))
+         (add-before 'build 'rename-import
+           (lambda _
+             (rename-file (string-append "src/github.com/go-spatial/tegola-" ,version)
+                          "src/github.com/go-spatial/tegola")
+             #t)))))
+    (home-page "http://tegola.io")
+    (synopsis "Vector tile server for maps")
+    (description "Tegola is a free vector tile server written in Go.  Tegola
+takes geospatial data and slices it into vector tiles that can be efficiently
+delivered to any client.")
+    (license (list
+               license:expat
+               ;; Some packages in vendor have other licenses
+               license:asl2.0
+               license:bsd-2
+               license:bsd-3
+               license:wtfpl2))))

From 3bd7611e4acbffc501f8cabdbf581ffc442ee72a Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 23 Sep 2018 22:36:45 +0200
Subject: [PATCH 179/909] gnu: Add imposm3.

* gnu/packages/geo.scm (imposm3): New variable.
---
 gnu/packages/geo.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 5641c742b4..c5b5dbcfd0 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -806,3 +806,47 @@ delivered to any client.")
                license:bsd-2
                license:bsd-3
                license:wtfpl2))))
+
+(define-public imposm3
+  (package
+    (name "imposm3")
+    (version "0.6.0-alpha.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/omniscale/imposm3/archive/v"
+                            version ".tar.gz"))
+    (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "06f0kwmv52yd5m9jlckqxqmkf0cnqy3hamakrvg9lspplyqrds80"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/omniscale/imposm3/cmd/imposm"
+       #:unpack-path "github.com/omniscale"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'rename-import
+           (lambda _
+             (rename-file (string-append "src/github.com/omniscale/imposm3-" ,version)
+                          "src/github.com/omniscale/imposm3")
+             #t))
+         (add-before 'build 'set-version
+           (lambda _
+             (substitute* "src/github.com/omniscale/imposm3/version.go"
+               (("0.0.0-dev") ,version))
+             #t)))))
+    (inputs
+     `(("geos" ,geos)
+       ("leveldb" ,leveldb)))
+    (home-page "https://imposm.org/")
+    (synopsis "OpenStreetMap importer for PostGIS")
+    (description "Imposm is an importer for OpenStreetMap data.  It reads PBF
+files and imports the data into PostgreSQL/PostGIS databases.  It is designed
+to create databases that are optimized for rendering/tile/map-services.")
+    (license (list
+               license:asl2.0
+               ;; Some dependencies in vendor have different licenses
+               license:expat
+               license:bsd-2
+               license:bsd-3))))

From 8fa3451c6fd56373555e2ada00f3978e1eed32a0 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 27 Sep 2018 22:16:31 +0200
Subject: [PATCH 180/909] gnu: Add protozero.

* gnu/packages/geo.scm (protozero): New variable.
---
 gnu/packages/geo.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index c5b5dbcfd0..dda981c90a 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -24,6 +24,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages geo)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
@@ -850,3 +851,26 @@ to create databases that are optimized for rendering/tile/map-services.")
                license:expat
                license:bsd-2
                license:bsd-3))))
+
+(define-public protozero
+  (package
+    (name "protozero")
+    (version "1.6.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/mapbox/protozero/archive/v"
+                            version ".tar.gz"))
+    (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "1xaj4phz1r7xn0vgdfvfkz8b0bizgb6mavjky1zqcvdmbwgwgly5"))))
+    (build-system cmake-build-system)
+    (home-page "https://github.com/mapbox/protozero")
+    (synopsis "Minimalistic protocol buffer decoder and encoder in C++")
+    (description "Protozero is a minimalistic protocol buffer decored and
+encoder in C++.  The developer using protozero has to manually translate the
+@file{.proto} description into code.")
+    (license (list
+               license:asl2.0; for folly
+               license:bsd-2))))

From 889e94e343b0784598134b333cc328ed41f387ba Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 27 Sep 2018 22:38:32 +0200
Subject: [PATCH 181/909] gnu: Add libosmium.

* gnu/packages/geo.scm (libosmium): New variable.
---
 gnu/packages/geo.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index dda981c90a..990c2a6b02 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -39,6 +39,8 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages documentation)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages glib)
@@ -874,3 +876,34 @@ encoder in C++.  The developer using protozero has to manually translate the
     (license (list
                license:asl2.0; for folly
                license:bsd-2))))
+
+(define-public libosmium
+  (package
+    (name "libosmium")
+    (version "2.14.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/osmcode/libosmium/archive/v"
+                version ".tar.gz"))
+    (file-name (string-append name "-" version ".tar.gz"))
+        (sha256
+         (base32
+          "0d9b46qiw7zkw1h9lygjdwqxnbhm3c7v8kydzw9f9f778cyagc94"))))
+    (build-system cmake-build-system)
+    (propagated-inputs
+     `(("boost" ,boost)
+       ("expat" ,expat)
+       ("gdal" ,gdal)
+       ("geos" ,geos)
+       ("proj.4" ,proj.4)
+       ("protozero" ,protozero)
+       ("sparsehash" ,sparsehash)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("doxygen" ,doxygen)))
+    (home-page "https://osmcode.org/libosmium/")
+    (synopsis "C++ library for working with OpenStreetMap data")
+    (description "Libosmium is a fast and flexible C++ library for working with
+OpenStreetMap data.")
+    (license license:boost1.0)))

From b0e2299ad8164b986ae0f9081dad30f3332c91e5 Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Sun, 23 Sep 2018 22:37:17 +0200
Subject: [PATCH 182/909] gnu: Add osm2pgsql.

* gnu/packages/geo.scm (osm2pgsql): New variable.
---
 gnu/packages/geo.scm | 48 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 990c2a6b02..9644bf9d9e 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -48,6 +48,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages image)
   #:use-module (gnu packages icu4c)
+  #:use-module (gnu packages lua)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
@@ -907,3 +908,50 @@ encoder in C++.  The developer using protozero has to manually translate the
     (description "Libosmium is a fast and flexible C++ library for working with
 OpenStreetMap data.")
     (license license:boost1.0)))
+
+(define-public osm2pgsql
+  (package
+    (name "osm2pgsql")
+    (version "0.96.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/openstreetmap/osm2pgsql/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "08y7776r4l9v9177a4q6cfdri0lpirky96m6g699hwl7v1vhw0mn"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "contrib/protozero")
+                  (delete-file-recursively "contrib/libosmium")
+                  #t))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f; tests fail because we need to setup a database
+       #:configure-flags
+       (list (string-append "-DOSMIUM_INCLUDE_DIR="
+                            (assoc-ref %build-inputs "libosmium")
+                            "/include")
+             (string-append "-DPROTOZERO_INCLUDE_DIR="
+                            (assoc-ref %build-inputs "protozero")
+                            "/include"))))
+    (inputs
+     `(("boost" ,boost)
+       ("expat" ,expat)
+       ("libosmium" ,libosmium)
+       ("lua" ,lua)
+       ("postgresql" ,postgresql)
+       ("proj.4" ,proj.4)
+       ("protozero" ,protozero)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("python-2" ,python-2)
+       ("python2-psycopg2" ,python2-psycopg2)))
+    (home-page "https://github.com/openstreetmap/osm2pgsql")
+    (synopsis "OSM data importer to postgresql")
+    (description "Osm2pgsql is a tool for loading OpenStreetMap data into a
+PostgreSQL / PostGIS database suitable for applications like rendering into a
+map, geocoding with Nominatim, or general analysis.")
+    (license license:gpl2+)))

From 6f91223fd4889301a099f75ecc855031a300fcfe Mon Sep 17 00:00:00 2001
From: Julien Lepiller <julien@lepiller.eu>
Date: Thu, 27 Sep 2018 22:12:46 +0200
Subject: [PATCH 183/909] gnu: Add tippecanoe.

* gnu/packages/geo.scm (tippecanoe): New variable.
---
 gnu/packages/geo.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 9644bf9d9e..4275476e34 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -955,3 +955,34 @@ OpenStreetMap data.")
 PostgreSQL / PostGIS database suitable for applications like rendering into a
 map, geocoding with Nominatim, or general analysis.")
     (license license:gpl2+)))
+
+(define-public tippecanoe
+  (package
+    (name "tippecanoe")
+    (version "1.31.5")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/mapbox/tippecanoe/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1057na1dkgjaryr7jr15lqkxpam111d3l5zdpdkqzzzpxmdjxqcf"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases (delete 'configure))
+       #:test-target "test"
+       #:make-flags
+       (list "CC=gcc"
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))))
+    (inputs
+     `(("perl" ,perl)
+       ("sqlite" ,sqlite)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/mapbox/tippecanoe")
+    (synopsis "Vector tile server for maps")
+    (description "Tippecanoe creates scale-independent view of data, so that
+the texture and density of features is visible at every zoom level, instead of
+dropping features at lower levels.")
+    (license license:bsd-2)))

From bfb22078fd3a184f60968938851ada97d7dead58 Mon Sep 17 00:00:00 2001
From: fis trivial <ybbs.daans@hotmail.com>
Date: Sat, 29 Sep 2018 04:05:15 +0000
Subject: [PATCH 184/909] gnu: pocl: Update to 1.2.

* gnu/packages/opencl.scm (pocl): Update to 1.2.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/opencl.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm
index d32e696438..da979253b0 100644
--- a/gnu/packages/opencl.scm
+++ b/gnu/packages/opencl.scm
@@ -294,23 +294,23 @@ back-end for the LLVM compiler framework.")
 (define-public pocl
   (package
     (name "pocl")
-    (version "1.1")
+    (version "1.2")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/pocl/pocl.git")
              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
        (sha256
-        (base32 "1z3sqn20ddv1030adchpzs65qng436gc2mb99p213mkh95jkh1l5"))))
+        (base32 "0fyiwd9nrqhl0jsac0bx17p9acpfzhyxp50mmp28mzn7psb9qidg"))
+       (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (native-inputs
      `(("libltdl" ,libltdl)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("clang" ,clang)
-       ("hwloc" ,hwloc "lib")
+       ("hwloc" ,hwloc-2.0 "lib")
        ("llvm" ,llvm)
        ("ocl-icd" ,ocl-icd)))
     (arguments

From 81e69ba85d6f613b4ff900f6aa50a8a2386ee271 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 29 Sep 2018 11:57:53 -0400
Subject: [PATCH 185/909] gnu: BIND: Update to 9.12.2-P2.

* gnu/packages/dns.scm (isc-bind): Update to 9.12.2-P2.
---
 gnu/packages/dns.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index 00135294be..4fc1c25229 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -104,7 +104,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
 (define-public isc-bind
   (package
     (name "bind")
-    (version "9.12.2-P1")
+    (version "9.12.2-P2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -112,7 +112,7 @@ and BOOTP/TFTP for network booting of diskless machines.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "192ld6w8f4n46hvdmmzzrfkd28apf4dwmbpbi3j2q1d2p315ajww"))))
+                "0gk9vwqlbdmn10m21f2awvmiccfbadvcwi8zsgm91awbx4k7h0l7"))))
     (build-system gnu-build-system)
     (outputs `("out" "utils"))
     (inputs

From 2a1267d3d7dbce9bf2c16ea5972eb7ee4717cf67 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 29 Sep 2018 11:58:59 -0400
Subject: [PATCH 186/909] gnu: isc-dhcp: Update bundled BIND to 9.11.4-P2.

* gnu/packages/admin.scm (isc-dhcp)[inputs]: Update bundled BIND to 9.11.4-P2.
---
 gnu/packages/admin.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index ded7ce3b97..a0ab431ddd 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -613,7 +613,7 @@ connection alive.")
          (bind-minor-version "11")
          (bind-patch-version "4")
          (bind-release-type "-P")         ; for patch release, use "-P"
-         (bind-release-version "1")      ; for patch release, e.g. "6"
+         (bind-release-version "2")      ; for patch release, e.g. "6"
          (bind-version (string-append bind-major-version
                                       "."
                                       bind-minor-version
@@ -730,7 +730,7 @@ connection alive.")
                                         "/bind-" bind-version ".tar.gz"))
                     (sha256
                      (base32
-                      "08zyy13b8ydfbg26b3y6mw299qs89ba90gymraqqjsgjicydrq5h"))))
+                      "04fq17zksd2b3w6w6padps5n7b6s2lasxpksbhl4378h56vgfnm8"))))
 
                 ;; When cross-compiling, we need the cross Coreutils and sed.
                 ;; Otherwise just use those from %FINAL-INPUTS.

From 44fa365e7774a31bc98adff4e87430a3d1e19e26 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 29 Sep 2018 15:55:23 -0400
Subject: [PATCH 187/909] gnu: linux-libre@4.4: Update to 4.4.159.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.159.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index cb8203da0b..dbe00b567f 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -452,8 +452,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.158"
-                    "1l3blfaw50a8l9bp735vzsmk1naq4l40qidza10dwkkrd2ip3n41"
+  (make-linux-libre "4.4.159"
+                    "12wrhni1ikmakwv55cgzsznx9llzp82irsisbjjs7bc8z2hzwr6l"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 63e98a4c416957e08bf3d267f52c780f4c6b84f2 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 29 Sep 2018 15:56:16 -0400
Subject: [PATCH 188/909] gnu: linux-libre@4.9: Update to 4.9.130.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.130.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index dbe00b567f..de13a36a36 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.129"
-                    "0y7p1xgbpn4nmr5pmqb58shr54lvryr5rxwm9m66knwzj332f3rh"
+  (make-linux-libre "4.9.130"
+                    "1l3ra1pbgz0wbpp1ci90sj9x9iamvagx1vdbdfbmpjsgh1cfnpmq"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 92011cbf7eb73469cae4478701ef3a1171841d52 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 29 Sep 2018 15:56:49 -0400
Subject: [PATCH 189/909] gnu: linux-libre@4.14: Update to 4.14.73.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.73.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index de13a36a36..042e7fd280 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.72")
-(define %linux-libre-4.14-hash "1ngz5p8mvga45y1n6hbw6niy0ji5mfl4vc3bxlckjg42dcp5qf64")
+(define %linux-libre-4.14-version "4.14.73")
+(define %linux-libre-4.14-hash "0s2aphqgasx0lnprb2hzaqgbcd5i9774gfyhz5a6sqj6dygr00xy")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From e72ca4111fce4b05bf2a685e451f26e06680e36c Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 29 Sep 2018 15:58:27 -0400
Subject: [PATCH 190/909] gnu: linux-libre: Update to 4.18.11.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.11.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 042e7fd280..ec2520cdff 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.10")
-(define %linux-libre-hash "1znc6kh3j8plmxail6hn2ss0r0fvbcp50s3xv5gxys7jc7k42znj")
+(define %linux-libre-version "4.18.11")
+(define %linux-libre-hash "1r4yf7gr7rf8igkg5jv781wa8vn6ii7fsdnffyshin1slnxbd79k")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch

From 17bea1803cf706d8db053d8d73302a4455684d29 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sat, 29 Sep 2018 21:18:45 -0400
Subject: [PATCH 191/909] Revert "services: Add Gitolite."

This reverts commit 258a6d944ed891fa92fa87a16731e5dfe0bac477.
---
 doc/guix.texi                    |  94 ----------------
 gnu/services/version-control.scm | 179 +------------------------------
 gnu/tests/version-control.scm    | 114 +-------------------
 3 files changed, 2 insertions(+), 385 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 94bb0ec4e1..e1046eb512 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -21028,100 +21028,6 @@ could instantiate a cgit service like this:
           (cgitrc "")))
 @end example
 
-@subsubheading Gitolite Service
-
-@cindex Gitolite service
-@cindex Git, hosting
-@uref{http://gitolite.com/gitolite/, Gitolite} is a tool for hosting Git
-repositories on a central server.
-
-Gitolite can handle multiple repositories and users, and supports flexible
-configuration of the permissions for the users on the repositories.
-
-The following example will configure Gitolite using the default @code{git}
-user, and the provided SSH public key.
-
-@example
-(service gitolite-service-type
-         (gitolite-configuration
-           (admin-pubkey (plain-file
-                           "yourname.pub"
-                           "ssh-rsa AAAA... guix@@example.com"))))
-@end example
-
-Gitolite is configured through a special admin repository which you can clone,
-for example, if you setup Gitolite on @code{example.com}, you would run the
-following command to clone the admin repository.
-
-@example
-git clone git@@example.com:gitolite-admin
-@end example
-
-When the Gitolite service is activated, the provided @code{admin-pubkey} will
-be inserted in to the @file{keydir} directory in the gitolite-admin
-repository.  If this results in a change in the repository, it will be
-committed using the message ``gitolite setup by GNU Guix''.
-
-@deftp {Data Type} gitolite-configuration
-Data type representing the configuration for @code{gitolite-service-type}.
-
-@table @asis
-@item @code{package} (default: @var{gitolite})
-Gitolite package to use.
-
-@item @code{user} (default: @var{git})
-User to use for Gitolite.  This will be user that you use when accessing
-Gitolite over SSH.
-
-@item @code{group} (default: @var{git})
-Group to use for Gitolite.
-
-@item @code{home-directory} (default: @var{"/var/lib/gitolite"})
-Directory in which to store the Gitolite configuration and repositories.
-
-@item @code{rc-file} (default: @var{(gitolite-rc-file)})
-A ``file-like'' object (@pxref{G-Expressions, file-like objects}),
-representing the configuration for Gitolite.
-
-@item @code{admin-pubkey} (default: @var{#f})
-A ``file-like'' object (@pxref{G-Expressions, file-like objects}) used to
-setup Gitolite.  This will be inserted in to the @file{keydir} directory
-within the gitolite-admin repository.
-
-To specify the SSH key as a string, use the @code{plain-file} function.
-
-@example
-(plain-file "yourname.pub" "ssh-rsa AAAA... guix@@example.com")
-@end example
-
-@end table
-@end deftp
-
-@deftp {Data Type} gitolite-rc-file
-Data type representing the Gitolite RC file.
-
-@table @asis
-@item @code{umask} (default: @code{#o0077})
-This controls the permissions Gitolite sets on the repositories and their
-contents.
-
-A value like @code{#o0027} will give read access to the group used by Gitolite
-(by default: @code{git}). This is necessary when using Gitolite with software
-like cgit or gitweb.
-
-@item @code{git-config-keys} (default: @code{""})
-Gitolite allows you to set git config values using the "config" keyword. This
-setting allows control over the config keys to accept.
-
-@item @code{roles} (default: @code{'(("READERS" . 1) ("WRITERS" . ))})
-Set the role names allowed to be used by users running the perms command.
-
-@item @code{enable} (default: @code{'("help" "desc" "info" "perms" "writable" "ssh-authkeys" "git-config" "daemon" "gitweb")})
-This setting controls the commands and features to enable within Gitolite.
-
-@end table
-@end deftp
-
 
 @node Game Services
 @subsubsection Game Services
diff --git a/gnu/services/version-control.scm b/gnu/services/version-control.scm
index cc8cd22021..58274c8bee 100644
--- a/gnu/services/version-control.scm
+++ b/gnu/services/version-control.scm
@@ -3,7 +3,6 @@
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
-;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,23 +40,7 @@
 
             git-http-configuration
             git-http-configuration?
-            git-http-nginx-location-configuration
-
-            <gitolite-configuration>
-            gitolite-configuration
-            gitolite-configuration-package
-            gitolite-configuration-user
-            gitolite-configuration-rc-file
-            gitolite-configuration-admin-pubkey
-
-            <gitolite-rc-file>
-            gitolite-rc-file
-            gitolite-rc-file-umask
-            gitolite-rc-file-git-config-keys
-            gitolite-rc-file-roles
-            gitolite-rc-file-enable
-
-            gitolite-service-type))
+            git-http-nginx-location-configuration))
 
 ;;; Commentary:
 ;;;
@@ -214,163 +197,3 @@ access to exported repositories under @file{/srv/git}."
             "")
         (list "fastcgi_param GIT_PROJECT_ROOT " git-root ";")
         "fastcgi_param PATH_INFO $1;"))))))
-
-
-;;;
-;;; Gitolite
-;;;
-
-(define-record-type* <gitolite-rc-file>
-  gitolite-rc-file make-gitolite-rc-file
-  gitolite-rc-file?
-  (umask           gitolite-rc-file-umask
-                   (default #o0077))
-  (git-config-keys gitolite-rc-file-git-config-keys
-                   (default ""))
-  (roles           gitolite-rc-file-roles
-                   (default '(("READERS" . 1)
-                              ("WRITERS" . 1))))
-  (enable          gitolite-rc-file-enable
-                   (default '("help"
-                              "desc"
-                              "info"
-                              "perms"
-                              "writable"
-                              "ssh-authkeys"
-                              "git-config"
-                              "daemon"
-                              "gitweb"))))
-
-(define-gexp-compiler (gitolite-rc-file-compiler
-                       (file <gitolite-rc-file>) system target)
-  (match file
-    (($ <gitolite-rc-file> umask git-config-keys roles enable)
-     (apply text-file* "gitolite.rc"
-      `("%RC = (\n"
-        "    UMASK => " ,(format #f "~4,'0o" umask) ",\n"
-        "    GIT_CONFIG_KEYS => '" ,git-config-keys "',\n"
-        "    ROLES => {\n"
-        ,@(map (match-lambda
-                 ((role . value)
-                  (simple-format #f "        ~A => ~A,\n" role value)))
-               roles)
-        "    },\n"
-        "\n"
-        "    ENABLE => [\n"
-        ,@(map (lambda (value)
-                 (simple-format #f "        '~A',\n" value))
-               enable)
-        "    ],\n"
-        ");\n"
-        "\n"
-        "1;\n")))))
-
-(define-record-type* <gitolite-configuration>
-  gitolite-configuration make-gitolite-configuration
-  gitolite-configuration?
-  (package        gitolite-configuration-package
-                  (default gitolite))
-  (user           gitolite-configuration-user
-                  (default "git"))
-  (group          gitolite-configuration-group
-                  (default "git"))
-  (home-directory gitolite-configuration-home-directory
-                  (default "/var/lib/gitolite"))
-  (rc-file        gitolite-configuration-rc-file
-                  (default (gitolite-rc-file)))
-  (admin-pubkey   gitolite-configuration-admin-pubkey))
-
-(define gitolite-accounts
-  (match-lambda
-    (($ <gitolite-configuration> package user group home-directory
-                                 rc-file admin-pubkey)
-     ;; User group and account to run Gitolite.
-     (list (user-group (name user) (system? #t))
-           (user-account
-            (name user)
-            (group group)
-            (system? #t)
-            (comment "Gitolite user")
-            (home-directory home-directory))))))
-
-(define gitolite-activation
-  (match-lambda
-    (($ <gitolite-configuration> package user group home
-                                 rc-file admin-pubkey)
-     #~(begin
-         (use-modules (ice-9 match)
-                      (guix build utils))
-
-         (let* ((user-info (getpwnam #$user))
-                (admin-pubkey #$admin-pubkey)
-                (pubkey-file (string-append
-                              #$home "/"
-                              (basename
-                               (strip-store-file-name admin-pubkey)))))
-
-           (simple-format #t "guix: gitolite: installing ~A\n" #$rc-file)
-           (copy-file #$rc-file #$(string-append home "/.gitolite.rc"))
-
-           ;; The key must be writable, so copy it from the store
-           (copy-file admin-pubkey pubkey-file)
-
-           (chmod pubkey-file #o500)
-           (chown pubkey-file
-                  (passwd:uid user-info)
-                  (passwd:gid user-info))
-
-           ;; Set the git configuration, to avoid gitolite trying to use
-           ;; the hostname command, as the network might not be up yet
-           (with-output-to-file #$(string-append home "/.gitconfig")
-             (lambda ()
-               (display "[user]
-        name = GNU Guix
-        email = guix@localhost
-")))
-           ;; Run Gitolite setup, as this updates the hooks and include the
-           ;; admin pubkey if specified. The admin pubkey is required for
-           ;; initial setup, and will replace the previous key if run after
-           ;; initial setup
-           (match (primitive-fork)
-             (0
-              ;; Exit with a non-zero status code if an exception is thrown.
-              (dynamic-wind
-                (const #t)
-                (lambda ()
-                  (setenv "HOME" (passwd:dir user-info))
-                  (setenv "USER" #$user)
-                  (setgid (passwd:gid user-info))
-                  (setuid (passwd:uid user-info))
-                  (primitive-exit
-                   (system* #$(file-append package "/bin/gitolite")
-                            "setup"
-                            "-m" "gitolite setup by GNU Guix"
-                            "-pk" pubkey-file)))
-                (lambda ()
-                  (primitive-exit 1))))
-             (pid (waitpid pid)))
-
-           (when (file-exists? pubkey-file)
-             (delete-file pubkey-file)))))))
-
-(define gitolite-service-type
-  (service-type
-   (name 'gitolite)
-   (extensions
-    (list (service-extension activation-service-type
-                             gitolite-activation)
-          (service-extension account-service-type
-                             gitolite-accounts)
-          (service-extension profile-service-type
-                             ;; The Gitolite package in Guix uses
-                             ;; gitolite-shell in the authorized_keys file, so
-                             ;; gitolite-shell needs to be on the PATH for
-                             ;; gitolite to work.
-                             (lambda (config)
-                               (list
-                                (gitolite-configuration-package config))))))
-   (description
-    "Setup @command{gitolite}, a Git hosting tool providing access over SSH..
-By default, the @code{git} user is used, but this is configurable.
-Additionally, Gitolite can integrate with with tools like gitweb or cgit to
-provide a web interface to view selected repositories.")))
diff --git a/gnu/tests/version-control.scm b/gnu/tests/version-control.scm
index 4409b8a12b..3b935a1b48 100644
--- a/gnu/tests/version-control.scm
+++ b/gnu/tests/version-control.scm
@@ -2,7 +2,6 @@
 ;;; Copyright © 2017, 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
-;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,17 +27,14 @@
   #:use-module (gnu services)
   #:use-module (gnu services version-control)
   #:use-module (gnu services cgit)
-  #:use-module (gnu services ssh)
   #:use-module (gnu services web)
   #:use-module (gnu services networking)
   #:use-module (gnu packages version-control)
-  #:use-module (gnu packages ssh)
   #:use-module (guix gexp)
   #:use-module (guix store)
   #:use-module (guix modules)
   #:export (%test-cgit
-            %test-git-http
-            %test-gitolite))
+            %test-git-http))
 
 (define README-contents
   "Hello!  This is what goes inside the 'README' file.")
@@ -304,111 +300,3 @@ HTTP-PORT."
    (name "git-http")
    (description "Connect to a running Git HTTP server.")
    (value (run-git-http-test))))
-
-
-;;;
-;;; Gitolite.
-;;;
-
-(define %gitolite-test-admin-keypair
-  (computed-file
-   "gitolite-test-admin-keypair"
-   (with-imported-modules (source-module-closure
-                           '((guix build utils)))
-     #~(begin
-         (use-modules (ice-9 match) (srfi srfi-26)
-                      (guix build utils))
-
-         (mkdir #$output)
-         (invoke #$(file-append openssh "/bin/ssh-keygen")
-                 "-f" (string-append #$output "/test-admin")
-                 "-t" "rsa"
-                 "-q"
-                 "-N" "")))))
-
-(define %gitolite-os
-  (simple-operating-system
-   (dhcp-client-service)
-   (service openssh-service-type)
-   (service gitolite-service-type
-            (gitolite-configuration
-             (admin-pubkey
-              (file-append %gitolite-test-admin-keypair "/test-admin.pub"))))))
-
-(define (run-gitolite-test)
-  (define os
-    (marionette-operating-system
-     %gitolite-os
-     #:imported-modules '((gnu services herd)
-                          (guix combinators))))
-
-  (define vm
-    (virtual-machine
-     (operating-system os)
-     (port-forwardings `((2222 . 22)))))
-
-  (define test
-    (with-imported-modules '((gnu build marionette)
-                             (guix build utils))
-      #~(begin
-          (use-modules (srfi srfi-64)
-                       (rnrs io ports)
-                       (gnu build marionette)
-                       (guix build utils))
-
-          (define marionette
-            (make-marionette (list #$vm)))
-
-          (mkdir #$output)
-          (chdir #$output)
-
-          (test-begin "gitolite")
-
-          ;; Wait for sshd to be up and running.
-          (test-assert "service running"
-            (marionette-eval
-             '(begin
-                (use-modules (gnu services herd))
-                (start-service 'ssh-daemon))
-             marionette))
-
-          (display #$%gitolite-test-admin-keypair)
-
-          (setenv "GIT_SSH_VARIANT" "ssh")
-          (setenv "GIT_SSH_COMMAND"
-                  (string-join
-                   '(#$(file-append openssh "/bin/ssh")
-                     "-i" #$(file-append %gitolite-test-admin-keypair
-                                         "/test-admin")
-                     "-o" "UserKnownHostsFile=/dev/null"
-                     "-o" "StrictHostKeyChecking=no")))
-
-          (test-assert "cloning the admin repository"
-            (invoke #$(file-append git "/bin/git")
-                    "clone" "-v"
-                    "ssh://git@localhost:2222/gitolite-admin"
-                    "/tmp/clone"))
-
-          (test-assert "admin key exists"
-            (file-exists? "/tmp/clone/keydir/test-admin.pub"))
-
-          (with-directory-excursion "/tmp/clone"
-            (invoke #$(file-append git "/bin/git")
-                    "-c" "user.name=Guix" "-c" "user.email=guix"
-                    "commit"
-                    "-m" "Test commit"
-                    "--allow-empty")
-
-            (test-assert "pushing, and the associated hooks"
-              (invoke #$(file-append git "/bin/git") "push")))
-
-          (test-end)
-          (exit (= (test-runner-fail-count (test-runner-current)) 0)))))
-
-  (gexp->derivation "gitolite" test))
-
-(define %test-gitolite
-  (system-test
-   (name "gitolite")
-   (description "Clone the Gitolite admin repository.")
-   (value (run-gitolite-test))))

From 3b362c8a8366b55a172817d7c347098accd3d56b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 30 Sep 2018 13:37:06 +0300
Subject: [PATCH 192/909] gnu: mtools: Update to 4.0.19.

* gnu/packages/mtools.scm (mtools): Update to 4.0.19.
---
 gnu/packages/mtools.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/mtools.scm b/gnu/packages/mtools.scm
index f49a035b41..e4750f579f 100644
--- a/gnu/packages/mtools.scm
+++ b/gnu/packages/mtools.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,7 +28,7 @@
 (define-public mtools
   (package
     (name "mtools")
-    (version "4.0.18")
+    (version "4.0.19")
     (source
      (origin
       (method url-fetch)
@@ -35,7 +36,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "1hxciksv7av5ilnkvwbidyxxr1gzn24lr0mz9z8drkml7780im1h"))))
+        "003qnj4rs22v2sih3is55scvav8xq9p1dp5b7gnyl67a60ky516r"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/mtools/")
     (synopsis "Access MS-DOS disks without mounting")

From cebec8bd1ca3871dead210c2e8404e3f5cec8ab7 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 30 Sep 2018 15:46:46 +0300
Subject: [PATCH 193/909] gnu: font-culmus: Update to 0.133.

* gnu/packages/fonts.scm (font-culmus): Update to 0.133.
---
 gnu/packages/fonts.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 218b04baa1..6d4abc637b 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1210,7 +1210,7 @@ ExtraLight, Light, Book, Medium, Semibold, Bold & ExtraBold")
 (define-public font-culmus
   (package
     (name "font-culmus")
-    (version "0.132")
+    (version "0.133")
     (source
      (origin
        (method url-fetch)
@@ -1219,7 +1219,7 @@ ExtraLight, Light, Book, Medium, Semibold, Bold & ExtraBold")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1djxalm26r7bcq33ckmfa15xfs6pmqzvcl64d5lqa1dl01bl4j4z"))))
+         "02akysgsqhi15cck54xcacm16q5raf4l7shgb8fnj7xr3c1pbfyp"))))
     (build-system font-build-system)
     (arguments
      `(#:phases

From f2bc53af70eea7b7147b9e7e40280941866ed128 Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Sun, 30 Sep 2018 14:08:42 -0400
Subject: [PATCH 194/909] gnu: Add porechop.

* gnu/packages/bioinformatics.scm (porechop): New variable.
---
 gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e74abf005f..b84498d042 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13869,3 +13869,33 @@ single-cell transcriptomic map of the human and mouse pancreas reveals inter-
 and intra-cell population structure.\" Baron et al. Cell Systems (2016)
 @url{https://www.ncbi.nlm.nih.gov/pubmed/27667365}.")
       (license license:gpl2+))))
+
+(define-public porechop
+  ;; The recommended way to install is to clone the git repository
+  ;; https://github.com/rrwick/Porechop#installation
+  (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861")
+        (revision "1"))
+    (package
+      (name "porechop")
+      (version (git-version "0.2.3" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rrwick/Porechop.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23"))))
+      (build-system python-build-system)
+      (home-page "https://github.com/rrwick/porechop")
+      (synopsis "Finding, trimming or splitting adapters, in Oxford Nanopore reads")
+      (description
+       "The porechop package is a tool for finding and removing adapters from Oxford
+Nanopore reads.  Adapters on the ends of reads are trimmed off, and when a read
+has an adapter in its middle, it is treated as chimeric and chopped into
+separate reads.  Porechop performs thorough alignments to effectively find
+adapters, even at low sequence identity.  Porechop also supports demultiplexing
+of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR
+Barcoding Kit or Rapid Barcoding Kit.")
+      (license license:gpl3+))))

From 0e2d3ce20e7bd71aaad5baa6b977b9684216b66e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 30 Sep 2018 21:12:06 +0200
Subject: [PATCH 195/909] gnu: sshuttle: Rely on $PATH to find a POSIX sh.

This fixes a regression introduced in commit
c32863e094d3489d2e08ccb3188988d7c6410976, where the sshuttle client
will try to invoke its own /gnu/store/.../bin/sh on the server.

Rely on $PATH instead of regressing to upstream's hard-coded /bin/sh.

* gnu/packages/vpn.scm (sshuttle)[arguments]: SUBSTITUTE* "sh" for
"/bin/sh".
---
 gnu/packages/vpn.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index de5df5039d..9b1f26aa7d 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -355,8 +355,7 @@ private network between hosts on the internet.")
              (substitute* "sshuttle/client.py"
                (("/usr/bin/env") (which "env")))
              (substitute* "sshuttle/ssh.py"
-               ;; Perhaps this is unreachable, but don't let's take risks.
-               (("/bin/sh") (which "sh")))
+               (("/bin/sh") "sh"))
              #t)))))
     (native-inputs
      `(("python-setuptools-scm" ,python-setuptools-scm)

From f9051e387056fb1c29d8e67b76754168b304449d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 30 Sep 2018 21:57:59 +0200
Subject: [PATCH 196/909] status: Always print the daemon's "waiting for locks"
 messages.

Reported by Ricardo Wurmus <rekado@elephly.net>.

* guix/status.scm (print-build-event) <build-log>: Let "waiting for
locks" messages through.
---
 guix/status.scm | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/guix/status.scm b/guix/status.scm
index b19f0199d1..c6956066fd 100644
--- a/guix/status.scm
+++ b/guix/status.scm
@@ -383,14 +383,20 @@ addition to build events."
   actual hash:   ~a~%"))
              expected actual))
     (('build-log line)
-     ;; The daemon prefixes early messages coming with 'guix substitute' with
-     ;; "substitute:".  These are useful ("updating substitutes from URL"), so
-     ;; let them through.
-     (if (string-prefix? "substitute: " line)
-         (begin
-           (format port line)
-           (force-output port))
-         (print-log-line line)))
+     ;; TODO: Better distinguish daemon messages and build log lines.
+     (cond ((string-prefix? "substitute: " line)
+            ;; The daemon prefixes early messages coming with 'guix
+            ;; substitute' with "substitute:".  These are useful ("updating
+            ;; substitutes from URL"), so let them through.
+            (format port line)
+            (force-output port))
+           ((string-prefix? "waiting for locks" line)
+            ;; This is when a derivation is already being built and we're just
+            ;; waiting for the build to complete.
+            (display (info (string-trim-right line)) port)
+            (newline))
+           (else
+            (print-log-line line))))
     (_
      event)))
 

From dde15fea25b86c75512f204de91bb0c82a152967 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 14:10:20 -0400
Subject: [PATCH 197/909] gnu: ghc: Use GHC 8.4.3 as the default GHC.

* gnu/packages/haskell.scm (ghc): Switch to ghc-8.
---
 gnu/packages/haskell.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6b774c358a..1e7a502d8f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -559,7 +559,7 @@ interactive environment for the functional language Haskell.")
                                 (file-pattern ".*\\.conf\\.d$")
                                 (file-type 'directory))))))
 
-(define-public ghc ghc-8.0)
+(define-public ghc ghc-8)
 
 (define-public ghc-hostname
   (package

From f54f04756f6d90c9fb3b5e45f3947329287f9b05 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 17:08:08 -0400
Subject: [PATCH 198/909] gnu: ghc-mtl: Remove built-in Haskell package.

* gnu/packages/agda.scm (agda)[inputs]: Remove ghc-mtl.
* gnu/packages/games.scm (raincat)[inputs]: Remove ghc-mtl.
* gnu/packages/haskell-check.scm (ghc-tasty-ant-xml, ghc-tasty-golden,
ghc-tasty, ghc-tasty-kat, ghc-tasty-rerun,
ghc-crypto-cipher-tests)[inputs]: Remove ghc-mtl.
* gnu/packages/haskell-crypto.scm (ghc-asn1-encoding, ghc-pem, ghc-x509,
ghc-x509-store, ghc-x509-validation, ghc-x509-system)[inputs]: Remove
ghc-mtl.
* gnu/packages/haskell-web.scm (ghc-http, ghc-http-conduit,
ghc-yesod-core)[inputs]: Remove ghc-mtl.
* gnu/packages/haskell.scm (ghc-convertible, ghc-libxml, ghc-cgi,
ghc-happy, ghc-haskell-src-exts, ghc-resourcet, cabal-install,
ghc-indents, ghc-regex-base, ghc-regex-tdfa-rc, ghc-trifecta,
ghc-zip-archive, ghc-logict, ghc-exceptions, ghc-smallcheck, ghc-syb,
ghc-fgl, ghc-chasingbottoms, ghc-parsec, ghc-megaparsec, ghc-edisonapi,
ghc-edisoncore, ghc-mmorph, ghc-ifelse, ghc-kan-extensions, ghc-lens,
ghc-cheapskate, ghc-free, ghc-adjunctions, ghc-equivalence, ghc-texmath,
ghc-texmath-for-pandoc-1, ghc-highlighting-kate, ghc-th-reify-many,
ghc-th-orphans, ghc-geniplate-mirror, ghc-conduit, ghc-filemanip,
ghc-juicypixels, ghc-hslua, ghc-hourglass, ghc-skylighting,
ghc-skylighting-for-pandoc-1, ghc-pandoc, ghc-pandoc-1,
ghc-pandoc-citeproc, ghc-regex-tdfa, ghc-stmonadtrans, ghc-constraints,
ghc-lifted-async, ghc-shelly, ghc-hslogger, ghc-json, shellcheck,
ghc-vector-algorithms, ghc-monad-par-extras, ghc-monad-par,
ghc-monadrandom, ghc-either, ghc-rebase, ghc-aws, ghc-monad-logger,
ghc-persistent, ghc-bytes, ghc-missingh, ghc-operational,
ghc-chart)[inputs]: Remove ghc-mtl.
(ghc-conduit-combinators)[native-inputs]: Remove ghc-mtl.
(ghc-mtl): Remove variable.
* gnu/packages/idris.scm (idris)[inputs]: Remove ghc-mtl.
* gnu/packages/tls.scm (ghc-tls)[inputs]: Remove ghc-mtl.
* gnu/packages/version-control.scm (darcs, git-annex)[inputs]: Remove
ghc-mtl.
* gnu/packages/wm.scm (xmonad, ghc-xmonad-contrib)[inputs]: Remove
ghc-mtl.
* gnu/packages/xml.scm (ghc-hxt)[inputs]: Remove ghc-mtl.
---
 gnu/packages/agda.scm            |   1 -
 gnu/packages/games.scm           |   1 -
 gnu/packages/haskell-check.scm   |   8 +-
 gnu/packages/haskell-crypto.scm  |  14 +--
 gnu/packages/haskell-web.scm     |   3 -
 gnu/packages/haskell.scm         | 154 ++++++-------------------------
 gnu/packages/idris.scm           |   1 -
 gnu/packages/tls.scm             |   3 +-
 gnu/packages/version-control.scm |   2 -
 gnu/packages/wm.scm              |   4 +-
 gnu/packages/xml.scm             |   1 -
 11 files changed, 33 insertions(+), 159 deletions(-)

diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm
index df4968c445..572de5bbeb 100644
--- a/gnu/packages/agda.scm
+++ b/gnu/packages/agda.scm
@@ -58,7 +58,6 @@
        ("ghc-hashtables" ,ghc-hashtables)
        ("ghc-ieee754" ,ghc-ieee754)
        ("ghc-monadplus" ,ghc-monadplus)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-murmur-hash" ,ghc-murmur-hash)
        ("ghc-uri-encode" ,ghc-uri-encode)
        ("ghc-parallel" ,ghc-parallel)
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 8be87f6f55..8155876313 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -2136,7 +2136,6 @@ on the screen and keyboard to display letters.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-random" ,ghc-random)
        ("ghc-glut" ,ghc-glut)
        ("freeglut" ,freeglut)
diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 31407ca259..4324c9c44d 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -54,7 +54,6 @@
     (inputs
      `(("ghc-generic-deriving" ,ghc-generic-deriving)
        ("ghc-xml" ,ghc-xml)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-stm" ,ghc-stm)
        ("ghc-tagged" ,ghc-tagged)
        ("ghc-tasty" ,ghc-tasty)))
@@ -140,7 +139,6 @@ Haskell test framework.")
     (inputs
      `(("ghc-temporary" ,ghc-temporary)
        ("ghc-tasty" ,ghc-tasty)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-tagged" ,ghc-tagged)
        ("ghc-async" ,ghc-async)
@@ -197,7 +195,6 @@ timer functions of different operating systems via a unified API.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-stm" ,ghc-stm)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-tagged" ,ghc-tagged)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
        ("ghc-regex-tdfa-rc" ,ghc-regex-tdfa-rc)
@@ -250,7 +247,6 @@ test framework.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-tasty" ,ghc-tasty)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
        ("ghc-tasty-hunit" ,ghc-tasty-hunit)))
     (home-page "https://github.com/vincenthz/tasty-kat")
@@ -299,8 +295,7 @@ test-framework.")
                 "0yg8cicfn3qaazvp4rbanzy3dyk95k3y1kkd4bykvkl9v4076788"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-optparse-applicative" ,ghc-optparse-applicative)
+     `(("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-reducers" ,ghc-reducers)
        ("ghc-split" ,ghc-split)
        ("ghc-stm" ,ghc-stm)
@@ -827,7 +822,6 @@ minimal dependencies.")
          "19wqignlq90qwpam01hnmmrxaxh5lkax9l1l6rlbi4a07nvp1dnz"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-quickcheck" ,ghc-quickcheck)
-              ("ghc-mtl" ,ghc-mtl)
               ("ghc-hunit" ,ghc-hunit)
               ("ghc-test-framework" ,ghc-test-framework)
               ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index b0be30cb6b..1326de0923 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -70,8 +70,7 @@ format.")
     (inputs
      `(("ghc-hourglass" ,ghc-hourglass)
        ("ghc-asn1-types" ,ghc-asn1-types)
-       ("ghc-text" ,ghc-text)
-       ("ghc-mtl" ,ghc-mtl)))
+       ("ghc-text" ,ghc-text)))
     (native-inputs
      `(("ghc-tasty" ,ghc-tasty)
        ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)))
@@ -345,8 +344,7 @@ to obtain cryptographically strong entropy.")
                 "162sk5sg22w21wqz5qv8kx6ibxp99v5p20g3nknhm1kddk3hha1p"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-base64-bytestring" ,ghc-base64-bytestring)))
+     `(("ghc-base64-bytestring" ,ghc-base64-bytestring)))
     (native-inputs
      `(("ghc-test-framework" ,ghc-test-framework)
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
@@ -431,7 +429,6 @@ libraries, like OpenSSL.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-memory" ,ghc-memory)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-hourglass" ,ghc-hourglass)
        ("ghc-pem" ,ghc-pem)
        ("ghc-asn1-types" ,ghc-asn1-types)
@@ -461,8 +458,7 @@ libraries, like OpenSSL.")
                 "0yw09nwkvr324qz4sc27c0p28bz2h6gns6lkaz9mz92mgqf2dza9"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-pem" ,ghc-pem)
+     `(("ghc-pem" ,ghc-pem)
        ("ghc-asn1-types" ,ghc-asn1-types)
        ("ghc-asn1-encoding" ,ghc-asn1-encoding)
        ("ghc-cryptonite" ,ghc-cryptonite)
@@ -490,7 +486,6 @@ collections, certificates, revocation lists, and exception lists.")
     (inputs
      `(("ghc-memory" ,ghc-memory)
        ("ghc-byteable" ,ghc-byteable)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-hourglass" ,ghc-hourglass)
        ("ghc-data-default-class" ,ghc-data-default-class)
        ("ghc-pem" ,ghc-pem)
@@ -520,8 +515,7 @@ list validation.")
                 "0k7zc0xp7r6kqmi39rpiicvq78xb0pr2cq6q5s3kmmsshllg13nr"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-pem" ,ghc-pem)
+     `(("ghc-pem" ,ghc-pem)
        ("ghc-x509" ,ghc-x509)
        ("ghc-x509-store" ,ghc-x509-store)))
     (home-page "https://github.com/vincenthz/hs-certificate")
diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index a043ffcc0d..9ef9486b3f 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -171,7 +171,6 @@ both client and server code).")
        ("ghc-old-time" ,ghc-old-time)
        ("ghc-parsec" ,ghc-parsec)
        ("ghc-puremd5" ,ghc-puremd5)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
        ("ghc-network-uri" ,ghc-network-uri)
        ("ghc-split" ,ghc-split)))
@@ -350,7 +349,6 @@ and HPACK.  Currently HTTP/2 16 framing and HPACK 10 is supported.")
        ("ghc-http-client" ,ghc-http-client)
        ("ghc-http-client-tls" ,ghc-http-client-tls)
        ("ghc-monad-control" ,ghc-monad-control)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-exceptions" ,ghc-exceptions)
        ("ghc-unliftio" ,ghc-unliftio)))
     (native-inputs
@@ -1039,7 +1037,6 @@ avoid any issues with characters.")
               ("ghc-text" ,ghc-text)
               ("ghc-shakespeare" ,ghc-shakespeare)
               ("ghc-blaze-builder" ,ghc-blaze-builder)
-              ("ghc-mtl" ,ghc-mtl)
               ("ghc-clientsession" ,ghc-clientsession)
               ("ghc-random" ,ghc-random)
               ("ghc-cereal" ,ghc-cereal)
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 1e7a502d8f..95e89a3b06 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -596,7 +596,6 @@ determine the hostname.")
     (inputs
      `(("ghc-old-time" ,ghc-old-time)
        ("ghc-old-locale" ,ghc-old-locale)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-text" ,ghc-text)))
     (home-page "https://hackage.haskell.org/package/convertible")
     (synopsis "Typeclasses and instances for converting between types")
@@ -649,8 +648,7 @@ between double precision floating point and text.")
          "01zvk86kg726lf2vnlr7dxiz7g3xwi5a4ak9gcfbwyhynkzjmsfi"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("libxml2" ,libxml2)))
+     `(("libxml2" ,libxml2)))
     (arguments
      `(#:configure-flags
        `(,(string-append "--extra-include-dirs="
@@ -1041,8 +1039,7 @@ tool lex or flex for C/C++.")
        ("ghc-exceptions" ,ghc-exceptions)
        ("ghc-multipart" ,ghc-multipart)
        ("ghc-network-uri" ,ghc-network-uri)
-       ("ghc-network" ,ghc-network)
-       ("ghc-mtl" ,ghc-mtl)))
+       ("ghc-network" ,ghc-network)))
     (native-inputs
      `(("ghc-doctest" ,ghc-doctest)
        ("ghc-quickcheck" ,ghc-quickcheck)))
@@ -1111,8 +1108,6 @@ postfix notation.  For more information on stack based languages, see
         (base32
          "186ky3bly0i3cc56qk3r7j7pxh2108aackq4n2lli7jmbnb3kxsd"))))
     (build-system haskell-build-system)
-    (inputs
-     `(("ghc-mtl" ,ghc-mtl)))
     (home-page "https://hackage.haskell.org/package/happy")
     (synopsis "Parser generator for Haskell")
     (description "Happy is a parser generator for Haskell.  Given a grammar
@@ -1199,7 +1194,6 @@ examination.")
     (inputs
      `(("cpphs" ,cpphs)
        ("ghc-happy" ,ghc-happy)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-pretty-show" ,ghc-pretty-show-for-haskell-src-exts)))
     (native-inputs
      `(("ghc-smallcheck" ,ghc-smallcheck)
@@ -1317,7 +1311,6 @@ unwanted suggestions, and to add your own custom suggestions.")
      `(("ghc-transformers-base" ,ghc-transformers-base)
        ("ghc-monad-control" ,ghc-monad-control)
        ("ghc-transformers-compat" ,ghc-transformers-compat)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-mmorph" ,ghc-mmorph)
        ("ghc-exceptions" ,ghc-exceptions)
        ("ghc-unliftio-core" ,ghc-unliftio-core)))
@@ -1812,7 +1805,6 @@ versions of GHC (i.e., < 6.10).")
    (build-system haskell-build-system)
    (inputs
     `(("ghc-http" ,ghc-http)
-      ("ghc-mtl" ,ghc-mtl)
       ("ghc-network-uri" ,ghc-network-uri)
       ("ghc-network" ,ghc-network)
       ("ghc-random" ,ghc-random)
@@ -1848,37 +1840,6 @@ configuration.  This library provides the common bits for writing custom
 @file{Setup.hs} files.")
     (license license:bsd-3)))
 
-(define-public ghc-mtl
-  (package
-    (name "ghc-mtl")
-    (version "2.2.1")
-    (outputs '("out" "doc"))
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://hackage.haskell.org/package/mtl/mtl-"
-             version
-             ".tar.gz"))
-       (sha256
-        (base32
-         "1icdbj2rshzn0m1zz5wa7v3xvkf6qw811p4s7jgqwvx1ydwrvrfa"))))
-    (build-system haskell-build-system)
-    ;; This is an official revision, relaxing the requirement transformers ==
-    ;; 0.4 to transformers >= 0.4 && < 0.6; see
-    ;; https://hackage.haskell.org/package/mtl-2.2.1/revision/1.cabal
-    (arguments
-     `(#:configure-flags (list "--allow-newer=transformers")))
-    (home-page "https://github.com/ekmett/mtl")
-    (synopsis
-     "Monad classes, using functional dependencies")
-    (description "Monad classes using functional dependencies, with instances
-for various monad transformers, inspired by the paper 'Functional Programming
-with Overloading and Higher-Order Polymorphism', by Mark P Jones, in 'Advanced
-School of Functional Programming', 1995.  See
-@uref{https://web.cecs.pdx.edu/~mpj/pubs/springschool.html, the paper}.")
-    (license license:bsd-3)))
-
 (define-public ghc-parsec-numbers
   (package
     (name "ghc-parsec-numbers")
@@ -2535,8 +2496,7 @@ isn't available, portable implementations are used.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-parsec" ,ghc-parsec)
-       ("ghc-concatenative" ,ghc-concatenative)
-       ("ghc-mtl" ,ghc-mtl)))
+       ("ghc-concatenative" ,ghc-concatenative)))
     (home-page "http://patch-tag.com/r/salazar/indents")
     (synopsis "Indentation sensitive parser-combinators for parsec")
     (description
@@ -2611,8 +2571,6 @@ supported systems.")
         (base32
          "0y1j4h2pg12c853nzmczs263di7xkkmlnsq5dlp5wgbgl49mgp10"))))
     (build-system haskell-build-system)
-    (inputs
-     `(("ghc-mtl" ,ghc-mtl)))
     (home-page
      "https://sourceforge.net/projects/lazy-regex")
     (synopsis "Replaces/Enhances Text.Regex")
@@ -2684,8 +2642,7 @@ Haskell library @code{regex-base}.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-regex-base" ,ghc-regex-base)
-       ("ghc-parsec" ,ghc-parsec)
-       ("ghc-mtl" ,ghc-mtl)))
+       ("ghc-parsec" ,ghc-parsec)))
     (home-page
      "https://hackage.haskell.org/package/regex-tdfa")
     (synopsis "Tagged DFA regex engine for Haskell")
@@ -2815,7 +2772,6 @@ the parsers provided by @code{parsec}, @code{attoparsec} and @code{base}'s
        ("ghc-fingertree" ,ghc-fingertree)
        ("ghc-hashable" ,ghc-hashable)
        ("ghc-lens" ,ghc-lens)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-parsers" ,ghc-parsers)
        ("ghc-profunctors" ,ghc-profunctors)
        ("ghc-quickcheck" ,ghc-quickcheck)
@@ -2904,7 +2860,6 @@ complicated text/binary file formats.")
      `(("ghc-old-time" ,ghc-old-time)
        ("ghc-digest" ,ghc-digest)
        ("zip" ,zip)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-temporary" ,ghc-temporary)
        ("ghc-text" ,ghc-text)
        ("ghc-zlib" ,ghc-zlib)))
@@ -3249,7 +3204,6 @@ syntax and semantics as Perl 5.")
         (base32
          "07hnirv6snnym2r7iijlfz00b60jpy2856zvqxh989q0in7bd0hi"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-mtl" ,ghc-mtl)))
     (home-page "http://code.haskell.org/~dolio/")
     (synopsis "Backtracking logic-programming monad")
     (description "This library provides a continuation-based, backtracking,
@@ -3332,7 +3286,6 @@ consuming feeds in both RSS (Really Simple Syndication) and Atom format.")
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
     (inputs
      `(("ghc-stm" ,ghc-stm)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-transformers-compat" ,ghc-transformers-compat)))
     (home-page "https://github.com/ekmett/exceptions/")
     (synopsis "Extensible optionally-pure exceptions")
@@ -3410,8 +3363,7 @@ This is a better maintained fork of the \"temporary\" package.")
          "195fj7w3v03d1y1nm2ylavzrwxjcdbq0lb6zsw1dwyx5jmwfc84h"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-logict" ,ghc-logict)
-       ("ghc-mtl" ,ghc-mtl)))
+     `(("ghc-logict" ,ghc-logict)))
     (home-page
      "https://github.com/feuerbach/smallcheck")
     (synopsis "Property-based testing library")
@@ -3495,8 +3447,7 @@ to cases.")
          "1p3cnqjm13677r4a966zffzhi9b3a321aln8zs8ckqj0d9z1z3d3"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-hunit" ,ghc-hunit)
-       ("ghc-mtl" ,ghc-mtl)))
+     `(("ghc-hunit" ,ghc-hunit)))
     (home-page
      "http://www.cs.uu.nl/wiki/GenericProgramming/SYB")
     (synopsis "Scrap Your Boilerplate")
@@ -3528,8 +3479,7 @@ variety of traversals.")
      `(#:configure-flags (list "--allow-newer=QuickCheck"
                                "--allow-newer=hspec")))
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-hspec" ,ghc-hspec)
+     `(("ghc-hspec" ,ghc-hspec)
        ("ghc-quickcheck" ,ghc-quickcheck)))
     (home-page "https://web.engr.oregonstate.edu/~erwig/fgl/haskell")
     (synopsis
@@ -3554,8 +3504,7 @@ encourages inductive, recursive definitions of graph algorithms.")
          "04jwwjs22mqc4hvpp4c3gpb79inrrq5sapks5khknspv2hslm61q"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-quickcheck" ,ghc-quickcheck)
+     `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-random" ,ghc-random)
        ("ghc-syb" ,ghc-syb)))
     (home-page "https://hackage.haskell.org/package/ChasingBottoms")
@@ -3764,8 +3713,7 @@ mainstream languages.")
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)))
     (inputs
-     `(("ghc-text" ,ghc-text)
-       ("ghc-mtl" ,ghc-mtl)))
+     `(("ghc-text" ,ghc-text)))
     (arguments
      `(#:tests? #f)) ; FIXME: currently missing libraries used for tests.
     (home-page
@@ -3814,7 +3762,6 @@ combinators.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-case-insensitive" ,ghc-case-insensitive)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-parser-combinators" ,ghc-parser-combinators)
        ("ghc-scientific" ,ghc-scientific)
        ("ghc-text" ,ghc-text)))
@@ -4043,7 +3990,6 @@ representing a store for a single element.")
        (sha256
         (base32 "0vmmlsj8ggbpwx6fkf5fvb6jp0zpx6iba6b28m80lllr2p8bi8wm"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-mtl" ,ghc-mtl)))
     (home-page "http://rwd.rdockins.name/edison/home/")
     (synopsis "Library of efficient, purely-functional data structures (API)")
     (description
@@ -4069,8 +4015,7 @@ finite maps and priority queues where the priority and element are distinct.")
         (base32 "06shxmcqxcahcn6zgl64vlqix4fnq53d97drcgsh94qp7gp201ry"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-quickcheck" ,ghc-quickcheck)
+     `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-edisonapi" ,ghc-edisonapi)))
     (home-page "http://rwd.rdockins.name/edison/home/")
     (synopsis "Library of efficient, purely-functional data structures")
@@ -4096,8 +4041,7 @@ with various performance characteristics.")
          "1i8dzrc5qi3ryc9vrrmpn3sihmramsbhhd592w4w2k5g26qr3hql"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-transformers-compat" ,ghc-transformers-compat)))
+     `(("ghc-transformers-compat" ,ghc-transformers-compat)))
     (home-page "https://hackage.haskell.org/package/mmorph")
     (synopsis "Monad morphisms")
     (description
@@ -4118,7 +4062,6 @@ manipulating monad transformer stacks.")
         (base32
          "1kfx1bwfjczj93a8yqz1n8snqiq5655qgzwv1lrycry8wb1vzlwa"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-mtl" ,ghc-mtl)))
     (home-page "http://hackage.haskell.org/package/IfElse")
     (synopsis "Monadic control flow with anaphoric variants")
     (description "This library provides functions for control flow inside of
@@ -4638,7 +4581,6 @@ given term should not exist.")
        ("ghc-contravariant" ,ghc-contravariant)
        ("ghc-distributive" ,ghc-distributive)
        ("ghc-free" ,ghc-free)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-semigroupoids" ,ghc-semigroupoids)
        ("ghc-tagged" ,ghc-tagged)))
     (home-page "https://github.com/ekmett/kan-extensions/")
@@ -4728,7 +4670,6 @@ in the @code{IO} monad, like @code{IORef}s or parts of the OpenGL state.")
        ("ghc-comonad" ,ghc-comonad)
        ("ghc-contravariant" ,ghc-contravariant)
        ("ghc-hashable" ,ghc-hashable)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-profunctors" ,ghc-profunctors)
        ("ghc-semigroups" ,ghc-semigroups)
        ("ghc-tagged" ,ghc-tagged)
@@ -4772,8 +4713,7 @@ indexed variants.")
          "1hiqi7h76shjzs2zj0j8g6wnq2hbiq1hmfafdazr97fba2zl2432"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-text" ,ghc-text)
+     `(("ghc-text" ,ghc-text)
        ("ghc-blaze-html" ,ghc-blaze-html)
        ("ghc-xss-sanitize" ,ghc-xss-sanitize)
        ("ghc-data-default" ,ghc-data-default)
@@ -4936,7 +4876,6 @@ semigroup.")
        ("ghc-bifunctors" ,ghc-bifunctors)
        ("ghc-comonad" ,ghc-comonad)
        ("ghc-distributive" ,ghc-distributive)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-semigroupoids" ,ghc-semigroupoids)
        ("ghc-semigroups" ,ghc-semigroups)))
     (home-page "https://github.com/ekmett/free/")
@@ -4971,7 +4910,6 @@ definition of @code{Monad}.")
        ("ghc-contravariant" ,ghc-contravariant)
        ("ghc-distributive" ,ghc-distributive)
        ("ghc-free" ,ghc-free)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-tagged" ,ghc-tagged)
        ("ghc-semigroupoids" ,ghc-semigroupoids)
        ("ghc-semigroups" ,ghc-semigroups)
@@ -4995,8 +4933,7 @@ for Haskell.")
         (base32 "0a85bdyyvjqs5z4kfhhf758210k9gi9dv42ik66a3jl0z7aix8kx"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-stmonadtrans" ,ghc-stmonadtrans)
+     `(("ghc-stmonadtrans" ,ghc-stmonadtrans)
        ("ghc-transformers-compat" ,ghc-transformers-compat)
        ("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-test-framework" ,ghc-test-framework)
@@ -5393,7 +5330,6 @@ building up, manipulating and serialising @code{Pandoc} structures.")
        ("ghc-utf8-string" ,ghc-utf8-string)
        ("ghc-xml" ,ghc-xml)
        ("ghc-parsec" ,ghc-parsec)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-pandoc-types" ,ghc-pandoc-types)))
     (home-page "https://github.com/jgm/texmath")
     (synopsis "Conversion between formats used to represent mathematics")
@@ -5417,8 +5353,7 @@ it can parse and apply LaTeX macros.")
                (base32
                 "129q33m56diiv35kdwfb07838wrg0mm88kxdqxfyl1zvf9nzkqkd"))))
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-network-uri" ,ghc-network-uri)
+     `(("ghc-network-uri" ,ghc-network-uri)
        ("ghc-pandoc-types" ,ghc-pandoc-types-for-pandoc-1)
        ("ghc-parsec" ,ghc-parsec)
        ("ghc-split" ,ghc-split)
@@ -5492,8 +5427,7 @@ and utilities for pretty printing.")
     (native-inputs
      `(("ghc-parsec" ,ghc-parsec)
        ("ghc-blaze-html" ,ghc-blaze-html)
-       ("ghc-utf8-string" ,ghc-utf8-string)
-       ("ghc-mtl" ,ghc-mtl)))
+       ("ghc-utf8-string" ,ghc-utf8-string)))
     (home-page "https://github.com/jgm/highlighting-kate")
     (synopsis "Syntax highlighting library")
     (description
@@ -5747,8 +5681,7 @@ instances.  This package provides orphan instances for @code{containers},
                 "1b76zjxkj0v0n8zj9l0nwav2irm0c43rx6qjihfw8klmmxvx59df"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-safe" ,ghc-safe)
+     `(("ghc-safe" ,ghc-safe)
        ("ghc-th-expand-syns" ,ghc-th-expand-syns)))
     (home-page "https://github.com/mgsloan/th-reify-many")
     (synopsis "Recurseively reify template haskell datatype info")
@@ -5775,7 +5708,6 @@ function which generates instances.")
      `(("ghc-th-lift" ,ghc-th-lift)
        ("ghc-th-lift-instances" ,ghc-th-lift-instances)
        ("ghc-th-reify-many" ,ghc-th-reify-many)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-generic-deriving" ,ghc-generic-deriving)))
     (native-inputs
      `(("ghc-hspec" ,ghc-hspec)))
@@ -5801,7 +5733,6 @@ package, and that's where the version number started.")
        (sha256
         (base32 "17vjps2118s5z3k39ij00lkmkxv3mqf8h59wv6qdamlgmhyr36si"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-mtl" ,ghc-mtl)))
     (home-page "https://github.com/danr/geniplate")
     (synopsis "Use Template Haskell to generate Uniplate-like functions")
     (description
@@ -5877,7 +5808,6 @@ template-haskell abstract syntax.")
        ("ghc-lifted-base" ,ghc-lifted-base)
        ("ghc-mono-traversable" ,ghc-mono-traversable)
        ("ghc-mmorph" ,ghc-mmorph)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-resourcet" ,ghc-resourcet)
        ("ghc-silently" ,ghc-silently)
        ("ghc-transformers-base" ,ghc-transformers-base)
@@ -6003,8 +5933,7 @@ back-ends.")
                 "0ilqr8jv41zxcj5qyicg29m8s30b9v70x6f9h2h2rw5ap8bxldl8"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-unix-compat" ,ghc-unix-compat)))
+     `(("ghc-unix-compat" ,ghc-unix-compat)))
     (home-page "https://github.com/bos/filemanip")
     (synopsis "File and directory manipulation for Haskell")
     (description
@@ -6048,8 +5977,7 @@ do on-demand loading.")
                 "14s57fgf6kd5n5al2kcvk1aaxbq1ph0r5h8blflrjkx83yl6r8yn"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-zlib" ,ghc-zlib)
+     `(("ghc-zlib" ,ghc-zlib)
        ("ghc-vector" ,ghc-vector)
        ("ghc-primitive" ,ghc-primitive)
        ("ghc-mmap" ,ghc-mmap)))
@@ -6078,7 +6006,6 @@ TIFF and GIF formats.")
      `(("lua" ,lua)
        ("ghc-exceptions" ,ghc-exceptions)
        ("ghc-fail" ,ghc-fail)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-text" ,ghc-text)))
     (native-inputs
      `(("ghc-tasty" ,ghc-tasty)
@@ -6176,8 +6103,7 @@ wrapping a bytestring with stronger and more meaniful name.")
                 "104d1yd84hclprg740nkz60vx589mnm094zriw6zczbgg8nkclym"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-old-locale" ,ghc-old-locale)))
+     `(("ghc-old-locale" ,ghc-old-locale)))
     (native-inputs
      `(("ghc-tasty" ,ghc-tasty)
        ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
@@ -6322,7 +6248,6 @@ the choice of SSL/TLS, and SOCKS.")
        ("ghc-colour" ,ghc-colour)
        ("ghc-diff" ,ghc-diff)
        ("ghc-hxt" ,ghc-hxt)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-pretty-show" ,ghc-pretty-show)
        ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin)
        ("ghc-safe" ,ghc-safe)
@@ -6388,7 +6313,6 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
        ("ghc-case-insensitive" ,ghc-case-insensitive)
        ("ghc-diff" ,ghc-diff)
        ("ghc-hxt" ,ghc-hxt)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-pretty-show" ,ghc-pretty-show)
        ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin)
        ("ghc-safe" ,ghc-safe)
@@ -6483,7 +6407,6 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
        ("ghc-http-client-tls" ,ghc-http-client-tls)
        ("ghc-http-types" ,ghc-http-types)
        ("ghc-juicypixels" ,ghc-juicypixels)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
        ("ghc-network-uri" ,ghc-network-uri)
        ("ghc-old-locale" ,ghc-old-locale)
@@ -6560,7 +6483,6 @@ provided for those who need a drop-in replacement for Markdown.pl.")
        ("ghc-http-client-tls" ,ghc-http-client-tls)
        ("ghc-http-types" ,ghc-http-types)
        ("ghc-juicypixels" ,ghc-juicypixels)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
        ("ghc-network-uri" ,ghc-network-uri)
        ("ghc-old-time" ,ghc-old-time)
@@ -6782,8 +6704,7 @@ the @code{conduit} package.")
          (add-after 'install 'post-install-check
            (assoc-ref %standard-phases 'check)))))
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-pandoc-types" ,ghc-pandoc-types)
+     `(("ghc-pandoc-types" ,ghc-pandoc-types)
        ("ghc-pandoc" ,ghc-pandoc)
        ("ghc-tagsoup" ,ghc-tagsoup)
        ("ghc-aeson" ,ghc-aeson)
@@ -6935,8 +6856,7 @@ regular expressions.  Parsers can be built using Applicative interface.")
          "0f8x8wyr6m21g8dnxvnvalz5bsq37l125l6qhs0fscbvprsxc4nb"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-parsec" ,ghc-parsec)
+     `(("ghc-parsec" ,ghc-parsec)
        ("ghc-regex-base" ,ghc-regex-base)))
     (home-page "https://github.com/ChrisKuklewicz/regex-tdfa")
     (synopsis "POSIX extended regular expressions in Haskell.")
@@ -7070,8 +6990,6 @@ an index.")
        (sha256
         (base32 "1nr26fnmi5fdjc6d00w13kjhmfyvb5b837d0006w4dj0yxndaksp"))))
     (build-system haskell-build-system)
-    (inputs
-     `(("ghc-mtl" ,ghc-mtl)))
     (home-page "https://hackage.haskell.org/package/STMonadTrans")
     (synopsis "Monad transformer version of the ST monad")
     (description
@@ -7288,7 +7206,6 @@ and edge labels with positional information, etc.
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hashable" ,ghc-hashable)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-transformers-compat" ,ghc-transformers-compat)))
     (home-page "https://github.com/ekmett/constraints/")
     (synopsis "Constraint manipulation")
@@ -7319,7 +7236,6 @@ a vocabulary for working with them.")
        ("ghc-monad-control" ,ghc-monad-control)
        ("ghc-constraints" ,ghc-constraints)
        ("ghc-hunit" ,ghc-hunit)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-tasty" ,ghc-tasty)
        ("ghc-tasty-hunit" ,ghc-tasty-hunit)
        ("ghc-tasty-th" ,ghc-tasty-th)))
@@ -7408,8 +7324,7 @@ which can't be decoded in the current locale encoding.")
          "023fbvbqs5gdwm30j5517gbdcc7fvz0md70dgwgpypkskj3i926y"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-unix-compat" ,ghc-unix-compat)
+     `(("ghc-unix-compat" ,ghc-unix-compat)
        ("ghc-system-filepath-bootstrap" ,ghc-system-filepath-bootstrap)
        ("ghc-system-fileio-bootstrap" ,ghc-system-fileio-bootstrap)
        ("ghc-monad-control" ,ghc-monad-control)
@@ -8102,8 +8017,7 @@ files in Haskell.")
                 "0as5gvlh6pi2gflakp695qnlizyyp059dqrhvjl4gjxalja6xjnp"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-network" ,ghc-network)
+     `(("ghc-network" ,ghc-network)
        ("ghc-old-locale" ,ghc-old-locale)))
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)))
@@ -8148,7 +8062,6 @@ handled safely, this is what you're left with.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-syb" ,ghc-syb)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-text" ,ghc-text)
        ("ghc-parsec" ,ghc-parsec)))
     (home-page "https://hackage.haskell.org/package/json")
@@ -8213,7 +8126,6 @@ generated SQL and optimize it for your backend.")
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-json" ,ghc-json)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-parsec" ,ghc-parsec)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)))
     (home-page "https://github.com/koalaman/shellcheck")
@@ -8546,7 +8458,6 @@ between 2 and 3 times faster than the Mersenne Twister.")
              #t)))))
     (inputs
      `(("ghc-vector" ,ghc-vector)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-mwc-random" ,ghc-mwc-random)))
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)))
@@ -8622,8 +8533,7 @@ module for more details.")
     (build-system haskell-build-system)
     (inputs `(("ghc-abstract-par" ,ghc-abstract-par)
               ("ghc-cereal" ,ghc-cereal)
-              ("ghc-random" ,ghc-random)
-              ("ghc-mtl" ,ghc-mtl)))
+              ("ghc-random" ,ghc-random)))
     (home-page "https://github.com/simonmar/monad-par")
     (synopsis "Combinators and extra features for Par monads for Haskell")
     (description "This Haskell package provides additional data structures,
@@ -8685,8 +8595,7 @@ This package also includes a simple reference implementation based on
               ("ghc-abstract-deque" ,ghc-abstract-deque)
               ("ghc-monad-par-extras" ,ghc-monad-par-extras)
               ("ghc-mwc-random" ,ghc-mwc-random)
-              ("ghc-parallel" ,ghc-parallel)
-              ("ghc-mtl" ,ghc-mtl)))
+              ("ghc-parallel" ,ghc-parallel)))
     (native-inputs `(("ghc-quickcheck" ,ghc-quickcheck)
                      ("ghc-hunit" ,ghc-hunit)
                      ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
@@ -8879,7 +8788,6 @@ statically known size.")
          "1h1nhswrcmhy3mq6vd530p0df51fcnnf4csbwnljar7cf0mb2h6y"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-transformers-compat" ,ghc-transformers-compat)
-              ("ghc-mtl" ,ghc-mtl)
               ("ghc-primitive" ,ghc-primitive)
               ("ghc-fail" ,ghc-fail)
               ("ghc-random" ,ghc-random)))
@@ -8908,7 +8816,6 @@ which consume random values.")
               ("ghc-free" ,ghc-free)
               ("ghc-monad-control" ,ghc-monad-control)
               ("ghc-manodrandom" ,ghc-monadrandom)
-              ("ghc-mtl" ,ghc-mtl)
               ("ghc-mmorph" ,ghc-mmorph)
               ("ghc-profunctors" ,ghc-profunctors)
               ("ghc-semigroups" ,ghc-semigroups)
@@ -9057,7 +8964,6 @@ parsing and printing @dfn{Universally Unique Identifiers} or UUIDs.")
               ("ghc-contravariant" ,ghc-contravariant)
               ("ghc-contravariant-extras" ,ghc-contravariant-extras)
               ("ghc-semigroups" ,ghc-semigroups)
-              ("ghc-mtl" ,ghc-mtl)
               ("ghc-either" ,ghc-either)
               ("ghc-fail" ,ghc-fail)
               ("ghc-base-prelude" ,ghc-base-prelude)))
@@ -9219,7 +9125,6 @@ data structures as non-empty.")
               ("ghc-mono-traversable" ,ghc-mono-traversable)))
     (native-inputs `(("ghc-hspec" ,ghc-hspec)
                      ("ghc-silently" ,ghc-silently)
-                     ("ghc-mtl" ,ghc-mtl)
                      ("ghc-safe" ,ghc-safe)
                      ("ghc-quickcheck" ,ghc-quickcheck)))
     (home-page "https://github.com/snoyberg/mono-traversable")
@@ -9258,7 +9163,6 @@ as well as a convenient Conduit module.")
        ("ghc-http-conduit" ,ghc-http-conduit)
        ("ghc-http-types" ,ghc-http-types)
        ("ghc-monad-control" ,ghc-monad-control)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
        ("ghc-old-locale" ,ghc-old-locale)
        ("ghc-safe" ,ghc-safe)
@@ -9411,7 +9315,6 @@ operators for looping.")
               ("ghc-transformers-base" ,ghc-transformers-base)
               ("ghc-monad-control" ,ghc-monad-control)
               ("ghc-monad-loops" ,ghc-monad-loops)
-              ("ghc-mtl" ,ghc-mtl)
               ("ghc-blaze-builder" ,ghc-blaze-builder)
               ("ghc-exceptions" ,ghc-exceptions)))
     (home-page "https://github.com/kazu-yamamoto/logger")
@@ -9652,7 +9555,6 @@ Haskell data types to and from HTTP API data.")
               ("ghc-blaze-html" ,ghc-blaze-html)
               ("ghc-blaze-markup" ,ghc-blaze-markup)
               ("ghc-silently" ,ghc-silently)
-              ("ghc-mtl" ,ghc-mtl)
               ("ghc-fast-logger" ,ghc-fast-logger)
               ("ghc-scientific" ,ghc-scientific)
               ("ghc-tagged" ,ghc-tagged)))
@@ -9932,7 +9834,6 @@ address string against RFC 5322.")
    (inputs `(("ghc-cereal" ,ghc-cereal)
              ("cabal-doctest" ,cabal-doctest)
              ("ghc-doctest" ,ghc-doctest-0.13)
-             ("ghc-mtl" ,ghc-mtl)
              ("ghc-scientific" ,ghc-scientific)
              ("ghc-text" ,ghc-text)
              ("ghc-transformers-compat" ,ghc-transformers-compat)
@@ -10032,7 +9933,6 @@ This package provides an orphan instance.")
     (inputs
      `(("ghc-network" ,ghc-network)
        ("ghc-parsec" ,ghc-parsec)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-hunit" ,ghc-hunit)
        ("ghc-regex-compat" ,ghc-regex-compat)
        ("ghc-hslogger" ,ghc-hslogger)
@@ -10088,8 +9988,7 @@ example code on the home page for a quick introduction.")
          "1x2abg2q9d26h1vzj40r6k7k3gqgappbs4g9d853vvg77837km4i"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-random" ,ghc-random)))
+     `(("ghc-random" ,ghc-random)))
     (home-page "http://wiki.haskell.org/Operational")
     (synopsis "Implementation of difficult monads made easy with operational semantics")
     (description
@@ -10146,7 +10045,6 @@ tools are not needed to actually run Gtk2Hs programs.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-old-locale" ,ghc-old-locale)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-lens" ,ghc-lens)
        ("ghc-colour" ,ghc-colour)
        ("ghc-data-default-class" ,ghc-data-default-class)
diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm
index 79f89d6f54..7f1af62c1f 100644
--- a/gnu/packages/idris.scm
+++ b/gnu/packages/idris.scm
@@ -106,7 +106,6 @@
        ("ghc-fingertree" ,ghc-fingertree)
        ("ghc-fsnotify" ,ghc-fsnotify)
        ("ghc-ieee754" ,ghc-ieee754)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index bdb63c0dbf..6c4c64e507 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -881,8 +881,7 @@ coding footprint.")
                 "1rdidf18i781c0vdvy9yn79yh08hmcacf6fp3sgghyiy3h0wyh5l"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-cereal" ,ghc-cereal)
+     `(("ghc-cereal" ,ghc-cereal)
        ("ghc-data-default-class" ,ghc-data-default-class)
        ("ghc-memory" ,ghc-memory)
        ("ghc-cryptonite" ,ghc-cryptonite)
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index d06055de45..c8ad067ff1 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1895,7 +1895,6 @@ be served with a HTTP file server of your choice.")
        ("ghc-hashable" ,ghc-hashable)
        ("ghc-html" ,ghc-html)
        ("ghc-mmap" ,ghc-mmap)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-old-time" ,ghc-old-time)
        ("ghc-parsec" ,ghc-parsec)
        ("ghc-random" ,ghc-random)
@@ -2188,7 +2187,6 @@ directory full of HOWTOs.")
        ("ghc-memory" ,ghc-memory)
        ("ghc-monad-control" ,ghc-monad-control)
        ("ghc-monad-logger" ,ghc-monad-logger)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-network" ,ghc-network)
        ("ghc-old-locale" ,ghc-old-locale)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 08f82ba2d2..163281ac67 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -467,7 +467,6 @@ desktop environment.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
-       ("ghc-mtl"                   ,ghc-mtl)
        ("ghc-quickcheck"            ,ghc-quickcheck)
        ("ghc-semigroups"            ,ghc-semigroups)
        ("ghc-setlocale"             ,ghc-setlocale)
@@ -560,8 +559,7 @@ Haskell, no knowledge of the language is required to install and use it.")
          "1660w3xhbfrlq8b8s1rviq2mcn1vyqpypli4023gqxwry52brk6y"))))
     (build-system haskell-build-system)
     (propagated-inputs
-     `(("ghc-mtl" ,ghc-mtl)
-       ("ghc-old-time" ,ghc-old-time)
+     `(("ghc-old-time" ,ghc-old-time)
        ("ghc-random" ,ghc-random)
        ("ghc-utf8-string" ,ghc-utf8-string)
        ("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index aa1395286f..2bf5ea3569 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -2078,7 +2078,6 @@ derivations of regular expressions.")
     (build-system haskell-build-system)
     (inputs
      `(("ghc-parsec" ,ghc-parsec)
-       ("ghc-mtl" ,ghc-mtl)
        ("ghc-hxt-charproperties" ,ghc-hxt-charproperties)
        ("ghc-hxt-unicode" ,ghc-hxt-unicode)
        ("ghc-hxt-regex-xmlschema" ,ghc-hxt-regex-xmlschema)

From bb6419f3745911aec87ad79c55bb953b36f246dd Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 30 Aug 2018 22:08:59 -0400
Subject: [PATCH 199/909] build-system: haskell: Add #:cabal-revision argument.

Add a #:cabal-revision argument for specifying which Cabal file revision
from Hackage should be used.

* guix/build-system/haskell.scm (source-url->revision-url): New function.
(lower): Accept a cabal-revision keyword argument, convert it to an
origin record, and add it to the resulting bag's host-inputs.
(haskell-build): Pass the cabal-revision input to the builder as an
argument.
* guix/build/haskell-build-system.scm (patch-cabal-file): New phase.
(%standard-phases): Add it.
---
 guix/build-system/haskell.scm       | 32 ++++++++++++++++++++++++++++-
 guix/build/haskell-build-system.scm | 12 +++++++++++
 2 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/guix/build-system/haskell.scm b/guix/build-system/haskell.scm
index 1cb734631c..1ec11c71d8 100644
--- a/guix/build-system/haskell.scm
+++ b/guix/build-system/haskell.scm
@@ -21,6 +21,7 @@
   #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix derivations)
+  #:use-module (guix download)
   #:use-module (guix search-paths)
   #:use-module (guix build-system)
   #:use-module (guix build-system gnu)
@@ -48,14 +49,35 @@
   (let ((haskell (resolve-interface '(gnu packages haskell))))
     (module-ref haskell 'ghc)))
 
+(define (source-url->revision-url url revision)
+  "Convert URL (a Hackage source URL) to the URL for the Cabal file at
+version REVISION."
+  (let* ((last-slash (string-rindex url #\/))
+         (next-slash (string-rindex url #\/ 0 last-slash)))
+    (string-append (substring url 0 next-slash)
+                   (substring url last-slash (- (string-length url)
+                                                (string-length ".tar.gz")))
+                   "/revision/" revision ".cabal")))
+
 (define* (lower name
                 #:key source inputs native-inputs outputs system target
                 (haskell (default-haskell))
+                cabal-revision
                 #:allow-other-keys
                 #:rest arguments)
   "Return a bag for NAME."
   (define private-keywords
-    '(#:target #:haskell #:inputs #:native-inputs))
+    '(#:target #:haskell #:cabal-revision #:inputs #:native-inputs))
+
+  (define (cabal-revision->origin cabal-revision)
+    (match cabal-revision
+      ((revision hash)
+       (origin
+         (method url-fetch)
+         (uri (source-url->revision-url (origin-uri source) revision))
+         (sha256 (base32 hash))
+         (file-name (string-append name "-" revision ".cabal"))))
+      (#f #f)))
 
   (and (not target)                               ;XXX: no cross-compilation
        (bag
@@ -64,6 +86,9 @@
          (host-inputs `(,@(if source
                               `(("source" ,source))
                               '())
+                        ,@(match (cabal-revision->origin cabal-revision)
+                            (#f '())
+                            (revision `(("cabal-revision" ,revision))))
                         ,@inputs
 
                         ;; Keep the standard inputs of 'gnu-build-system'.
@@ -103,6 +128,11 @@ provides a 'Setup.hs' file as its build system."
                                    source)
                                   (source
                                    source))
+                      #:cabal-revision ,(match (assoc-ref inputs
+                                                          "cabal-revision")
+                                          (((? derivation? revision))
+                                           (derivation->output-path revision))
+                                          (revision revision))
                       #:configure-flags ,configure-flags
                       #:haddock-flags ,haddock-flags
                       #:system ,system
diff --git a/guix/build/haskell-build-system.scm b/guix/build/haskell-build-system.scm
index 26519ce5a6..be4f5b583b 100644
--- a/guix/build/haskell-build-system.scm
+++ b/guix/build/haskell-build-system.scm
@@ -27,6 +27,7 @@
   #:use-module (ice-9 regex)
   #:use-module (ice-9 match)
   #:use-module (ice-9 vlist)
+  #:use-module (ice-9 ftw)
   #:export (%standard-phases
             haskell-build))
 
@@ -265,8 +266,19 @@ given Haskell package."
       (run-setuphs "haddock" haddock-flags)
       #t))
 
+(define* (patch-cabal-file #:key cabal-revision #:allow-other-keys)
+  (when cabal-revision
+    ;; Cabal requires there to be a single file with the suffix ".cabal".
+    (match (scandir "." (cut string-suffix? ".cabal" <>))
+      ((original)
+       (format #t "replacing ~s with ~s~%" original cabal-revision)
+       (copy-file cabal-revision original))
+      (_ (error "Could not find a Cabal file to patch."))))
+  #t)
+
 (define %standard-phases
   (modify-phases gnu:%standard-phases
+    (add-after 'unpack 'patch-cabal-file patch-cabal-file)
     (delete 'bootstrap)
     (add-before 'configure 'setup-compiler setup-compiler)
     (add-before 'install 'haddock haddock)

From 127586adfb4228576d124ad5fa5cb6eacc29ea0f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 09:45:36 -0400
Subject: [PATCH 200/909] guix: import: stackage: Fix JSON accessors.

* guix/import/stackage.scm (lts-info-ghc-version, lst-info-packages): Use
assoc-ref for accessing parsed JSON.
---
 guix/import/stackage.scm | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/guix/import/stackage.scm b/guix/import/stackage.scm
index afd5d997ae..1c1e73a723 100644
--- a/guix/import/stackage.scm
+++ b/guix/import/stackage.scm
@@ -43,15 +43,12 @@
 
 (define (lts-info-ghc-version lts-info)
   "Retruns the version of the GHC compiler contained in LTS-INFO."
-  (match lts-info
-    ((("snapshot" ("ghc" . version) _ _) _)  version)
-    (_ #f)))
+  (and=> (assoc-ref lts-info "snapshot")
+         (cut assoc-ref <> "ghc")))
 
 (define (lts-info-packages lts-info)
-  "Returns the alist of packages contained in LTS-INFO."
-  (match lts-info
-    ((("packages" pkg ...) . _) pkg)
-    (_ '())))
+  "Retruns the alist of packages contained in LTS-INFO."
+  (or (assoc-ref lts-info "packages") '()))
 
 (define (leave-with-message fmt . args)
   (raise (condition (&message (message (apply format #f fmt args))))))

From 988dee48d048af6bf324c07a6d7f615b4c768fcc Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:12:05 -0400
Subject: [PATCH 201/909] gnu: cabal-doctest: Update Cabal file to r1.

* gnu/packages/haskell.scm (cabal-doctest): Update Cabal file to r1.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 95e89a3b06..7fa63eb116 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1832,6 +1832,9 @@ installation of Haskell libraries and programs.")
         (base32
          "0bgd4jdmzxq5y465r4sf4jv2ix73yvblnr4c9wyazazafddamjny"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "1bk85avgc93yvcggwbk01fy8nvg6753wgmaanhkry0hz55h7mpld")))
     (home-page "https://github.com/phadej/cabal-doctest")
     (synopsis "Setup.hs helper for running doctests")
     (description

From 6bacde7cd7c47dd8f83265f53a4098dace9569f1 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:22:20 -0400
Subject: [PATCH 202/909] gnu: ghc-basement: Update to 0.0.8.

* gnu/packages/haskell.scm (ghc-basement): Update to 0.0.8.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7fa63eb116..e6a88f295d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9197,7 +9197,7 @@ Web Services.")
 (define-public ghc-basement
   (package
     (name "ghc-basement")
-    (version "0.0.7")
+    (version "0.0.8")
     (source
      (origin
        (method url-fetch)
@@ -9205,7 +9205,7 @@ Web Services.")
                            "basement/basement-" version ".tar.gz"))
        (sha256
         (base32
-         "0w2g4k9bs2ph00p0fgrmcrng8ypdz6xis0r10g380nzkg2rvj0dm"))))
+         "194jw567di4q2758943q9rrwkbf9gl261my7qc21i9xhyabipx67"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/haskell-foundation/foundation")
     (synopsis "Basic primitives for Foundation starter pack")

From d3cc0eb2f35df66262402c2432adeff4694f202d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:22:43 -0400
Subject: [PATCH 203/909] gnu: ghc-base-prelude: Update to 1.3.

* gnu/packages/haskell.scm (ghc-base-prelude): Update to 1.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e6a88f295d..9c79eb654d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8701,7 +8701,7 @@ classy-prelude.")
 (define-public ghc-base-prelude
   (package
     (name "ghc-base-prelude")
-    (version "1.2.0.1")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
@@ -8710,7 +8710,7 @@ classy-prelude.")
                            "base-prelude-" version ".tar.gz"))
        (sha256
         (base32
-         "17hivs7lmsglagdlzxd9q9zsddmgqin2788mpq911zwnb57lj6l1"))))
+         "1zk728sd09hh2r4xwz4lazsrrgg5cshydn64932sm0vckplndk73"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/nikita-volkov/base-prelude")
     (synopsis "The most complete prelude formed solely from the Haskell's base

From 0ff8558a4d337a89d4d6bb43bf70a0dc3a008f67 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:23:41 -0400
Subject: [PATCH 204/909] gnu: ghc-cmdargs: Update to 0.10.20.

* gnu/packages/haskell.scm (ghc-cmdargs): Update to 0.10.20.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9c79eb654d..f5a5299379 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1053,7 +1053,7 @@ tool lex or flex for C/C++.")
 (define-public ghc-cmdargs
   (package
     (name "ghc-cmdargs")
-    (version "0.10.18")
+    (version "0.10.20")
     (source
      (origin
        (method url-fetch)
@@ -1062,7 +1062,7 @@ tool lex or flex for C/C++.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1lnmcsf6p9yrwwz1zvrw5lbc32xpff7b70yz4ylawaflnlz6wrlh"))))
+         "0cbkmgrcnwgigg6z88y3c09gm7g6dwm7gzbgr53h8k1xik29s9hf"))))
     (build-system haskell-build-system)
     (home-page
      "http://community.haskell.org/~ndm/cmdargs/")

From d05d03dda05588cd31e1d5d05c1583c8d17dfa6e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:28:08 -0400
Subject: [PATCH 205/909] gnu: ghc-colour: Update to 2.3.4.

* gnu/packages/haskell.scm (ghc-colour): Update to 2.3.4.
[arguments]: Disable tests.
---
 gnu/packages/haskell.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index f5a5299379..e1dfb9b1f0 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7073,7 +7073,7 @@ the @code{mtl-tf} package.")
 (define-public ghc-colour
 (package
   (name "ghc-colour")
-  (version "2.3.3")
+  (version "2.3.4")
   (source
    (origin
      (method url-fetch)
@@ -7082,7 +7082,11 @@ the @code{mtl-tf} package.")
            version ".tar.gz"))
      (sha256
       (base32
-       "1qmn1778xzg07jg9nx4k1spdz2llivpblf6wwrps1qpqjhsac5cd"))))
+       "1sy51nz096sv91nxqk6yk7b92b5a40axv9183xakvki2nc09yhqg"))))
+  (arguments
+   ;; The tests for this package have the following dependency cycle:
+   ;; ghc-test-framework -> ghc-ansi-terminal -> ghc-colour.
+   `(#:tests? #f))
   (build-system haskell-build-system)
   (home-page "https://www.haskell.org/haskellwiki/Colour")
   (synopsis "Model for human colour perception")

From 7d887a2ceccdbec2abb6eaf5ae97c12849a7cbc6 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:33:08 -0400
Subject: [PATCH 206/909] gnu: ghc-easy-file: Update to 0.2.2.

* gnu/packages/haskell.scm (ghc-easy-file): Update to 0.2.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e1dfb9b1f0..9df5e030a0 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4253,7 +4253,7 @@ library for Haskell.")
 (define-public ghc-easy-file
   (package
     (name "ghc-easy-file")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method url-fetch)
@@ -4263,7 +4263,7 @@ library for Haskell.")
              ".tar.gz"))
        (sha256
         (base32
-         "0v75081bx4qzlqy29hh639nzlr7dncwza3qxbzm9njc4jarf31pz"))))
+         "0zmlcz723051qpn8l8vi51c5rx1blwrw4094jcshkmj8p9r2xxaj"))))
     (build-system haskell-build-system)
     (home-page
      "https://github.com/kazu-yamamoto/easy-file")

From a7427ff7780bc7907b7e7fe1446d21625ceeddb1 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:33:58 -0400
Subject: [PATCH 207/909] gnu: ghc-entropy: Update to 0.4.1.1.

* gnu/packages/haskell-crypto.scm (ghc-entropy): Update to 0.4.1.1.
---
 gnu/packages/haskell-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index 1326de0923..6a1eff6821 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -314,7 +314,7 @@ are implemented as FFI bindings to efficient code from zlib.")
 (define-public ghc-entropy
   (package
     (name "ghc-entropy")
-    (version "0.3.8")
+    (version "0.4.1.1")
     (source
      (origin
        (method url-fetch)
@@ -323,7 +323,7 @@ are implemented as FFI bindings to efficient code from zlib.")
                            "entropy-" version ".tar.gz"))
        (sha256
         (base32
-         "1l3lfigqvdlmxkz1wl7zdkmc0i2r5p6z4xzhiw8xdsbsw7aljfkl"))))
+         "1ahz5g148l6sax3dy505na2513i99c7bxix68jja5kbx4f271zcf"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/TomMD/entropy")
     (synopsis "Provides platform independent entropy source for Haskell")

From 6b850af42d20016c8a33d575b6388acdfb6a0a88 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:28:57 -0400
Subject: [PATCH 208/909] gnu: ghc-geniplate-mirror: Update to 0.7.6.

* gnu/packages/haskell.scm (ghc-geniplate-mirror): Update to 0.7.6.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9df5e030a0..98cd790865 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5726,7 +5726,7 @@ package, and that's where the version number started.")
 (define-public ghc-geniplate-mirror
   (package
     (name "ghc-geniplate-mirror")
-    (version "0.7.5")
+    (version "0.7.6")
     (source
      (origin
        (method url-fetch)
@@ -5734,7 +5734,7 @@ package, and that's where the version number started.")
                            "/geniplate-mirror"
                            "/geniplate-mirror-" version ".tar.gz"))
        (sha256
-        (base32 "17vjps2118s5z3k39ij00lkmkxv3mqf8h59wv6qdamlgmhyr36si"))))
+        (base32 "1y0m0bw5zpm1y1y6d9qmxj3swl8j8hlw1shxbr5awycf6k884ssb"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/danr/geniplate")
     (synopsis "Use Template Haskell to generate Uniplate-like functions")

From a3aaf87a99316f694d2c220c5e578eaad55accbf Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:29:30 -0400
Subject: [PATCH 209/909] gnu: ghc-happy: Update to 1.19.9.

* gnu/packages/haskell.scm (ghc-happy): Update to 1.19.9.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 98cd790865..98c2c3f67e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1096,7 +1096,7 @@ postfix notation.  For more information on stack based languages, see
 (define-public ghc-happy
   (package
     (name "ghc-happy")
-    (version "1.19.8")
+    (version "1.19.9")
     (source
      (origin
        (method url-fetch)
@@ -1106,7 +1106,7 @@ postfix notation.  For more information on stack based languages, see
              ".tar.gz"))
        (sha256
         (base32
-         "186ky3bly0i3cc56qk3r7j7pxh2108aackq4n2lli7jmbnb3kxsd"))))
+         "138xpxdb7x62lpmgmb6b3v3vgdqqvqn4273jaap3mjmc2gla709y"))))
     (build-system haskell-build-system)
     (home-page "https://hackage.haskell.org/package/happy")
     (synopsis "Parser generator for Haskell")

From 9959625056ad70b45632799535a350da3aac73b0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:45:49 -0400
Subject: [PATCH 210/909] gnu: ghc-ieee754: Update to 0.8.0.

* gnu/packages/haskell.scm (ghc-ieee754): Update to 0.8.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 98c2c3f67e..f1e26bb69c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7862,7 +7862,7 @@ specific Windows, Mac, and Linux file system event notification.")
 (define-public ghc-ieee754
   (package
     (name "ghc-ieee754")
-    (version "0.7.8")
+    (version "0.8.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -7870,7 +7870,7 @@ specific Windows, Mac, and Linux file system event notification.")
                     "ieee754-" version ".tar.gz"))
               (sha256
                (base32
-                "1zvfnnd5nm5kgr60214cdyks0kqdqyzpwk5sdh0s60yr8b7fyjny"))))
+                "1lcs521g9lzy9d7337vg4w7q7s8500rfqy7rcifcz6pm6yfgyb8f"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/patperry/hs-ieee754")
     (synopsis "Utilities for dealing with IEEE floating point numbers")

From f06b5f23c0f6677e3692928250dbde68ec5d6bd7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:47:51 -0400
Subject: [PATCH 211/909] gnu: ghc-microlens: Update to 0.4.9.1.

* gnu/packages/haskell.scm (ghc-microlens): Update to 0.4.9.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index f1e26bb69c..c674c970b6 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9665,7 +9665,7 @@ functions.")
 (define-public ghc-microlens
   (package
     (name "ghc-microlens")
-    (version "0.4.8.3")
+    (version "0.4.9.1")
     (source
      (origin
        (method url-fetch)
@@ -9674,7 +9674,7 @@ functions.")
                            "microlens-" version ".tar.gz"))
        (sha256
         (base32
-         "17qx2mbqdrlnkc3gxq8njbp7qw8nh51drmz6fc8khgj9bls5ni2k"))))
+         "0j2nzf0vpx2anvsrg2w0vy2z4jn3kkcs2n6glkzblhn1j9piqh51"))))
     (build-system haskell-build-system)
     (home-page
      "https://github.com/aelve/microlens")

From e433898d8cb407479b700132cd800114d4bb3768 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:50:11 -0400
Subject: [PATCH 212/909] gnu: ghc-network-info: Update to 0.2.0.10.

* gnu/packages/haskell.scm (ghc-network-info): Update to 0.2.0.10.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c674c970b6..9452555540 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8856,7 +8856,7 @@ ByteStrings in the style of other common *nix hex dump tools.")
 (define-public ghc-network-info
   (package
     (name "ghc-network-info")
-    (version "0.2.0.8")
+    (version "0.2.0.10")
     (source
      (origin
        (method url-fetch)
@@ -8865,7 +8865,7 @@ ByteStrings in the style of other common *nix hex dump tools.")
                            "network-info-" version ".tar.gz"))
        (sha256
         (base32
-         "0xndvg776241fgjmynxfpy81f1csjmh8dg33yf0c8m71ychz3pzc"))))
+         "0anmgzcpnz7nw3n6vq0r25m1s9l2svpwi83wza0lzkrlbnbzd02n"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/jystic/network-info")
     (synopsis "Access the local computer's basic network configuration")

From 12eb67dcc94cfd6c110576d50cb6cd28c7fc2e74 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 15:12:07 -0400
Subject: [PATCH 213/909] gnu: ghc-old-locale: Update Cabal file to r2.

* gnu/packages/haskell.scm (ghc-old-locale): Update Cabal file to r2.
[arguments]: Remove unneeded "--allow-newer" configure flag.
---
 gnu/packages/haskell.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9452555540..e0ebe09dd3 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1686,7 +1686,8 @@ configurations to coexist without resorting to mutable global variables or
         (base32 "0l3viphiszvz5wqzg7a45zp40grwlab941q5ay29iyw8p3v8pbyv"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=base")))
+     `(#:cabal-revision
+       ("2" "04b9vn007hlvsrx4ksd3r8r3kbyaj2kvwxchdrmd4370qzi8p6gs")))
     (home-page "https://hackage.haskell.org/package/old-locale")
     (synopsis "Adapt to locale conventions")
     (description

From 62f97b121725689a3ba81285ff857749b44603f9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:51:30 -0400
Subject: [PATCH 214/909] gnu: ghc-parallel: Update to 3.2.2.0.

* gnu/packages/haskell.scm (ghc-parallel): Update to 3.2.2.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e0ebe09dd3..aa471fa0ad 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2093,7 +2093,7 @@ case with other forms of concurrent communication, such as locks or
 (define-public ghc-parallel
   (package
     (name "ghc-parallel")
-    (version "3.2.1.0")
+    (version "3.2.2.0")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -2104,7 +2104,7 @@ case with other forms of concurrent communication, such as locks or
              ".tar.gz"))
        (sha256
         (base32
-         "09l52k1gsn667lmv0pp052cbwkzkbhfivp51f2xkrlfzf6xwvqsd"))))
+         "1xkfi96w6yfpppd0nw1rnszdxmvifwzm699ilv6332ra3akm610p"))))
     (build-system haskell-build-system)
     (home-page "https://hackage.haskell.org/package/parallel")
     (synopsis "Parallel programming library")

From e21822026672b8348b8ec1582609e8931a087634 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:57:19 -0400
Subject: [PATCH 215/909] gnu: ghc-parser-combinators: Update to 1.0.0.

* gnu/packages/haskell.scm (ghc-parser-combinators): Update to 1.0.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index aa471fa0ad..7de08a7d2d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3732,7 +3732,7 @@ is also parametric in the input stream type.")
 (define-public ghc-parser-combinators
   (package
     (name "ghc-parser-combinators")
-    (version "0.4.0")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
@@ -3741,7 +3741,7 @@ is also parametric in the input stream type.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1azkz0a6ikym02s8wydjcklp7rz8k512bs4s9lp9g1g03m0yj95i"))))
+         "1pwfdsklqwvaynwpdzmx1bs35mp6dpsyaqdnzxnqcrxwf5h8sk75"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/mrkkrp/parser-combinators")
     (synopsis "Commonly useful parser combinators")

From 30a8c0d81e5b0195e566b3c8e11afd7ba75b3eba Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:02:11 -0400
Subject: [PATCH 216/909] gnu: ghc-sdl: Update to 0.6.7.0.

* gnu/packages/haskell.scm (ghc-sdl): Update to 0.6.7.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7de08a7d2d..51170adbfb 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1349,7 +1349,7 @@ OpenAL.")
 (define-public ghc-sdl
   (package
     (name "ghc-sdl")
-    (version "0.6.5.1")
+    (version "0.6.7.0")
     (source
      (origin
        (method url-fetch)
@@ -1359,7 +1359,7 @@ OpenAL.")
              ".tar.gz"))
        (sha256
         (base32
-         "1sa3zx3vrs1gbinxx33zwq0x2bsf3i964bff7419p7vzidn36k46"))))
+         "00y67v80a8l09i3k76z09lg25kw72ivl09nag8ckdlk4a0cfnzfq"))))
     (build-system haskell-build-system)
     (inputs
      `(("sdl" ,sdl)))

From 42f2732e13c0d36f7e70b2131a629a54c59987f7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:03:30 -0400
Subject: [PATCH 217/909] gnu: ghc-setlocale: Update to 1.0.0.8.

* gnu/packages/haskell.scm (ghc-setlocale): Update to 1.0.0.8.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 51170adbfb..fa588b8dbe 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1936,7 +1936,7 @@ environment variables.")
 (define-public ghc-setlocale
   (package
     (name "ghc-setlocale")
-    (version "1.0.0.6")
+    (version "1.0.0.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1944,7 +1944,7 @@ environment variables.")
                     version "/setlocale-" version ".tar.gz"))
               (sha256
                (base32
-                "1rl8qb8vzv8fdbczy2dxwgn4cb68lfrjdxf2w8nn9wy1acqzcyjq"))))
+                "0sdrsmkhw08483d73ysgm2926fdbhii61br03lqpqw0lfzj4ilbd"))))
     (build-system haskell-build-system)
     (home-page "https://hackage.haskell.org/package/setlocale")
     (synopsis "Haskell bindings to setlocale")

From c2e393cccb3280e0a5ff517999f468e37fe2b54c Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:03:55 -0400
Subject: [PATCH 218/909] gnu: ghc-simple-reflect: Update to 0.3.3.

* gnu/packages/haskell.scm (ghc-simple-reflect): Update to 0.3.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index fa588b8dbe..e711d46bd8 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -938,7 +938,7 @@ documentation-generation tool for Haskell libraries.")
 (define-public ghc-simple-reflect
   (package
     (name "ghc-simple-reflect")
-    (version "0.3.2")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
@@ -948,7 +948,7 @@ documentation-generation tool for Haskell libraries.")
              ".tar.gz"))
        (sha256
         (base32
-         "1dpcf6w3cf1sfl9bnlsx04x7aghw029glj5d05qzrsnms2rlw8iq"))))
+         "0ayvrx5cm8n6db21jiyjmk5h93pw7cz1707hih09hlhk9jh5x0h7"))))
     (build-system haskell-build-system)
     (home-page
      "https://twanvl.nl/blog/haskell/simple-reflection-of-expressions")

From 4112a2e7c44c999cb65270e020fbe8f241874829 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:07:18 -0400
Subject: [PATCH 219/909] gnu: ghc-stringbuilder: Update to 0.5.1.

* gnu/packages/haskell.scm (ghc-stringbuilder): Update to 0.5.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e711d46bd8..ddbd9098d0 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2007,7 +2007,7 @@ parts.")
 (define-public ghc-stringbuilder
   (package
     (name "ghc-stringbuilder")
-    (version "0.5.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
@@ -2017,7 +2017,7 @@ parts.")
              ".tar.gz"))
        (sha256
         (base32
-         "1ap95xphqnrhv64c2a137wqslkdmb2jjd9ldb17gs1pw48k8hrl9"))))
+         "1fh3csx1wcssn8xyvl4ip4aprh9l4qyz2kk8mgjvqvc0vb2bsy6q"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: circular dependencies with tests
                                ; enabled

From 5fe52835d926d8fa79495dbd0d6e3e47d07e9bc8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:12:22 -0400
Subject: [PATCH 220/909] gnu: ghc-th-abstraction: Update to 0.2.8.0.

* gnu/packages/haskell.scm (ghc-th-abstraction): Update to 0.2.8.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ddbd9098d0..ad84eeeff5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5584,7 +5584,7 @@ asynchronous exceptions.")
 (define-public ghc-th-abstraction
   (package
     (name "ghc-th-abstraction")
-    (version "0.2.6.0")
+    (version "0.2.8.0")
     (source
      (origin
        (method url-fetch)
@@ -5593,7 +5593,7 @@ asynchronous exceptions.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0g42h6wnj2awc5ryhbvx009wd8w75pn66bjzsq1z4s3xajd2hbp5"))))
+         "0n17w4q2ykd0nica4sck2wng6md56rfad8x0icl0l8vnzb9nn4ya"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/glguy/th-abstraction")
     (synopsis "Nicer interface for reified information about data types")

From d7f14885bbb12edd86ae66782a06e32046bc469e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:12:56 -0400
Subject: [PATCH 221/909] gnu: ghc-transformers-compat: Update to 0.6.2.

* gnu/packages/haskell.scm (ghc-transformers-compat): Update to 0.6.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ad84eeeff5..4183c9c49d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2415,7 +2415,7 @@ compatibility to run on old versions of the platform.")
 (define-public ghc-transformers-compat
   (package
     (name "ghc-transformers-compat")
-    (version "0.5.1.4")
+    (version "0.6.2")
     (source
      (origin
        (method url-fetch)
@@ -2424,7 +2424,7 @@ compatibility to run on old versions of the platform.")
              "/transformers-compat-" version ".tar.gz"))
        (sha256
         (base32
-         "17yam0199fh9ndsn9n69jx9nvbsmymzzwbi23dck3dk4q57fz0fq"))))
+         "1gp4a8kvniwgm8947ghb4iwv4b7wd6ry4kvv4nfnym4agf5j41nw"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/ekmett/transformers-compat/")
     (synopsis "Small compatibility shim between transformers 0.3 and 0.4")

From 58c102e08d28d69851fa779fdb4ee0701b23eb24 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:14:42 -0400
Subject: [PATCH 222/909] gnu: ghc-unbounded-delays: Update to 0.1.1.0.

* gnu/packages/haskell.scm (ghc-unbounded-delays): Update to 0.1.1.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4183c9c49d..0d4501328a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4426,7 +4426,7 @@ having to unsafely pass dummy arguments.")
 (define-public ghc-unbounded-delays
   (package
     (name "ghc-unbounded-delays")
-    (version "0.1.0.9")
+    (version "0.1.1.0")
     (source
      (origin
        (method url-fetch)
@@ -4436,7 +4436,7 @@ having to unsafely pass dummy arguments.")
              ".tar.gz"))
        (sha256
         (base32
-         "1f4h87503m3smhip432q027wj3zih18pmz2rnafh60589ifcl420"))))
+         "1ir9fghbrc214c97bwafk5ck6cacxz1pdnq4i18p604d1b8zg9wa"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/basvandijk/unbounded-delays")
     (synopsis "Unbounded thread delays and timeouts")

From 06dae8ffe92100d7f5818f68a24642a032fc2593 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:17:26 -0400
Subject: [PATCH 223/909] gnu: ghc-unexceptionalio: Update to 0.4.0.

* gnu/packages/haskell.scm (ghc-unexceptionalio): Update to 0.4.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0d4501328a..63564b23b5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8040,14 +8040,14 @@ handler built in.")
 (define-public ghc-unexceptionalio
   (package
     (name "ghc-unexceptionalio")
-    (version "0.3.0")
+    (version "0.4.0")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://hackage.haskell.org/package/"
                            "unexceptionalio-" version "/" "unexceptionalio-"
                            version ".tar.gz"))
-       (sha256 (base32 "1f7h7zwky4scdcyjspg4ksfh7x6yra0wjybxq70p7vcwpgk2nzlj"))))
+       (sha256 (base32 "09gynk472l7nn5l2w320n4dwigwp0wh0shfp6dyw6r5h2jdxz18p"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/singpolyma/unexceptionalio")
     (synopsis "IO without any non-error, synchronous exceptions")

From 32a9a3808711feac2ee30379256c1ac95d29857b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:18:01 -0400
Subject: [PATCH 224/909] gnu: ghc-unix-compat: Update to 0.5.1.

* gnu/packages/haskell.scm (ghc-unix-compat): Update to 0.5.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 63564b23b5..3ebefeea3a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2464,7 +2464,7 @@ for Unix time in Haskell.")
 (define-public ghc-unix-compat
   (package
     (name "ghc-unix-compat")
-    (version "0.4.2.0")
+    (version "0.5.1")
     (source
      (origin
        (method url-fetch)
@@ -2474,7 +2474,7 @@ for Unix time in Haskell.")
              ".tar.gz"))
        (sha256
         (base32
-         "036nv05w0yjxc3rfpar60ddjrlzc40mdgr5k6ihvwlvqfmq1gw9m"))))
+         "0llwl7rp63fy2ychwdclz1afj45pbin5pfl01dvn6rwhvmwhr7d3"))))
     (build-system haskell-build-system)
     (home-page
      "https://github.com/jystic/unix-compat")

From f871a555026b94e2f3a34ae9410388a1ce0368ac Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:20:28 -0400
Subject: [PATCH 225/909] gnu: ghc-unliftio-core: Update Cabal file to r1.

* gnu/packages/haskell.scm (ghc-unliftio-core): Update Cabal file to r1.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 3ebefeea3a..32a530853e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9655,6 +9655,9 @@ functions for the ghc-persistent package.")
         (base32
          "1193fplsjm1lcr05xwvkj1rsyzx74i755f6kw3ikmxbsv0bv0l3m"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "16bjwcsaghqqmyi69rq65dn3ydifyfaabq3ns37apdm00mwqbcj2")))
     (home-page
      "https://github.com/fpco/unliftio/tree/master/unliftio-core#readme")
     (synopsis "The MonadUnliftIO typeclass for unlifting monads to IO")

From c325dde2702540332d30b5525be1dc1441dd0281 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 30 Aug 2018 10:53:19 -0400
Subject: [PATCH 226/909] gnu: ghc-utf8-string: Update Cabal file to r3.

* gnu/packages/haskell.scm (ghc-utf8-string): Update Cabal file to r3.
[arguments]: Remove unneeded "--allow-newer" configure flag.
---
 gnu/packages/haskell.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 32a530853e..d8cb73c83a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1903,7 +1903,8 @@ configuration.  This library provides the common bits for writing custom
         (base32 "0h7imvxkahiy8pzr8cpsimifdfvv18lizrb33k6mnq70rcx9w2zv"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=base")))
+     `(#:cabal-revision
+       ("3" "02vhj5gykkqa2dyn7s6gn8is1b5fdn9xcqqvlls268g7cpv6rk38")))
     (home-page "https://github.com/glguy/utf8-string/")
     (synopsis "Support for reading and writing UTF8 Strings")
     (description

From 061832f1f96dbe60b5e0961650e37017a0116675 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:21:00 -0400
Subject: [PATCH 227/909] gnu: ghc-wl-pprint: Update to 1.2.1.

* gnu/packages/haskell.scm (ghc-wl-pprint): Update to 1.2.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d8cb73c83a..696f42118d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3634,7 +3634,7 @@ a variety of ways.")
 (define-public ghc-wl-pprint
   (package
     (name "ghc-wl-pprint")
-    (version "1.2")
+    (version "1.2.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3642,7 +3642,7 @@ a variety of ways.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "166zvk4zwn2zaa9kx66m1av38m34qp6h4i65bri2sfnxgvx0700r"))))
+                "0kn7y8pdrv8f87zhd5mifcl8fy3b2zvnzmzwhdqhxxlyzwiq6z0c"))))
     (build-system haskell-build-system)
     (home-page "https://hackage.haskell.org/package/wl-pprint")
     (synopsis "Wadler/Leijen pretty printer")

From 6c76f51f96737d5e0fc2148343b4f5605a6e95a4 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:21:29 -0400
Subject: [PATCH 228/909] gnu: ghc-xhtml: Update to 3000.2.2.1.

* gnu/packages/haskell-web.scm (ghc-xhtml): Update to 3000.2.2.1.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 9ef9486b3f..0a53136f97 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -708,7 +708,7 @@ documents.")
 (define-public ghc-xhtml
   (package
     (name "ghc-xhtml")
-    (version "3000.2.1")
+    (version "3000.2.2.1")
     (source
      (origin
        (method url-fetch)
@@ -718,7 +718,7 @@ documents.")
              ".tar.gz"))
        (sha256
         (base32
-         "1n6wgzxbj8xf0wf1il827qidphnffb5vzhwzqlxhh70c2y10f0ik"))))
+         "0939kwpinq6l4n3nyvd1gzyl7f83gymw0wzqndlgy1yc7q0nkj2w"))))
     (build-system haskell-build-system)
     (home-page "https://github.com/haskell/xhtml")
     (synopsis "XHTML combinator library")

From e09ef4fccaddfeb74ecab8cc7ab9a24be9b019f9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 6 Sep 2018 14:08:08 -0400
Subject: [PATCH 229/909] gnu: ghc-zlib: Relax test framework dependency
 constraints.

* gnu/packages/haskell.scm (ghc-zlib)[arguments]: Remove "--allow-newer"
configure flag and add a phase that removes dependency version constraints
from some of the test frameworks.
---
 gnu/packages/haskell.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 696f42118d..9ed7554bb0 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2044,7 +2044,15 @@ literals.")
         (base32
          "1vbzf0awb6zb456xf48za1kl22018646cfzq4frvxgb9ay97vk0d"))))
     (build-system haskell-build-system)
-    (arguments `(#:configure-flags (list "--allow-newer=tasty")))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'strip-test-framework-constraints
+           (lambda _
+             (substitute* "zlib.cabal"
+               (("tasty            >= 0\\.8 && < 0\\.12") "tasty")
+               (("tasty-hunit      >= 0\\.8 && < 0\\.10") "tasty-hunit")
+               (("tasty-quickcheck == 0\\.8\\.\\*") "tasty-quickcheck")))))))
     (inputs `(("zlib" ,zlib)))
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From 8642b86a0080343d000aafc54b518f0cb4d2d286 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:22:01 -0400
Subject: [PATCH 230/909] gnu: hscolour: Update to 1.24.4.

* gnu/packages/haskell.scm (hscolour): Update to 1.24.4.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9ed7554bb0..93d855dd12 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2974,7 +2974,7 @@ parser isolation, and labeled blocks for better error messages.")
 (define-public hscolour
   (package
     (name "hscolour")
-    (version "1.24.1")
+    (version "1.24.4")
     (source
      (origin
        (method url-fetch)
@@ -2984,7 +2984,7 @@ parser isolation, and labeled blocks for better error messages.")
              ".tar.gz"))
        (sha256
         (base32
-         "1j3rpzjygh3igvnd1n2xn63bq68rs047cjxr2qi6xyfnivgf6vz4"))))
+         "079jwph4bwllfp03yfr26s5zc6m6kw3nhb1cggrifh99haq34cr4"))))
     (build-system haskell-build-system)
     (home-page "https://hackage.haskell.org/package/hscolour")
     (synopsis "Script to colourise Haskell code")

From ecefe4ce870e69009117d8e14382ad9c2e69720d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:20:26 -0400
Subject: [PATCH 231/909] gnu: ghc-ansi-terminal: Update to 0.8.0.4.

* gnu/packages/haskell.scm (ghc-ansi-terminal): Update to 0.8.0.4.
[inputs]: Add ghc-colour.
---
 gnu/packages/haskell.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 93d855dd12..cc5dc152f6 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3943,7 +3943,7 @@ package into this package.")
 (define-public ghc-ansi-terminal
   (package
     (name "ghc-ansi-terminal")
-    (version "0.6.2.3")
+    (version "0.8.0.4")
     (source
      (origin
        (method url-fetch)
@@ -3953,8 +3953,10 @@ package into this package.")
              ".tar.gz"))
        (sha256
         (base32
-         "0hpfw0k025y681m9ml1c712skrb1p4vh7z5x1f0ci9ww7ssjrh2d"))))
+         "0428gq8m3fdnb7ldcsyk97qcch76hcxbgh2666p6f76fs2qbhg7b"))))
     (build-system haskell-build-system)
+    (inputs
+     `(("ghc-colour" ,ghc-colour)))
     (home-page "https://github.com/feuerbach/ansi-terminal")
     (synopsis "ANSI terminal support for Haskell")
     (description "This package provides ANSI terminal support for Haskell.  It

From e95cc1087a13ab4c26244c31b7e6512c37042a5b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 09:53:24 -0400
Subject: [PATCH 232/909] gnu: Add ghc-bsb-http-chunked.

* gnu/packages/haskell-web.scm (ghc-bsb-http-chunked): New variable.
---
 gnu/packages/haskell-web.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 0a53136f97..190bec8dd2 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -524,6 +524,30 @@ functionality.")
 Haskell's Web Application Interface (WAI).")
     (license license:expat)))
 
+(define-public ghc-bsb-http-chunked
+  (package
+    (name "ghc-bsb-http-chunked")
+    (version "0.0.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/"
+             "bsb-http-chunked/bsb-http-chunked-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "1x6m6xkrcw6jiaig1bb2wb5pqyw31x8xr9k9pxgq2g3ng44pbjr8"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-bytestring-builder" ,ghc-bytestring-builder)))
+    (home-page "http://github.com/sjakobi/bsb-http-chunked")
+    (synopsis "Chunked HTTP transfer encoding for bytestring builders")
+    (description "This Haskell library contains functions for encoding
+bytestring builders for chunked Hypertext Transfer Protocol (HTTP) 1.1
+transfers.")
+    (license license:bsd-3)))
+
 (define-public ghc-warp
   (package
     (name "ghc-warp")

From 95415545ab5b33e7e4d813b97d101c810b1ae338 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:28:17 -0400
Subject: [PATCH 233/909] gnu: ghc-foundation: Update to 0.0.21.

* gnu/packages/haskell.scm (ghc-foundation): Update to 0.0.21.
[arguments]: Add a phase to create missing "Setup.hs" file.
---
 gnu/packages/haskell.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index cc5dc152f6..860834d795 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9233,7 +9233,7 @@ packages.")
 (define-public ghc-foundation
   (package
     (name "ghc-foundation")
-    (version "0.0.20")
+    (version "0.0.21")
     (source
      (origin
        (method url-fetch)
@@ -9241,8 +9241,18 @@ packages.")
                            "foundation/foundation-" version ".tar.gz"))
        (sha256
         (base32
-         "0bg4g0xf4pb2vmahnfp8c4f0a3v0av73lb5g8bwnp170khxfcsms"))))
+         "1q43y8wfj0wf9gdq2kzphwjwq6m5pvryy1lqgk954aq5z3ks1lsf"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'add-setup-script
+           (lambda _
+             ;; The usual "Setup.hs" script is missing from the source.
+             (with-output-to-file "Setup.hs"
+               (lambda ()
+                 (format #t "import Distribution.Simple~%")
+                 (format #t "main = defaultMain~%"))))))))
     (inputs `(("ghc-basement" ,ghc-basement)))
     (home-page "https://github.com/haskell-foundation/foundation")
     (synopsis "Alternative prelude with batteries and no dependencies")

From acf13271302ae531b577b42502d790bd7e5a46d5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:28:37 -0400
Subject: [PATCH 234/909] gnu: ghc-generics-sop: Update to 0.3.2.0.

* gnu/packages/haskell.scm (ghc-generics-sop): Update to 0.3.2.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 860834d795..567bf75b5d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9464,7 +9464,7 @@ from aeson.")
 (define-public ghc-generics-sop
   (package
     (name "ghc-generics-sop")
-    (version "0.3.1.0")
+    (version "0.3.2.0")
     (source
      (origin
        (method url-fetch)
@@ -9473,7 +9473,7 @@ from aeson.")
                            "generics-sop-" version ".tar.gz"))
        (sha256
         (base32
-         "1bazlhgmxcwv7vd44jhdx74cnhmaz6yy47jxfycapjj4mjrnp0x7"))))
+         "168v62i845jh9jbfaz3ldz8svz4wmzq9mf2vhb7pxlnbkk8fqq1h"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-transformers-compat" ,ghc-transformers-compat)))
     (home-page "https://github.com/well-typed/generics-sop")

From c18122265e45419df9cbc6a8db9ec1fb5a450e5f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:32:26 -0400
Subject: [PATCH 235/909] gnu: ghc-microlens-th: Update to 0.4.2.2.

* gnu/packages/haskell.scm (ghc-microlens-th): Update to 0.4.2.2.
[inputs]: Add ghc-th-abstraction.
---
 gnu/packages/haskell.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 567bf75b5d..4bfde42b2b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9715,7 +9715,7 @@ stripped.  As the result, this package has no dependencies.")
 (define-public ghc-microlens-th
   (package
     (name "ghc-microlens-th")
-    (version "0.4.1.3")
+    (version "0.4.2.2")
     (source
      (origin
        (method url-fetch)
@@ -9724,9 +9724,10 @@ stripped.  As the result, this package has no dependencies.")
                            "microlens-th-" version ".tar.gz"))
        (sha256
         (base32
-         "15a12cqxlgbcn1n73zwrxnp2vfm8b0ma0a0sdd8zmjbs8zy3np4f"))))
+         "02nj7lnl61yffi3c6wn341arxhld5r0vj6nzcb5zmqjhnqsv8c05"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-microlens" ,ghc-microlens)))
+    (inputs `(("ghc-microlens" ,ghc-microlens)
+              ("ghc-th-abstraction" ,ghc-th-abstraction)))
     (home-page
      "https://github.com/aelve/microlens")
     (synopsis "Automatic generation of record lenses for

From 8b5d1142c28ba51442c1190aa9b2dc54d151d6c5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:32:51 -0400
Subject: [PATCH 236/909] gnu: ghc-mmorph: Update to 1.1.2.

* gnu/packages/haskell.scm (ghc-mmorph): Update to 1.1.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4bfde42b2b..a7e7404932 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4043,7 +4043,7 @@ with various performance characteristics.")
 (define-public ghc-mmorph
   (package
     (name "ghc-mmorph")
-    (version "1.0.6")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
@@ -4053,7 +4053,7 @@ with various performance characteristics.")
              ".tar.gz"))
        (sha256
         (base32
-         "1i8dzrc5qi3ryc9vrrmpn3sihmramsbhhd592w4w2k5g26qr3hql"))))
+         "1gjz1ib968lqybma7my1n19qq6cdj6a7nskrlnwy4jy9jrwzs2n9"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-transformers-compat" ,ghc-transformers-compat)))

From d58fda7d65f28a25e514aef45f09188b934a4ea5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:33:22 -0400
Subject: [PATCH 237/909] gnu: ghc-monadrandom: Update to 0.5.1.1.

* gnu/packages/haskell.scm (ghc-monadrandom): Update to 0.5.1.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a7e7404932..4798636c65 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8795,7 +8795,7 @@ statically known size.")
 (define-public ghc-monadrandom
   (package
     (name "ghc-monadrandom")
-    (version "0.4.2.3")
+    (version "0.5.1.1")
     (source
      (origin
        (method url-fetch)
@@ -8804,7 +8804,7 @@ statically known size.")
                            "MonadRandom-" version ".tar.gz"))
        (sha256
         (base32
-         "1h1nhswrcmhy3mq6vd530p0df51fcnnf4csbwnljar7cf0mb2h6y"))))
+         "0w44jl1n3kqvqaflh82l1wj3xxbhzfs3kf4m8rk7w6fgg8llmnmb"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-transformers-compat" ,ghc-transformers-compat)
               ("ghc-primitive" ,ghc-primitive)

From e37775110e8909665ddb10889759567474fb2d7f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:09:36 -0400
Subject: [PATCH 238/909] gnu: ghc-old-time: Update Cabal file to r2.

* gnu/packages/haskell.scm (ghc-old-time): Update Cabal file to r2.
[arguments]: Remove unneeded "--allow-newer" configure flag.
---
 gnu/packages/haskell.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4798636c65..8228d8b480 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1711,7 +1711,8 @@ date and time formats.")
          "1h9b26s3kfh2k0ih4383w90ibji6n0iwamxp6rfp2lbq1y5ibjqw"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=base")))
+     `(#:cabal-revision
+       ("2" "1j6ln1dkvhdvnwl33bp0xf9lhc4sybqk0aw42p8cq81xwwzbn7y9")))
     (inputs
      `(("ghc-old-locale" ,ghc-old-locale)))
     (home-page "https://hackage.haskell.org/package/old-time")

From 6b19c5a477c08b0f168519d730ff9edb1357005c Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:15:15 -0400
Subject: [PATCH 239/909] gnu: ghc-pretty-show: Update to 1.7.

* gnu/packages/haskell.scm (ghc-pretty-show): Update to 1.7.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 8228d8b480..4a5a7a9f5b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1138,7 +1138,7 @@ Happy works in a similar way to the yacc tool for C.")
 (define-public ghc-pretty-show
   (package
     (name "ghc-pretty-show")
-    (version "1.6.12")
+    (version "1.7")
     (source
      (origin
        (method url-fetch)
@@ -1146,7 +1146,7 @@ Happy works in a similar way to the yacc tool for C.")
                            "pretty-show-" version ".tar.gz"))
        (sha256
         (base32
-         "1fblcxw4z4ry14brin1mvwccs6hqqlhi7xhwv1f23szjq25cjacn"))))
+         "0br7pkxqqqhby2j2v1g847lgqsrasx56g1jw3dhmjh4flzs6warq"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-haskell-lexer" ,ghc-haskell-lexer)

From cfd1a7d0663402d6c180db22e932567add683a4c Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:37:02 -0400
Subject: [PATCH 240/909] gnu: ghc-sdl-image: Update to 0.6.2.0.

* gnu/packages/haskell.scm (ghc-sdl-image): Update to 0.6.2.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4a5a7a9f5b..59fbb514c1 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1406,7 +1406,7 @@ MIDI, Ogg Vorbis, and SMPEG MP3 libraries.")
 (define-public ghc-sdl-image
   (package
     (name "ghc-sdl-image")
-    (version "0.6.1.2")
+    (version "0.6.2.0")
     (source
      (origin
        (method url-fetch)
@@ -1416,7 +1416,7 @@ MIDI, Ogg Vorbis, and SMPEG MP3 libraries.")
              ".tar.gz"))
        (sha256
         (base32
-         "1ybdwlqi5nqzpsbh2md5mxhwmjn910iqysf6nykwjxlmvhcjk281"))))
+         "1gxwrvswgwjw6g7ym52gik22l9l3ljy592phv97jdmcf3gi6qcg1"))))
     (build-system haskell-build-system)
     (arguments
      `(#:configure-flags

From 214fae871ba3a6a19c43993d98c40514b1880045 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:39:10 -0400
Subject: [PATCH 241/909] gnu: ghc-sdl-mixer: Update to 0.6.3.0.

* gnu/packages/haskell.scm (ghc-sdl-mixer): Update to 0.6.3.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 59fbb514c1..99d056e62f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1375,7 +1375,7 @@ award winning Linux port of \"Civilization: Call To Power.\"")
 (define-public ghc-sdl-mixer
   (package
     (name "ghc-sdl-mixer")
-    (version "0.6.2.0")
+    (version "0.6.3.0")
     (source
      (origin
        (method url-fetch)
@@ -1385,7 +1385,7 @@ award winning Linux port of \"Civilization: Call To Power.\"")
              ".tar.gz"))
        (sha256
         (base32
-         "1fhray79d80dk2aj9mx3ks05mm48sd832g8zgxli226jx471fs8r"))))
+         "0k26hqgdh789ka3mv4dsk6rin6x6vwcs6hjmnsqq7j3mnrh1342r"))))
     (build-system haskell-build-system)
     (arguments
      `(#:configure-flags

From c9fa2a286ceff8495e2c9bdfcce94c15468677ef Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:39:29 -0400
Subject: [PATCH 242/909] gnu: ghc-statevar: Update to 1.1.1.1.

* gnu/packages/haskell.scm (ghc-statevar): Update to 1.1.1.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 99d056e62f..b70df5bf2e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4637,7 +4637,7 @@ call stacks with different versions of the compiler.")
 (define-public ghc-statevar
   (package
     (name "ghc-statevar")
-    (version "1.1.0.4")
+    (version "1.1.1.1")
     (source
      (origin
        (method url-fetch)
@@ -4647,7 +4647,7 @@ call stacks with different versions of the compiler.")
              ".tar.gz"))
        (sha256
         (base32
-         "1dzz9l0haswgag9x56q7n57kw18v7nhmzkjyr61nz9y9npn8vmks"))))
+         "08r2iw0gdmfs4f6wraaq19vfmkjdbics3dbhw39y7mdjd98kcr7b"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-stm" ,ghc-stm)))

From 70ee3228bb4125814c7812c4a36352031040e9a3 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 16:40:07 -0400
Subject: [PATCH 243/909] gnu: ghc-tagged: Update Cabal file to r2.

* gnu/packages/haskell.scm (ghc-tagged): Update Cabal file to r2.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b70df5bf2e..881936efb5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4427,6 +4427,9 @@ periodic, on-demand actions in Haskell.")
         (base32
          "16cdzh0bw16nvjnyyy5j9s60malhz4nnazw96vxb0xzdap4m2z74"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("2" "0r2knfcq0b4s652vlvlnfwxlc2mkc2ra9kl8bp4zdn1awmfy0ia5")))
     (inputs
      `(("ghc-transformers-compat" ,ghc-transformers-compat)))
     (home-page "https://hackage.haskell.org/package/tagged")

From 44f717efff4b2d789597ee00b94f0d12dd4df1bc Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:08:57 -0400
Subject: [PATCH 244/909] gnu: ghc-text: Update to 1.2.3.0.

* gnu/packages/haskell.scm (ghc-text): Update to 1.2.3.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 881936efb5..7d59b5ada5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2149,7 +2149,7 @@ are not exception safe and can be broken by @code{killThread}.")
 (define-public ghc-text
   (package
     (name "ghc-text")
-    (version "1.2.2.2")
+    (version "1.2.3.0")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -2160,7 +2160,7 @@ are not exception safe and can be broken by @code{killThread}.")
              ".tar.gz"))
        (sha256
         (base32
-         "1y9d0zjs2ls0c574mr5xw7y3y49s62sd3wcn9lhpwz8a6q352iii"))))
+         "06iir7q99rnffzxi8gagn8w1k9m49368sbidgz634fv1gxib3q10"))))
     (build-system haskell-build-system)
     ;; The test dependencies depend on ghc-text: ghc-test-framework -> ghc-xml -> ghc-text
     (arguments `(#:tests? #f))

From 08c3993f4f4cdb323aa79bc7de6dce6a6324050d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 21:12:41 -0400
Subject: [PATCH 245/909] gnu: ghc-th-lift: Update to 0.7.11.

* gnu/packages/haskell.scm (ghc-th-lift): Update to 0.7.11.
[inputs]: Add ghc-th-abstraction.
---
 gnu/packages/haskell.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7d59b5ada5..63a7825ed4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5622,15 +5622,17 @@ Template Haskell.")
 (define-public ghc-th-lift
   (package
     (name "ghc-th-lift")
-    (version "0.7.8")
+    (version "0.7.11")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "th-lift/th-lift-" version ".tar.gz"))
               (sha256
                (base32
-                "0ay10b78x3969rpqqrgzy8srkl6iby2cljbf3mm17na8x22k7y1c"))))
+                "131360zxb0hazbqwbkk6ab2p77jkxr79bwwm618mrwrwkm3x2g6m"))))
     (build-system haskell-build-system)
+    (inputs
+     `(("ghc-th-abstraction" ,ghc-th-abstraction)))
     (home-page "https://github.com/mboes/th-lift")
     (synopsis "Derive Template Haskell's Lift class for datatypes")
     (description

From 9b6d49e84ab6e3f30753d247437f659c66a8bcd7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:09:31 -0400
Subject: [PATCH 246/909] gnu: ghc-time-locale-compat: Update to 0.1.1.5.

* gnu/packages/haskell.scm (ghc-time-locale-compat): Update to 0.1.1.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 63a7825ed4..7d63ec7596 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2802,7 +2802,7 @@ with slicing and Clang-style colored diagnostics.")
 (define-public ghc-time-locale-compat
   (package
     (name "ghc-time-locale-compat")
-    (version "0.1.1.3")
+    (version "0.1.1.5")
     (source
      (origin
        (method url-fetch)
@@ -2811,7 +2811,7 @@ with slicing and Clang-style colored diagnostics.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1vdcfr2hp9qh3ag90x6ikbdf42wiqpdylnplffna54bpnilbyi4i"))))
+         "0b2hmj8wwrfkndwzgm11qr496ca2ahwdxcj3m0ii91bxvrk1bzq7"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-old-locale" ,ghc-old-locale)))
     (home-page "https://github.com/khibino/haskell-time-locale-compat")

From f46cbe1ec4312f3b2e234f1806612b5a60cd74d4 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:09:48 -0400
Subject: [PATCH 247/909] gnu: ghc-transformers-base: Update to 0.4.5.2.

* gnu/packages/haskell.scm (ghc-transformers-base): Update to 0.4.5.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7d63ec7596..b778e603c8 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2397,7 +2397,7 @@ Hashing\" by Claessen, Pałka for details and the rationale of the design.")
 (define-public ghc-transformers-base
   (package
     (name "ghc-transformers-base")
-    (version "0.4.4")
+    (version "0.4.5.2")
     (source
      (origin
        (method url-fetch)
@@ -2407,7 +2407,7 @@ Hashing\" by Claessen, Pałka for details and the rationale of the design.")
              ".tar.gz"))
        (sha256
         (base32
-         "11r3slgpgpra6zi2kjg3g60gvv17b1fh6qxipcpk8n86qx7lk8va"))))
+         "1s256bi0yh0x2hp2gwd30f3mg1cv53zz397dv1yhfsnfzmihrj6h"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-stm" ,ghc-stm)

From 2a7c296a5df83c42537ea6fc09ef4c96d443a405 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:10:12 -0400
Subject: [PATCH 248/909] gnu: ghc-blaze-builder: Update to 0.4.1.0.

* gnu/packages/haskell.scm (ghc-blaze-builder): Update to 0.4.1.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b778e603c8..2d6b9ebd25 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4209,7 +4209,7 @@ pragmas in your code.")
 (define-public ghc-blaze-builder
   (package
     (name "ghc-blaze-builder")
-    (version "0.4.0.2")
+    (version "0.4.1.0")
     (source
      (origin
        (method url-fetch)
@@ -4219,7 +4219,7 @@ pragmas in your code.")
              ".tar.gz"))
        (sha256
         (base32
-         "1m33y6p5xldni8p4fzg8fmsyqvkfmnimdamr1xjnsmgm3dkf9lws"))))
+         "05681dih2d8s96an945wkbwl05w8ddbcfx8n3r3ck79ydyb8pz4i"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f))          ; FIXME: Missing test libraries.
     (inputs

From 343c23988ad70f3760691ef1cade25a6a20215bd Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 22:53:34 -0400
Subject: [PATCH 249/909] gnu: ghc-system-filepath-bootstrap: Update to 0.4.14.

* gnu/packages/haskell.scm (ghc-system-filepath-bootstrap): Update to 0.4.14.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 2d6b9ebd25..16638af2c5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7278,7 +7278,7 @@ instance of @code{MonadBase} or @code{MonadBaseControl}.")
 (define ghc-system-filepath-bootstrap
   (package
     (name "ghc-system-filepath-bootstrap")
-    (version "0.4.13.4")
+    (version "0.4.14")
     (source
      (origin
        (method url-fetch)
@@ -7287,7 +7287,7 @@ instance of @code{MonadBase} or @code{MonadBaseControl}.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1yy5zsmmimhg6iaw9fmpwrxvxrgi5s6bfyqfihdsnx4bjvn7sp9l"))))
+         "14yras4pz2dh55xpwmazcgxijvi8913pjgzb9iw50mjq1lycwmhn"))))
     (build-system haskell-build-system)
     (arguments
      `(#:tests? #f))

From 6a9730a0c41b7033a600593b2c2720d610919126 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:11:55 -0400
Subject: [PATCH 250/909] gnu: ghc-chell: Update to 0.4.0.2.

* gnu/packages/haskell.scm (ghc-chell): Update to 0.4.0.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 16638af2c5..8ef95a4800 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7399,7 +7399,7 @@ easily work with command-line options.")
 (define-public ghc-chell
   (package
     (name "ghc-chell")
-    (version "0.4.0.1")
+    (version "0.4.0.2")
     (source
      (origin
        (method url-fetch)
@@ -7408,7 +7408,7 @@ easily work with command-line options.")
              version ".tar.gz"))
        (sha256
         (base32
-         "0lb95abzxl4a87nfqxsxpb3a39pd52cci43hcvj8615hyhqvs2jz"))))
+         "10ingy9qnbmc8cqh4i9pskcw43l0mzk8f3d76b3qz3fig5ary3j9"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-options-bootstrap" ,ghc-options-bootstrap)

From 0ceaff6f2fb463cf96b461fc78062128cda20be0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:12:56 -0400
Subject: [PATCH 251/909] gnu: ghc-cmark-gfm: Update to 0.1.5.

* gnu/packages/haskell.scm (ghc-cmark-gfm): Update to 0.1.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 8ef95a4800..be26a146d7 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5488,7 +5488,7 @@ sources, and does not require prior installation of the C library.")
 (define-public ghc-cmark-gfm
   (package
     (name "ghc-cmark-gfm")
-    (version "0.1.3")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
@@ -5497,7 +5497,7 @@ sources, and does not require prior installation of the C library.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1fkisbrydmdx5h8yad09fzk8h1b1j53r02g7vb81izgdwj9b673k"))))
+         "13b0mqks5c1q989slgsa3ixr5vvkfyic4ynzgv00kgl5qrs7hqk7"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-text" ,ghc-text)))

From 8d75edc01055712004598d66d6d5875e31ff61a8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:13:30 -0400
Subject: [PATCH 252/909] gnu: ghc-mime-types: Update to 0.1.0.8.

* gnu/packages/haskell-web.scm (ghc-mime-types): Update to 0.1.0.8.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 190bec8dd2..54eedf5044 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -688,7 +688,7 @@ Haskell.")
 (define-public ghc-mime-types
   (package
     (name "ghc-mime-types")
-    (version "0.1.0.7")
+    (version "0.1.0.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -696,7 +696,7 @@ Haskell.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1fg9cqpp5lswk8ajlq4f41n12c2v2naz179l8dsz6zisjqj4l5l3"))))
+                "14ccl2842ya17zyj0bpc7vzklbyqvvydpbypn69h2fmhgji192x8"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-text" ,ghc-text)))

From d9c620bab0e84ddb882a608027b4d0a537a66c4d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:13:59 -0400
Subject: [PATCH 253/909] gnu: ghc-monad-control: Update to 1.0.2.3.

* gnu/packages/haskell.scm (ghc-monad-control): Update to 1.0.2.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index be26a146d7..1050777b43 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4088,7 +4088,7 @@ monads with anaphoric variants on @code{if} and @code{when} and a C-like
 (define-public ghc-monad-control
   (package
     (name "ghc-monad-control")
-    (version "1.0.1.0")
+    (version "1.0.2.3")
     (source
      (origin
        (method url-fetch)
@@ -4097,7 +4097,7 @@ monads with anaphoric variants on @code{if} and @code{when} and a C-like
              "/monad-control-" version ".tar.gz"))
        (sha256
         (base32
-         "1x018gi5irznx5rgzmkr2nrgh26r8cvqwkcfc6n6y05pdjf21c6l"))))
+         "1c92833gr6cadidjdp8mlznkpp8lyxl0w3y7d19y8yi3klc3843c"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-stm" ,ghc-stm)

From 8ebdab0dc4fa389f5238203eb785a1d17cb1d478 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:14:39 -0400
Subject: [PATCH 254/909] gnu: ghc-parsec: Update to 3.1.13.0.

* gnu/packages/haskell.scm (ghc-parsec): Update to 3.1.13.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 1050777b43..7994b6c33c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3712,7 +3712,7 @@ mainstream languages.")
 (define-public ghc-parsec
   (package
     (name "ghc-parsec")
-    (version "3.1.11")
+    (version "3.1.13.0")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -3722,7 +3722,7 @@ mainstream languages.")
              version
              ".tar.gz"))
        (sha256
-        (base32 "0vk7q9j2128q191zf1sg0ylj9s9djwayqk9747k0a5fin4f2b1vg"))))
+        (base32 "1wc09pyn70p8z6llink10c8pqbh6ikyk554911yfwxv1g91swqbq"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)))

From 09b52698babe9a09a4f0aba2f34e1732094b88a1 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 13:20:13 -0400
Subject: [PATCH 255/909] gnu: ghc-quickcheck: Update to 2.11.3.

This commit also removes extra versions of ghc-quickcheck that have no
dependents.

* gnu/packages/haskell-check.scm (ghc-quickcheck): Update to 2.11.3.
[arguments]: Remove "-f base4" configure flag.
(ghc-quickcheck-latest): Delete variable.
(ghc-quickcheck-2.9): Delete variable.
---
 gnu/packages/haskell-check.scm | 34 +++-------------------------------
 1 file changed, 3 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 4324c9c44d..57e7f0edc1 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -421,7 +421,7 @@ use HUnit assertions as QuickCheck properties.")
 (define-public ghc-quickcheck
   (package
     (name "ghc-quickcheck")
-    (version "2.10.1")
+    (version "2.11.3")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -432,11 +432,10 @@ use HUnit assertions as QuickCheck properties.")
              ".tar.gz"))
        (sha256
         (base32
-         "1rfmns3lj3hl93k1jws85ajkkw7z9ll8cw292n9m7zald1w5dfqx"))))
+         "0xhqk35fkzlbjcqbabg6962jkv8d688nzmz7ng4bm84x2d95d328"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:tests? #f  ; FIXME: currently missing libraries used for tests.
-       #:configure-flags '("-f base4")))
+     `(#:tests? #f))  ; FIXME: currently missing libraries used for tests.
     (inputs
      `(("ghc-random" ,ghc-random)
        ("ghc-tf-random" ,ghc-tf-random)))
@@ -450,33 +449,6 @@ hold in a large number of randomly generated cases.  Specifications are
 expressed in Haskell, using combinators defined in the QuickCheck library.")
     (license license:bsd-3)))
 
-(define-public ghc-quickcheck-2.9
-  (package
-    (inherit ghc-quickcheck)
-    (name "ghc-quickcheck")
-    (version "2.9.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://hackage.haskell.org/package/QuickCheck-2.9.2/QuickCheck-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "119np67qvx8hyp9vkg4gr2wv3lj3j6ay2vl4hxspkg43ymb1cp0m"))))))
-
-(define-public ghc-quickcheck-latest
-  (package (inherit ghc-quickcheck)
-    (version "2.11.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://hackage.haskell.org/package/QuickCheck/QuickCheck-"
-             version
-             ".tar.gz"))
-       (sha256
-        (base32
-         "0xhqk35fkzlbjcqbabg6962jkv8d688nzmz7ng4bm84x2d95d328"))))))
-
 (define-public ghc-test-framework
   (package
     (name "ghc-test-framework")

From e7e74518221a97496d8e1e4b0de61ccf25135ae9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:17:08 -0400
Subject: [PATCH 256/909] gnu: ghc-reflection: Update to 2.1.4.

* gnu/packages/haskell.scm (ghc-reflection): Update to 2.1.4.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7994b6c33c..5df71e87e7 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1649,7 +1649,7 @@ unlit literate code files; and an option to turn off macro-expansion.")
 (define-public ghc-reflection
   (package
     (name "ghc-reflection")
-    (version "2.1.2")
+    (version "2.1.4")
     (source
      (origin
        (method url-fetch)
@@ -1659,7 +1659,7 @@ unlit literate code files; and an option to turn off macro-expansion.")
              ".tar.gz"))
        (sha256
         (base32
-         "0f9w0akbm6p8h7kzgcd2f6nnpw1wy84pqn45vfz1ch5j0hn8h2d9"))))
+         "0kf4a5ijw6jfnfibjcrpdy9vzh1n6v2pxia8dhyyqdissiwc8bzj"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-tagged" ,ghc-tagged)))
     (home-page "https://github.com/ekmett/reflection")

From 80d06b8d98094a1f0661264e9b6cedae7ebe7cfe Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:17:57 -0400
Subject: [PATCH 257/909] gnu: ghc-syb: Update to 0.7.

* gnu/packages/haskell.scm (ghc-syb): Update to 0.7.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5df71e87e7..ae708bd94b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3447,7 +3447,7 @@ to cases.")
 (define-public ghc-syb
   (package
     (name "ghc-syb")
-    (version "0.6")
+    (version "0.7")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -3458,7 +3458,7 @@ to cases.")
              ".tar.gz"))
        (sha256
         (base32
-         "1p3cnqjm13677r4a966zffzhi9b3a321aln8zs8ckqj0d9z1z3d3"))))
+         "1da2zz7gqm4xbkx5vpd74dayx1svaxyl145fl14mq15lbb77sxdq"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hunit" ,ghc-hunit)))

From 0588525b0612b394fb1ce18571206c27e4c8f8be Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:18:23 -0400
Subject: [PATCH 258/909] gnu: ghc-unix-time: Update to 0.3.8.

* gnu/packages/haskell.scm (ghc-unix-time): Update to 0.3.8.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ae708bd94b..b3441650be 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2447,7 +2447,7 @@ but also need those types.")
 (define-public ghc-unix-time
   (package
     (name "ghc-unix-time")
-    (version "0.3.7")
+    (version "0.3.8")
     (source
      (origin
        (method url-fetch)
@@ -2457,7 +2457,7 @@ but also need those types.")
              ".tar.gz"))
        (sha256
         (base32
-         "1qdlc9raih8s0m3x8x3n7q3ngh4faw2alv9l78sp6gnx648k0c8i"))))
+         "051slgpid5cxiaw203ky0ql3823h28fcjs08axkzd4265wrvv8fw"))))
     (build-system haskell-build-system)
     (arguments
      `(#:tests? #f)) ; FIXME: Test fails with "System.Time not found".  This

From 7de7ec7d45e46232771be423b8e575383f154642 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:19:15 -0400
Subject: [PATCH 259/909] gnu: ghc-alex: Update to 3.2.4.

* gnu/packages/haskell.scm (ghc-alex): Update to 3.2.4.
[arguments]: Add a phase to set environment variables for tests.
[native-inputs]: Add which.
---
 gnu/packages/haskell.scm | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b3441650be..f1c358065b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -994,7 +994,7 @@ package are to parse or generate Haskell 98 code.")
 (define-public ghc-alex
   (package
     (name "ghc-alex")
-    (version "3.2.3")
+    (version "3.2.4")
     (source
      (origin
        (method url-fetch)
@@ -1004,9 +1004,20 @@ package are to parse or generate Haskell 98 code.")
              ".tar.gz"))
        (sha256
         (base32
-         "0bi1cs9b8ir33h1fl6x2xw4ymygapqbr713ridpf7rmk2wa7jqqs"))))
+         "0cpjixgsr0b2x4s6hz4aa6gnmjw9i7xd9nlfi8m37zqlidq4v3nm"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-check-variables
+           (lambda _
+             (setenv "PATH" (string-append (getcwd) "/dist/build/alex:"
+                                           (getenv "PATH")))
+             (setenv "alex_datadir" (string-append (getcwd) "/data"))
+             #t)))))
     (inputs `(("ghc-quickcheck" ,ghc-quickcheck)))
+    (native-inputs
+     `(("which" ,which)))
     (home-page "https://www.haskell.org/alex/")
     (synopsis
      "Tool for generating lexical analysers in Haskell")

From fa9c33dc8e012316f3dc3d4d6d0aa7e6cd7df70d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:19:48 -0400
Subject: [PATCH 260/909] gnu: ghc-chasingbottoms: Update to 1.3.1.4.

* gnu/packages/haskell.scm (ghc-chasingbottoms): Update to 1.3.1.4.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index f1c358065b..c4eee42a6a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3518,7 +3518,7 @@ encourages inductive, recursive definitions of graph algorithms.")
 (define-public ghc-chasingbottoms
   (package
     (name "ghc-chasingbottoms")
-    (version "1.3.1.3")
+    (version "1.3.1.4")
     (source
      (origin
        (method url-fetch)
@@ -3526,7 +3526,7 @@ encourages inductive, recursive definitions of graph algorithms.")
                            "ChasingBottoms-" version ".tar.gz"))
        (sha256
         (base32
-         "04jwwjs22mqc4hvpp4c3gpb79inrrq5sapks5khknspv2hslm61q"))))
+         "06cynx6hcbfpky7qq3b3mjjgwbnaxkwin3znbwq4b9ikiw0ng633"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From 4a3f50e36c09e18e10be894141ea996fcae1aa52 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 22:42:54 -0400
Subject: [PATCH 261/909] gnu: ghc-chell-quickcheck: Allow newer QuickCheck.

* gnu/packages/haskell.scm (ghc-chell-quickcheck)[arguments]: Add a phase
that patches the Cabal file to allow newer versions of QuickCheck.
(ghc-chell-quickcheck-bootstrap)[arguments]: Ditto.
---
 gnu/packages/haskell.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c4eee42a6a..1294671e76 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7455,7 +7455,14 @@ testing strategies.")
        ("ghc-random" ,ghc-random)
        ("ghc-quickcheck" ,ghc-quickcheck)))
     (arguments
-     `(#:tests? #f))
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "chell-quickcheck.cabal"
+               (("QuickCheck >= 2\\.3 && < 2\\.11")
+                "QuickCheck >= 2.3 && < 2.12")))))))
     (home-page "https://john-millikin.com/software/chell/")
     (synopsis "QuickCheck support for the Chell testing library")
     (description "More complex tests for @code{chell}.")
@@ -7475,6 +7482,14 @@ testing strategies.")
         (base32
          "1iicsys9igx7m7n4l2b8djardmjy2ah5ibzp7kzs758h460fq53a"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "chell-quickcheck.cabal"
+               (("QuickCheck >= 2\\.3 && < 2\\.11")
+                "QuickCheck >= 2.3 && < 2.12")))))))
     (inputs
      `(("ghc-chell" ,ghc-chell)
        ("ghc-chell-quickcheck-bootstrap" ,ghc-chell-quickcheck-bootstrap)

From 38922e49ca4f62e8e10fad8c0a3ee58a4e49d45d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:22:21 -0400
Subject: [PATCH 262/909] gnu: ghc-edisoncore: Update to 1.3.2.1.

* gnu/packages/haskell.scm (ghc-edisoncore): Update to 1.3.2.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 1294671e76..86ec0b2cd5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4032,14 +4032,14 @@ finite maps and priority queues where the priority and element are distinct.")
 (define-public ghc-edisoncore
   (package
     (name "ghc-edisoncore")
-    (version "1.3.1.1")
+    (version "1.3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://hackage.haskell.org/package/EdisonCore"
                            "/EdisonCore-" version ".tar.gz"))
        (sha256
-        (base32 "06shxmcqxcahcn6zgl64vlqix4fnq53d97drcgsh94qp7gp201ry"))))
+        (base32 "0fgj5iwiv3v2gdgx7kjcr15dcs4x1kvmjspp3p99wyhh0x6h3ikk"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From 3ea018c7428d3a08a143dcf917bea0e89bf8f704 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:24:24 -0400
Subject: [PATCH 263/909] gnu: ghc-haskell-src: Update to 1.0.3.0.

* gnu/packages/haskell.scm (ghc-haskell-src): Update to 1.0.3.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 86ec0b2cd5..44e8960b5e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -965,7 +965,7 @@ them.")
 (define-public ghc-haskell-src
   (package
     (name "ghc-haskell-src")
-    (version "1.0.2.0")
+    (version "1.0.3.0")
     (source
      (origin
        (method url-fetch)
@@ -975,7 +975,7 @@ them.")
              ".tar.gz"))
        (sha256
         (base32
-         "19lilhpwnjb7cks9fq1ipnc8f7dwxy0ri3dgjkdxs3i355byw99a"))))
+         "1g4dj1f0j68bhn4ixfac63wjzy6gsp6kwgxryb1k5nl3i0g99d5l"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-happy" ,ghc-happy)

From 568cafd56a341266dd3926e54136610728e7ba28 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:27:11 -0400
Subject: [PATCH 264/909] gnu: ghc-hs-bibutils: Update to 6.6.0.0.

* gnu/packages/haskell.scm (ghc-hs-bibutils): Update to 6.6.0.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 44e8960b5e..101fca3a0e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6543,7 +6543,7 @@ provided for those who need a drop-in replacement for Markdown.pl.")
 (define-public ghc-hs-bibutils
   (package
     (name "ghc-hs-bibutils")
-    (version "6.2.0.1")
+    (version "6.6.0.0")
     (source
      (origin
        (method url-fetch)
@@ -6552,7 +6552,7 @@ provided for those who need a drop-in replacement for Markdown.pl.")
              version ".tar.gz"))
        (sha256
         (base32
-         "0c56sjgg82kjcg5rrplnyn7vf02ccsj3kkcbgc87zxlv0j880rjb"))))
+         "0n2sz2zl4naspryd49ii858qkjp2lapns5a2gr8zm6vvn5sh1f0l"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-syb" ,ghc-syb)))
     (home-page "https://hackage.haskell.org/package/hs-bibutils")

From ddfb799e5d3dda9c773ec752f5638433c0a65185 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:31:17 -0400
Subject: [PATCH 265/909] gnu: ghc-indents: Update to 0.5.0.0.

* gnu/packages/haskell.scm (ghc-indents): Update to 0.5.0.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 101fca3a0e..fa00f68b83 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2509,7 +2509,7 @@ isn't available, portable implementations are used.")
 (define-public ghc-indents
   (package
     (name "ghc-indents")
-    (version "0.3.3")
+    (version "0.5.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2517,7 +2517,7 @@ isn't available, portable implementations are used.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "16lz21bp9j14xilnq8yym22p3saxvc9fsgfcf5awn2a6i6n527xn"))))
+                "1ly3v41jacc6lrsvg4j3m5a6zs90gr8dyif5m6bf34hj1k5cgg0n"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-parsec" ,ghc-parsec)

From 1a8f5eb2e1b4e0bfe36010ca6bfb568618ecc588 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:32:04 -0400
Subject: [PATCH 266/909] gnu: ghc-json: Update to 0.9.2.

* gnu/packages/haskell.scm (ghc-json): Update to 0.9.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index fa00f68b83..c8dcefeb12 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8101,7 +8101,7 @@ handled safely, this is what you're left with.")
 (define-public ghc-json
   (package
     (name "ghc-json")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
@@ -8109,7 +8109,7 @@ handled safely, this is what you're left with.")
                            "json-" version ".tar.gz"))
        (sha256
         (base32
-         "18l5027vc68hnnxrxlnyl59vkkg95a92m1zzms0dqiby2r6pxdcn"))))
+         "13kkfgx58z18jphbg56jn08jn72wi3kvfndlwwx87hqwg7x1dfz6"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-syb" ,ghc-syb)

From 4a2100b8ae3dd3297f2748f312da3586795776bd Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:32:40 -0400
Subject: [PATCH 267/909] gnu: ghc-lifted-base: Update to 0.2.3.12.

* gnu/packages/haskell.scm (ghc-lifted-base): Update to 0.2.3.12.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c8dcefeb12..f195563516 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5074,7 +5074,7 @@ It is modeled after doctest for Python, see
 (define-public ghc-lifted-base
   (package
     (name "ghc-lifted-base")
-    (version "0.2.3.8")
+    (version "0.2.3.12")
     (source
      (origin
        (method url-fetch)
@@ -5084,7 +5084,7 @@ It is modeled after doctest for Python, see
              ".tar.gz"))
        (sha256
         (base32
-         "17yz4n7q96x4cp8vxai8csn2vmpigxvipkfh48arahf91f0xy18n"))))
+         "1i8p8d3rkdh21bhgjjh32vd7qqjr7jq7p59qds0aw2kmargsjd61"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: Missing testing libraries.
     (inputs

From 4729cfacebe95de6283a4e9efca319f3af400991 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:33:13 -0400
Subject: [PATCH 268/909] gnu: ghc-multipart: Update to 0.1.3.

* gnu/packages/haskell-web.scm (ghc-multipart): Update to 0.1.3.
[inputs]: Add ghc-stringsearch.
---
 gnu/packages/haskell-web.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 54eedf5044..bb4f419e66 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -911,7 +911,7 @@ of a JSON value into a @code{Data.Aeson.Value}.")
 (define-public ghc-multipart
   (package
     (name "ghc-multipart")
-    (version "0.1.2")
+    (version "0.1.3")
     (source
      (origin
        (method url-fetch)
@@ -921,9 +921,11 @@ of a JSON value into a @code{Data.Aeson.Value}.")
              ".tar.gz"))
        (sha256
         (base32
-         "0g04jhyw1ib1s7c9bcldyyn4n90qd9x7dmvic4vgq57bgcqgnhz5"))))
+         "1x4n4yyva22dhfr1pg5ki112qvvzb4hyd7bwpm189iq4gcp52q4z"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-parsec" ,ghc-parsec)))
+    (inputs
+     `(("ghc-parsec" ,ghc-parsec)
+       ("ghc-stringsearch" ,ghc-stringsearch)))
     (home-page
      "http://www.github.com/silkapp/multipart")
     (synopsis

From 3e6fe51f9a332315e9d90c3b0e6cd8299b7df3b8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:35:41 -0400
Subject: [PATCH 269/909] gnu: ghc-regex-tdfa: Update to 1.2.3.1.

* gnu/packages/haskell.scm (ghc-regex-tdfa): Update to 1.2.3.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index f195563516..f44eadbbe8 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6876,7 +6876,7 @@ regular expressions.  Parsers can be built using Applicative interface.")
 (define-public ghc-regex-tdfa
   (package
     (name "ghc-regex-tdfa")
-    (version "1.2.2")
+    (version "1.2.3.1")
     (source
      (origin
        (method url-fetch)
@@ -6885,7 +6885,7 @@ regular expressions.  Parsers can be built using Applicative interface.")
              version ".tar.gz"))
        (sha256
         (base32
-         "0f8x8wyr6m21g8dnxvnvalz5bsq37l125l6qhs0fscbvprsxc4nb"))))
+         "0l7ajnh4hpgggf2a1r9dg0hx2fy679vd2kada5y7r02hy3nfxala"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-parsec" ,ghc-parsec)

From 17539a7ed1abba1f69045baf505581d0b5f2ccd2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:59:40 -0400
Subject: [PATCH 270/909] gnu: ghc-safe: Update to 0.3.17.

* gnu/packages/haskell.scm (ghc-safe): Update to 0.3.17.
[native-inputs]: Add ghc-quickcheck.
---
 gnu/packages/haskell.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index f44eadbbe8..a4bb28eecd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3144,7 +3144,7 @@ style.")
 (define-public ghc-safe
   (package
     (name "ghc-safe")
-    (version "0.3.9")
+    (version "0.3.17")
     (source
      (origin
        (method url-fetch)
@@ -3154,8 +3154,10 @@ style.")
              ".tar.gz"))
        (sha256
         (base32
-         "1jdnp5zhvalf1xy8i872n29nljfjz6lnl9ghj80ffisrnnkrwcfh"))))
+         "0p3yaf5slvyz1cyy51jq64c5rlp8yzwim8iy2dlnk42if4gc9ibr"))))
     (build-system haskell-build-system)
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)))
     (home-page "https://github.com/ndmitchell/safe#readme")
     (synopsis "Library of safe (exception free) functions")
     (description "This library provides wrappers around @code{Prelude} and

From 5285d61490f1c4fbdbdc82ad6e6daaab863e1a46 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:36:52 -0400
Subject: [PATCH 271/909] gnu: ghc-split: Update to 0.2.3.3.

* gnu/packages/haskell.scm (ghc-split): Update to 0.2.3.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a4bb28eecd..a555cea5e9 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3700,7 +3700,7 @@ colored output using the ansi-terminal package.")
 (define-public ghc-split
   (package
     (name "ghc-split")
-    (version "0.2.3.1")
+    (version "0.2.3.3")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -3711,7 +3711,7 @@ colored output using the ansi-terminal package.")
              ".tar.gz"))
        (sha256
         (base32
-         "12660m16c6sib3laaxn6w9s453pyx1b49myrmzfij372vq5bc5bn"))))
+         "04qlmkcyklznl03gsjg95b4nzb6i96gdapqg60rny9szgi7ngk8x"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)))

From 46f8898118ae2b27d42c005a520064d5c53c0ab9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:37:49 -0400
Subject: [PATCH 272/909] gnu: ghc-th-expand-syns: Update to 0.4.4.0.

* gnu/packages/haskell.scm (ghc-th-expand-syns): Update to 0.4.4.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a555cea5e9..2601db0a99 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5682,7 +5682,7 @@ instances.  This package provides orphan instances for @code{containers},
 (define-public ghc-th-expand-syns
   (package
     (name "ghc-th-expand-syns")
-    (version "0.4.0.0")
+    (version "0.4.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -5690,7 +5690,7 @@ instances.  This package provides orphan instances for @code{containers},
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1sjy7a17zwyvlbkc8gklii67sy78wpnw35fyb00lsbnpk4cryd2r"))))
+                "01prlvh3py5hq5ccjidfyp9ixq2zd88dkbsidyjrpkja6v8m43yc"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-syb" ,ghc-syb)))

From 9e3e6ee026c95deafef7f4532a1333863f3e5d81 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:39:54 -0400
Subject: [PATCH 273/909] gnu: ghc-utility-ht: Update to 0.0.14.

* gnu/packages/haskell.scm (ghc-utility-ht): Update to 0.0.14.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 2601db0a99..575a7be4a8 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7808,14 +7808,14 @@ Accessor to access state in transformers State monad.")
 (define-public ghc-utility-ht
   (package
     (name "ghc-utility-ht")
-    (version "0.0.12")
+    (version "0.0.14")
     (home-page "https://hackage.haskell.org/package/utility-ht")
     (source
      (origin
        (method url-fetch)
        (uri (string-append home-page "/utility-ht-" version ".tar.gz"))
        (sha256
-        (base32 "1vq5bd51rl9l5lgfmaqxgiggddk38hzgngcj7qgrqnalcd1myi54"))))
+        (base32 "1a7bgk7wv7sqbxbiv7kankiimr3wij7zdm7s83zwsf886ghyxhk9"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-quickcheck" ,ghc-quickcheck)))
     (synopsis "Haskell helper functions for Lists, Maybes, Tuples, Functions")

From 57203a15cb2d1c6164b20d16cbb60c02b63dc305 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 30 Aug 2018 10:57:38 -0400
Subject: [PATCH 274/909] gnu: ghc-vector: Update Cabal file to r3.

* gnu/packages/haskell.scm (ghc-vector): Update Cabal file to r3.
---
 gnu/packages/haskell.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 575a7be4a8..caa8c681cc 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3823,7 +3823,10 @@ speed, flexibility, and quality of parse errors.")
     (build-system haskell-build-system)
     ;; FIXME: To simplify upgrading all Haskell packages, we leave the tests
     ;; disabled for now.
-    (arguments `(#:tests? #f))
+    (arguments
+     `(#:cabal-revision
+       ("3" "0y5rh8k710i2a3p1h2rghvr5cfg78p5h0kbfi7ifxqqf6pzlyr1x")
+       #:tests? #f))
     (inputs
      `(("ghc-primitive" ,ghc-primitive)
        ("ghc-random" ,ghc-random)

From 50eff0d5ff2d50038f652a44f12410160651c389 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:41:35 -0400
Subject: [PATCH 275/909] gnu: ghc-boxes: Update to 0.1.5.

* gnu/packages/haskell.scm (ghc-boxes): Update to 0.1.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index caa8c681cc..481502857b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5226,14 +5226,14 @@ notation}.")
 (define-public ghc-boxes
   (package
     (name "ghc-boxes")
-    (version "0.1.4")
+    (version "0.1.5")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://hackage.haskell.org/package/boxes/boxes-"
                            version ".tar.gz"))
        (sha256
-        (base32 "1n7xiplzd3s1a39nizwjcgsh3wi2348mp21c3fk19v98ialfjgjf"))))
+        (base32 "1hsnmw95i58d4bkpxby3ddsj1cawypw4mdyb18m393s5i8p7iq9q"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-split" ,ghc-split)

From 38f0d04e5971d4228824300f278cd7d6930d8893 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:43:08 -0400
Subject: [PATCH 276/909] gnu: ghc-juicypixels: Update to 3.2.9.5.

* gnu/packages/haskell.scm (ghc-juicypixels): Update to 3.2.9.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 481502857b..e1c81f28b2 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6003,7 +6003,7 @@ do on-demand loading.")
 (define-public ghc-juicypixels
   (package
     (name "ghc-juicypixels")
-    (version "3.2.9.3")
+    (version "3.2.9.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -6011,7 +6011,7 @@ do on-demand loading.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "14s57fgf6kd5n5al2kcvk1aaxbq1ph0r5h8blflrjkx83yl6r8yn"))))
+                "0mf3ihr0xy2wc2wzb9a17g0n3p60x7pvm8akwpvhdy8klvs6r744"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-zlib" ,ghc-zlib)

From 19b29882878a6558e5f16d587265eb3a0c0cdec6 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:43:52 -0400
Subject: [PATCH 277/909] gnu: ghc-language-c: Update to 0.8.1.

* gnu/packages/haskell.scm (ghc-language-c): Update to 0.8.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e1c81f28b2..aaf9f6c6a2 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7950,7 +7950,7 @@ dependency.")
 (define-public ghc-language-c
   (package
     (name "ghc-language-c")
-    (version "0.5.0")
+    (version "0.8.1")
     (source
      (origin
        (method url-fetch)
@@ -7958,7 +7958,7 @@ dependency.")
                            "language-c/language-c-" version ".tar.gz"))
        (sha256
         (base32
-         "08i2bl7jmmymn2sldzlbz6ig7lx3wfwhlpadzibs3fx72z08pmc6"))))
+         "0sdkjj0hq8p69fcdm6ljbjkjvrsrb8a6rl5dq6dj6byj32ajrm3d"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-syb" ,ghc-syb)))
     (native-inputs

From 5209fc22e1fe1c24f154b0eeecc2b5587aa64a1f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:46:48 -0400
Subject: [PATCH 278/909] gnu: ghc-th-reify-many: Update to 0.1.8.

* gnu/packages/haskell.scm (ghc-th-reify-many): Update to 0.1.8.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index aaf9f6c6a2..fce0c81c3e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5707,7 +5707,7 @@ instances.  This package provides orphan instances for @code{containers},
 (define-public ghc-th-reify-many
   (package
     (name "ghc-th-reify-many")
-    (version "0.1.6")
+    (version "0.1.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -5715,7 +5715,7 @@ instances.  This package provides orphan instances for @code{containers},
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1b76zjxkj0v0n8zj9l0nwav2irm0c43rx6qjihfw8klmmxvx59df"))))
+                "0hzy6hvhvcd6i60vx5cp2b7ggmnnjh9rx4h8bm8xw4grglcaxjnf"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-safe" ,ghc-safe)

From d9404fc122530b21e00ec3d150742d9c20dee66a Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:36:42 -0400
Subject: [PATCH 279/909] gnu: ghc-vector-algorithms: Update to 0.7.0.4.

* gnu/packages/haskell.scm (ghc-vector-algorithms): Update to 0.7.0.4.
[arguments]: Remove unneeded "--allow-newer=vector" configure flag; remove
test-patching phase.
[inputs]: Remove ghc-mwc-random.
---
 gnu/packages/haskell.scm | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index fce0c81c3e..6036a12ee1 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8490,7 +8490,7 @@ between 2 and 3 times faster than the Mersenne Twister.")
 (define-public ghc-vector-algorithms
   (package
     (name "ghc-vector-algorithms")
-    (version "0.7.0.1")
+    (version "0.7.0.4")
     (source
      (origin
        (method url-fetch)
@@ -8499,22 +8499,10 @@ between 2 and 3 times faster than the Mersenne Twister.")
                            "vector-algorithms-" version ".tar.gz"))
        (sha256
         (base32
-         "0w4hf598lpxfg58rnimcqxrbnpqq2jmpjx82qa5md3q6r90hlipd"))))
+         "0mfa8ig9v69l41p2vb5jl4qmaln5y1rlzarr2mlgm8g1nvq8qqdg"))))
     (build-system haskell-build-system)
-    ;; The limits have been adjusted in a revision of the cabal file.
-    (arguments
-     '(#:configure-flags (list "--allow-newer=vector")
-       #:phases
-       (modify-phases %standard-phases
-         ;; The tests cannot be built due to type errors.
-         (add-after 'unpack 'do-not-build-quickcheck-tests
-           (lambda _
-             (substitute* "vector-algorithms.cabal"
-               (("\\!flag\\(properties\\)") "True"))
-             #t)))))
     (inputs
-     `(("ghc-vector" ,ghc-vector)
-       ("ghc-mwc-random" ,ghc-mwc-random)))
+     `(("ghc-vector" ,ghc-vector)))
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)))
     (home-page "https://github.com/bos/math-functions")

From bc8bda501cb8d9156afe001a440589b893d7b110 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:37:21 -0400
Subject: [PATCH 280/909] gnu: ghc-test-framework: Update to 0.8.2.0.

* gnu/packages/haskell.scm (ghc-semigroups-bootstrap, ghc-hashable-bootstrap,
ghc-nats-bootstrap, ghc-unordered-containers-bootstrap): New variables for
breaking a dependency cycle with ghc-test-framework.
* gnu/packages/haskell-check.scm (ghc-test-framework): Update to 0.8.2.0.
[arguments]: Add a phase to patch the Cabal file to allow a newer QuickCheck.
[inputs]: Add ghc-semigroups-bootstrap.
---
 gnu/packages/haskell-check.scm | 16 +++++++++++----
 gnu/packages/haskell.scm       | 37 ++++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 57e7f0edc1..a9ff6af041 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -452,7 +452,7 @@ expressed in Haskell, using combinators defined in the QuickCheck library.")
 (define-public ghc-test-framework
   (package
     (name "ghc-test-framework")
-    (version "0.8.1.1")
+    (version "0.8.2.0")
     (source
      (origin
        (method url-fetch)
@@ -460,10 +460,17 @@ expressed in Haskell, using combinators defined in the QuickCheck library.")
                            "test-framework-" version ".tar.gz"))
        (sha256
         (base32
-         "0wxjgdvb1c4ykazw774zlx86550848wbsvgjgcrdzcgbb9m650vq"))))
+         "1hhacrzam6b8f10hyldmjw8pb7frdxh04rfg3farxcxwbnhwgbpm"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=time")))
+     `(#:tests? #f  ; FIXME: Tests do not build.
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "test-framework.cabal"
+               (("QuickCheck     >= 2\\.3 && < 2\\.10")
+                "QuickCheck     >= 2.3 && < 2.12")))))))
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-quickcheck" ,ghc-quickcheck)))
@@ -475,7 +482,8 @@ expressed in Haskell, using combinators defined in the QuickCheck library.")
        ("ghc-random" ,ghc-random)
        ("ghc-regex-posix" ,ghc-regex-posix)
        ("ghc-xml" ,ghc-xml)
-       ("ghc-libxml" ,ghc-libxml)))
+       ("ghc-libxml" ,ghc-libxml)
+       ("ghc-semigroups" ,ghc-semigroups-bootstrap)))
     (home-page "https://batterseapower.github.io/test-framework/")
     (synopsis "Framework for running and organising tests")
     (description
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6036a12ee1..a12e7e894b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2266,6 +2266,14 @@ data structures.  The package provides instances for basic types and a way to
 combine hash values.")
     (license license:bsd-3)))
 
+(define-public ghc-hashable-bootstrap
+  (package
+    (inherit ghc-hashable)
+    (name "ghc-hashable-bootstrap")
+    (arguments `(#:tests? #f))
+    (native-inputs '())
+    (properties '((hidden? #t)))))
+
 (define-public ghc-hashable-time
   (package
     (name "ghc-hashable-time")
@@ -3580,6 +3588,15 @@ optimized for performance critical use, both in terms of large data quantities
 and high speed.")
     (license license:bsd-3)))
 
+(define-public ghc-unordered-containers-bootstrap
+  (package
+    (inherit ghc-unordered-containers)
+    (name "ghc-unordered-containers-bootstrap")
+    (arguments `(#:tests? #f))
+    (inputs
+     `(("ghc-hashable" ,ghc-hashable-bootstrap)))
+    (properties '(hidden? #t))))
+
 (define-public ghc-uniplate
   (package
     (name "ghc-uniplate")
@@ -4569,6 +4586,14 @@ Compatibility package for older packages.")
     (description "This library provides the natural numbers for Haskell.")
     (license license:bsd-3)))
 
+(define-public ghc-nats-bootstrap
+  (package
+    (inherit ghc-nats)
+    (name "ghc-nats-bootstrap")
+    (inputs
+     `(("ghc-hashable" ,ghc-hashable-bootstrap)))
+    (properties '((hidden? #t)))))
+
 (define-public ghc-void
   (package
     (name "ghc-void")
@@ -4889,6 +4914,18 @@ where every element did not have to have an inverse, thus the name
 semigroup.")
     (license license:bsd-3)))
 
+(define-public ghc-semigroups-bootstrap
+  (package
+    (inherit ghc-semigroups)
+    (name "ghc-semigroups-bootstrap")
+    (inputs
+     `(("ghc-nats" ,ghc-nats-bootstrap)
+       ("ghc-tagged" ,ghc-tagged)
+       ("ghc-unordered-containers" ,ghc-unordered-containers-bootstrap)
+       ("ghc-text" ,ghc-text)
+       ("ghc-hashable" ,ghc-hashable-bootstrap)))
+    (properties '(hidden? #t))))
+
 (define-public ghc-free
   (package
     (name "ghc-free")

From aeb1c6abd5b0f6e02ad569bb50e1fb740165f094 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 30 Aug 2018 11:12:46 -0400
Subject: [PATCH 281/909] gnu: ghc-test-framework-hunit: Update Cabal file to
 r3.

* gnu/packages/haskell-check.scm (ghc-test-framework-hunit): Update Cabal
file to r3.
[arguments]: Remove unneeded "--allow-newer" configure flag.
---
 gnu/packages/haskell-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index a9ff6af041..3bef4e5802 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -508,9 +508,9 @@ reporting and test statistics output.")
         (base32
          "1y0b6vg8nfm43v90lxxcydhi6qlxhfy4vpxbzm5ic2w55bh8xjwm"))))
     (build-system haskell-build-system)
-    ;; The official revision of the cabal file allows for HUnit lower than 1.7
     (arguments
-     `(#:configure-flags (list "--allow-newer=HUnit")))
+     `(#:cabal-revision
+       ("3" "0i9mlalv7cl1iq43ld5myrnpszq5rxmd79hk495dcb08rglhgl3z")))
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
        ("ghc-hunit" ,ghc-hunit)

From c2d2f27537367ac9248cc0162a86e258bcb4a673 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 30 Aug 2018 11:16:01 -0400
Subject: [PATCH 282/909] gnu: ghc-test-framework-quickcheck2: Update Cabal
 file to r1.

* gnu/packages/haskell-check.scm (ghc-test-framework-quickcheck2): Update
Cabal file to r1.
---
 gnu/packages/haskell-check.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 3bef4e5802..ef19645346 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -535,6 +535,9 @@ reporting and test statistics output.")
         (base32
          "0vj834337r6jzr3258cv68ly2sv5999mklpsrfngyk51kywsyqyp"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "147ngmfdkskyg7mwsp5w73a4dbx3rp5s38bci3z03kn1m093lxff")))
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
        ("ghc-quickcheck" ,ghc-quickcheck)

From d09b2ad42801e974eb433593891b51f9894147d9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:07:16 -0400
Subject: [PATCH 283/909] gnu: ghc-x11: Update to 1.9.

* gnu/packages/haskell.scm (ghc-x11): Update to 1.9.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a12e7e894b..1b66d88faa 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1968,14 +1968,14 @@ environment variables.")
 (define-public ghc-x11
   (package
     (name "ghc-x11")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://hackage.haskell.org/package/X11/"
                            "X11-" version ".tar.gz"))
        (sha256
-        (base32 "13lxq36856fzp61y4api78vssykyh8fm2aplr0nsj18ymdm1c6sl"))))
+        (base32 "1f8dy6ckkyvpcv7zlniyv01cqjb9lgqscm8pml58cvwc7n38w4qh"))))
     (build-system haskell-build-system)
     (inputs
      `(("libx11" ,libx11)

From 5e4058ad85416bc256bc414df4985bbfd4e5eeac Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 21:19:12 -0400
Subject: [PATCH 284/909] gnu: ghc-bytestring-handle: Allow newer base and
 QuickCheck.

* gnu/packages/haskell.scm (ghc-bytestring-handle)[arguments]: Add a phase
that patches the Cabal file to allow newer versions of base and QuickCheck.
---
 gnu/packages/haskell.scm | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 1b66d88faa..d8cd4cbba5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7008,6 +7008,16 @@ this problem.")
         (base32
          "18f17aja1ivhr3zyg2cccn2m03hdn5jf5410dndkhf12gvgiqs7y"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "bytestring-handle.cabal"
+               (("QuickCheck >= 2\\.1\\.2 && < 2\\.11")
+                "QuickCheck >= 2.1.2 && < 2.12")
+               (("base >= 4\\.2 && < 4\\.11")
+                "base >= 4.2 && < 4.12")))))))
     (inputs
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-quickcheck" ,ghc-quickcheck)

From 91ffeed70a451620dcd4f87d29bb4c40e5057f47 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:52:17 -0400
Subject: [PATCH 285/909] gnu: ghc-cereal: Update to 0.5.7.0.

* gnu/packages/haskell.scm (ghc-cereal): Update to 0.5.7.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d8cd4cbba5..eb1c34c1fe 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2939,7 +2939,7 @@ Dual to @code{Traversable}.")
 (define-public ghc-cereal
   (package
     (name "ghc-cereal")
-    (version "0.5.3.0")
+    (version "0.5.7.0")
     (source
      (origin
        (method url-fetch)
@@ -2949,7 +2949,7 @@ Dual to @code{Traversable}.")
              ".tar.gz"))
        (sha256
         (base32
-         "1x4aib7nnaf4x2b9zlndq5n5zsqniw78jifkf55nhnbmvryf05n3"))))
+         "1j7imh2mzqcljld7sx0av69699955rpy3hzivi5723i6a9nszgbs"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From 5f4327df7fb03363f6cc0be9a97886aff6f76953 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:16:24 -0400
Subject: [PATCH 286/909] gnu: ghc-deepseq-generics: Update Cabal file to r2.

* gnu/packages/haskell.scm (ghc-deepseq-generics): Update Cabal file to r2.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index eb1c34c1fe..b6657f115f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5295,6 +5295,9 @@ using a simple box model.")
                (base32
                 "17bwghc15mc9pchfd1w46jh2p3wzc86aj6a537wqwxn08rayzcxh"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("2" "1pnidf8w8x0w5fsqgv8hhrw07slmhxwy5x4fikgk0bd6k76aqicb")))
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-test-framework" ,ghc-test-framework)

From d340ee858f82c9e34da87deb2a62d27b22415959 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 23:35:30 -0400
Subject: [PATCH 287/909] gnu: ghc-edit-distance: Replace "--allow-newer" flag.

* gnu/packages/haskell.scm (ghc-edit-distance)[arguments]: Replace
"--allow-newer" configure flag with a phase that patches the Cabal file.
---
 gnu/packages/haskell.scm | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b6657f115f..ec262f143f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6208,7 +6208,13 @@ representations of current time.")
         (base32 "0jkca97zyv23yyilp3jydcrzxqhyk27swhzh82llvban5zp8b21y"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck")))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "edit-distance.cabal"
+               (("QuickCheck >= 2\\.4 && <2\\.9")
+                "QuickCheck >= 2.4 && < 2.12")))))))
     (inputs
      `(("ghc-random" ,ghc-random)
        ("ghc-test-framework" ,ghc-test-framework)

From 5f192d52a31d58e25c809e18cb4361f2df611532 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:53:55 -0400
Subject: [PATCH 288/909] gnu: ghc-exceptions: Update to 0.10.0.

* gnu/packages/haskell.scm (ghc-exceptions): Update to 0.10.0.
[arguments]: Remove unneeded "--allow-newer=QuickCheck" configure flag.
[native-inputs]: Add ghc-quickcheck, ghc-test-framework, and
ghc-test-framework-hunit.
---
 gnu/packages/haskell.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ec262f143f..ee88b89c9a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3302,7 +3302,7 @@ consuming feeds in both RSS (Really Simple Syndication) and Atom format.")
 (define-public ghc-exceptions
   (package
     (name "ghc-exceptions")
-    (version "0.8.3")
+    (version "0.10.0")
     (source
      (origin
        (method url-fetch)
@@ -3312,12 +3312,12 @@ consuming feeds in both RSS (Really Simple Syndication) and Atom format.")
              ".tar.gz"))
        (sha256
         (base32
-         "1gl7xzffsqmigam6zg0jsglncgzxqafld2p6kb7ccp9xirzdjsjd"))))
+         "1ms9zansv0pwzwdjncvx4kf18lnkjy2p61hvjhvxmjx5bqp93p8y"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck")))
     (native-inputs
-     `(("ghc-test-framework" ,ghc-test-framework)
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
     (inputs
      `(("ghc-stm" ,ghc-stm)

From 9c072f820e05736e4e6536192d0af213e0277408 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:54:47 -0400
Subject: [PATCH 289/909] gnu: ghc-fingertree: Update to 0.1.4.1.

* gnu/packages/haskell.scm (ghc-fingertree): Update to 0.1.4.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ee88b89c9a..e23ebb6afe 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4348,7 +4348,7 @@ will eventually deliver a value of type @code{a}.")
 (define-public ghc-fingertree
   (package
     (name "ghc-fingertree")
-    (version "0.1.3.0")
+    (version "0.1.4.1")
     (source
      (origin
        (method url-fetch)
@@ -4357,7 +4357,7 @@ will eventually deliver a value of type @code{a}.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1ryjj7qrx70ckcjlr02x9zh86kfp76azbxq05r7hawqkaqg44sfs"))))
+         "192fyzv0pn1437wdpqg1l80rswkk4rw3w61r4bq7dhv354bdqy4p"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)

From c496fb987316251a5ff8d491d83bd76b13fa9d25 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:58:23 -0400
Subject: [PATCH 290/909] gnu: ghc-hashable: Update to 1.2.7.0.

* gnu/packages/haskell.scm (ghc-hashable): Update to 1.2.7.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e23ebb6afe..85889b20dc 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2235,7 +2235,7 @@ IO operations.")
 (define-public ghc-hashable
   (package
     (name "ghc-hashable")
-    (version "1.2.6.1")
+    (version "1.2.7.0")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -2246,7 +2246,7 @@ IO operations.")
              ".tar.gz"))
        (sha256
         (base32
-         "0ymv2mcrrgbdc2w39rib171fwnhg7fgp0sy4h8amrh1vw64qgjll"))))
+         "1gra8gq3kb7b2sd845h55yxlrfqx3ii004c6vjhga8v0b30fzdgc"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-text" ,ghc-text)

From c1c35c3b0e853b2a422cd40ddef35ec741d23481 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:59:41 -0400
Subject: [PATCH 291/909] gnu: ghc-sha: Update to 1.6.4.4.

* gnu/packages/haskell-crypto.scm (ghc-sha): Update to 1.6.4.4.
---
 gnu/packages/haskell-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index 6a1eff6821..c675564a77 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -391,14 +391,14 @@ interface.")
 (define-public ghc-sha
   (package
     (name "ghc-sha")
-    (version "1.6.4.2")
+    (version "1.6.4.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "SHA/SHA-" version ".tar.gz"))
               (sha256
                (base32
-                "134ajm87fm4lpsw86m9q8apv20dw4bpk46raa389zr6bcdpifw64"))))
+                "0i4b2wjisivdy72synal711ywhx05mfqfba5n65rk8qidggm1nbb"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From b925e1f537c37f46c324b737888ce8290deb1ea8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:49:09 -0400
Subject: [PATCH 292/909] gnu: ghc-async: Update to 2.2.1.

* gnu/packages/haskell.scm (ghc-async): Update to 2.2.1.
[inputs]: Add ghc-hashable.
---
 gnu/packages/haskell.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 85889b20dc..3bd1757f80 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4320,7 +4320,7 @@ library for Haskell.")
 (define-public ghc-async
   (package
     (name "ghc-async")
-    (version "2.1.1.1")
+    (version "2.2.1")
     (source
      (origin
        (method url-fetch)
@@ -4330,10 +4330,11 @@ library for Haskell.")
              ".tar.gz"))
        (sha256
         (base32
-         "1qj4fp1ynwg0l453gmm27vgkzb5k5m2hzdlg5rdqi9kf8rqy90yd"))))
+         "09whscli1q5z7lzyq9rfk0bq1ydplh6pjmc6qv0x668k5818c2wg"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-stm" ,ghc-stm)
+       ("ghc-hashable" ,ghc-hashable)
        ("ghc-hunit" ,ghc-hunit)
        ("ghc-test-framework" ,ghc-test-framework)
        ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))

From f5aa584541f076773e5b226e09ae3fcc8d8142c2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:00:05 -0400
Subject: [PATCH 293/909] gnu: ghc-case-insensitive: Update to 1.2.0.11.

* gnu/packages/haskell.scm (ghc-case-insensitive): Update to 1.2.0.11.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 3bd1757f80..c82fd2aafe 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3434,7 +3434,7 @@ writing to stdout and other handles.")
 (define-public ghc-case-insensitive
   (package
     (name "ghc-case-insensitive")
-    (version "1.2.0.7")
+    (version "1.2.0.11")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -3445,7 +3445,7 @@ writing to stdout and other handles.")
              ".tar.gz"))
        (sha256
         (base32
-         "1j6ahvrz1g5q89y2difyk838yhwjc8z67zr0v2z512qdznc3h38n"))))
+         "1qrpxfirsxckg7jv28f5ah2qc8lh95hp7rnqkbqs1ahcwlbnvkm7"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hunit" ,ghc-hunit)))

From 0f108b33a727f338a8a71757a132d5b599c7237c Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:01:17 -0400
Subject: [PATCH 294/909] gnu: ghc-crypto-api: Update to 0.13.3.

* gnu/packages/haskell-crypto.scm (ghc-crypto-api): Update to 0.13.3.
---
 gnu/packages/haskell-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index c675564a77..f27d7dc23a 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -107,7 +107,7 @@ when ASN1 pattern matching is not convenient.")
 (define-public ghc-crypto-api
   (package
     (name "ghc-crypto-api")
-    (version "0.13.2")
+    (version "0.13.3")
     (source
      (origin
        (method url-fetch)
@@ -116,7 +116,7 @@ when ASN1 pattern matching is not convenient.")
                            "crypto-api-" version ".tar.gz"))
        (sha256
         (base32
-         "1vc27qcgbg7hf50rkqhlrs58zn1888ilh4b6wrrm07bnm48xacak"))))
+         "19bsmkqkpnvh01b77pmyarx00fic15j4hvg4pzscrj4prskrx2i9"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-cereal" ,ghc-cereal)
               ("ghc-tagged" ,ghc-tagged)

From 24e18bf937f80aa28f2f9d3d1b587b2cc1ae9c9e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:01:33 -0400
Subject: [PATCH 295/909] gnu: ghc-errors: Update to 2.3.0.

* gnu/packages/haskell.scm (ghc-errors): Update to 2.3.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c82fd2aafe..c81b37a7c3 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8405,7 +8405,7 @@ matching patterns against file paths.")
 (define-public ghc-errors
   (package
     (name "ghc-errors")
-    (version "2.2.2")
+    (version "2.3.0")
     (source
      (origin
        (method url-fetch)
@@ -8414,7 +8414,7 @@ matching patterns against file paths.")
                            "errors-" version ".tar.gz"))
        (sha256
         (base32
-         "13sflhglcm5skwrxb48fw96skdcx7ydiy4zg22200733pxhjncpn"))))
+         "0x8znwn31qcx6kqx99wp7bc86kckfb39ncz3zxvj1s07kxlfawk7"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-exceptions" ,ghc-exceptions)

From 75c07ef5199179cba554a733048d21649f6c0d15 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:13:10 -0400
Subject: [PATCH 296/909] gnu: ghc-hashable-time: Update Cabal file to r1.

* gnu/packages/haskell.scm (ghc-hashable-time): Update Cabal file to r1.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c81b37a7c3..bfc061c107 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2289,6 +2289,9 @@ combine hash values.")
         (base32
          "0k932nyd08l3xxbh2g3n76py2f4kd9yw4s5a065vjz0xp6wjnxdm"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "0rv40xkg3gj8jnqsry1gq3f5s5la6d5arg8fzkirnwdpcgha1as6")))
     (inputs `(("ghc-hashable" ,ghc-hashable)))
     (home-page "http://hackage.haskell.org/package/hashable-time")
     (synopsis "Hashable instances for Data.Time")

From fef71dbc9d28cccda627922d036ebf70844dbc84 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 6 Sep 2018 14:13:09 -0400
Subject: [PATCH 297/909] gnu: ghc-hashtables: Update to 1.2.3.1.

* gnu/packages/haskell.scm (ghc-hashtables): Update to 1.2.3.1.
[arguments]: Remove unneeded "--allow-newer" configure flag.
---
 gnu/packages/haskell.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index bfc061c107..c4dbbc7d75 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7804,7 +7804,7 @@ Haskell, using gnuplot for rendering.")
 (define-public ghc-hashtables
   (package
     (name "ghc-hashtables")
-    (version "1.2.1.0")
+    (version "1.2.3.1")
     (source
      (origin
        (method url-fetch)
@@ -7812,10 +7812,8 @@ Haskell, using gnuplot for rendering.")
              "https://hackage.haskell.org/package/hashtables/hashtables-"
              version ".tar.gz"))
        (sha256
-        (base32 "1b6w9xznk42732vpd8ili60k12yq190xnajgga0iwbdpyg424lgg"))))
+        (base32 "1giw9caajr07slf09j7zry9b0kvm4yj9q78zy1mawzi6gk3wglcg"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:configure-flags (list "--allow-newer=vector")))
     (inputs
      `(("ghc-hashable" ,ghc-hashable)
        ("ghc-primitive" ,ghc-primitive)

From d62f695119ff036762c93c5b8464c9ca5448e2c5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:04:02 -0400
Subject: [PATCH 298/909] gnu: ghc-nats: Update to 1.1.2.

* gnu/packages/haskell.scm (ghc-nats): Update to 1.1.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c4dbbc7d75..6230270f30 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4570,7 +4570,7 @@ Compatibility package for older packages.")
 (define-public ghc-nats
   (package
     (name "ghc-nats")
-    (version "1.1.1")
+    (version "1.1.2")
     (source
      (origin
        (method url-fetch)
@@ -4580,7 +4580,7 @@ Compatibility package for older packages.")
              ".tar.gz"))
        (sha256
         (base32
-         "1kfl2yy97nb7q0j17v96rl73xvi3z4db9bk0xychc76dax41n78k"))))
+         "1v40drmhixck3pz3mdfghamh73l4rp71mzcviipv1y8jhrfxilmr"))))
     (build-system haskell-build-system)
     (arguments `(#:haddock? #f))
     (inputs

From 6062c4610ebab3b4ba5dcd954972ff1a0ee09eb5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:04:41 -0400
Subject: [PATCH 299/909] gnu: ghc-psqueues: Update to 0.2.7.0.

* gnu/packages/haskell.scm (ghc-psqueues): Update to 0.2.7.0.
[arguments]: Remove unneeded "--allow-newer=QuickCheck" configure flag.
---
 gnu/packages/haskell.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6230270f30..b9f40fe90f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8309,7 +8309,7 @@ bytestrings and their hexademical representation.")
 (define-public ghc-psqueues
   (package
     (name "ghc-psqueues")
-    (version "0.2.6.0")
+    (version "0.2.7.0")
     (source
      (origin
        (method url-fetch)
@@ -8318,10 +8318,8 @@ bytestrings and their hexademical representation.")
                            "psqueues-" version ".tar.gz"))
        (sha256
         (base32
-         "0n39s1i88j6s7vvsdhpbhcr3gpbwlzabwcc3nbd7nqb4kb4i0sls"))))
+         "1sjgc9bxh63kkdp59nbirx3xazr02ia5yhp4f4a0jnq1hj465wsc"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck")))
     (inputs
      `(("ghc-hashable" ,ghc-hashable)))
     (native-inputs

From e0b8cc34a483beb19a6651a3fac8ad2eeb89cd46 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:06:16 -0400
Subject: [PATCH 300/909] gnu: ghc-unordered-containers: Update to 0.2.9.0.

* gnu/packages/haskell.scm (ghc-unordered-containers): Update to 0.2.9.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b9f40fe90f..4cec8d0ba7 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3561,7 +3561,7 @@ Partial and Infinite Values\"}.")
 (define-public ghc-unordered-containers
   (package
     (name "ghc-unordered-containers")
-    (version "0.2.7.1")
+    (version "0.2.9.0")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -3571,7 +3571,7 @@ Partial and Infinite Values\"}.")
              "/unordered-containers-" version ".tar.gz"))
        (sha256
         (base32
-         "00npqiphivjp2d7ryqsdavfn4m5v3w1lq2azhdsrfh0wsvqpg4ig"))))
+         "0l4264p0av12cc6i8gls13q8y27x12z2ar4x34n3x59y99fcnc37"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-chasingbottoms" ,ghc-chasingbottoms)

From e59983ece567b9131b45113777a317394ed68e25 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:36:17 -0400
Subject: [PATCH 301/909] gnu: ghc-hinotify: Update to 0.3.10.

* gnu/packages/haskell.scm (ghc-hinotify): Update to 0.3.10.
[inputs]: Add ghc-async.
---
 gnu/packages/haskell.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4cec8d0ba7..6e9185cb3f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7921,7 +7921,7 @@ helper functions for Lists, Maybes, Tuples, Functions.")
 (define-public ghc-hinotify
   (package
     (name "ghc-hinotify")
-    (version "0.3.8.1")
+    (version "0.3.10")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -7929,8 +7929,10 @@ helper functions for Lists, Maybes, Tuples, Functions.")
                     "hinotify-" version ".tar.gz"))
               (sha256
                (base32
-                "03c1f4d7x805zdiq2w26kl09xrfjw19saycdkhnixzv2qcr6xm1p"))))
+                "17ax3n68a5c2ddazp86aciliskrh6znd3bnry0wcllmb6dbpsaxg"))))
     (build-system haskell-build-system)
+    (inputs
+     `(("ghc-async" ,ghc-async)))
     (home-page "https://github.com/kolmodin/hinotify.git")
     (synopsis "Haskell binding to inotify")
     (description "This library provides a wrapper to the Linux kernel's inotify

From 42c000dcf568f98208b3fe7390ac89decc170912 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:15:13 -0400
Subject: [PATCH 302/909] gnu: ghc-semigroups: Update to 0.18.5.

* gnu/packages/haskell.scm (ghc-semigroups): Update to 0.18.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6e9185cb3f..762df9b6fd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4889,7 +4889,7 @@ just a @code{Semigroup} are added.")
 (define-public ghc-semigroups
   (package
     (name "ghc-semigroups")
-    (version "0.18.2")
+    (version "0.18.5")
     (source
      (origin
        (method url-fetch)
@@ -4899,7 +4899,7 @@ just a @code{Semigroup} are added.")
              ".tar.gz"))
        (sha256
         (base32
-         "1r6hsn3am3dpf4rprrj4m04d9318v9iq02bin0pl29dg4a3gzjax"))))
+         "17g29h62g1k51ghhvzkw72zksjgi6vs6bfipkj81pqw1dsprcamb"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-nats" ,ghc-nats)

From 48f8ba91ca948154f3b75a50aa014c72aff3ffff Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:22:09 -0400
Subject: [PATCH 303/909] gnu: ghc-chunked-data: Update to 0.3.1.

* gnu/packages/haskell.scm (ghc-chunked-data): Update to 0.3.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 762df9b6fd..ad27832f1f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8776,7 +8776,7 @@ and regression and autocorrelation analysis.
 (define-public ghc-chunked-data
   (package
     (name "ghc-chunked-data")
-    (version "0.3.0")
+    (version "0.3.1")
     (source
      (origin
        (method url-fetch)
@@ -8785,7 +8785,7 @@ and regression and autocorrelation analysis.
                            "chunked-data-" version ".tar.gz"))
        (sha256
         (base32
-         "0bszq6fijnr4pmadzz89smj7kfmzx0ca3wd9ga8gv0in9jk9vgp1"))))
+         "16m7y7fwrirbjbqqcsfmr4yxa9qvfax6r7pw0zl9ky71ms0wa47p"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-vector" ,ghc-vector)
               ("ghc-semigroups" ,ghc-semigroups)

From 2927343183efdcdd6bbd732bb1211540ba6ece51 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:22:58 -0400
Subject: [PATCH 304/909] gnu: ghc-glob: Update to 0.9.2.

* gnu/packages/haskell.scm (ghc-glob): Update to 0.9.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ad27832f1f..df1746b1a2 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8376,7 +8376,7 @@ Typical applications of Priority Search Queues include:
 (define-public ghc-glob
   (package
     (name "ghc-glob")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
@@ -8385,7 +8385,7 @@ Typical applications of Priority Search Queues include:
                            "Glob-" version ".tar.gz"))
        (sha256
         (base32
-         "0rzmsknl02p332dxmm36fyrz3dpma7bchn0ymyjipxvqil20pjw0"))))
+         "1rbwcq9w9951qsnp13vqcm9r01yax2yh1wk8s4zxa3ckk9717iwg"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-dlist" ,ghc-dlist)

From c839da85129858fb7b374c5f903f1d32ae676abc Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:42:16 -0400
Subject: [PATCH 305/909] gnu: ghc-hmatrix: Update to 0.19.0.0.

* gnu/packages/haskell.scm (ghc-hmatrix): Update to 0.19.0.0.
[inputs]: Add ghc-semigroups.
---
 gnu/packages/haskell.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index df1746b1a2..76feb10a12 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7675,7 +7675,7 @@ and Fortran complex data types.")
 (define-public ghc-hmatrix
   (package
     (name "ghc-hmatrix")
-    (version "0.18.1.0")
+    (version "0.19.0.0")
     (source
      (origin
        (method url-fetch)
@@ -7683,12 +7683,13 @@ and Fortran complex data types.")
              "https://hackage.haskell.org/package/hmatrix/hmatrix-"
              version ".tar.gz"))
        (sha256
-        (base32 "07zkwvg872hfk6jyn4s54ws8mvclynazaxf7fsbqi16dmf9dn61c"))))
+        (base32 "10jd69nby29dggghcyjk6ykyr5wrn97nrv1dkpyrp0y5xm12xssj"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-random" ,ghc-random)
        ("ghc-split" ,ghc-split)
        ("ghc-storable-complex" ,ghc-storable-complex)
+       ("ghc-semigroups" ,ghc-semigroups)
        ("ghc-vector" ,ghc-vector)
        ;;("openblas" ,openblas)
        ("lapack" ,lapack)))

From e99625b5aeed7d000de947afc57454444894d8c5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:26:23 -0400
Subject: [PATCH 306/909] gnu: ghc-void: Update to 0.7.2.

* gnu/packages/haskell.scm (ghc-void): Update to 0.7.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 76feb10a12..38bdd7c05b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4601,7 +4601,7 @@ Compatibility package for older packages.")
 (define-public ghc-void
   (package
     (name "ghc-void")
-    (version "0.7.1")
+    (version "0.7.2")
     (source
      (origin
        (method url-fetch)
@@ -4611,7 +4611,7 @@ Compatibility package for older packages.")
              ".tar.gz"))
        (sha256
         (base32
-         "1x15x2axz84ndw2bf60vjqljhrb0w95lddaljsxrl0hcd29zvw69"))))
+         "0aygw0yb1h3yhmfl3bkwh5d3h0l4mmsxz7j53vdm6jryl1kgxzyk"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-semigroups" ,ghc-semigroups)

From c64e832f1008bec9a11481b4f48b5f619ce0319d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:29:18 -0400
Subject: [PATCH 307/909] gnu: xmonad: Update to 0.14.2.

* gnu/packages/wm.scm (xmonad): Update to 0.14.2.
---
 gnu/packages/wm.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 163281ac67..db345cd2fd 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -455,7 +455,7 @@ desktop environment.")
 (define-public xmonad
   (package
     (name "xmonad")
-    (version "0.14")
+    (version "0.14.2")
     (synopsis "Tiling window manager")
     (source (origin
               (method url-fetch)
@@ -463,7 +463,7 @@ desktop environment.")
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0lq3k0ap7jxrrswpd954mqa6h8diccbif5srcgbmr39y6y8x0mm4"))))
+                "0gqyivpw8z1x73p1l1fpyq1wc013a1c07r6xn1a82liijs91b949"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)

From 0b0e45d829df59ee8cb4973f674e44ebf7c60843 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:32:09 -0400
Subject: [PATCH 308/909] gnu: ghc-contravariant: Update to 1.4.1.

* gnu/packages/haskell.scm (ghc-contravariant): Update to 1.4.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 38bdd7c05b..d826f5d8a7 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4863,7 +4863,7 @@ just a @code{Semigroup} are added.")
 (define-public ghc-contravariant
   (package
     (name "ghc-contravariant")
-    (version "1.4")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
@@ -4873,7 +4873,7 @@ just a @code{Semigroup} are added.")
              ".tar.gz"))
        (sha256
         (base32
-         "117fff8kkrvlmr8cb2jpj71z7lf2pdiyks6ilyx89mry6zqnsrp1"))))
+         "1vfhk8c5cxmmakx7rflap1ipkx5q0j5vnlrcz7yz6y53kxhksgf9"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-void" ,ghc-void)

From 3c00bc13a5b78f0cfb240d60b4e283b1873b7ed9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:58:48 -0400
Subject: [PATCH 309/909] gnu: ghc-hmatrix-gsl: Update to 0.19.0.1.

* gnu/packages/haskell.scm (ghc-hmatrix-gsl): Update to 0.19.0.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d826f5d8a7..5ea7ed8831 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7706,7 +7706,7 @@ numerical computations based on BLAS and LAPACK.")
 (define-public ghc-hmatrix-gsl
   (package
     (name "ghc-hmatrix-gsl")
-    (version "0.18.0.1")
+    (version "0.19.0.1")
     (source
      (origin
        (method url-fetch)
@@ -7714,7 +7714,7 @@ numerical computations based on BLAS and LAPACK.")
              "https://hackage.haskell.org/package/hmatrix-gsl/hmatrix-gsl-"
              version ".tar.gz"))
        (sha256
-        (base32 "0mflm7zg6c6a5vy092pa429rzpyv5drc1589r3x4fbmvcyqc79gx"))))
+        (base32 "0v6dla426x4ywaq59jm89ql1i42n39iw6z0j378xwb676v9kfxhm"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hmatrix" ,ghc-hmatrix)

From 9d1944a4939ae006b6f53c4203c49bc727c55dfd Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 5 Sep 2018 14:22:28 -0400
Subject: [PATCH 310/909] gnu: ghc-tasty: Update to 1.1.0.3.

* gnu/packages/haskell.scm (ghc-integer-logarithms-bootstrap,
ghc-scientific-bootstrap, ghc-attoparsec-bootstrap,
ghc-wcwidth-bootstrap): New variables to break a dependency cycle from
ghc-tasty.
* gnu/packages/haskell-check.scm (ghc-tasty): Update to 1.1.0.3.
[inputs]: Add ghc-wcwidth-bootstrap; remove ghc-regex-tdfa-rc.
---
 gnu/packages/haskell-check.scm |  8 +++----
 gnu/packages/haskell.scm       | 42 ++++++++++++++++++++++++++++++++++
 2 files changed, 46 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index ef19645346..913835a807 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -181,7 +181,7 @@ timer functions of different operating systems via a unified API.")
 (define-public ghc-tasty
   (package
     (name "ghc-tasty")
-    (version "0.11.0.4")
+    (version "1.1.0.3")
     (source
      (origin
        (method url-fetch)
@@ -191,18 +191,18 @@ timer functions of different operating systems via a unified API.")
              ".tar.gz"))
        (sha256
         (base32
-         "05pxjzgbgjdn7477xry0ssjrnmnsydqiq6nm6ck8n2da1baliqp0"))))
+         "14riid753hjqr6lca1kgxpnvq0wykf0k3qc5jpag42hh8bszav22"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-stm" ,ghc-stm)
        ("ghc-tagged" ,ghc-tagged)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
-       ("ghc-regex-tdfa-rc" ,ghc-regex-tdfa-rc)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-unbounded-delays" ,ghc-unbounded-delays)
        ("ghc-async" ,ghc-async)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
-       ("ghc-clock-bootstrap" ,ghc-clock-bootstrap)))
+       ("ghc-clock-bootstrap" ,ghc-clock-bootstrap)
+       ("ghc-wcwidth" ,ghc-wcwidth-bootstrap)))
     (home-page "http://documentup.com/feuerbach/tasty")
     (synopsis "Modern and extensible testing framework")
     (description "Tasty is a modern testing framework for Haskell.  It lets
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5ea7ed8831..b50bf3d5d4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2877,6 +2877,17 @@ aimed particularly at dealing efficiently with network protocols and
 complicated text/binary file formats.")
     (license license:bsd-3)))
 
+(define-public ghc-attoparsec-bootstrap
+  (package
+    (inherit ghc-attoparsec)
+    (name "ghc-attoparsec-bootstrap")
+    (arguments `(#:tests? #f))
+    (inputs
+     `(("ghc-scientific" ,ghc-scientific-bootstrap)
+       ("ghc-text" ,ghc-text)))
+    (native-inputs '())
+    (properties '(hidden? #t))))
+
 (define-public ghc-zip-archive
   (package
     (name "ghc-zip-archive")
@@ -5227,6 +5238,14 @@ occurrences of a substring (the first in case of overlaps) with another.")
 in migrated modules.")
     (license license:expat)))
 
+(define-public ghc-integer-logarithms-bootstrap
+  (package
+    (inherit ghc-integer-logarithms)
+    (name "ghc-integer-logarithms-bootstrap")
+    (arguments `(#:tests? #f))
+    (native-inputs '())
+    (properties '(hidden? #t))))
+
 (define-public ghc-scientific
   (package
     (name "ghc-scientific")
@@ -5264,6 +5283,19 @@ and space efficient.  They are represented using
 notation}.")
     (license license:bsd-3)))
 
+(define-public ghc-scientific-bootstrap
+  (package
+    (inherit ghc-scientific)
+    (name "ghc-scientific-bootstrap")
+    (arguments `(#:tests? #f))
+    (inputs
+     `(("ghc-integer-logarithms" ,ghc-integer-logarithms-bootstrap)
+       ("ghc-text" ,ghc-text)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-primitive" ,ghc-primitive)))
+    (native-inputs '())
+    (properties '(hidden? #t))))
+
 (define-public ghc-boxes
   (package
     (name "ghc-boxes")
@@ -10199,4 +10231,14 @@ The command line tool can compile a width table to Haskell code that assigns
 widths to the Char type.")
     (license license:bsd-3)))
 
+(define-public ghc-wcwidth-bootstrap
+  (package
+    (inherit ghc-wcwidth)
+    (name "ghc-wcwidth-bootstrap")
+    (inputs
+     `(("ghc-setlocale" ,ghc-setlocale)
+       ("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-attoparsec" ,ghc-attoparsec-bootstrap)))
+    (properties '(hidden? #t))))
+
 ;;; haskell.scm ends here

From c1cf4c70f2828c86febb3c5eb2efd5e2e4173afa Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:39:34 -0400
Subject: [PATCH 311/909] gnu: ghc-contravariant-extras: Update to 0.3.4.

* gnu/packages/haskell.scm (ghc-contravariant-extras): Update to 0.3.4.
[inputs]: Add ghc-semigroups.
---
 gnu/packages/haskell.scm | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b50bf3d5d4..a8a90f919d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8888,7 +8888,7 @@ statically known size.")
 (define-public ghc-contravariant-extras
   (package
     (name "ghc-contravariant-extras")
-    (version "0.3.3.1")
+    (version "0.3.4")
     (source
      (origin
        (method url-fetch)
@@ -8897,11 +8897,13 @@ statically known size.")
                            "contravariant-extras-" version ".tar.gz"))
        (sha256
         (base32
-         "1mbrgjybdx8fjdck4ldwi8955w4qnmm0ql56zix7dyn0s7s9spgk"))))
+         "0gg62ccl94kvh7mnvdq09pifqxjx2kgs189si90nmg44bafj7a9n"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-tuple-th" ,ghc-tuple-th)
-              ("ghc-contravariant" ,ghc-contravariant)
-              ("ghc-base-prelude" ,ghc-base-prelude)))
+    (inputs
+     `(("ghc-tuple-th" ,ghc-tuple-th)
+       ("ghc-contravariant" ,ghc-contravariant)
+       ("ghc-base-prelude" ,ghc-base-prelude)
+       ("ghc-semigroups" ,ghc-semigroups)))
     (home-page "https://github.com/nikita-volkov/contravariant-extras")
     (synopsis "Extras for the @code{ghc-contravariant} Haskell package")
     (description "This Haskell package provides extras for the

From 722d3bd80b3c740e4b3244b61ced62dc33eb1e81 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:03:10 -0400
Subject: [PATCH 312/909] gnu: ghc-hmatrix-special: Update to 0.19.0.0.

* gnu/packages/haskell.scm (ghc-hmatrix-special): Update to 0.19.0.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a8a90f919d..d621c00840 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7764,7 +7764,7 @@ using GSL.")
 (define-public ghc-hmatrix-special
   (package
     (name "ghc-hmatrix-special")
-    (version "0.4.0.1")
+    (version "0.19.0.0")
     (source
      (origin
        (method url-fetch)
@@ -7773,7 +7773,7 @@ using GSL.")
          "https://hackage.haskell.org/package/hmatrix-special/hmatrix-special-"
          version ".tar.gz"))
        (sha256
-        (base32 "0kpcqdchi7ikzhqacy4rh4dxz3v37paxyb84wqa66sysb72wkabj"))))
+        (base32 "1mywr61kr852sbff26n9x95kswx9l4ycbv6s68qsbkh02xzqq7qz"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hmatrix" ,ghc-hmatrix)

From 665615e93beb0c1825b7e37bfbd265ca32d5f8a4 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:16:12 -0400
Subject: [PATCH 313/909] gnu: ghc-tasty-expected-failure: Update to 0.11.1.1.

* gnu/packages/haskell-check.scm (ghc-tasty-expected-failure): Update to 0.11.1.1.
---
 gnu/packages/haskell-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 913835a807..561cf0402f 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -312,7 +312,7 @@ been added since previous test run.")
 (define-public ghc-tasty-expected-failure
   (package
     (name "ghc-tasty-expected-failure")
-    (version "0.11.0.4")
+    (version "0.11.1.1")
     (source
      (origin
        (method url-fetch)
@@ -321,7 +321,7 @@ been added since previous test run.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0r555f18d2gj96pjyc13chn1nxaxl81am4xgip3mvvjhw8s5mva1"))))
+         "1i2s809m644b7hgiblqay9j364r3fjj1rwbrahsn1pgr5q6mr6ji"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-tagged" ,ghc-tagged)

From 58182daa3f284922893c7b5574b74e9cd40b0831 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:16:30 -0400
Subject: [PATCH 314/909] gnu: ghc-tasty-hunit: Update to 0.10.0.1.

* gnu/packages/haskell-check.scm (ghc-tasty-hunit): Update to 0.10.0.1.
[inputs]: Add ghc-call-stack.
---
 gnu/packages/haskell-check.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 561cf0402f..232975e6b4 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -213,7 +213,7 @@ and any other types of tests into a single test suite.")
 (define-public ghc-tasty-hunit
   (package
     (name "ghc-tasty-hunit")
-    (version "0.9.2")
+    (version "0.10.0.1")
     (source
      (origin
        (method url-fetch)
@@ -223,10 +223,11 @@ and any other types of tests into a single test suite.")
              ".tar.gz"))
        (sha256
         (base32
-         "08qnxaw34wfnzi9irs1jd4d0zczqm3k5ffkd4zwhkz0dflmgq7mf"))))
+         "0j3hgga6c3s8h5snzivb8a75h96207ia2rlbxzj07xbf4zpkp44g"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-tasty" ,ghc-tasty)))
+     `(("ghc-call-stack" ,ghc-call-stack-boot)
+       ("ghc-tasty" ,ghc-tasty)))
     (home-page "http://documentup.com/feuerbach/tasty")
     (synopsis "HUnit support for the Tasty test framework")
     (description "This package provides HUnit support for the Tasty Haskell

From 59a50276043d2054eb7f74a64a4e5cc8b8f1157e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:25:50 -0400
Subject: [PATCH 315/909] gnu: ghc-tasty-quickcheck: Update to 0.10.

* gnu/packages/haskell-check.scm (ghc-tasty-quickcheck): Update to 0.10.
---
 gnu/packages/haskell-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 232975e6b4..0ab0b9a61d 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -96,7 +96,7 @@ Haskell test framework.")
 (define-public ghc-tasty-quickcheck
   (package
     (name "ghc-tasty-quickcheck")
-    (version "0.8.4")
+    (version "0.10")
     (source
      (origin
        (method url-fetch)
@@ -105,7 +105,7 @@ Haskell test framework.")
              "tasty-quickcheck-" version ".tar.gz"))
        (sha256
         (base32
-         "15rjxib5jmjq0hzj47x15kgp3awc73va4cy1pmpf7k3hvfv4qprn"))))
+         "0vr6szbbz3s5461i0zr8zpq347zfvidfzv5gf3xwxhm0yk731z8h"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From c70f00e203e913226c08c5bba4bc2b9c57571117 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:31:40 -0400
Subject: [PATCH 316/909] gnu: ghc-blaze-markup: Update to 0.8.2.1.

* gnu/packages/haskell.scm (ghc-blaze-markup): Update to 0.8.2.1.
[arguments]: Add a phase that patches the Cabal file to allow newer
versions of tasty.
---
 gnu/packages/haskell.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d621c00840..92703ee668 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4284,7 +4284,7 @@ interoperate with code that uses the new implementation.")
 (define-public ghc-blaze-markup
   (package
     (name "ghc-blaze-markup")
-    (version "0.8.2.0")
+    (version "0.8.2.1")
     (source
      (origin
        (method url-fetch)
@@ -4293,8 +4293,16 @@ interoperate with code that uses the new implementation.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0m3h3ryxj5r74mv5g5dnfq5jbbwmvkl7ray18vi20d5vd93sydj4"))))
+         "0ih1c3qahkdgzbqihdhny5s313l2m66fbb88w8jbx7yz56y7rawh"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "blaze-markup.cabal"
+               (("tasty            >= 1\\.0  && < 1\\.1")
+                "tasty            >= 1.0  && < 1.2")))))))
     (inputs
      `(("ghc-blaze-builder" ,ghc-blaze-builder)
        ("ghc-text" ,ghc-text)))

From 083c9c73757c97afc1e3cdbeb200c2ab1dc33547 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:32:33 -0400
Subject: [PATCH 317/909] gnu: ghc-cookie: Update to 0.4.4.

* gnu/packages/haskell-web.scm (ghc-cookie): Update to 0.4.4.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index bb4f419e66..72defb3446 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -64,7 +64,7 @@ for screen-scraping.")
 (define-public ghc-cookie
   (package
     (name "ghc-cookie")
-    (version "0.4.3")
+    (version "0.4.4")
     (source
      (origin
        (method url-fetch)
@@ -74,7 +74,7 @@ for screen-scraping.")
              ".tar.gz"))
        (sha256
         (base32
-         "0qpdydhb9gw590ffabqg70x7xvjpg8l74idqnrfbhv5yrr7hryzv"))))
+         "1qy09i0jh2z9i9avy2khf8a8afq4fqgnv0fyrszgfg4kmq2fsi9j"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-old-locale" ,ghc-old-locale)

From 6ef7c05c8d9bb9f77cd1d4145d85c938899e114f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:06:10 -0400
Subject: [PATCH 318/909] gnu: ghc-cryptohash-md5: Update Cabal file to r2.

* gnu/packages/haskell-crypto.scm (ghc-cryptohash-md5): Update Cabal
file to r2.
---
 gnu/packages/haskell-crypto.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index f27d7dc23a..b1db19bdeb 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -210,7 +210,9 @@ that hides the C implementation.")
          "1y8q7s2bn4gdknw1wjikdnar2b5pgz3nv3220lxrlgpsf23x82vi"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:tests? #f)) ; tests require old version of ghc-hunit (0.9)
+     `(#:cabal-revision
+       ("2" "0vyb9cfvpfxpslxvvhd48gw37i9g8ry5x63xwxd9q7xfiqhs7p3a")
+       #:tests? #f)) ; tests require old version of ghc-hunit (0.9)
     (native-inputs `(("ghc-base16-bytestring" ,ghc-base16-bytestring)
                      ("ghc-puremd5" ,ghc-puremd5)
                      ("ghc-tasty" ,ghc-tasty)

From f89bf67491d62755a9777c71c453e3b308ab8220 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:07:32 -0400
Subject: [PATCH 319/909] gnu: ghc-cryptohash-sha1: Update Cabal file to r2.

* gnu/packages/haskell-crypto.scm (ghc-cryptohash-sha1): Update Cabal
file to r2.
---
 gnu/packages/haskell-crypto.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index b1db19bdeb..87e6cd3c15 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -238,7 +238,9 @@ that hides the C implementation.")
          "1aqdxdhxhl9jldh951djpwxx8z7gzaqspxl7iwpl84i5ahrsyy9w"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:tests? #f)) ; tests require old version of ghc-hunit (0.9)
+     `(#:cabal-revision
+       ("2" "0xas0nbq9bfdzlj6k565ibizv1cqvzfzsdj6q9pdiiwyxqblqc3m")
+       #:tests? #f)) ; tests require old version of ghc-hunit (0.9)
     (native-inputs `(("ghc-base16-bytestring" ,ghc-base16-bytestring)
                      ("ghc-sha" ,ghc-sha)
                      ("ghc-tasty" ,ghc-tasty)

From bef2ee1c588ad6f207f84e1a43e2ade2c4839bce Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:34:20 -0400
Subject: [PATCH 320/909] gnu: ghc-hourglass: Update to 0.2.12.

* gnu/packages/haskell.scm (ghc-hourglass): Update to 0.2.12.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 92703ee668..5875e9b02e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6214,14 +6214,14 @@ wrapping a bytestring with stronger and more meaniful name.")
 (define-public ghc-hourglass
   (package
     (name "ghc-hourglass")
-    (version "0.2.10")
+    (version "0.2.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "hourglass/hourglass-" version ".tar.gz"))
               (sha256
                (base32
-                "104d1yd84hclprg740nkz60vx589mnm094zriw6zczbgg8nkclym"))))
+                "0jnay5j13vpz6i1rkaj3j0d9v8jfpri499xn3l7wd01f81f5ncs4"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-old-locale" ,ghc-old-locale)))

From 6b05cfb4e47c28d3432d01d58ae4157d816d9d67 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 5 Sep 2018 14:55:56 -0400
Subject: [PATCH 321/909] gnu: ghc-integer-logarithms: Replace "--allow-newer"
 flag.

* gnu/packages/haskell.scm (ghc-integer-logarithms)[arguments]: Replace
"--allow-newer" configure flag with a phase that patches the Cabal file.
---
 gnu/packages/haskell.scm | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5875e9b02e..9dbeae194c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5227,7 +5227,13 @@ occurrences of a substring (the first in case of overlaps) with another.")
          "1wj8kgjg5bn2yrs4zh9qfjv85cx6w998j9pi39yrbv305944mb9j"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=tasty")))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "integer-logarithms.cabal"
+               (("tasty >= 0\\.10 && < 1\\.1")
+                "tasty >= 0.10 && < 1.2")))))))
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-smallcheck" ,ghc-smallcheck)

From 221c3563162926a44be20ba3899d4f8b7601b3c9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:34:59 -0400
Subject: [PATCH 322/909] gnu: ghc-tar: Update to 0.5.1.0.

* gnu/packages/haskell.scm (ghc-tar): Update to 0.5.1.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9dbeae194c..fdc77c3d95 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7091,7 +7091,7 @@ this problem.")
 (define-public ghc-tar
   (package
     (name "ghc-tar")
-    (version "0.5.0.3")
+    (version "0.5.1.0")
     (source
      (origin
        (method url-fetch)
@@ -7100,7 +7100,7 @@ this problem.")
              version ".tar.gz"))
        (sha256
         (base32
-         "18qq94j9bm91iswnxq2dm5dws5c7wm4k01q2rpf8py35cf3svnfq"))))
+         "0s2brvaxg5fki2jdkccmnpssiy6a3wjh24p6a3dkkdvjcixnk7f8"))))
     (build-system haskell-build-system)
     ;; FIXME: 2/24 tests fail.
     (arguments `(#:tests? #f))

From fe3ecc307f87d3f2d12dbeecbd180c68ab16d483 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 15:18:15 -0400
Subject: [PATCH 323/909] gnu: ghc-uuid-types: Relax test framework dependency
 constraints.

* gnu/packages/haskell.scm (ghc-uuid-types)[arguments]: Remove
"--allow-newer" configure flags and add a phase that removes dependency
version constraints from all of the test frameworks.
---
 gnu/packages/haskell.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index fdc77c3d95..a5f1628854 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9034,8 +9034,16 @@ IPv4, IPv6 and MAC addresses.")
          "1zdka5jnm1h6k36w3nr647yf3b5lqb336g3fkprhd6san9x52xlj"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck"
-                               "--allow-newer=HUnit")))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'strip-test-framework-constraints
+           (lambda _
+             (substitute* "uuid-types.cabal"
+               (("HUnit >=1\\.2 && < 1\\.4") "HUnit")
+               (("QuickCheck >=2\\.4 && < 2\\.9") "QuickCheck")
+               (("tasty >= 0\\.10 && < 0\\.12") "tasty")
+               (("tasty-hunit == 0\\.9\\.\\*") "tasty-hunit")
+               (("tasty-quickcheck == 0\\.8\\.\\*") "tasty-quickcheck")))))))
     (inputs `(("ghc-hashable" ,ghc-hashable)
               ("ghc-random" ,ghc-random)
               ("ghc-text" ,ghc-text)))

From 4f2f0eb02f1e5435846e8437e47d754af79b6b6c Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 20:51:46 -0400
Subject: [PATCH 324/909] gnu: ghc-vector-binary-instances: Update Cabal file
 to r1.

* gnu/packages/haskell.scm (ghc-vector-binary-instances): Update Cabal
file to r1.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a5f1628854..9a5632c47d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3889,6 +3889,9 @@ optimisation framework.")
         (base32
          "1y236jb72iab9ska1mc48z6yb0xgwmj45laaqdyjxksd84z7hbrb"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "196frl4akhfk7xf1nxzn8lmq99dxhzhsimanswn9yy7ym8zhki4i")))
     (inputs
      `(("ghc-vector" ,ghc-vector)))
     (native-inputs

From b8afa2da58bb04ea5ac021547601e956341f814e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:39:02 -0400
Subject: [PATCH 325/909] gnu: ghc-blaze-html: Update to 0.9.1.1.

* gnu/packages/haskell-web.scm (ghc-blaze-html): Update to 0.9.1.1.
[arguments]: Remove unneeded "--allow-newer" configure flags.
---
 gnu/packages/haskell-web.scm | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 72defb3446..a60bf007af 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -754,7 +754,7 @@ Strict, Transitional and Frameset variants.")
 (define-public ghc-blaze-html
   (package
     (name "ghc-blaze-html")
-    (version "0.9.0.1")
+    (version "0.9.1.1")
     (source
      (origin
        (method url-fetch)
@@ -763,11 +763,8 @@ Strict, Transitional and Frameset variants.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0r0acv47nh75bmf7kjyfvhcwz8f02rn9x0a1l80pzgyczfrsmkmf"))))
+         "06xv8fqhclfjj61z74cgggn4lmx1s7diakxg84mnkgfvk11983pa"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck"
-                               "--allow-newer=HUnit")))
     (inputs
      `(("ghc-blaze-builder" ,ghc-blaze-builder)
        ("ghc-text" ,ghc-text)

From 3a066eb5ee852338d7de1d37ddc524df92efe2a2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:40:01 -0400
Subject: [PATCH 326/909] gnu: ghc-extra: Update to 1.6.9.

* gnu/packages/haskell.scm (ghc-extra): Update to 1.6.9.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9a5632c47d..9f2b6f2bef 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3062,7 +3062,7 @@ Strings.")
 (define-public ghc-extra
   (package
     (name "ghc-extra")
-    (version "1.6.3")
+    (version "1.6.9")
     (source
      (origin
        (method url-fetch)
@@ -3072,7 +3072,7 @@ Strings.")
              ".tar.gz"))
        (sha256
         (base32
-         "06ds0jlx6sljwdf63l154qbzia9mnsri79i9qm3xikky3nj9ia1m"))))
+         "0xxcpb00pgwi9cmy6a7ghh6rblxry42p8pz5ssfgj20fs1xwzj1b"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-clock" ,ghc-clock)

From 9720cca2e53e1c3310d91a465084269c84e90f7c Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:59:18 -0400
Subject: [PATCH 327/909] gnu: ghc-pem: Update to 0.2.4.

* gnu/packages/haskell-crypto.scm (ghc-pem): Update to 0.2.4.
[inputs]: Remove ghc-base64-bytestring; add ghc-basement and ghc-memory.
---
 gnu/packages/haskell-crypto.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index 87e6cd3c15..bb0ee074c2 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -338,17 +338,18 @@ to obtain cryptographically strong entropy.")
 (define-public ghc-pem
   (package
     (name "ghc-pem")
-    (version "0.2.2")
+    (version "0.2.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "pem/pem-" version ".tar.gz"))
               (sha256
                (base32
-                "162sk5sg22w21wqz5qv8kx6ibxp99v5p20g3nknhm1kddk3hha1p"))))
+                "1m7qjsxrd8m88cvkqmr8kscril500j2a9y0iynvksjyjkhdlq33p"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-base64-bytestring" ,ghc-base64-bytestring)))
+     `(("ghc-basement" ,ghc-basement)
+       ("ghc-memory" ,ghc-memory)))
     (native-inputs
      `(("ghc-test-framework" ,ghc-test-framework)
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)

From 4828f040df32b2fef214034d3eddce94052f760e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:41:46 -0400
Subject: [PATCH 328/909] gnu: ghc-securemem: Update to 0.1.10.

* gnu/packages/haskell.scm (ghc-securemem): Update to 0.1.10.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9f2b6f2bef..5d5815a8d4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9535,7 +9535,7 @@ interpolates variables according to the type being inserted.")
 (define-public ghc-securemem
   (package
     (name "ghc-securemem")
-    (version "0.1.9")
+    (version "0.1.10")
     (source
      (origin
        (method url-fetch)
@@ -9544,7 +9544,7 @@ interpolates variables according to the type being inserted.")
                            "securemem-" version ".tar.gz"))
        (sha256
         (base32
-         "0dkhhjxa7njc3qbgvd5a23rkvr39vj2kn2a9nk6yjg7a8b2hvdpy"))))
+         "19hnw2cfbsfjynxq1bq9f6djbxhsc1k751ml0y1ab3ah913mm29j"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-byteable" ,ghc-byteable)
               ("ghc-memory" ,ghc-memory)))

From a11ce10666aa19f6be3c4d261812866163ed97f2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 16:07:50 -0400
Subject: [PATCH 329/909] gnu: ghc-uuid: Update Cabal file to r2 and relax
 dependencies.

* gnu/packages/haskell.scm (ghc-uuid): Update Cabal file to r2.
[arguments]: Add a phase to remove test framework dependency version
constraints.
---
 gnu/packages/haskell.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5d5815a8d4..da29e156ec 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9078,8 +9078,18 @@ functions.")
          "09xhk42yhxvqmka0iqrv3338asncz8cap3j0ic0ps896f2581b6z"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck"
-                               "--allow-newer=HUnit")))
+     `(#:cabal-revision
+       ("2" "0m185q62jkfb5jsv358nxbnrkv8y8hd0qqvgvh22wvc5g9ipz0r9")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'strip-test-framework-constraints
+           (lambda _
+             (substitute* "uuid.cabal"
+               (("HUnit            >= 1\\.2   && < 1\\.4") "HUnit")
+               (("QuickCheck       >= 2\\.4   && < 2\\.10") "QuickCheck")
+               (("tasty            >= 0\\.10  && < 0\\.12") "tasty")
+               (("tasty-hunit      == 0\\.9\\.\\*") "tasty-hunit")
+               (("tasty-quickcheck == 0\\.8\\.\\*") "tasty-quickcheck")))))))
     (inputs `(("ghc-cryptohash-sha1" ,ghc-cryptohash-sha1)
               ("ghc-cryptohash-md5" ,ghc-cryptohash-md5)
               ("ghc-entropy" ,ghc-entropy)

From a98973651ed8bafdeadfacf376b9a71254e0ea8e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:45:22 -0400
Subject: [PATCH 330/909] gnu: ghc-highlighting-kate: Update to 0.6.4.

* gnu/packages/haskell.scm (ghc-highlighting-kate): Update to 0.6.4.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index da29e156ec..007bcf0836 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5539,7 +5539,7 @@ and utilities for pretty printing.")
 (define-public ghc-highlighting-kate
   (package
     (name "ghc-highlighting-kate")
-    (version "0.6.3")
+    (version "0.6.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -5547,7 +5547,7 @@ and utilities for pretty printing.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "03c4flh4h1jd48bx0qmplax3q8w6wj1dhbh6j0xhaf5h95fbinki"))))
+                "1bqv00gfmrsf0jjr4qf3lhshvfkyzmhbi3pjb6mafbnsyn2k7f6q"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-diff" ,ghc-diff)

From 19533b321695356cf892e79afde4c428306426a2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:46:25 -0400
Subject: [PATCH 331/909] gnu: ghc-base-orphans: Update to 0.7.

* gnu/packages/haskell.scm (ghc-base-orphans): Update to 0.7.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 007bcf0836..0b59d3c071 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4428,7 +4428,7 @@ command line options in Haskell.")
 (define-public ghc-base-orphans
   (package
     (name "ghc-base-orphans")
-    (version "0.6")
+    (version "0.7")
     (source
      (origin
        (method url-fetch)
@@ -4438,7 +4438,7 @@ command line options in Haskell.")
              ".tar.gz"))
        (sha256
         (base32
-         "03mdww5j0gwai7aqlx3m71ldmjcr99jzpkcclzjfclk6a6kjla67"))))
+         "057f9npnqk71ccfh95djfkpd54dzazphj06grwxa3fyhwcwxrb8a"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From 3ff7232ae724a82a774680fa05598685181dec97 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:00:35 -0400
Subject: [PATCH 332/909] gnu: ghc-constraints: Update to 0.10.1.

* gnu/packages/haskell.scm (ghc-constraints): Update to 0.10.1.
[inputs]: Add ghc-semigroups.
[native-inputs]: Add ghc-hspec and ghc-hspec-discover.
---
 gnu/packages/haskell.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0b59d3c071..9bb81cda6d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7343,7 +7343,7 @@ and edge labels with positional information, etc.
 (define-public ghc-constraints
   (package
     (name "ghc-constraints")
-    (version "0.8")
+    (version "0.10.1")
     (source
      (origin
        (method url-fetch)
@@ -7352,11 +7352,15 @@ and edge labels with positional information, etc.
              version ".tar.gz"))
        (sha256
         (base32
-         "120mmv9rwbahslisc1z8zx9lw7v6hl5fzid4l0hiy5as6ijqgl2c"))))
+         "1xy3vv78jxc17hm0z7qqspxjwv7l2jbcbj670yrl2f053qkfr02q"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-hashable" ,ghc-hashable)
+       ("ghc-semigroups" ,ghc-semigroups)
        ("ghc-transformers-compat" ,ghc-transformers-compat)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("hspec-discover" ,hspec-discover)))
     (home-page "https://github.com/ekmett/constraints/")
     (synopsis "Constraint manipulation")
     (description

From 98993f605b3562f4b9df5061da37df4e75a1c4fe Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 21:03:38 -0400
Subject: [PATCH 333/909] gnu: ghc-fgl: Replace "--allow-newer" flags.

* gnu/packages/haskell.scm (ghc-fgl)[arguments]: Replace "--allow-newer"
configure flags with a phase that patches the Cabal file.
---
 gnu/packages/haskell.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9bb81cda6d..4ddd6dc47c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3525,8 +3525,15 @@ variety of traversals.")
          "1i6cp4b3w7sjk7y1dq3fh6bci2sm5h3lnbbaw9ln19nwncg2wwll"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck"
-                               "--allow-newer=hspec")))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "fgl.cabal"
+               (("QuickCheck >= 2\\.8 && < 2\\.10")
+                "QuickCheck >= 2.8 && < 2.12")
+               (("hspec >= 2\\.1 && < 2\\.5")
+                "hspec >= 2.1 && < 2.6")))))))
     (inputs
      `(("ghc-hspec" ,ghc-hspec)
        ("ghc-quickcheck" ,ghc-quickcheck)))

From b408c5a768345907f69772e42a75d7e4ecaa97c0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:49:02 -0400
Subject: [PATCH 334/909] gnu: ghc-generic-deriving: Update to 1.12.2.

* gnu/packages/haskell.scm (ghc-generic-deriving): Update to 1.12.2.
[inputs]: Add ghc-th-abstraction.
---
 gnu/packages/haskell.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4ddd6dc47c..b942d2d4ce 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3190,7 +3190,7 @@ exceptions.")
 (define-public ghc-generic-deriving
   (package
     (name "ghc-generic-deriving")
-    (version "1.11.1")
+    (version "1.12.2")
     (source
      (origin
        (method url-fetch)
@@ -3200,8 +3200,10 @@ exceptions.")
              ".tar.gz"))
        (sha256
         (base32
-         "1sdh5hpcwvh3b6zvgfk3pr3hla8p88l82njnih880c0gk5zl53dk"))))
+         "1i7d6cpj9yhaqb79zays3nqchhaacacjz9bkc0zlwj73y5gvi22n"))))
     (build-system haskell-build-system)
+    (inputs
+     `(("ghc-th-abstraction" ,ghc-th-abstraction)))
     (native-inputs
      `(("ghc-hspec" ,ghc-hspec)
        ("hspec-discover" ,hspec-discover)))

From 16b4b6d1b93cefc565500ff35cac434a9dda21bb Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 20:35:11 -0400
Subject: [PATCH 335/909] gnu: ghc-half: Update to 0.3.

* gnu/packages/haskell.scm (ghc-half): Update to 0.3.
[native-inputs]: Add ghc-hspec and ghc-quickcheck.
---
 gnu/packages/haskell.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b942d2d4ce..6327b4fe84 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1447,7 +1447,7 @@ PNG, PNM, TGA, TIFF, XCF, XPM, XV.")
 (define-public ghc-half
   (package
     (name "ghc-half")
-    (version "0.2.2.3")
+    (version "0.3")
     (source
      (origin
        (method url-fetch)
@@ -1456,8 +1456,11 @@ PNG, PNM, TGA, TIFF, XCF, XPM, XV.")
              version ".tar.gz"))
        (sha256
         (base32
-         "0p4sb7vv9cljv48wlx65wgdnkryrk5d6yfh7g4yrm20w1p449hl5"))))
+         "14r0nx8hm5fic9gz0ybjjw4kyc758zfgvhhwvzsshpx5caq6zch6"))))
     (build-system haskell-build-system)
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-quickcheck" ,ghc-quickcheck)))
     (home-page "https://github.com/ekmett/half")
     (synopsis "Half-precision floating-point computations")
     (description "This library provides a half-precision floating-point

From 1cf4f2729f05872eb3d7a2eade1bde5120e502f8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:49:28 -0400
Subject: [PATCH 336/909] gnu: ghc-logging-facade: Update to 0.3.0.

* gnu/packages/haskell.scm (ghc-logging-facade): Update to 0.3.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6327b4fe84..3a607bfb4e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5975,7 +5975,7 @@ space as enumerator/iteratee and pipes.")
 (define-public ghc-logging-facade
   (package
     (name "ghc-logging-facade")
-    (version "0.1.1")
+    (version "0.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -5983,7 +5983,7 @@ space as enumerator/iteratee and pipes.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "18ldv6rsff480rqpbs3iabjpvn1fhw0i2a0g80jnhxg9ajfz5yb0"))))
+                "0d0lwxxgd16is9aw6v3ps4r9prv3dj8xscmm45fvzq3nicjiawcf"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-hspec" ,ghc-hspec)

From 073f5ae1fe78de76c46659e4c938f1b8ef84652a Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 00:00:06 -0400
Subject: [PATCH 337/909] gnu: Add ghc-newtype-generics.

* gnu/packages/haskell.scm (ghc-newtype-generics): New variable.
---
 gnu/packages/haskell.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 3a607bfb4e..5c49e9074a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -823,6 +823,32 @@ code pages on Windows.  On all other operating systems, the library does
 nothing.")
   (license license:bsd-3)))
 
+(define-public ghc-newtype-generics
+  (package
+    (name "ghc-newtype-generics")
+    (version "0.5.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "newtype-generics/newtype-generics-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0igyisw2djg19v9vkna1rwf47k97mvkvk4bbkmswznvbm00z15gj"))))
+    (build-system haskell-build-system)
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("hspec-discover" ,hspec-discover)))
+    (home-page "http://github.com/sjakobi/newtype-generics")
+    (synopsis "Typeclass and set of functions for working with newtypes")
+    (description "The @code{Newtype} typeclass represents the packing and
+unpacking of a newtype, and allows you to operate under that newtype with
+functions such as @code{ala}.  Generics support was added in version 0.4,
+making this package a full replacement for the original newtype package,
+and an alternative to newtype-th.")
+    (license license:bsd-3)))
+
 (define-public ghc-haddock-library
   (package
     (name "ghc-haddock-library")

From 96d214a6d9d0585589432de4e2a77523c4590743 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:50:33 -0400
Subject: [PATCH 338/909] gnu: ghc-unliftio: Update to 0.2.7.0.

* gnu/packages/haskell.scm (ghc-unliftio): Update to 0.2.7.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5c49e9074a..7b187899ac 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9936,7 +9936,7 @@ used both from lens and microlens).")
 (define-public ghc-unliftio
   (package
     (name "ghc-unliftio")
-    (version "0.2.4.0")
+    (version "0.2.7.0")
     (source
      (origin
        (method url-fetch)
@@ -9946,7 +9946,7 @@ used both from lens and microlens).")
              ".tar.gz"))
        (sha256
         (base32
-         "0vpncmwaq5zb6bziqfns4qdgxmq8ky0rlxna2yngxp170s5zxx9z"))))
+         "0qql93lq5w7qghl454cc3s1i8v1jb4h08n82fqkw0kli4g3g9njs"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: hspec-discover not in PATH
     (inputs

From f9a97fb553fc26f2ea443f7e425b39fea51e47cd Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:00:43 -0400
Subject: [PATCH 339/909] gnu: ghc-doctest: Update to 0.16.0.

* gnu/packages/haskell.scm (ghc-doctest): Update to 0.16.0.
[inputs]: Add ghc-code-page.
---
 gnu/packages/haskell.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7b187899ac..75ba7f7993 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5115,7 +5115,7 @@ monad transformer (instead of the IO monad).")
 (define-public ghc-doctest
   (package
     (name "ghc-doctest")
-    (version "0.11.0")
+    (version "0.16.0")
     (source
      (origin
        (method url-fetch)
@@ -5125,13 +5125,14 @@ monad transformer (instead of the IO monad).")
              ".tar.gz"))
        (sha256
         (base32
-         "0xv4vx1r3mk7cmiwywzrq25545cx3i7imhcx33mk47r88j5c49fj"))))
+         "0hkccch65s3kp0b36h7bqhilnpi4bx8kngncm7ma9vbd3dwacjdv"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f))          ; FIXME: missing test framework
     (inputs
      `(("ghc-syb" ,ghc-syb)
        ("ghc-paths" ,ghc-paths)
        ("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-code-page" ,ghc-code-page)
        ("ghc-hunit" ,ghc-hunit)
        ("ghc-hspec" ,ghc-hspec)
        ("ghc-quickcheck" ,ghc-quickcheck)

From 11afd13d70389abeadb274639ddfe1166c8ff4b6 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 22:40:43 -0400
Subject: [PATCH 340/909] gnu: ghc-fgl-arbitrary: Replace "--allow-newer"
 flags.

* gnu/packages/haskell.scm (ghc-fgl-arbitrary)[arguments]: Replace
"--allow-newer" configure flags with a phase that patches the Cabal file.
---
 gnu/packages/haskell.scm | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 75ba7f7993..76e2d22001 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7316,8 +7316,15 @@ supported.  A module of colour names (\"Data.Colour.Names\") is provided.")
          "0ln1szgfy8fa78l3issq4fx3aqnnd54w3cb4wssrfi48vd5rkfjm"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck"
-                               "--allow-newer=hspec")))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "fgl-arbitrary.cabal"
+               (("QuickCheck >= 2\\.3 && < 2\\.10")
+                "QuickCheck >= 2.3 && < 2.12")
+               (("hspec >= 2\\.1 && < 2\\.5")
+                "hspec >= 2.1 && < 2.6")))))))
     (inputs
      `(("ghc-fgl" ,ghc-fgl)
        ("ghc-quickcheck" ,ghc-quickcheck)

From cd40c4d6c360ce52aaf006cb1b0f9190cb5e4d14 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 14:20:06 -0400
Subject: [PATCH 341/909] gnu: Add ghc-memotrie.

* gnu/packages/haskell.scm (ghc-memotrie): New variable.
---
 gnu/packages/haskell.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 76e2d22001..1ae8eb993a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -849,6 +849,29 @@ making this package a full replacement for the original newtype package,
 and an alternative to newtype-th.")
     (license license:bsd-3)))
 
+(define-public ghc-memotrie
+  (package
+    (name "ghc-memotrie")
+    (version "0.6.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/MemoTrie/MemoTrie-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "157p0pi6rrq74a35mq6zkkycv4ah7xhkbrcmnkb9xf7pznw4aq0x"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-newtype-generics" ,ghc-newtype-generics)))
+    (home-page "https://github.com/conal/MemoTrie")
+    (synopsis "Trie-based memo functions")
+    (description "This package provides a functional library for creating
+efficient memo functions using tries.")
+    (license license:bsd-3)))
+
 (define-public ghc-haddock-library
   (package
     (name "ghc-haddock-library")

From 1aacec9e3d4294d3dadd153170878a9a4748ca24 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:14:17 -0400
Subject: [PATCH 342/909] gnu: ghc-openglraw: Update to 3.3.1.0.

* gnu/packages/haskell.scm (ghc-openglraw): Update to 3.3.1.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 1ae8eb993a..70847aec1f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1539,7 +1539,7 @@ arithmetic.")
 (define-public ghc-openglraw
   (package
     (name "ghc-openglraw")
-    (version "3.2.7.0")
+    (version "3.3.1.0")
     (source
      (origin
        (method url-fetch)
@@ -1549,7 +1549,7 @@ arithmetic.")
              ".tar.gz"))
        (sha256
         (base32
-         "024aln102d1mmsdalq9jd5mmwjbnrb8gxcak73lybrc7q87kswk2"))))
+         "1x8w3x308jldj2c1xqcq3a3sc2jc06pdpgqkgjsmixi1skv4a1vb"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-half" ,ghc-half)

From ded4ac387173cedbaf917479bdf763cffbb22e73 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:05:45 -0400
Subject: [PATCH 343/909] gnu: ghc-temporary: Update to 1.3.

* gnu/packages/haskell.scm (ghc-temporary): Update to 1.3.
[inputs]: Add ghc-random.
[native-inputs]: Add ghc-base-compat, ghc-tasty, and ghc-tasty-hunit.
---
 gnu/packages/haskell.scm | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 70847aec1f..dfe3756649 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3399,7 +3399,7 @@ for Haskell.")
 (define-public ghc-temporary
   (package
     (name "ghc-temporary")
-    (version "1.2.0.4")
+    (version "1.3")
     (source
      (origin
        (method url-fetch)
@@ -3409,9 +3409,15 @@ for Haskell.")
              ".tar.gz"))
        (sha256
         (base32
-         "0qk741yqnpd69sksgks2vb7zi50rglp9m498lzw4sh268a017rsi"))))
+         "144qhwfwg37l3k313raf4ssiz16jbgwlm1nf4flgqpsbd69jji4c"))))
     (build-system haskell-build-system)
-    (inputs `(("ghc-exceptions" ,ghc-exceptions)))
+    (inputs
+     `(("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-random" ,ghc-random)))
+    (native-inputs
+     `(("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)))
     (home-page "https://www.github.com/batterseapower/temporary")
     (synopsis "Temporary file and directory support")
     (description "The functions for creating temporary files and directories

From 7307a2f8a41fa11a56baa88ae22934572b1900f2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:21:12 -0400
Subject: [PATCH 344/909] gnu: ghc-th-orphans: Update to 0.13.6.

* gnu/packages/haskell.scm (ghc-th-orphans): Update to 0.13.6.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index dfe3756649..8676948aa3 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5893,14 +5893,14 @@ function which generates instances.")
 (define-public ghc-th-orphans
   (package
     (name "ghc-th-orphans")
-    (version "0.13.2")
+    (version "0.13.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "th-orphans/th-orphans-" version ".tar.gz"))
               (sha256
                (base32
-                "0102vkyzpgnp2fys8pvw4khrhrh2y1b8dp1slgvn020vg4s351mc"))))
+                "0sfl3pn9kq9da3ji3lsgzgzy82vz6yvsg80dmakc1jvk7awycibp"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-th-lift" ,ghc-th-lift)

From bb7d443d85a3dfc8577ae14fc5d38315c61b233b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:21:43 -0400
Subject: [PATCH 345/909] gnu: ghc-x509: Update to 1.7.3.

* gnu/packages/haskell-crypto.scm (ghc-x509): Update to 1.7.3.
---
 gnu/packages/haskell-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index bb0ee074c2..cff678d724 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -423,14 +423,14 @@ libraries, like OpenSSL.")
 (define-public ghc-x509
   (package
     (name "ghc-x509")
-    (version "1.6.4")
+    (version "1.7.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "x509/x509-" version ".tar.gz"))
               (sha256
                (base32
-                "0hixx76wpb4qxida017ka5zr6lrsycahrqyw8z90q9mxvndpy3my"))))
+                "0mkk29g32fs70bqkikg83v45h9jig9c8aail3mrdqwxpkfa0yx21"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-memory" ,ghc-memory)

From 68dc0c294a6090db2bac109c61b2308eeffb797e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 23:56:01 -0400
Subject: [PATCH 346/909] gnu: ghc-distributive: Update Cabal file to r6.

* gnu/packages/haskell.scm (ghc-distributive): Update Cabal file to r6.
[native-inputs]: Replace ghc-doctest-0.12 with ghc-doctest.
---
 gnu/packages/haskell.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 8676948aa3..cac1fcddc3 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2985,6 +2985,9 @@ modifying, and extracting files from zip archives in Haskell.")
         (base32
          "0y566r97sfyvhsmd4yxiz4ns2mqgwf5bdbp56wgxl6wlkidq0wwi"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("6" "06bd38rf31yrvvy989r44pm0id3dsxwcp6nxg7wk6ccj3n2b8rzk")))
     (inputs
      `(("ghc-tagged" ,ghc-tagged)
        ("ghc-base-orphans" ,ghc-base-orphans)
@@ -2993,7 +2996,7 @@ modifying, and extracting files from zip archives in Haskell.")
        ("ghc-generic-deriving" ,ghc-generic-deriving)))
     (native-inputs
      `(("cabal-doctest" ,cabal-doctest)
-       ("ghc-doctest" ,ghc-doctest-0.12)
+       ("ghc-doctest" ,ghc-doctest)
        ("ghc-hspec" ,ghc-hspec)
        ("hspec-discover" ,hspec-discover)))
     (home-page "https://github.com/ekmett/distributive/")

From 211b213367c7bafb0701e03c777c31902b9a8415 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:22:40 -0400
Subject: [PATCH 347/909] gnu: ghc-gluraw: Update to 2.0.0.4.

* gnu/packages/haskell.scm (ghc-gluraw): Update to 2.0.0.4.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index cac1fcddc3..911cdccfc0 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1599,7 +1599,7 @@ programs.")
 (define-public ghc-gluraw
   (package
     (name "ghc-gluraw")
-    (version "2.0.0.2")
+    (version "2.0.0.4")
     (source
      (origin
        (method url-fetch)
@@ -1609,7 +1609,7 @@ programs.")
              ".tar.gz"))
        (sha256
         (base32
-         "1phmvxr0kkxq89ykmr8rj77inj8dvcxd6h72z1ncdgdazfz3sjw8"))))
+         "1i2xi35n5z0d372px9mh6cyhgg1m0cfaiy3fnspkf6kbn9fgsqxq"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-openglraw" ,ghc-openglraw)))

From f9f2877d54fdf72e0579bce6cfca87b8712144be Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:14:14 -0400
Subject: [PATCH 348/909] gnu: ghc-gnuplot: Update to 0.5.5.2.

* gnu/packages/haskell.scm (ghc-gnuplot): Update to 0.5.5.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 911cdccfc0..df4ba82a30 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8019,7 +8019,7 @@ helper functions for Lists, Maybes, Tuples, Functions.")
 (define-public ghc-gnuplot
   (package
     (name "ghc-gnuplot")
-    (version "0.5.4.1")
+    (version "0.5.5.2")
     (source
      (origin
        (method url-fetch)
@@ -8027,7 +8027,7 @@ helper functions for Lists, Maybes, Tuples, Functions.")
              "mirror://hackage/package/gnuplot/gnuplot-"
              version ".tar.gz"))
        (sha256
-        (base32 "1xz8prw9xjk0rsyrkp9bsmxykzrbhpv9qhhkdapy75mdbmgwjm7s"))))
+        (base32 "1mlppnc13ygjzmf6ldydys4wvy35yb3xjwwfgf9rbi7nfcqjr6mn"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-temporary" ,ghc-temporary)

From ad91386a277f7b084ce59c6e7f1c9f57ec5501e4 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Mon, 3 Sep 2018 22:30:50 -0400
Subject: [PATCH 349/909] gnu: ghc-graphviz: Remove unneeded configure flag.

* gnu/packages/haskell.scm (ghc-graphviz)[arguments]: Remove unneeded
"--allow-newer=QuickCheck" configure flag.
---
 gnu/packages/haskell.scm | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index df4ba82a30..6198180194 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7382,8 +7382,6 @@ for generating graph-like data structures.")
                (base32
                 "0kj7ap0gnliviq2p8lscw1m06capnsa90vpvcys24nqy5nw2wrp7"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck")))
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-colour" ,ghc-colour)

From a15411176342ba58914d9119296ad6da7f7aa35b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:08:39 -0400
Subject: [PATCH 350/909] gnu: ghc-markdown-unlit: Update to 0.5.0.

* gnu/packages/haskell.scm (ghc-markdown-unlit): Update to 0.5.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6198180194..d754ecdc1b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8165,7 +8165,7 @@ and a large set of GNU extensions.")
 (define-public ghc-markdown-unlit
   (package
     (name "ghc-markdown-unlit")
-    (version "0.4.0")
+    (version "0.5.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -8173,7 +8173,7 @@ and a large set of GNU extensions.")
                     "markdown-unlit-" version ".tar.gz"))
               (sha256
                (base32
-                "1kj2bffl7ndd8ygwwa3r1mbpwbxbfhyfgnbla8k8g9i6ffp0qrbw"))))
+                "1gy79vr85vcp13rdjh0hz7zv6daqqffww4j0cqn2lpjjh9xhsbg7"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-base-compat" ,ghc-base-compat)

From b3cd1712a8acc59b1d7302627bb997912aad9a28 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:14:19 -0400
Subject: [PATCH 351/909] gnu: ghc-mockery: Update to 0.3.5.

* gnu/packages/haskell.scm (ghc-mockery): Update to 0.3.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d754ecdc1b..9b906e1524 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6057,14 +6057,14 @@ back-ends.")
 (define-public ghc-mockery
   (package
     (name "ghc-mockery")
-    (version "0.3.3")
+    (version "0.3.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "mockery/mockery-" version ".tar.gz"))
               (sha256
                (base32
-                "1m7sq2vclgir3qbpngzl3g87ks4034blwwf7p3h02c0jlcwpl5b1"))))
+                "09ypgm3z69gq8mj6y66ss58kbjnk15r8frwcwbqcfbfksfnfv8dp"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-temporary" ,ghc-temporary)

From 5a92fb411c0cac4032c885d977192f212daaa493 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:26:03 -0400
Subject: [PATCH 352/909] gnu: ghc-network: Update to 2.6.3.6.

* gnu/packages/haskell.scm (ghc-network): Update to 2.6.3.6.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9b906e1524..935b126077 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4004,7 +4004,7 @@ interface.")
 (define-public ghc-network
   (package
     (name "ghc-network")
-    (version "2.6.3.1")
+    (version "2.6.3.6")
     (outputs '("out" "doc"))
     (source
      (origin
@@ -4015,7 +4015,7 @@ interface.")
              ".tar.gz"))
        (sha256
         (base32
-         "1rl2gl37cf4k0ddsq93q15fwdz1l25nhl4w205krbh7d5dg5y12p"))))
+         "198mam7ahny48p9fajznbqq16a8ya2gw0xm3gnm1si1rmc4hdplv"))))
     (build-system haskell-build-system)
     ;; The regression tests depend on an unpublished module.
     (arguments `(#:tests? #f))

From 10ae734585c9f11fd0bd5353120d026d058e1950 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:50:16 -0400
Subject: [PATCH 353/909] gnu: ghc-typed-process: Update to 0.2.3.0.

* gnu/packages/haskell.scm (ghc-typed-process): Update to 0.2.3.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 935b126077..d7b09065dd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6764,7 +6764,7 @@ better for some purposes.")
 (define-public ghc-typed-process
   (package
     (name "ghc-typed-process")
-    (version "0.2.2.0")
+    (version "0.2.3.0")
     (source
      (origin
        (method url-fetch)
@@ -6773,7 +6773,7 @@ better for some purposes.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0c6gvgvjyncbni9a5bvpbglknd4yclr3d3hfg9bhgahmkj40dva2"))))
+         "0j36vrc9w841m5qbwqra1lwiznx31xfnhin1sm8x2c2739csbpn0"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-async" ,ghc-async)

From 0618a71b1e5d0e5d79b440509791c49740a43f38 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:50:55 -0400
Subject: [PATCH 354/909] gnu: ghc-wave: Update to 0.1.5.

* gnu/packages/haskell.scm (ghc-wave): Update to 0.1.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d7b09065dd..b804117d84 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8223,7 +8223,7 @@ Rust syntax.  It is intended to be useful for two different purposes:
 (define-public ghc-wave
   (package
     (name "ghc-wave")
-    (version "0.1.4")
+    (version "0.1.5")
     (source (origin
       (method url-fetch)
       (uri (string-append
@@ -8232,7 +8232,7 @@ Rust syntax.  It is intended to be useful for two different purposes:
              ".tar.gz"))
       (sha256
         (base32
-          "1g5nmqfk6p25v9ismwz4i66ay91bd1qh39xwj0hm4z6a5mw8frk8"))))
+          "03zycmwrchhqvi37fdvlzz2d1vl4hy0i8xyys1zznw38qfq0h2i5"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-cereal" ,ghc-cereal)

From 245a2555bcdd551cc6e0fe8fde6ccffa1248f741 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:26:37 -0400
Subject: [PATCH 355/909] gnu: ghc-x509-store: Update to 1.6.6.

* gnu/packages/haskell-crypto.scm (ghc-x509-store): Update to 1.6.6.
[native-inputs]: Add ghc-tasty and ghc-tasty-hunit.
---
 gnu/packages/haskell-crypto.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index cff678d724..9903555e6b 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -452,7 +452,7 @@ libraries, like OpenSSL.")
 (define-public ghc-x509-store
   (package
     (name "ghc-x509-store")
-    (version "1.6.2")
+    (version "1.6.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -460,7 +460,7 @@ libraries, like OpenSSL.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0yw09nwkvr324qz4sc27c0p28bz2h6gns6lkaz9mz92mgqf2dza9"))))
+                "0dbndqmnmyixxc7308nyq3zlkhz9dff4rbcw2a49c77rbicny9va"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-pem" ,ghc-pem)
@@ -468,6 +468,9 @@ libraries, like OpenSSL.")
        ("ghc-asn1-encoding" ,ghc-asn1-encoding)
        ("ghc-cryptonite" ,ghc-cryptonite)
        ("ghc-x509" ,ghc-x509)))
+    (native-inputs
+     `(("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)))
     (home-page "https://github.com/vincenthz/hs-certificate")
     (synopsis "X.509 collection accessing and storing methods")
     (description

From 74f490ec0b1fab0d5df54a5b5b79b9f511197aa5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:21:18 -0400
Subject: [PATCH 356/909] gnu: ghc-zip-archive: Update to 0.3.3.

* gnu/packages/haskell.scm (ghc-zip-archive): Update to 0.3.3.
[inputs]: Remove ghc-old-time and zip.
[native-inputs]: Add unzip.
---
 gnu/packages/haskell.scm | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b804117d84..7c5fef6c9b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2943,7 +2943,7 @@ complicated text/binary file formats.")
 (define-public ghc-zip-archive
   (package
     (name "ghc-zip-archive")
-    (version "0.3.0.5")
+    (version "0.3.3")
     (source
      (origin
        (method url-fetch)
@@ -2953,17 +2953,16 @@ complicated text/binary file formats.")
              ".tar.gz"))
        (sha256
         (base32
-         "1iwpzjck4jg9bz1yqky051i2wljsqc14q5zbi10dydfp8ip3d0yw"))))
+         "0kf8xyac168bng8a0za2jwrbss7a4ralvci9g54hnvl0gkkxx2lq"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-old-time" ,ghc-old-time)
-       ("ghc-digest" ,ghc-digest)
-       ("zip" ,zip)
+     `(("ghc-digest" ,ghc-digest)
        ("ghc-temporary" ,ghc-temporary)
        ("ghc-text" ,ghc-text)
        ("ghc-zlib" ,ghc-zlib)))
     (native-inputs
-     `(("ghc-hunit" ,ghc-hunit)))
+     `(("ghc-hunit" ,ghc-hunit)
+       ("unzip" ,unzip)))
     (home-page "https://hackage.haskell.org/package/zip-archive")
     (synopsis "Zip archive library for Haskell")
     (description "The zip-archive library provides functions for creating,

From 0f9e74e9f7bef9157c7869cd9cb6ed50a8364e2d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 30 Aug 2018 11:39:41 -0400
Subject: [PATCH 357/909] gnu: ghc-attoparsec: Enable tests and allow newer
 QuickCheck.

* gnu/packages/haskell.scm (ghc-attoparsec)[arguments]: Enable tests and
add a phase that patches the Cabal file to allow a newer QuickCheck and
removes a failing test.
---
 gnu/packages/haskell.scm | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7c5fef6c9b..5c1bb6f309 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2909,10 +2909,19 @@ with slicing and Clang-style colored diagnostics.")
         (base32
          "0j6qcwd146yzlkc9mcvzvnixsyl65n2a68l28322q5v9p4g4g4yx"))))
     (build-system haskell-build-system)
-    ;; FIXME: at least on test fails with QuickCheck > 2.9.2.  Once upstream
-    ;; has updated the tests to work with a later version of QuickCheck we can
-    ;; re-enable them.
-    (arguments `(#:tests? #f))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-for-newer-quickcheck
+           (lambda _
+             (substitute* "attoparsec.cabal"
+               (("QuickCheck >= 2\\.7 && < 2\\.10")
+                "QuickCheck >= 2.7 && < 2.12"))
+             ;; This test fails because of the newer QuickCheck:
+             ;; <https://github.com/bos/attoparsec/issues/134>.
+             (substitute* "tests/QC/ByteString.hs"
+               ((", testProperty \"satisfyWith\" satisfyWith")
+                "")))))))
     (inputs
      `(("ghc-scientific" ,ghc-scientific)
        ("ghc-text" ,ghc-text)))

From 40a8d0762f7f872696cf23d5111fbecb28dbdd5f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:27:32 -0400
Subject: [PATCH 358/909] gnu: ghc-bytes: Update to 0.15.5.

* gnu/packages/haskell.scm (ghc-bytes): Update to 0.15.5.
[inputs]: Replace ghc-doctest-0.13 with ghc-doctest.
---
 gnu/packages/haskell.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5c1bb6f309..d2db25c019 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10092,7 +10092,7 @@ address string against RFC 5322.")
 (define-public ghc-bytes
   (package
    (name "ghc-bytes")
-   (version "0.15.4")
+   (version "0.15.5")
    (source
     (origin
      (method url-fetch)
@@ -10103,11 +10103,11 @@ address string against RFC 5322.")
      (file-name (string-append name "-" version ".tar.gz"))
      (sha256
       (base32
-       "121x3iqlm8pghw8cd9g30cnqbl7jrdpfjxdanmqdqllajw6xivrm"))))
+       "063il2vrn0p88r9gzndh4ijs0mxj37khkc9ym9bqdsv7ngk3b683"))))
    (build-system haskell-build-system)
    (inputs `(("ghc-cereal" ,ghc-cereal)
              ("cabal-doctest" ,cabal-doctest)
-             ("ghc-doctest" ,ghc-doctest-0.13)
+             ("ghc-doctest" ,ghc-doctest)
              ("ghc-scientific" ,ghc-scientific)
              ("ghc-text" ,ghc-text)
              ("ghc-transformers-compat" ,ghc-transformers-compat)

From c2828c8149ee06577c861f21acfcf4418bd711f8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:29:10 -0400
Subject: [PATCH 359/909] gnu: ghc-comonad: Update to 5.0.4.

* gnu/packages/haskell.scm (ghc-comonad): Update to 5.0.4.
[native-inputs]: Add cabal-doctest and ghc-doctest.
---
 gnu/packages/haskell.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d2db25c019..0e883d1ff3 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3043,7 +3043,7 @@ parser isolation, and labeled blocks for better error messages.")
 (define-public ghc-comonad
   (package
     (name "ghc-comonad")
-    (version "5")
+    (version "5.0.4")
     (source
      (origin
        (method url-fetch)
@@ -3053,10 +3053,11 @@ parser isolation, and labeled blocks for better error messages.")
              ".tar.gz"))
        (sha256
         (base32
-         "0anb36m9z52y9xsipxzj9w1b41b2rj8r389cxd6d20dplnfv3rbq"))))
+         "09g870c4flp4k3fgbibsd0mmfjani1qcpbcl685v8x89kxzrva3q"))))
     (build-system haskell-build-system)
     (native-inputs
-     `(("ghc-doctest" ,ghc-doctest)))
+     `(("cabal-doctest" ,cabal-doctest)
+       ("ghc-doctest" ,ghc-doctest)))
     (inputs
      `(("ghc-contravariant" ,ghc-contravariant)
        ("ghc-distributive" ,ghc-distributive)

From 14b0ade66fac4d8f9945f14c2031bd41352139b5 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:33:24 -0400
Subject: [PATCH 360/909] gnu: ghc-haskell-src-exts: Update to 1.20.2.

* gnu/packages/haskell.scm (ghc-haskell-src-exts): Update to 1.20.2.
[inputs]: Replace ghc-pretty-show-for-haskell-src-exts with ghc-pretty-show.
(ghc-pretty-show-for-haskell-src-exts): Remove.
---
 gnu/packages/haskell.scm | 19 +++----------------
 1 file changed, 3 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0e883d1ff3..5772e6a4a4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1223,23 +1223,10 @@ complex generic values into an interactive Html page, for easier
 examination.")
     (license license:expat)))
 
-(define-public ghc-pretty-show-for-haskell-src-exts
-  (package (inherit ghc-pretty-show)
-    (name "ghc-pretty-show")
-    (version "1.6.10")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/pretty-show/"
-                           "pretty-show-" version ".tar.gz"))
-       (sha256
-        (base32
-         "133s4l1gk46saf6ycm785rswycy8g3j0qqrv93b5wp8cp50kd0ww"))))))
-
 (define-public ghc-haskell-src-exts
   (package
     (name "ghc-haskell-src-exts")
-    (version "1.20.1")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
@@ -1249,12 +1236,12 @@ examination.")
              ".tar.gz"))
        (sha256
         (base32
-         "1jsjl9hja2dpcfq4mzlfpwyr6axwnwgacfb7aa070kz4lbygzaa8"))))
+         "1sm3z4v1p5yffg01ldgavz71s3bvfhjfa13k428rk14bpkl8crlz"))))
     (build-system haskell-build-system)
     (inputs
      `(("cpphs" ,cpphs)
        ("ghc-happy" ,ghc-happy)
-       ("ghc-pretty-show" ,ghc-pretty-show-for-haskell-src-exts)))
+       ("ghc-pretty-show" ,ghc-pretty-show)))
     (native-inputs
      `(("ghc-smallcheck" ,ghc-smallcheck)
        ("ghc-tasty" ,ghc-tasty)

From b9a6398692b78db8ce6038ffcba534c0d4b77e97 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:31:42 -0400
Subject: [PATCH 361/909] gnu: ghc-iproute: Update to 1.7.5.

* gnu/packages/haskell.scm (ghc-iproute): Update to 1.7.5.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5772e6a4a4..fa57aebe66 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2583,7 +2583,7 @@ lines continued at an indented level below.")
 (define-public ghc-iproute
   (package
     (name "ghc-iproute")
-    (version "1.7.1")
+    (version "1.7.5")
     (source
      (origin
        (method url-fetch)
@@ -2593,7 +2593,7 @@ lines continued at an indented level below.")
              ".tar.gz"))
        (sha256
         (base32
-         "1viyxq3m1aifl05w0hxwrhhhcfpmvwz4ymil2gngi4nfm0yd1f2p"))))
+         "1vw1nm3s8vz1hqnjnqd3wh5rr4q3m2r4izn5ynhf93h9185qwqzd"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: Tests cannot find System.ByteOrder,
                                ; exported by ghc-byteorder.  Doctest issue.

From 81caf9488546f438c7d6397959e827f6af9273cb Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:32:07 -0400
Subject: [PATCH 362/909] gnu: ghc-megaparsec: Update to 6.5.0.

* gnu/packages/haskell.scm (ghc-megaparsec): Update to 6.5.0.
[arguments]: Update Cabal file to r4.
---
 gnu/packages/haskell.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index fa57aebe66..142c96f63c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3873,7 +3873,7 @@ combinators.")
 (define-public ghc-megaparsec
   (package
     (name "ghc-megaparsec")
-    (version "6.4.0")
+    (version "6.5.0")
     (source
      (origin
        (method url-fetch)
@@ -3882,8 +3882,11 @@ combinators.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0h9azhs0dfrc359vrbd1jljrg3yfdbwd4p62cxqkn7mnh8913jpd"))))
+         "12iggy7qpf8x93jm64zf0g215xwy779bqyfyjk2bhmxqqr1yzgdy"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("4" "0ij3asi5vwlhbgwsy6nhli9a0qb7926mg809fsgyl1rnhs9fvpx1")))
     (inputs
      `(("ghc-case-insensitive" ,ghc-case-insensitive)
        ("ghc-parser-combinators" ,ghc-parser-combinators)

From ce88eae9a30d23d10cc771fb06659da293d1ae9b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:44:29 -0400
Subject: [PATCH 363/909] gnu: ghc-opengl: Update to 3.0.2.2.

* gnu/packages/haskell.scm (ghc-opengl): Update to 3.0.2.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 142c96f63c..d1046a81bf 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1610,7 +1610,7 @@ basis for a nicer interface.")
 (define-public ghc-opengl
   (package
     (name "ghc-opengl")
-    (version "3.0.1.0")
+    (version "3.0.2.2")
     (source
      (origin
        (method url-fetch)
@@ -1620,7 +1620,7 @@ basis for a nicer interface.")
              ".tar.gz"))
        (sha256
         (base32
-         "1nm2mzrn1h2nnfs9vl5p088hqpll7rdvcsyqsn8q641im9jhqp7l"))))
+         "19vxwvx2n8zq2klj176l25n2b64ybp0b8mhm4p46gvpcivz41fjc"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-text" ,ghc-text)

From fc0424875f4f7c39ed1b5f88192ae4b77445ac3d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 22:47:48 -0400
Subject: [PATCH 364/909] gnu: ghc-quickcheck-instances: Update Cabal file to
 r1.

* gnu/packages/haskell-check.scm (ghc-quickcheck-instances) Update Cabal
file to r1.
[arguments]: Remove unneeded "--allow-newer" configure flag.
---
 gnu/packages/haskell-check.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 0ab0b9a61d..d8c2e47dbe 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -352,7 +352,8 @@ development.")
          "1bh1pzz5fdcqvzdcirqxna6fnjms02min5md716299g5niz46w55"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=base-compat")))
+     `(#:cabal-revision
+       ("1" "1sngfq3v71bvgjsl8cj5kh65m3fziwy8dkvwjzs0kxfrzr87faly")))
     (inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-base-compat" ,ghc-base-compat)

From fd358b34c356b9caaa73ea4df84efeeb67b88dce Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:32:48 -0400
Subject: [PATCH 365/909] gnu: ghc-socks: Update to 0.5.6.

* gnu/packages/haskell.scm (ghc-socks): Update to 0.5.6.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d1046a81bf..689a24a12f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6383,14 +6383,14 @@ set, memory copy, ..) and more")
 (define-public ghc-socks
   (package
     (name "ghc-socks")
-    (version "0.5.5")
+    (version "0.5.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "socks/socks-" version ".tar.gz"))
               (sha256
                (base32
-                "0s689w1hh9g8ifl75xhzbv96ir07hwn04b4lgvbxzl8swa9ylir6"))))
+                "0f44qy74i0n6ll3jym0a2ipafkpw1h67amcpqmj8iq95h21wsqzs"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-cereal" ,ghc-cereal)

From ddbe020756f65176d7a693b02f54e71bdd1b0685 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:33:57 -0400
Subject: [PATCH 366/909] gnu: ghc-x509-system: Update to 1.6.6.

* gnu/packages/haskell-crypto.scm (ghc-x509-system): Update to 1.6.6.
---
 gnu/packages/haskell-crypto.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index 9903555e6b..a4e0a22faf 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -512,7 +512,7 @@ list validation.")
 (define-public ghc-x509-system
   (package
     (name "ghc-x509-system")
-    (version "1.6.4")
+    (version "1.6.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -520,7 +520,7 @@ list validation.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0k7zc0xp7r6kqmi39rpiicvq78xb0pr2cq6q5s3kmmsshllg13nr"))))
+                "06a4m9c7vlr9nhp9gmqbb46arf0yj1dkdm4nip03hzy67spdmp20"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-pem" ,ghc-pem)

From bb84b01d51c3293fdd56e0907be87ac94f593197 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:34:16 -0400
Subject: [PATCH 367/909] gnu: ghc-x509-validation: Update to 1.6.10.

* gnu/packages/haskell-crypto.scm (ghc-x509-validation): Update to 1.6.10.
[native-inputs]: Add ghc-tasty and ghc-tasty-hunit.
---
 gnu/packages/haskell-crypto.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index a4e0a22faf..ff44970be0 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -481,7 +481,7 @@ collections, certificates, revocation lists, and exception lists.")
 (define-public ghc-x509-validation
   (package
     (name "ghc-x509-validation")
-    (version "1.6.5")
+    (version "1.6.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -489,7 +489,7 @@ collections, certificates, revocation lists, and exception lists.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "190w1sr3w6w49v3yvqz4grb0v09ym4gll3n8bxwijvbvcybk3xyi"))))
+                "1ms51scawldgyfcim5a2qlgyn3rnrclyh205d6djaa1569vrs73n"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-memory" ,ghc-memory)
@@ -502,6 +502,9 @@ collections, certificates, revocation lists, and exception lists.")
        ("ghc-x509" ,ghc-x509)
        ("ghc-x509-store" ,ghc-x509-store)
        ("ghc-cryptonite" ,ghc-cryptonite)))
+    (native-inputs
+     `(("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)))
     (home-page "https://github.com/vincenthz/hs-certificate")
     (synopsis "X.509 certificate and revocation list validation")
     (description

From 2dbecb3a7515eb50e54c431d9830ca7a30d42af1 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:38:09 -0400
Subject: [PATCH 368/909] gnu: ghc-aeson: Update to 1.3.1.1.

* gnu/packages/haskell-web.scm (ghc-aeson): Update to 1.3.1.1.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index a60bf007af..2e863965ae 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -783,7 +783,7 @@ Strict, Transitional and Frameset variants.")
 (define-public ghc-aeson
   (package
     (name "ghc-aeson")
-    (version "1.2.4.0")
+    (version "1.3.1.1")
     (source
      (origin
        (method url-fetch)
@@ -793,7 +793,7 @@ Strict, Transitional and Frameset variants.")
              ".tar.gz"))
        (sha256
         (base32
-         "16zwpd07cmhs58wwsqbhxy3b58gqw8w5nr7nf6lwi4nvznjdn09l"))))
+         "1i1ig840fvsb1lnklcv32zsc0zscirc301lw1mpfxhc6h4pk0gw4"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
     (inputs

From 8e4394a571ac8a25cc08a5a42f401011c5aa37a1 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 14:01:22 -0400
Subject: [PATCH 369/909] gnu: ghc-attoparsec-iso8601: Update Cabal file to r1.

* gnu/packages/haskell.scm (ghc-attoparsec-iso8601): Update Cabal file to r1.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 689a24a12f..397132d4dd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9684,6 +9684,9 @@ connections.")
         (base32
          "12l55b76bhya9q89mfmqmy6sl5v39b6gzrw5rf3f70vkb23nsv5a"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "06f7pgmmc8456p3hc1y23kz1y127gfczy7s00wz1rls9g2sm2vi4")))
     (inputs `(("ghc-attoparsec" ,ghc-attoparsec)
               ("ghc-base-compat" ,ghc-base-compat)
               ("ghc-text" ,ghc-text)))

From 8574e6c704f3e89e243b36793fedbfa0ea3bade0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:38:44 -0400
Subject: [PATCH 370/909] gnu: ghc-bifunctors: Update to 5.5.3.

* gnu/packages/haskell.scm (ghc-bifunctors): Update to 5.5.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 397132d4dd..45a43d6272 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4886,7 +4886,7 @@ cross-site scripting (@dfn{XSS}) attacks.")
 (define-public ghc-bifunctors
   (package
     (name "ghc-bifunctors")
-    (version "5.5.2")
+    (version "5.5.3")
     (source
      (origin
        (method url-fetch)
@@ -4896,7 +4896,7 @@ cross-site scripting (@dfn{XSS}) attacks.")
              ".tar.gz"))
        (sha256
         (base32
-         "04fbsysm6zl8kmvqgffmrqa9bxl9dl2gibrd51asqzg737mb4ark"))))
+         "1jn9rxg643xnlhrknmjz88nblcpsr45xwjkwwnn5nxpasa7m4d6l"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-base-orphans" ,ghc-base-orphans)

From 892d5546472e214849fced1a5ab23a7afab53e94 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 6 Sep 2018 13:55:55 -0400
Subject: [PATCH 371/909] gnu: ghc-cgi: Adjust dependency constraints.

* gnu/packages/haskell.scm (ghc-cgi)[arguments]: Remove "--allow-newer"
configure flag; add a phase that patches the Cabal file to allow newer
versions of exceptions, time, doctest, and QuickCheck.
---
 gnu/packages/haskell.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 45a43d6272..ba8491429b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1093,7 +1093,19 @@ tool lex or flex for C/C++.")
          "1hbpplss1m4rdpm4ibip6fpimlhssqa14fl338kl2jbc463i64cj"))))
     (build-system haskell-build-system)
     (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck")))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "cgi.cabal"
+               (("exceptions < 0\\.9")
+                "exceptions < 0.11")
+               (("time >= 1\\.5 && < 1\\.7")
+                "time >= 1.5 && < 1.9")
+               (("doctest >= 0\\.8 && < 0\\.12")
+                "doctest >= 0.8 && < 0.17")
+               (("QuickCheck >= 2\\.8\\.1 && < 2\\.10")
+                "QuickCheck >= 2.8.1 && < 2.12")))))))
     (inputs
      `(("ghc-parsec" ,ghc-parsec)
        ("ghc-exceptions" ,ghc-exceptions)

From 146198f89890035f5ffe32cebdf026cc38740fa2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:39:51 -0400
Subject: [PATCH 372/909] gnu: ghc-email-validate: Update to 2.3.2.6.

* gnu/packages/haskell.scm (ghc-email-validate): Update to 2.3.2.6.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ba8491429b..c65bff34c4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10053,7 +10053,7 @@ system dependencies.")
 (define-public ghc-email-validate
   (package
     (name "ghc-email-validate")
-    (version "2.3.2.1")
+    (version "2.3.2.6")
     (source
      (origin
        (method url-fetch)
@@ -10064,7 +10064,7 @@ system dependencies.")
              ".tar.gz"))
        (sha256
         (base32
-         "0qvxysiap3r4mi3xff5nsk9qv6diqxfgwj186bypbamzvzlz0lav"))))
+         "0chgylvc8xmhp933rdbmpg5sv4y7yg2h6kbf0ip1dzmbd5p55pa5"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-attoparsec" ,ghc-attoparsec)

From 2dee63943b3b9c215264c926e27a7af9e93ec886 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:55:11 -0400
Subject: [PATCH 373/909] gnu: ghc-glut: Update to 2.7.0.14.

* gnu/packages/haskell.scm (ghc-glut): Update to 2.7.0.14.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c65bff34c4..4fd8e69ee9 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1571,7 +1571,7 @@ found at runtime, a userError is thrown.")
 (define-public ghc-glut
   (package
     (name "ghc-glut")
-    (version "2.7.0.10")
+    (version "2.7.0.14")
     (source
      (origin
        (method url-fetch)
@@ -1581,7 +1581,7 @@ found at runtime, a userError is thrown.")
              ".tar.gz"))
        (sha256
         (base32
-         "0sbm943bg896nf3qjmlnsg3zzrr3pl330rzh9g0hwv47nzwwn4ab"))))
+         "01i162fly4q1751fp60lgkzlb8kr0qqbvmxj74zc6skb19qggy2w"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-statevar" ,ghc-statevar)

From 255a31f8413073c5c5e78d85adb9d466b09c18df Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:40:23 -0400
Subject: [PATCH 374/909] gnu: ghc-haskell-src-exts-util: Update to 0.2.3.

* gnu/packages/haskell.scm (ghc-haskell-src-exts-util): Update to 0.2.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4fd8e69ee9..f545e5ee93 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1271,7 +1271,7 @@ patterns as per the HaRP extension as well as HSX-style embedded XML syntax.")
 (define-public ghc-haskell-src-exts-util
   (package
     (name "ghc-haskell-src-exts-util")
-    (version "0.2.2")
+    (version "0.2.3")
     (source
      (origin
        (method url-fetch)
@@ -1280,7 +1280,7 @@ patterns as per the HaRP extension as well as HSX-style embedded XML syntax.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "14rhwcrdz3kfb69c64qn8kybl7wnpajrjlfz5p95ca4bva4mwclg"))))
+         "1803718paq89f8pdck4mb88hv2k1ah9lxzq0lgjgwi9n88ryycz8"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-data-default" ,ghc-data-default)

From dcfee7b6d56b4308433c2d23b8ae1700460f62f3 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:25:38 -0400
Subject: [PATCH 375/909] gnu: ghc-haskell-src-meta: Update to 0.8.0.3.

* gnu/packages/haskell.scm (ghc-haskell-src-meta): Update to 0.8.0.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index f545e5ee93..aad8649170 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5978,7 +5978,7 @@ info for more informative bug reports.")
 (define-public ghc-haskell-src-meta
   (package
     (name "ghc-haskell-src-meta")
-    (version "0.8.0.2")
+    (version "0.8.0.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -5986,7 +5986,7 @@ info for more informative bug reports.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "12rc4v5dbbbcwdp7j8isvnm9vqpazv124j5kdfwlgwgwjhxi8ysb"))))
+                "08jq156zv4m0fjq6712n99c1jwxnpa6kj6sq8ch0r1l0a1ay6ww4"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-haskell-src-exts" ,ghc-haskell-src-exts)

From 867ac7fe58f6defe202e040803e41fc3f8e3d646 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:40:25 -0400
Subject: [PATCH 376/909] gnu: ghc-hslua: Update to 0.9.5.2.

* gnu/packages/haskell.scm (ghc-hslua): Update to 0.9.5.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index aad8649170..b43844fb7f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6203,14 +6203,14 @@ TIFF and GIF formats.")
 (define-public ghc-hslua
   (package
     (name "ghc-hslua")
-    (version "0.9.5")
+    (version "0.9.5.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "hslua/hslua-" version ".tar.gz"))
               (sha256
                (base32
-                "1j2zk7f7nyywg2b0n6kb2yf6ljc7cn2sk9jz0h76g3ag2b70l12n"))))
+                "1rdvv01p214zfjh6fcqjjgqwi8y42wad6cqzhlcv5gvclzw2ck8f"))))
     (build-system haskell-build-system)
     (arguments
      `(#:configure-flags '("-fsystem-lua")))

From 40e1af35bee20984563a4bf48810777d4b7c488b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:41:19 -0400
Subject: [PATCH 377/909] gnu: ghc-http-date: Update to 0.0.8.

* gnu/packages/haskell-web.scm (ghc-http-date): Update to 0.0.8.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 2e863965ae..742d3abcba 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -261,7 +261,7 @@ libraries, such as http-conduit.")
 (define-public ghc-http-date
   (package
     (name "ghc-http-date")
-    (version "0.0.6.1")
+    (version "0.0.8")
     (source
      (origin
        (method url-fetch)
@@ -270,7 +270,7 @@ libraries, such as http-conduit.")
                            "http-date-" version ".tar.gz"))
        (sha256
         (base32
-         "0dknh28kyarnzqrsc80ssalxjrq0qbv7ir49247p2grb7rh0dqgj"))))
+         "09slbzqayjnqqz9zybk7slgzvizgplikqgg4b2flzgks91466k0g"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-attoparsec" ,ghc-attoparsec)))

From 774f3984146dffb33573ff119dee056580bacff6 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:42:31 -0400
Subject: [PATCH 378/909] gnu: ghc-parsers: Update to 0.12.9.

* gnu/packages/haskell.scm (ghc-parsers): Update to 0.12.9.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b43844fb7f..bdb1205082 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2800,7 +2800,7 @@ copious examples.")
 (define-public ghc-parsers
   (package
     (name "ghc-parsers")
-    (version "0.12.4")
+    (version "0.12.9")
     (source
      (origin
        (method url-fetch)
@@ -2810,7 +2810,7 @@ copious examples.")
              ".tar.gz"))
        (sha256
         (base32
-         "07najh7f9y3ahh42z96sw4hnd0kc4x3wm0xlf739y0gh81ys5097"))))
+         "1r05sc1mcglk8w596kq9a1brfn9c2vll8lq16j07ln0vsz4jzrc1"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: Test fails with "cannot satisfy
                                ; -package attoparsec-0.13.0.1"

From 310d782eaf1f8db59f6e8746132ffe93341db67e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:17:42 -0400
Subject: [PATCH 379/909] gnu: ghc-tasty-th: Update to 0.1.7.

* gnu/packages/haskell-check.scm (ghc-tasty-th): Update to 0.1.7.
[inputs]: Add ghc-haskell-src-exts and ghc-tasty-hunit.
---
 gnu/packages/haskell-check.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index d8c2e47dbe..ce1030eef1 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -260,7 +260,7 @@ tasty.")
 (define-public ghc-tasty-th
   (package
     (name "ghc-tasty-th")
-    (version "0.1.4")
+    (version "0.1.7")
     (source
      (origin
        (method url-fetch)
@@ -269,10 +269,12 @@ tasty.")
              version ".tar.gz"))
        (sha256
         (base32
-         "0dff9si8i1qp0s7p4hlk0l29vq7wxfglw6mvlgmld43h7rllv88q"))))
+         "0b2ivrw2257m4cy4rjnkwqlarh83j1y3zywnmaqqqbvy667sqnj3"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-tasty" ,ghc-tasty)))
+     `(("ghc-haskell-src-exts" ,ghc-haskell-src-exts)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)))
     (home-page "https://github.com/bennofs/tasty-th")
     (synopsis "Automatically generate tasty TestTrees")
     (description

From 66c5de39485fe543f1dd6a0df86dffa1dd33ade7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:42:50 -0400
Subject: [PATCH 380/909] gnu: ghc-tls: Update to 1.4.1.

* gnu/packages/tls.scm (ghc-tls): Update to 1.4.1.
---
 gnu/packages/tls.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 6c4c64e507..bf462981ee 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -871,14 +871,14 @@ coding footprint.")
 (define-public ghc-tls
   (package
     (name "ghc-tls")
-    (version "1.3.8")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "tls/tls-" version ".tar.gz"))
               (sha256
                (base32
-                "1rdidf18i781c0vdvy9yn79yh08hmcacf6fp3sgghyiy3h0wyh5l"))))
+                "1y083724mym28n6xfaz7pcc7zqxdhjpaxpbvzxfbs25qq2px3smv"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-cereal" ,ghc-cereal)

From bad349d8a620a055bcec4293a27e60bb20f3ce0e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:43:13 -0400
Subject: [PATCH 381/909] gnu: ghc-uri-bytestring: Update to 0.3.2.0.

* gnu/packages/haskell.scm (ghc-uri-bytestring): Update to 0.3.2.0.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index bdb1205082..40c77c9439 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9734,7 +9734,7 @@ each constructor are represented using an n-ary product.")
 (define-public ghc-uri-bytestring
   (package
     (name "ghc-uri-bytestring")
-    (version "0.3.1.0")
+    (version "0.3.2.0")
     (source
      (origin
        (method url-fetch)
@@ -9743,7 +9743,7 @@ each constructor are represented using an n-ary product.")
                            "uri-bytestring-" version ".tar.gz"))
        (sha256
         (base32
-         "04qjv1sgyrdg538290p9hqnvyxnahvr5cjwl8vm1rn9j0fv3ymq9"))))
+         "1q04j5ybvk37zk2m0bkjwyhblz0ymdj0cn4rvsvdca1ikn5xdv5c"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-attoparsec" ,ghc-attoparsec)
               ("ghc-fail" ,ghc-fail)

From 5ebadb584bc642d58bf6c8dbb54468e4b7f266bd Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:44:15 -0400
Subject: [PATCH 382/909] gnu: agda: Update to 2.5.4.1.

* gnu/packages/agda.scm (agda): Update to 2.5.4.1.
---
 gnu/packages/agda.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm
index 572de5bbeb..418025bc37 100644
--- a/gnu/packages/agda.scm
+++ b/gnu/packages/agda.scm
@@ -30,7 +30,7 @@
 (define-public agda
   (package
     (name "agda")
-    (version "2.5.3")
+    (version "2.5.4.1")
     (source
      (origin
        (method url-fetch)
@@ -39,7 +39,7 @@
              version ".tar.gz"))
        (sha256
         (base32
-         "0r80vw7vnvbgq47y50v050malv7zvv2p2kg6f47i04r0b2ix855a"))))
+         "0bxpibsk98n9xp42d92ma5vj2fam8rsnl61fbhr3askfjdvalnbp"))))
     (build-system haskell-build-system)
     (inputs
      `(("cpphs" ,cpphs)

From 22b5a1a47719f57fd6cfe391e517f1e7a3def7fe Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:44:40 -0400
Subject: [PATCH 383/909] gnu: ghc-aeson-compat: Update to 0.3.8.

* gnu/packages/haskell.scm (ghc-aeson-compat): Update to 0.3.8.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 40c77c9439..94ebae2629 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9845,7 +9845,7 @@ way.")
 (define-public ghc-aeson-compat
   (package
     (name "ghc-aeson-compat")
-    (version "0.3.7.1")
+    (version "0.3.8")
     (source
      (origin
        (method url-fetch)
@@ -9854,7 +9854,7 @@ way.")
                            "aeson-compat-" version ".tar.gz"))
        (sha256
         (base32
-         "1jya3lm9imclhb8qqihv39hhb62vvs3qpws7pc5fc23vwg0hsx2r"))))
+         "0j4v13pgk21zy8hqkbx8hw0n05jdl17qphxz9rj4h333pr547r3i"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f))  ;  FIXME: Tests require QuickCheck >= 2.10
     (inputs `(("ghc-base-compat" ,ghc-base-compat)

From d1d27a67bbb9d8e790cc411067daba7a737fe8fe Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:45:20 -0400
Subject: [PATCH 384/909] gnu: ghc-aeson-pretty: Update to 0.8.7.

* gnu/packages/haskell-web.scm (ghc-aeson-pretty): Update to 0.8.7.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 742d3abcba..4c29964e67 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -842,7 +842,7 @@ naming: in Greek mythology, Aeson was the father of Jason.)")
 (define-public ghc-aeson-pretty
   (package
     (name "ghc-aeson-pretty")
-    (version "0.8.5")
+    (version "0.8.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -850,7 +850,7 @@ naming: in Greek mythology, Aeson was the father of Jason.)")
                     version ".tar.gz"))
               (sha256
                (base32
-                "1yd98972srlbkn0f2jhrb3f443j9wnq2fnw5gbxjxzmkcinfh5yx"))))
+                "1m977gs0s9gf3lwzlbs5y7bl6ansc5pywmn2qjk09l5bwg2yrhf1"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-aeson" ,ghc-aeson)

From f4585fd1fda9912801b02490aaa02e7eac1ba00a Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:48:11 -0400
Subject: [PATCH 385/909] gnu: ghc-connection: Update to 0.2.8.

* gnu/packages/haskell.scm (ghc-connection): Update to 0.2.8.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 94ebae2629..c158a1be59 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6416,7 +6416,7 @@ set, memory copy, ..) and more")
 (define-public ghc-connection
   (package
     (name "ghc-connection")
-    (version "0.2.6")
+    (version "0.2.8")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -6424,7 +6424,7 @@ set, memory copy, ..) and more")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1c1prsgad669cmf6qrqlb5hmh0dnam2imijqzpwcr4ja14l6rh83"))))
+                "1swkb9w5vx9ph7x55y51dc0srj2z27nd9ibgn8c0qcl6hx7g9cbh"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-byteable" ,ghc-byteable)

From dfe5f60f2d1790bf931d5519814225570d37f755 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:48:34 -0400
Subject: [PATCH 386/909] gnu: ghc-doctemplates: Update to 0.2.2.1.

* gnu/packages/haskell.scm (ghc-doctemplates): Update to 0.2.2.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c158a1be59..b72fa27423 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6540,7 +6540,7 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
 (define-public ghc-doctemplates
   (package
     (name "ghc-doctemplates")
-    (version "0.2.1")
+    (version "0.2.2.1")
     (source
      (origin
        (method url-fetch)
@@ -6549,7 +6549,7 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1bfs2kl5j5al2w2y4qpbn68p0xsnb65r7h51l356kpkzc326646p"))))
+         "1gyckfg3kgvzhxw14i7iwrw0crygvsp86sy53bbr1yn7bxbgn33b"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-aeson" ,ghc-aeson)

From 085f26d1e12b077950f1262b24f7f8c15c8cb033 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 09:25:40 -0400
Subject: [PATCH 387/909] gnu: ghc-hslua-module-text: Update Cabal file to r1.

* gnu/packages/haskell.scm (ghc-hslua-module-text): Update Cabal file to r1.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b72fa27423..d604526cdd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6268,6 +6268,9 @@ described in @url{https://www.lua.org/}.")
         (base32
          "0bcfpb1dhnxp0gr376ai4w7vczr9zrjl1r3r6w7kcxivfkwq9cxf"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "0vajlsd7y6pwa08635q0cx8z5c1c55bk7fvavw7g2vmyvxqjzx6n")))
     (inputs
      `(("ghc-hslua" ,ghc-hslua)
        ("ghc-text" ,ghc-text)))

From de02e56bcb6ac6baef80a015d587208fd97319f7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:49:42 -0400
Subject: [PATCH 388/909] gnu: ghc-http-api-data: Update to 0.3.8.1.

* gnu/packages/haskell.scm (ghc-http-api-data): Update to 0.3.8.1.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d604526cdd..521f02c2f0 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9771,7 +9771,7 @@ parser that uses ByteStrings for parsing and representing the URI data.")
 (define-public ghc-http-api-data
   (package
     (name "ghc-http-api-data")
-    (version "0.3.7.1")
+    (version "0.3.8.1")
     (source
      (origin
        (method url-fetch)
@@ -9780,7 +9780,7 @@ parser that uses ByteStrings for parsing and representing the URI data.")
                            "http-api-data-" version ".tar.gz"))
        (sha256
         (base32
-         "1zbmf0kkfsw7pfznisi205gh7jd284gfarxsyiavd2iw26akwqwc"))))
+         "1cq6459b8wz6nvkvpi89dg189n5q2xdq4rdq435hf150555vmskf"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f))  ;  FIXME: Tests require QuickCheck >= 2.9
     (inputs `(("ghc-attoparsec" ,ghc-attoparsec)

From a57c91a192d34d3ad1d80e3d40d2495b96eaa7b0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:23:33 -0400
Subject: [PATCH 389/909] gnu: ghc-lifted-async: Update to 0.10.0.2.

* gnu/packages/haskell.scm (ghc-lifted-async): Update to 0.10.0.2.
[inputs]: Add ghc-tasty-expected-failure.
---
 gnu/packages/haskell.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 521f02c2f0..d50aef9170 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7462,7 +7462,7 @@ a vocabulary for working with them.")
 (define-public ghc-lifted-async
   (package
     (name "ghc-lifted-async")
-    (version "0.9.0")
+    (version "0.10.0.2")
     (source
      (origin
        (method url-fetch)
@@ -7471,7 +7471,7 @@ a vocabulary for working with them.")
              version ".tar.gz"))
        (sha256
         (base32
-         "00fnwfcnc6niq9jbbb9rap9rkdgv5qhcglwanzc5fi8834j94c1r"))))
+         "1073r512c1x2m1v0jar9bwqg656slg7jd1jhsyj6m8awgx1l1mwf"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-async" ,ghc-async)
@@ -7481,6 +7481,7 @@ a vocabulary for working with them.")
        ("ghc-constraints" ,ghc-constraints)
        ("ghc-hunit" ,ghc-hunit)
        ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-expected-failure" ,ghc-tasty-expected-failure)
        ("ghc-tasty-hunit" ,ghc-tasty-hunit)
        ("ghc-tasty-th" ,ghc-tasty-th)))
     (home-page "https://github.com/maoe/lifted-async")

From 4979dcd195366faa70534ced47982613eee9eb0f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 09:28:53 -0400
Subject: [PATCH 390/909] gnu: ghc-pandoc-types: Remove unneeded
 "--allow-newer" flag.

* gnu/packages/haskell.scm (ghc-pandoc-types)[arguments]: Remove the
unneeded "--allow-newer=QuickCheck" confingure flag.
---
 gnu/packages/haskell.scm | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d50aef9170..d359ce4a70 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5481,8 +5481,6 @@ and bytestrings.")
                (base32
                 "1q6v2bynij724fv347mhqxdscwifzrx5jb9mq80608qf638fn717"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck")))
     (inputs
      `(("ghc-syb" ,ghc-syb)
        ("ghc-aeson" ,ghc-aeson)

From bf73366886e5c8c1b37e35f23b9cf21b011521e8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 21:56:59 -0400
Subject: [PATCH 391/909] gnu: ghc-profunctors: Update Cabal file to r2.

* gnu/packages/haskell.scm (ghc-profunctors): Update Cabal file to r2.
---
 gnu/packages/haskell.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d359ce4a70..5a6fbb2d95 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3163,6 +3163,9 @@ this package makes them available back to GHC 7.2.")
         (base32
          "0s1pwjidbn761xk43pmzyvn99hm3psdifjd78ylki7f97aiyd0g9"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("2" "1ywlg9z8nlhd2avgb8c6gbkv8zyk7hvc25926bafyg0m0k8y1amq")))
     (inputs
      `(("ghc-base-orphans" ,ghc-base-orphans)
        ("ghc-bifunctors" ,ghc-bifunctors)

From 07f38c6a2685fff4bfaf996ed14adc04188cc159 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 22:08:31 -0400
Subject: [PATCH 392/909] gnu: ghc-semigroupoids: Update to 5.2.2.

* gnu/packages/haskell.scm (ghc-semigroupoids): Update to 5.2.2.
[arguments]: Enable tests and update Cabal file to r4.
[inputs]: Add ghc-hashable and ghc-unordered-containers.
[native-inputs]: Add cabal-doctests and ghc-doctests.
(ghc-semigroupoids-5.2.2): Remove variable.
---
 gnu/packages/haskell.scm | 31 +++++++++++--------------------
 1 file changed, 11 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5a6fbb2d95..87adbb1aab 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4932,7 +4932,7 @@ cross-site scripting (@dfn{XSS}) attacks.")
 (define-public ghc-semigroupoids
   (package
     (name "ghc-semigroupoids")
-    (version "5.1")
+    (version "5.2.2")
     (source
      (origin
        (method url-fetch)
@@ -4942,9 +4942,11 @@ cross-site scripting (@dfn{XSS}) attacks.")
              ".tar.gz"))
        (sha256
         (base32
-         "0dgqc59p4xx5cl8qkpm6sn4wd3n59rq7l6din76hf10bnklqrb0n"))))
+         "17i96y4iqj8clcs090lf6k0ij3j16nj14vsfwz0mm9nd6i4gbpp4"))))
     (build-system haskell-build-system)
-    (arguments `(#:tests? #f)) ; FIXME: doctest packagedb propagation problem.
+    (arguments
+     `(#:cabal-revision
+       ("4" "0pqfrxzypjq6z8lgdkzq4vhcyqkpk5326hny0r6snpc3gm78r4ij")))
     (inputs
      `(("ghc-base-orphans" ,ghc-base-orphans)
        ("ghc-transformers-compat" ,ghc-transformers-compat)
@@ -4952,8 +4954,13 @@ cross-site scripting (@dfn{XSS}) attacks.")
        ("ghc-comonad" ,ghc-comonad)
        ("ghc-contravariant" ,ghc-contravariant)
        ("ghc-distributive" ,ghc-distributive)
+       ("ghc-hashable" ,ghc-hashable)
        ("ghc-semigroups" ,ghc-semigroups)
-       ("ghc-tagged" ,ghc-tagged)))
+       ("ghc-tagged" ,ghc-tagged)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)))
+    (native-inputs
+     `(("cabal-doctest" ,cabal-doctest)
+       ("ghc-doctest" ,ghc-doctest)))
     (home-page "https://github.com/ekmett/semigroupoids")
     (synopsis "Semigroupoids operations for Haskell")
     (description "This library provides a wide array of (semi)groupoids and
@@ -10084,22 +10091,6 @@ system dependencies.")
 address string against RFC 5322.")
     (license license:bsd-3)))
 
-(define-public ghc-semigroupoids-5.2.2
-  (package
-    (inherit ghc-semigroupoids)
-    (name "ghc-semigroupoids")
-    (version "5.2.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://hackage.haskell.org/package/"
-                                  "semigroupoids-" version "/semigroupoids-"
-                                   version ".tar.gz"))
-              (sha256
-               (base32
-                "17i96y4iqj8clcs090lf6k0ij3j16nj14vsfwz0mm9nd6i4gbpp4"))))
-    (inputs `(("ghc-unordered-containers" ,ghc-unordered-containers)
-              ,@(package-inputs ghc-semigroupoids)))))
-
 (define-public ghc-bytes
   (package
    (name "ghc-bytes")

From 01a67f89d1ec6bd981b8c99ef24186ff5c1527c1 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:51:09 -0400
Subject: [PATCH 393/909] gnu: ghc-shakespeare: Update to 2.0.15.

* gnu/packages/haskell.scm (ghc-shakespeare): Update to 2.0.15.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 87adbb1aab..bb08f3f096 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9614,7 +9614,7 @@ code locations of messages.")
 (define-public ghc-shakespeare
   (package
     (name "ghc-shakespeare")
-    (version "2.0.14")
+    (version "2.0.15")
     (source
      (origin
        (method url-fetch)
@@ -9623,7 +9623,7 @@ code locations of messages.")
                            "shakespeare-" version ".tar.gz"))
        (sha256
         (base32
-         "0j5zx8ka7d7scvb9shm7k3376qzl3k4kpim9aqqfs6n86901zpl4"))))
+         "1vk4b19zvwy4mpwaq9z3l3kfmz75gfyf7alhh0y112gspgpccm23"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-parsec" ,ghc-parsec)
               ("ghc-text" ,ghc-text)

From aac78f6be3ae6dc3531ce198021fe58ff86f8528 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 4 Sep 2018 00:09:27 -0400
Subject: [PATCH 394/909] gnu: Add ghc-tls-session-manager.

* gnu/packages/haskell-web.scm (ghc-tls-session-manager): New variable.
---
 gnu/packages/haskell-web.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 4c29964e67..5278cb9259 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -600,6 +600,32 @@ transfers.")
 based WAI (Web Application Interface in Haskell).")
     (license license:expat)))
 
+(define-public ghc-tls-session-manager
+  (package
+  (name "ghc-tls-session-manager")
+  (version "0.0.0.2")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (string-append
+            "https://hackage.haskell.org/package/"
+            "tls-session-manager/tls-session-manager-"
+             version ".tar.gz"))
+      (sha256
+        (base32
+          "0rvmln545vghsx8zhxp44f0f6pzma8cylarmfhhysy55ipywr1n5"))))
+  (build-system haskell-build-system)
+  (inputs
+    `(("ghc-auto-update" ,ghc-auto-update)
+      ("ghc-clock" ,ghc-clock)
+      ("ghc-psqueues" ,ghc-psqueues)
+      ("ghc-tls" ,ghc-tls)))
+  (home-page "http://hackage.haskell.org/package/tls-session-manager")
+  (synopsis "In-memory TLS session manager")
+  (description "This Haskell library provides a TLS session manager with
+limitation, automatic pruning, energy saving and replay resistance.")
+  (license license:bsd-3)))
+
 (define-public ghc-warp-tls
   (package
     (name "ghc-warp-tls")

From 3f135acc357871fabde46ea9eedcf2153b3f4244 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:54:11 -0400
Subject: [PATCH 395/909] gnu: ghc-xss-sanitize: Update to 0.3.6.

* gnu/packages/haskell-web.scm (ghc-xss-sanitize): Update to 0.3.6.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 5278cb9259..ac7420c981 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -657,7 +657,7 @@ a WAI handler, via the native Haskell TLS implementation.")
 (define-public ghc-xss-sanitize
   (package
     (name "ghc-xss-sanitize")
-    (version "0.3.5.7")
+    (version "0.3.6")
     (source
      (origin
        (method url-fetch)
@@ -666,7 +666,7 @@ a WAI handler, via the native Haskell TLS implementation.")
              version ".tar.gz"))
        (sha256
         (base32
-         "005cmhaw9xbzkcn42jmhvcvk63bzmg4lml368xwmqdvh7r0mcn4m"))))
+         "1d72s3a6520iwwc1wbn9v2znqgbw6a5wwzb23iq8ny9ccnjyx1dk"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-tagsoup" ,ghc-tagsoup)

From 2d67fe8936f6f71493d97f40654d7931ef3621c0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:10:02 -0400
Subject: [PATCH 396/909] gnu: raincat: Update to 1.2.

* gnu/packages/games.scm (raincat): Update to 1.2.
---
 gnu/packages/games.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 8155876313..1fab9fe34a 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -2122,7 +2122,7 @@ on the screen and keyboard to display letters.")
 (define-public raincat
   (package
     (name "raincat")
-    (version "1.1.1.3")
+    (version "1.2")
     (source
      (origin
        (method url-fetch)
@@ -2132,7 +2132,7 @@ on the screen and keyboard to display letters.")
              ".tar.gz"))
        (sha256
         (base32
-         "1aalh68h6799mv4vyg30zpskl5jkn6x2j1jza7p4lrflyifxzar8"))))
+         "1zyxkvjxkadwakg03xnjii1hx0gs45ap9rfkpi4kxipzxppq1klk"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)

From 955738723bd55b470feb33633da58fc76bada068 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:54:58 -0400
Subject: [PATCH 397/909] gnu: ghc-free: Update to 5.0.2.

* gnu/packages/haskell.scm (ghc-free): Update to 5.0.2.
[inputs]: Add ghc-transformers-base and ghc-transformers-compat.
---
 gnu/packages/haskell.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index bb08f3f096..e9dac65588 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5046,7 +5046,7 @@ semigroup.")
 (define-public ghc-free
   (package
     (name "ghc-free")
-    (version "4.12.4")
+    (version "5.0.2")
     (source
      (origin
        (method url-fetch)
@@ -5056,7 +5056,7 @@ semigroup.")
              ".tar.gz"))
        (sha256
         (base32
-         "1147s393442xf4gkpbq0rd1p286vmykgx85mxhk5d1c7wfm4bzn9"))))
+         "15m3n9vhz7z3kzv1w3wlfa3x8jp4cbrkwmrcjr7jlx39iqffn1gg"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-prelude-extras" ,ghc-prelude-extras)
@@ -5066,7 +5066,9 @@ semigroup.")
        ("ghc-comonad" ,ghc-comonad)
        ("ghc-distributive" ,ghc-distributive)
        ("ghc-semigroupoids" ,ghc-semigroupoids)
-       ("ghc-semigroups" ,ghc-semigroups)))
+       ("ghc-semigroups" ,ghc-semigroups)
+       ("ghc-transformers-base" ,ghc-transformers-base)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)))
     (home-page "https://github.com/ekmett/free/")
     (synopsis "Unrestricted monads for Haskell")
     (description "This library provides free monads, which are useful for many

From 89d44801696f6d0b5458d30e77412f72a637e61d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:55:31 -0400
Subject: [PATCH 398/909] gnu: ghc-http-client-tls: Update to 0.3.5.3.

* gnu/packages/haskell-web.scm (ghc-http-client-tls): Update to 0.3.5.3.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index ac7420c981..ac8df3921c 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -229,7 +229,7 @@ for more user-friendly packages.")
 (define-public ghc-http-client-tls
   (package
     (name "ghc-http-client-tls")
-    (version "0.3.5.1")
+    (version "0.3.5.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
@@ -237,7 +237,7 @@ for more user-friendly packages.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0n4mi8z77qaggfyq17z79cl304nf1f4h6gag60v4wjwghvmj7yn1"))))
+                "0qj3pcpgbsfsc4m52dz35khhl4hf1i0nmcpa445z82d9567vy6j7"))))
     (build-system haskell-build-system)
     ;; Tests require Internet access
     (arguments `(#:tests? #f))

From 8e06e15b7d5d890b2811a60973ce9e51fc80e606 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 22:41:31 -0400
Subject: [PATCH 399/909] gnu: Add ghc-invariant.

* gnu/packages/haskell.scm (ghc-invariant): New variable.
---
 gnu/packages/haskell.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e9dac65588..32b3384c60 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4730,6 +4730,43 @@ Compatibility package for older packages.")
 given term should not exist.")
     (license license:bsd-3)))
 
+(define-public ghc-invariant
+  (package
+    (name "ghc-invariant")
+    (version "0.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/invariant/invariant-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0aqj7z55632qdg45074kgn9qfdxzb0a2f8lgjzr0l0i4mm2rr37b"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-bifunctors" ,ghc-bifunctors)
+       ("ghc-comonad" ,ghc-comonad)
+       ("ghc-contravariant" ,ghc-contravariant)
+       ("ghc-profunctors" ,ghc-profunctors)
+       ("ghc-semigroups" ,ghc-semigroups)
+       ("ghc-statevar" ,ghc-statevar)
+       ("ghc-stm" ,ghc-stm)
+       ("ghc-tagged" ,ghc-tagged)
+       ("ghc-th-abstraction" ,ghc-th-abstraction)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("hspec-discover" ,hspec-discover)))
+    (home-page "https://github.com/nfrisby/invariant-functors")
+    (synopsis "Haskell98 invariant functors")
+    (description "Haskell98 invariant functors (also known as exponential
+functors).  For more information, see Edward Kmett's article
+@uref{http://comonad.com/reader/2008/rotten-bananas/, Rotten Bananas}.")
+    (license license:bsd-2)))
+
 (define-public ghc-kan-extensions
   (package
     (name "ghc-kan-extensions")

From d8717c89b434ad887b8c4b66f9d6e229d547ebe2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:55:51 -0400
Subject: [PATCH 400/909] gnu: ghc-reducers: Update to 3.12.3.

* gnu/packages/haskell.scm (ghc-reducers): Update to 3.12.3.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 32b3384c60..12fb9121b9 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3182,7 +3182,7 @@ this package makes them available back to GHC 7.2.")
 (define-public ghc-reducers
   (package
     (name "ghc-reducers")
-    (version "3.12.2")
+    (version "3.12.3")
     (source
      (origin
        (method url-fetch)
@@ -3192,7 +3192,7 @@ this package makes them available back to GHC 7.2.")
              ".tar.gz"))
        (sha256
         (base32
-         "1gbaa5x4zbvnbklcb0d4q4m8hk6w0gz4s0c4m288czi1nw43dl65"))))
+         "09wf8pl9ycglcv6qj5ba26gkg2s5iy81hsx9xp0q8na0cwvp71ki"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-fingertree" ,ghc-fingertree)

From 61849d425f9b5351f06553419b23cfffaba7ee29 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 5 Sep 2018 14:28:18 -0400
Subject: [PATCH 401/909] gnu: ghc-skylighting: Update to 0.7.2.

* gnu/packages/haskell.scm (ghc-skylighting-core): New variable.
(ghc-skylighting): Simplify by inheriting from ghc-skylighting-core.
---
 gnu/packages/haskell.scm | 37 +++++++++++++++++++++++++++----------
 1 file changed, 27 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 12fb9121b9..d8ceb0a755 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6494,17 +6494,18 @@ needs.  It provides a very simple API to create sockets to a destination with
 the choice of SSL/TLS, and SOCKS.")
     (license license:bsd-3)))
 
-(define-public ghc-skylighting
+(define-public ghc-skylighting-core
   (package
-    (name "ghc-skylighting")
-    (version "0.5.1")
+    (name "ghc-skylighting-core")
+    (version "0.7.2")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://hackage.haskell.org/package/skylighting-"
-                                  version "/skylighting-" version ".tar.gz"))
+              (uri (string-append "https://hackage.haskell.org/package/"
+                                  "skylighting-core/skylighting-core-"
+                                  version ".tar.gz"))
               (sha256
                (base32
-                "0l5lhhqqlfaq1fs7pn3n3b25kmazk8p4ahwvhagbrhcbm5hsigdg"))))
+                "066fwmwsd7xcvwlinfk2izlzq0xp8697i6lnbgsbl71jdybyackq"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-aeson" ,ghc-aeson)
@@ -6514,21 +6515,21 @@ the choice of SSL/TLS, and SOCKS.")
        ("ghc-blaze-html" ,ghc-blaze-html)
        ("ghc-case-insensitive" ,ghc-case-insensitive)
        ("ghc-colour" ,ghc-colour)
-       ("ghc-diff" ,ghc-diff)
        ("ghc-hxt" ,ghc-hxt)
-       ("ghc-pretty-show" ,ghc-pretty-show)
        ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin)
        ("ghc-safe" ,ghc-safe)
        ("ghc-text" ,ghc-text)
        ("ghc-utf8-string" ,ghc-utf8-string)))
     (native-inputs
-     `(("ghc-hunit" ,ghc-hunit)
+     `(("ghc-diff" ,ghc-diff)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-pretty-show" ,ghc-pretty-show)
        ("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-tasty" ,ghc-tasty)
        ("ghc-tasty-golden" ,ghc-tasty-golden)
        ("ghc-tasty-hunit" ,ghc-tasty-hunit)
        ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)))
-    (home-page "https://hackage.haskell.org/package/skylighting")
+    (home-page "https://github.com/jgm/skylighting")
     (synopsis "Syntax highlighting library")
     (description "Skylighting is a syntax highlighting library with support
 for over one hundred languages.  It derives its tokenizers from XML syntax
@@ -6537,6 +6538,22 @@ supported by that framework can be added.  An optional command-line program is
 provided.  Skylighting is intended to be the successor to highlighting-kate.")
     (license license:gpl2)))
 
+(define-public ghc-skylighting
+  (package
+    (inherit ghc-skylighting-core)
+    (name "ghc-skylighting")
+    (version "0.7.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://hackage.haskell.org/package/skylighting-"
+                                  version "/skylighting-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1rh3z1a7a4clvksdw1qlpmhxqkfahwypi70k91whgfamzsqpxdch"))))
+    (inputs
+     `(("ghc-skylighting-core" ,ghc-skylighting-core)
+       ,@(package-inputs ghc-skylighting-core)))))
+
 (define-public ghc-skylighting-for-pandoc-1
   (package (inherit ghc-skylighting)
     (version "0.1.1.5")

From 128c4c40e48db02e313d782d7aeb705418bde035 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:18:28 -0400
Subject: [PATCH 402/909] gnu: ghc-vault: Update to 0.3.1.2.

* gnu/packages/haskell.scm (ghc-vault): Update to 0.3.1.2.
[inputs]: Add ghc-semigroupoids.
---
 gnu/packages/haskell.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d8ceb0a755..da48a64b0a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4102,7 +4102,7 @@ cursor, and changing the title.")
 (define-public ghc-vault
   (package
     (name "ghc-vault")
-    (version "0.3.0.6")
+    (version "0.3.1.2")
     (source
      (origin
        (method url-fetch)
@@ -4112,11 +4112,12 @@ cursor, and changing the title.")
              ".tar.gz"))
        (sha256
         (base32
-         "0j7gcs440q7qlgzi2hn36crgp2c0w69k40g6vj9hxlm31zk3shqb"))))
+         "072mbrihsdsb8c6xvg6lvk0rqjgvxvi8qkg4n6wwym5hq0pfa04y"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-unordered-containers" ,ghc-unordered-containers)
-       ("ghc-hashable" ,ghc-hashable)))
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-semigroupoids" ,ghc-semigroupoids)))
     (home-page
      "https://github.com/HeinrichApfelmus/vault")
     (synopsis "Persistent store for arbitrary values")

From 38563d9140bdd35215d36cffae890d7db891d597 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:57:06 -0400
Subject: [PATCH 403/909] gnu: ghc-adjunctions: Update to 4.4.

* gnu/packages/haskell.scm (ghc-adjunctions): Update to 4.4.
[inputs] Add ghc-transformers-compat.
[native-inputs]: Add ghc-generic-deriving, ghc-hspec, and hspec-discover.
---
 gnu/packages/haskell.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index da48a64b0a..394c541693 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5121,7 +5121,7 @@ definition of @code{Monad}.")
 (define-public ghc-adjunctions
   (package
     (name "ghc-adjunctions")
-    (version "4.3")
+    (version "4.4")
     (source
      (origin
        (method url-fetch)
@@ -5131,7 +5131,7 @@ definition of @code{Monad}.")
              ".tar.gz"))
        (sha256
         (base32
-         "1k1ykisf96i4g2zm47c45md7p42c4vsp9r73392pz1g8mx7s2j5r"))))
+         "1sbal7cbhm12crfnfhkk322jnzgx7lhw3jzq0p463bipagsjwz2h"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-profunctors" ,ghc-profunctors)
@@ -5142,7 +5142,12 @@ definition of @code{Monad}.")
        ("ghc-tagged" ,ghc-tagged)
        ("ghc-semigroupoids" ,ghc-semigroupoids)
        ("ghc-semigroups" ,ghc-semigroups)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)
        ("ghc-void" ,ghc-void)))
+    (native-inputs
+     `(("ghc-generic-deriving" ,ghc-generic-deriving)
+       ("ghc-hspec" ,ghc-hspec)
+       ("hspec-discover" ,hspec-discover)))
     (home-page "https://github.com/ekmett/adjunctions/")
     (synopsis "Adjunctions and representable functors")
     (description "This library provides adjunctions and representable functors

From 751a8c0b43268aa5b33bae9fe5615c9dcf5abcfb Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:57:23 -0400
Subject: [PATCH 404/909] gnu: ghc-either: Update to 5.0.1.

* gnu/packages/haskell.scm (ghc-either): Update to 5.0.1.
[native-inputs]: Add ghc-quickcheck, ghc-test-framework, and
ghc-test-framework-quickcheck2.
---
 gnu/packages/haskell.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 394c541693..734dc2c2ca 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9119,7 +9119,7 @@ which consume random values.")
 (define-public ghc-either
   (package
     (name "ghc-either")
-    (version "4.4.1.1")
+    (version "5.0.1")
     (source
      (origin
        (method url-fetch)
@@ -9128,7 +9128,7 @@ which consume random values.")
                            "either-" version ".tar.gz"))
        (sha256
         (base32
-         "1lrlwqqnm6ibfcydlv5qvvssw7bm0c6yypy0rayjzv1znq7wp1xh"))))
+         "064hjfld7dkzs78sy30k5qkiva3hx24rax6dvzz5ygr2c0zypdkc"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-bifunctors" ,ghc-bifunctors)
               ("ghc-exceptions" ,ghc-exceptions)
@@ -9140,6 +9140,10 @@ which consume random values.")
               ("ghc-semigroups" ,ghc-semigroups)
               ("ghc-semigroupoids" ,ghc-semigroupoids)
               ("ghc-transformers-base" ,ghc-transformers-base)))
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
     (home-page "https://github.com/ekmett/either")
     (synopsis "Provides an either monad transformer for Haskell")
     (description "This Haskell package provides an either monad transformer.")

From b587518960e560309ec69d480eef7fc6aa8abcd2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 23:22:32 -0400
Subject: [PATCH 405/909] gnu: ghc-fsnotify: Update to 0.3.0.1.

* gnu/packages/haskell.scm (ghc-fsnotify): Update to 0.3.0.1.
[inputs]: Remove ghc-temporary-rc; add ghc-temporary, ghc-random, and
ghc-shelly.
---
 gnu/packages/haskell.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 734dc2c2ca..d1e7145d0b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8158,7 +8158,7 @@ accessed or modified.")
 (define-public ghc-fsnotify
   (package
     (name "ghc-fsnotify")
-    (version "0.2.1")
+    (version "0.3.0.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -8166,7 +8166,7 @@ accessed or modified.")
                     "fsnotify-" version ".tar.gz"))
               (sha256
                (base32
-                "0asl313a52qx2w6dw25g845683xsl840bwjh118nkwi5v1xipkzb"))))
+                "19bdbz9wb9jvln6yg6qm0hz0w84bypvkxf0wjhgrgd52f9gidlny"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-text" ,ghc-text)
@@ -8175,7 +8175,9 @@ accessed or modified.")
        ("ghc-hinotify" ,ghc-hinotify)
        ("ghc-tasty" ,ghc-tasty)
        ("ghc-tasty-hunit" ,ghc-tasty-hunit)
-       ("ghc-temporary-rc" ,ghc-temporary-rc)))
+       ("ghc-random" ,ghc-random)
+       ("ghc-shelly" ,ghc-shelly)
+       ("ghc-temporary" ,ghc-temporary)))
     (home-page "https://github.com/haskell-fswatch/hfsnotify")
     (synopsis "Cross platform library for file change notification.")
     (description "Cross platform library for file creation, modification, and

From f752336c80fb221800d719001ea268039b5fcb29 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:59:18 -0400
Subject: [PATCH 406/909] gnu: ghc-tasty-rerun: Update to 1.1.12.

* gnu/packages/haskell-check.scm (ghc-tasty-rerun): Update to 1.1.12.
---
 gnu/packages/haskell-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index ce1030eef1..42b7fd167b 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -287,7 +287,7 @@ test-framework.")
 (define-public ghc-tasty-rerun
   (package
     (name "ghc-tasty-rerun")
-    (version "1.1.8")
+    (version "1.1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -295,7 +295,7 @@ test-framework.")
                     "tasty-rerun-" version ".tar.gz"))
               (sha256
                (base32
-                "0yg8cicfn3qaazvp4rbanzy3dyk95k3y1kkd4bykvkl9v4076788"))))
+                "05lp4zy6lwd916snq6hs43848n62j9vdfl3s8sfivqydrax0vvd8"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-optparse-applicative" ,ghc-optparse-applicative)

From 19da4c3cd99b338333e0d13a05795cf9597393c7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:53:50 -0400
Subject: [PATCH 407/909] gnu: ghc-wai: Update to 3.2.1.2.

* gnu/packages/haskell-web.scm (ghc-wai): Update to 3.2.1.2.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index ac8df3921c..a6df96fc46 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -385,7 +385,7 @@ which allow you to avoid direct usage of conduits.")
 (define-public ghc-wai
   (package
     (name "ghc-wai")
-    (version "3.2.1.1")
+    (version "3.2.1.2")
     (source
      (origin
        (method url-fetch)
@@ -395,7 +395,7 @@ which allow you to avoid direct usage of conduits.")
              ".tar.gz"))
        (sha256
         (base32
-         "08afasnirja21vr0bmzcywz4w29x736dmdv7h8nnh1l8bn7sd02x"))))
+         "0jr3b2789wa4m6mxkz12ynz4lfsqmgbrcy0am8karyqr3x3528r8"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-bytestring-builder" ,ghc-bytestring-builder)

From 8b1573b1e41452d2ddea503dd61bf6b84e542af9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:00:11 -0400
Subject: [PATCH 408/909] gnu: ghc-kan-extensions: Update to 5.2.

* gnu/packages/haskell.scm (ghc-kan-extensions): Update to 5.2.
[inputs]: Add ghc-invariant and ghc-transformers-compat.
---
 gnu/packages/haskell.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d1e7145d0b..6bc3e49823 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4771,7 +4771,7 @@ functors).  For more information, see Edward Kmett's article
 (define-public ghc-kan-extensions
   (package
     (name "ghc-kan-extensions")
-    (version "5.0.1")
+    (version "5.2")
     (source
      (origin
        (method url-fetch)
@@ -4781,7 +4781,7 @@ functors).  For more information, see Edward Kmett's article
              ".tar.gz"))
        (sha256
         (base32
-         "1qm0kf4krmyjbjynn96ab0h3q117vwcia5nin7n2b8b4f3jrzph1"))))
+         "1lyvyiwwh962j2nnnsqzlvp5zq6z8p3spvhmji99cjvldxc7wwkb"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-adjunctions" ,ghc-adjunctions)
@@ -4789,8 +4789,10 @@ functors).  For more information, see Edward Kmett's article
        ("ghc-contravariant" ,ghc-contravariant)
        ("ghc-distributive" ,ghc-distributive)
        ("ghc-free" ,ghc-free)
+       ("ghc-invariant" ,ghc-invariant)
        ("ghc-semigroupoids" ,ghc-semigroupoids)
-       ("ghc-tagged" ,ghc-tagged)))
+       ("ghc-tagged" ,ghc-tagged)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)))
     (home-page "https://github.com/ekmett/kan-extensions/")
     (synopsis "Kan extensions library")
     (description "This library provides Kan extensions, Kan lifts, various

From 6d2fd200f472d0f23d751991eb6093a1b3f816da Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:00:28 -0400
Subject: [PATCH 409/909] gnu: ghc-rebase: Update to 1.2.4.

* gnu/packages/haskell.scm (ghc-rebase): Update to 1.2.4.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6bc3e49823..0bd4c9de20 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9284,7 +9284,7 @@ parsing and printing @dfn{Universally Unique Identifiers} or UUIDs.")
 (define-public ghc-rebase
   (package
     (name "ghc-rebase")
-    (version "1.1")
+    (version "1.2.4")
     (source
      (origin
        (method url-fetch)
@@ -9293,7 +9293,7 @@ parsing and printing @dfn{Universally Unique Identifiers} or UUIDs.")
                            "rebase-" version ".tar.gz"))
        (sha256
         (base32
-         "1qkhnpcc4g2vd6jmbf3b6psqkan6hyawqzrwzqdd931hsb02l6ia"))))
+         "1gah2qwfpzwamnikbc5h4nv6dgvv9h16di9ka7946za3nibyasya"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-stm" ,ghc-stm)
               ("ghc-hashable" ,ghc-hashable)

From 7b19f0a8030b9f7d9606a9908bb59284aabeca3b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:56:47 -0400
Subject: [PATCH 410/909] gnu: ghc-wai-logger: Update to 2.3.2.

* gnu/packages/haskell-web.scm (ghc-wai-logger): Update to 2.3.2.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index a6df96fc46..5300a5701a 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -420,7 +420,7 @@ communication between web applications and web servers.")
 (define-public ghc-wai-logger
   (package
     (name "ghc-wai-logger")
-    (version "2.3.0")
+    (version "2.3.2")
     (source
      (origin
        (method url-fetch)
@@ -430,7 +430,7 @@ communication between web applications and web servers.")
              ".tar.gz"))
        (sha256
         (base32
-         "1w0b0vinsyqr37wciljkz8g5dcmfi2r210lq194a0wkycly9kkch"))))
+         "0w5ldq4gplc16zzk5ikmbbjw79imaqvw8p6lylaw3hlsbn3zzm4d"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: Tests cannot find libraries exported
                                ; by propagated-inputs.

From 53812aa77f5c8a490191c069a13a927d365618c7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:36:30 -0400
Subject: [PATCH 411/909] gnu: idris: Update to 1.3.0.

* gnu/packages/idris.scm (idris): Update to 1.3.0.
[inputs]: Remove ghc-aeson-1.1.2.0, ghc-cheapskate-0.1.0.5, and
ghc-trifecta-1.6.2.1; add ghc-aeson, ghc-cheapskate, and ghc-megaparsec.
[arguments]: Add a phase that patches the Cabal file to allow newer
versions of aeson.
(ghc-aeson-1.1.2.0, ghc-cheapskate-0.1.0.5, ghc-trifecta-1.6.2.1): Remove.
---
 gnu/packages/idris.scm | 61 +++++++-----------------------------------
 1 file changed, 10 insertions(+), 51 deletions(-)

diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm
index 7f1af62c1f..f80d6b3894 100644
--- a/gnu/packages/idris.scm
+++ b/gnu/packages/idris.scm
@@ -31,56 +31,10 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages))
 
-(define ghc-aeson-1.1.2.0
-  (package (inherit ghc-aeson)
-    (version "1.1.2.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://hackage.haskell.org/package/aeson/aeson-"
-             version
-             ".tar.gz"))
-       (sha256
-        (base32
-         "1zy5z8pzvh53qkjm0nm3f4rwqfqg3867ck8ncd6mrxpcyvxqqj1p"))))))
-
-(define ghc-trifecta-1.6.2.1
-  (package (inherit ghc-trifecta)
-    (version "1.6.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://hackage.haskell.org/package/trifecta/"
-             "trifecta-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1rgv62dlmm4vkdymx5rw5jg3w8ifpzg1745rvs1m4kzdx16p5cxs"))))))
-
-;; ghc-cheapskate appeared too new. This follows LTS Haskell.
-(define ghc-cheapskate-0.1.0.5
-  (package
-    (inherit ghc-cheapskate)
-    (version "0.1.0.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://hackage.haskell.org/package/cheapskate/cheapskate-"
-             version
-             ".tar.gz"))
-       (sha256
-        (base32
-         "0cpsmfx5z2xykg71sv8j7pl8ga6pzyjnjdb9bxn00vcpqkzvfqvs"))))
-    (arguments
-     ;; LTS Haskell says data-default >=0.5 && <0.8
-     `(#:configure-flags (list "--allow-newer=data-default")))))
-
 (define-public idris
   (package
     (name "idris")
-    (version "1.0")
+    (version "1.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -88,12 +42,12 @@
                     "idris-" version "/idris-" version ".tar.gz"))
               (sha256
                (base32
-                "1srbz0cyvd0k1yqgbrwnfj94yg5y3z533q1kzac96z1h7v454s5h"))))
+                "1w5i2z88li4niykwc6yrgxgfp25ll6ih95cip0ri7d8i7ik03c48"))))
     (build-system haskell-build-system)
     (inputs
      `(("gmp" ,gmp)
        ("ncurses" ,ncurses)
-       ("ghc-aeson" ,ghc-aeson-1.1.2.0)
+       ("ghc-aeson" ,ghc-aeson)
        ("ghc-annotated-wl-pprint" ,ghc-annotated-wl-pprint)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
        ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
@@ -101,11 +55,12 @@
        ("ghc-base64-bytestring" ,ghc-base64-bytestring)
        ("ghc-blaze-html" ,ghc-blaze-html)
        ("ghc-blaze-markup" ,ghc-blaze-markup)
-       ("ghc-cheapskate" ,ghc-cheapskate-0.1.0.5)
+       ("ghc-cheapskate" ,ghc-cheapskate)
        ("ghc-code-page" ,ghc-code-page)
        ("ghc-fingertree" ,ghc-fingertree)
        ("ghc-fsnotify" ,ghc-fsnotify)
        ("ghc-ieee754" ,ghc-ieee754)
+       ("ghc-megaparsec" ,ghc-megaparsec)
        ("ghc-network" ,ghc-network)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)
@@ -113,7 +68,6 @@
        ("ghc-split" ,ghc-split)
        ("ghc-terminal-size" ,ghc-terminal-size)
        ("ghc-text" ,ghc-text)
-       ("ghc-trifecta" ,ghc-trifecta-1.6.2.1)
        ("ghc-uniplate" ,ghc-uniplate)
        ("ghc-unordered-containers" ,ghc-unordered-containers)
        ("ghc-utf8-string" ,ghc-utf8-string)
@@ -131,6 +85,11 @@
            (lambda _
              (setenv "CC" "gcc")
              #t))
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "idris.cabal"
+               (("aeson >= 0\\.6 && < 1\\.3")
+                "aeson >= 0.6 && < 1.4"))))
          (add-after 'install 'fix-libs-install-location
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))

From 9516ef4f934e21fb059cff55d3e5047245178430 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 23:04:23 -0400
Subject: [PATCH 412/909] gnu: Add ghc-rerebase.

* gnu/packages/haskell.scm (ghc-rerebase): New variable.
---
 gnu/packages/haskell.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0bd4c9de20..3423164dc1 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9338,6 +9338,29 @@ The package is intended to rapidly evolve with the contribution from
 the community, with the missing features being added with pull-requests.")
     (license license:expat)))
 
+(define-public ghc-rerebase
+  (package
+    (name "ghc-rerebase")
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/rerebase/rerebase-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "11v6rmz7ql2rdx6mhb3lsal952lwihclfhh0m7fcnii5br0906ks"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-rebase" ,ghc-rebase)))
+    (home-page "https://github.com/nikita-volkov/rerebase")
+    (synopsis "Reexports from ``base'' with many other standard libraries")
+    (description "A rich drop-in replacement for ``base''.  For details and
+documentation please visit @uref{https://github.com/nikita-volkov/rerebase,
+the project's home page}.")
+    (license license:expat)))
+
 (define-public ghc-vector-builder
   (package
     (name "ghc-vector-builder")

From 6369346e5427ea506be15d1b3fa2fed4ac27659d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:59:53 -0400
Subject: [PATCH 413/909] gnu: ghc-wai-extra: Update to 3.0.24.2.

* gnu/packages/haskell-web.scm (ghc-wai-extra): Update to 3.0.24.2.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 5300a5701a..10bcbd2899 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -453,7 +453,7 @@ communication between web applications and web servers.")
 (define-public ghc-wai-extra
   (package
     (name "ghc-wai-extra")
-    (version "3.0.18")
+    (version "3.0.24.2")
     (source
      (origin
        (method url-fetch)
@@ -463,7 +463,7 @@ communication between web applications and web servers.")
              ".tar.gz"))
        (sha256
         (base32
-         "0r079mqqdv14fp97w0rigdpwk6b88grpjlqsjc5y8bbc0skf5za2"))))
+         "07gcgq59dki5drkjci9ka34xjsy3bqilbsx0lsc4905w9jlyfbci"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-ansi-terminal" ,ghc-ansi-terminal)

From c237721ea5491dfd115151cad06dfb9faee71d36 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:00:52 -0400
Subject: [PATCH 414/909] gnu: ghc-vector-builder: Update to 0.3.6.

* gnu/packages/haskell.scm (ghc-vector-builder): Update to 0.3.6.
[native-inputs]: Add ghc-attoparsec and ghc-rerebase; remove ghc-rebase.
---
 gnu/packages/haskell.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 3423164dc1..2272fd4d51 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9364,7 +9364,7 @@ the project's home page}.")
 (define-public ghc-vector-builder
   (package
     (name "ghc-vector-builder")
-    (version "0.3.1")
+    (version "0.3.6")
     (source
      (origin
        (method url-fetch)
@@ -9373,17 +9373,18 @@ the project's home page}.")
                            "vector-builder-" version ".tar.gz"))
        (sha256
         (base32
-         "1l6sfgd2s107zkp1qd1w6jdjcbznp31769qf99pxar087f697wvp"))))
+         "06d2pa1fb3ydrl7l6rjazqyxv5i73v65x2f5fp0ypjxfbm6jsmn8"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-vector" ,ghc-vector)
               ("ghc-semigroups" ,ghc-semigroups)
               ("ghc-base-prelude" ,ghc-base-prelude)))
-    (native-inputs `(("ghc-tasty" ,ghc-tasty)
+    (native-inputs `(("ghc-attoparsec" ,ghc-attoparsec)
+                     ("ghc-tasty" ,ghc-tasty)
                      ("ghc-tasty-hunit" ,ghc-tasty-hunit)
                      ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
                      ("ghc-hunit" ,ghc-hunit)
                      ("ghc-quickcheck-instances" ,ghc-quickcheck-instances)
-                     ("ghc-rebase" ,ghc-rebase)))
+                     ("ghc-rerebase" ,ghc-rerebase)))
     (home-page "https://github.com/nikita-volkov/vector-builder")
     (synopsis "Vector builder for Haskell")
     (description "This Haskell package provides an API for constructing vectors.

From ca96ba99aecd825945590c35365cf6920e3f5e89 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:01:10 -0400
Subject: [PATCH 415/909] gnu: ghc-foldl: Update to 1.4.3.

* gnu/packages/haskell.scm (ghc-foldl): Update to 1.4.3.
[inputs]: Add ghc-semigroups and ghc-semigroupoids.
---
 gnu/packages/haskell.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 2272fd4d51..ecd465d4da 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9399,7 +9399,7 @@ vector. ")
 (define-public ghc-foldl
   (package
     (name "ghc-foldl")
-    (version "1.3.5")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
@@ -9408,7 +9408,7 @@ vector. ")
                            "foldl-" version ".tar.gz"))
        (sha256
         (base32
-         "10qsp7dj2xsq4q2xm6x6b12y5pq32qf7my41hnkmdwwbccvhdxb2"))))
+         "13n0ca3hw5jzqf6rxsdbhbwkn61a9zlm13f0f205s60j3sc72jzk"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-mwc-randam" ,ghc-mwc-random)
               ("ghc-primitive" ,ghc-primitive)
@@ -9417,7 +9417,9 @@ vector. ")
               ("ghc-unordered-containers" ,ghc-unordered-containers)
               ("ghc-hashable" ,ghc-hashable)
               ("ghc-contravariant" ,ghc-contravariant)
+              ("ghc-semigroups" ,ghc-semigroups)
               ("ghc-profunctors" ,ghc-profunctors)
+              ("ghc-semigroupoids" ,ghc-semigroupoids)
               ("ghc-comonad" ,ghc-comonad)
               ("ghc-vector-builder" ,ghc-vector-builder)))
     (home-page "https://github.com/Gabriel439/Haskell-Foldl-Library")

From 24d919ffbdfed549b02f765e5854f54ada5bc5f7 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:02:44 -0400
Subject: [PATCH 416/909] gnu: ghc-wai-conduit: Update to 3.0.0.4.

* gnu/packages/haskell-web.scm (ghc-wai-conduit): Update to 3.0.0.4.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 10bcbd2899..ed1e02f4aa 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -502,7 +502,7 @@ functionality.")
 (define-public ghc-wai-conduit
   (package
     (name "ghc-wai-conduit")
-    (version "3.0.0.3")
+    (version "3.0.0.4")
     (source
      (origin
        (method url-fetch)
@@ -511,7 +511,7 @@ functionality.")
                            "wai-conduit-" version ".tar.gz"))
        (sha256
         (base32
-         "1zvsiwjq2mvkb9sjgp3ly9m968m7a2jjzr4id6jpi3mmqykj15z4"))))
+         "07yn41rn2skd5p3wqqa09wa761vj7ibl8l19gh4bi4i8slxhk417"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-conduit" ,ghc-conduit)

From 1613ee19f60e22d793f2f93fe070ce6e17d78d2d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:05:02 -0400
Subject: [PATCH 417/909] gnu: ghc-yaml: Update to 0.8.32.

* gnu/packages/haskell.scm (ghc-yaml): Update to 0.8.32.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ecd465d4da..e2666e132c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6148,14 +6148,14 @@ back-ends.")
 (define-public ghc-yaml
   (package
     (name "ghc-yaml")
-    (version "0.8.28")
+    (version "0.8.32")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://hackage.haskell.org/package/"
                                   "yaml/yaml-" version ".tar.gz"))
               (sha256
                (base32
-                "0swgkzkfrwj0ac7lssn8rnrdfmh3lcsdn5fbq2iwv55di6jbc0pp"))))
+                "0cbsyh4ilvjzq1q7pxls43k6pdqxg1l85xzibcwpbvmlvrizh86w"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-conduit" ,ghc-conduit)

From 6f7280b09083e1a174101804faff6576eb0dd422 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:10:55 -0400
Subject: [PATCH 418/909] gnu: ghc-monad-logger: Update to 0.3.29.

* gnu/packages/haskell.scm (ghc-monad-logger): Update to 0.3.29.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e2666e132c..a109a5d19c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9673,7 +9673,7 @@ operators for looping.")
 (define-public ghc-monad-logger
   (package
     (name "ghc-monad-logger")
-    (version "0.3.25.1")
+    (version "0.3.29")
     (source
      (origin
        (method url-fetch)
@@ -9682,7 +9682,7 @@ operators for looping.")
                            "monad-logger-" version ".tar.gz"))
        (sha256
         (base32
-         "0yv4fsi566zrn30j2g5l901lyqgmflhvzy4hji7ikcbh5d45m920"))))
+         "1z516s4pa9n94zf0l45mylssg07xr1d1m6zrz900p0iv3vfd07mv"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-transformers-compat" ,ghc-transformers-compat)
               ("ghc-text" ,ghc-text)

From 23aa12fc092c69228c6a636897f17c535605b35e Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:11:24 -0400
Subject: [PATCH 419/909] gnu: ghc-simple-sendfile: Update to 0.2.27.

* gnu/packages/haskell.scm (ghc-simple-sendfile): Update to 0.2.27.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a109a5d19c..d3eae809e9 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8482,7 +8482,7 @@ advanced user's otherwise working script to fail under future circumstances.
 (define-public ghc-simple-sendfile
   (package
     (name "ghc-simple-sendfile")
-    (version "0.2.25")
+    (version "0.2.27")
     (source
      (origin
        (method url-fetch)
@@ -8491,7 +8491,7 @@ advanced user's otherwise working script to fail under future circumstances.
                            "simple-sendfile-" version ".tar.gz"))
        (sha256
         (base32
-         "0k99j9xfcf83c55jmn202hdinhjaa4yn3dal4rvjk2w2rlhqirha"))))
+         "1bwwqzcm56m2w4ymsa054sxmpbj76h9pvb0jf8zxp8lr41cp51gn"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-conduit" ,ghc-conduit)

From 478365e36a59355001d46ee136dc550fccfb9c16 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:12:16 -0400
Subject: [PATCH 420/909] gnu: hlint: Update to 2.1.10.

* gnu/packages/haskell.scm (hlint): Update to 2.1.10.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d3eae809e9..85692c4689 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1319,7 +1319,7 @@ specify refactorings without depending on GHC.")
 (define-public hlint
   (package
     (name "hlint")
-    (version "2.1.1")
+    (version "2.1.10")
     (source
      (origin
        (method url-fetch)
@@ -1328,7 +1328,7 @@ specify refactorings without depending on GHC.")
              "/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0mmfavd158l5ig5wb1b1zbhbraj8hhqvbk4mg85n6c8ndpr4grd4"))))
+         "19as2m9g75cr6n1agzvsij0cvqhb0wbjlk31w4y5d5mns87dki0w"))))
     (build-system haskell-build-system)
     (inputs
      `(("cpphs" ,cpphs)

From c4a68deaad5e32894f881035613c2cdaedf9f61a Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 22 Sep 2018 09:47:49 -0400
Subject: [PATCH 421/909] gnu: Add ghc-echo.

* gnu/packages/haskell.scm (ghc-echo): New variable.
---
 gnu/packages/haskell.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 85692c4689..079d8561ce 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1852,6 +1852,32 @@ Writer monad), where list append quickly becomes too expensive.")
 versions of GHC (i.e., < 6.10).")
     (license license:bsd-3)))
 
+(define-public ghc-echo
+  (package
+    (name "ghc-echo")
+    (version "0.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/echo/echo-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "1vw5ykpwhr39wc0hhcgq3r8dh59zq6ib4zxbz1qd2wl21wqhfkvh"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "0br8wfiybcw5hand4imiw0i5hacdmrax1dv8g95f35gazffbx42l")))
+    (home-page "https://github.com/RyanGlScott/echo")
+    (synopsis "Echo terminal input portably")
+    (description "The @code{base} library exposes the @code{hGetEcho} and
+@code{hSetEcho} functions for querying and setting echo status, but
+unfortunately, neither function works with MinTTY consoles on Windows.
+This library provides an alternative interface which works with both
+MinTTY and other consoles.")
+    (license license:bsd-3)))
+
 (define-public cabal-install
  (package
   (name "cabal-install")

From bf7e5884321ee4f4c4f3c83a647b92817b511453 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 22 Sep 2018 09:43:20 -0400
Subject: [PATCH 422/909] gnu: Add ghc-cryptohash-sha256.

* gnu/packages/haskell-crypto.scm (ghc-cryptohash-sha256): New variable.
---
 gnu/packages/haskell-crypto.scm | 36 +++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index ff44970be0..0d9617e03d 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -253,6 +253,42 @@ pure API to the @uref{https://en.wikipedia.org/wiki/SHA-1, SHA-1 hash algorithm}
 including @uref{https://en.wikipedia.org/wiki/HMAC, HMAC support}, with
 performance close to the fastest implementations available in other languages.
 
+The implementation is made in C with a haskell FFI wrapper that hides
+the C implementation.")
+    (license license:bsd-3)))
+
+(define-public ghc-cryptohash-sha256
+  (package
+    (name "ghc-cryptohash-sha256")
+    (version "0.11.101.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "cryptohash-sha256-" version "/"
+                           "cryptohash-sha256-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1p85vajcgw9hmq8zsz9krzx0vxh7aggwbg5w9ws8w97avcsn8xaj"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "19birnmwga1yh82l4jqc3fygqkqcf5y8dlldnxfswngkzc3rvwp3")
+       #:tests? #f)) ; tests require old version of ghc-hunit (0.9)
+    (inputs
+     `(("ghc-base16-bytestring" ,ghc-base16-bytestring)))
+    (native-inputs
+     `(("ghc-sha" ,ghc-sha)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
+       ("ghc-hunit" ,ghc-hunit)))
+    (home-page "https://github.com/hvr/cryptohash-sha1")
+    (synopsis "SHA-256 implementation for Haskell")
+    (description "This Haskell package provides an incremental and
+one-pass, pure API to the @uref{https://en.wikipedia.org/wiki/SHA-2,
+SHA-256 cryptographic hash algorithm}, with performance close to the
+fastest implementations available in other languages.
+
 The implementation is made in C with a haskell FFI wrapper that hides
 the C implementation.")
     (license license:bsd-3)))

From 5a88cff239c238ba04b7ec45fae66aae077a0958 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 22 Sep 2018 09:46:06 -0400
Subject: [PATCH 423/909] ghc: Add ghc-ed25519.

* gnu/packages/haskell-crypto.scm (ghc-ed25519): New variable.
---
 gnu/packages/haskell-crypto.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/haskell-crypto.scm b/gnu/packages/haskell-crypto.scm
index 0d9617e03d..9bdcdb2f9e 100644
--- a/gnu/packages/haskell-crypto.scm
+++ b/gnu/packages/haskell-crypto.scm
@@ -701,3 +701,33 @@ percent.
 @item Monte Carlo value for Pi is 3.132465868 (error 0.29 percent).
 @end itemize")
     (license license:bsd-3)))
+
+(define-public ghc-ed25519
+  (package
+    (name "ghc-ed25519")
+    (version "0.0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/ed25519/ed25519-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0v8msqvgzimhs7p5ri25hrb1ni2wvisl5rmdxy89fc59py79b9fq"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("2" "1cq6h3jqkb1kvd9fjfhsllg5gq78sdiyf2gy9862xhlbv6wil19f")
+       ;; We omit these test suites because they require old versions of
+       ;; packages and packages we do not have.
+       #:configure-flags
+       '("--flags=-test-hlint -test-doctests -test-properties")))
+    (home-page "http://thoughtpolice.github.com/hs-ed25519")
+    (synopsis "Ed25519 cryptographic signatures")
+    (description "This package provides a simple, fast, self-contained
+copy of the Ed25519 public-key signature system with a clean interface.
+It also includes support for detached signatures, and thorough
+documentation on the design and implementation, including usage
+guidelines.")
+    (license license:expat)))

From 45e421ff219caa89ed3ad13981e5cb7886ac9326 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 22 Sep 2018 09:49:02 -0400
Subject: [PATCH 424/909] gnu: Add ghc-hackage-security.

* gnu/packages/haskell.scm (ghc-hackage-security): New variable.
---
 gnu/packages/haskell.scm | 46 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 079d8561ce..2b256a0f5d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1878,6 +1878,52 @@ This library provides an alternative interface which works with both
 MinTTY and other consoles.")
     (license license:bsd-3)))
 
+(define-public ghc-hackage-security
+  (package
+    (name "ghc-hackage-security")
+    (version "0.5.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "hackage-security/hackage-security-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "08bwawc7ramgdh54vcly2m9pvfchp0ahhs8117jajni6x4bnx66v"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:tests? #f)) ; Tests fail because of framework updates.
+    (inputs
+     `(("ghc-base16-bytestring" ,ghc-base16-bytestring)
+       ("ghc-base64-bytestring" ,ghc-base64-bytestring)
+       ("ghc-cryptohash-sha256" ,ghc-cryptohash-sha256)
+       ("ghc-ed25519" ,ghc-ed25519)
+       ("ghc-network" ,ghc-network)
+       ("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-tar" ,ghc-tar)
+       ("ghc-zlib" ,ghc-zlib)))
+    (native-inputs
+     `(("ghc-network-uri" ,ghc-network-uri)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-tar" ,ghc-tar)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)
+       ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
+       ("ghc-temporary" ,ghc-temporary)
+       ("ghc-zlib" ,ghc-zlib)))
+    (home-page "https://github.com/haskell/hackage-security")
+    (synopsis "Hackage security library")
+    (description "This Hackage security library provides both server and
+client utilities for securing @uref{http://hackage.haskell.org/, the
+Hackage package server}.  It is based on
+@uref{http://theupdateframework.com/, The Update Framework}, a set of
+recommendations developed by security researchers at various universities
+in the US as well as developers on the @uref{https://www.torproject.org/,
+Tor project}.")
+    (license license:bsd-3)))
+
 (define-public cabal-install
  (package
   (name "cabal-install")

From 246cdfac2f551ef010ac98495c5ead1a688f37bb Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 22 Sep 2018 09:50:32 -0400
Subject: [PATCH 425/909] gnu: Add ghc-resolv.

* gnu/packages/haskell.scm (ghc-resolv): New variable.
---
 gnu/packages/haskell.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 2b256a0f5d..a1047abd86 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1924,6 +1924,35 @@ in the US as well as developers on the @uref{https://www.torproject.org/,
 Tor project}.")
     (license license:bsd-3)))
 
+(define-public ghc-resolv
+  (package
+    (name "ghc-resolv")
+    (version "0.1.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/resolv/resolv-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0wh7wj56l3f2bylz563g5g04a4nydj8acv60hpwa7k3mn792xca9"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("1" "15ay4n3x8c09cb3h4z1nan84yd3n9zpgvi6h114hk98bq10k8mma")
+       #:tests? #f)) ; The required test frameworks are too old.
+    (inputs
+     `(("ghc-base16-bytestring" ,ghc-base16-bytestring)))
+    (home-page "https://github.com/haskell/hackage-security")
+    (synopsis "Domain Name Service (DNS) lookup via @code{libresolv}")
+    (description "This package implements an API for accessing the
+@uref{https://tools.ietf.org/html/rfc1035, Domain Name Service (DNS)}
+resolver service via the standard @code{libresolv} system library (whose
+API is often available directly via the standard @code{libc} C library) on
+Unix systems.")
+    (license license:gpl3)))
+
 (define-public cabal-install
  (package
   (name "cabal-install")

From f707db294ae088e297b3eef22632e26571320be4 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:12:40 -0400
Subject: [PATCH 426/909] gnu: cabal-install: Update to 2.2.0.0.

* gnu/packages/haskell.scm (cabal-install): Update to 2.2.0.0.
[inputs] Add ghc-async, ghc-base16-bytestring, ghc-cryptohash-sha256,
ghc-echo, ghc-edit-distance, ghc-hackage-security, ghc-hashable,
ghc-resolv, and ghc-tar.
---
 gnu/packages/haskell.scm | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a1047abd86..b23a61961c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1956,7 +1956,7 @@ Unix systems.")
 (define-public cabal-install
  (package
   (name "cabal-install")
-   (version "1.22.6.0")
+   (version "2.2.0.0")
    (source
     (origin
      (method url-fetch)
@@ -1965,15 +1965,24 @@ Unix systems.")
             version
             ".tar.gz"))
       (sha256
-       (base32 "1d5h7h2wjwc2s3dvsvzjgmmfrfl2312ym2h6kyjgm9wnaqw9w8wx"))))
+       (base32 "1nd3ch7qr4dpfxhgkcq2lnhvszx2kjgnn1kwb44vk9y5jgfs4mn8"))))
    (arguments `(#:tests? #f)) ; FIXME: testing libraries are missing.
    (build-system haskell-build-system)
    (inputs
-    `(("ghc-http" ,ghc-http)
+    `(("ghc-async" ,ghc-async)
+      ("ghc-base16-bytestring" ,ghc-base16-bytestring)
+      ("ghc-cryptohash-sha256" ,ghc-cryptohash-sha256)
+      ("ghc-echo" ,ghc-echo)
+      ("ghc-edit-distance" ,ghc-edit-distance)
+      ("ghc-hackage-security" ,ghc-hackage-security)
+      ("ghc-hashable" ,ghc-hashable)
+      ("ghc-http" ,ghc-http)
       ("ghc-network-uri" ,ghc-network-uri)
       ("ghc-network" ,ghc-network)
       ("ghc-random" ,ghc-random)
+      ("ghc-resolv" ,ghc-resolv)
       ("ghc-stm" ,ghc-stm)
+      ("ghc-tar" ,ghc-tar)
       ("ghc-zlib" ,ghc-zlib)))
    (home-page "https://www.haskell.org/cabal/")
    (synopsis "Command-line interface for Cabal and Hackage")

From fbdf4031891fa1f0c5a82b9c7c773bcb64ea40b2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 28 Aug 2018 22:54:31 -0400
Subject: [PATCH 427/909] gnu: ghc-feed: Update to 1.0.0.0.

* gnu/packages/haskell.scm (ghc-feed): Update to 1.0.0.0.
[arguments]: Update Cabal file to r4.
[inputs]: Add ghc-base-compat, ghc-safe, ghc-text, ghc-xml-conduit, and
ghc-xml-types; remove ghc-xml.
---
 gnu/packages/haskell.scm | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index b23a61961c..2347a4deb1 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3465,7 +3465,7 @@ online}.")
 (define-public ghc-feed
   (package
     (name "ghc-feed")
-    (version "0.3.12.0")
+    (version "1.0.0.0")
     (source
      (origin
        (method url-fetch)
@@ -3473,14 +3473,21 @@ online}.")
                            "feed/feed-" version ".tar.gz"))
        (sha256
         (base32
-         "0hkrsinspg70bbm3hwqdrvivws6zya1hyk0a3awpaz82j4xnlbfc"))))
+         "05rgg7x1984mgfhkmz792xj8lhwjgznixhygzr8blf517lns2nck"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("4" "0baavcavm3ywykcr9cm07aqr7sna98jba2n68lyn3kany8ri214d")))
     (inputs
-     `(("ghc-old-locale" ,ghc-old-locale)
+     `(("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-old-locale" ,ghc-old-locale)
        ("ghc-old-time" ,ghc-old-time)
+       ("ghc-safe" ,ghc-safe)
+       ("ghc-text" ,ghc-text)
        ("ghc-time-locale-compat" ,ghc-time-locale-compat)
        ("ghc-utf8-string" ,ghc-utf8-string)
-       ("ghc-xml" ,ghc-xml)))
+       ("ghc-xml-conduit" ,ghc-xml-conduit)
+       ("ghc-xml-types" ,ghc-xml-types)))
     (native-inputs
      `(("ghc-hunit" ,ghc-hunit)
        ("ghc-test-framework" ,ghc-test-framework)

From b9f67d10bcbd969884e3f579d1dd9ff585b2016a Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:14:08 -0400
Subject: [PATCH 428/909] gnu: ghc-lens: Update to 4.16.1.

* gnu/packages/haskell.scm (ghc-lens): Update to 4.16.1.
[arguments]: Update Cabal file to r2.
[inputs]: Remove ghc-doctest-0.13.
[native-inputs]: Add ghc-doctest.
---
 gnu/packages/haskell.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 2347a4deb1..351420c108 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4971,7 +4971,7 @@ in the @code{IO} monad, like @code{IORef}s or parts of the OpenGL state.")
 (define-public ghc-lens
   (package
     (name "ghc-lens")
-    (version "4.15.4")
+    (version "4.16.1")
     (source
      (origin
        (method url-fetch)
@@ -4979,12 +4979,14 @@ in the @code{IO} monad, like @code{IORef}s or parts of the OpenGL state.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "1lkwlnhgpgnsz046mw4qs0fa7h4l012gilrr3nf3spllsy3pnbkl"))))
+         "1im4drhbydbawd6i0jsrzpqihnmx4ywpkg7yg94ddwsw3mxwkgpm"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("2" "11h83lj5mba4grhz1qx3irz10ysm9c3k7k6i6xv2cr60q8xin3ri")))
     (inputs
      `(("ghc-base-orphans" ,ghc-base-orphans)
        ("ghc-bifunctors" ,ghc-bifunctors)
-       ("ghc-doctest" ,ghc-doctest-0.13)
        ("ghc-distributive" ,ghc-distributive)
        ("ghc-exceptions" ,ghc-exceptions)
        ("ghc-free" ,ghc-free)
@@ -5010,6 +5012,7 @@ in the @code{IO} monad, like @code{IORef}s or parts of the OpenGL state.")
        ("hlint" ,hlint)))
     (native-inputs
      `(("cabal-doctest" ,cabal-doctest)
+       ("ghc-doctest" ,ghc-doctest)
        ("ghc-hunit" ,ghc-hunit)
        ("ghc-test-framework" ,ghc-test-framework)
        ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)

From bc368781b6b3d81442a1dda44d93361b18eb987a Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:14:48 -0400
Subject: [PATCH 429/909] gnu: ghc-persistent: Update to 2.8.2.

* gnu/packages/haskell.scm (ghc-persistent): Update to 2.8.2.
[inputs]: Add ghc-void.
---
 gnu/packages/haskell.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 351420c108..e07b3423fd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10027,7 +10027,7 @@ Haskell data types to and from HTTP API data.")
 (define-public ghc-persistent
   (package
     (name "ghc-persistent")
-    (version "2.7.3.1")
+    (version "2.8.2")
     (source
      (origin
        (method url-fetch)
@@ -10036,7 +10036,7 @@ Haskell data types to and from HTTP API data.")
                            "persistent-" version ".tar.gz"))
        (sha256
         (base32
-         "1jbvavdvr9qz5ld7vf6l1jgiadhmxx6zc4vqsdk9ivfq6d5wlg1p"))))
+         "1h0yijbf1yiwl50klyafy4ln99j8bib4kgbzviw7fc4y4mwv4sv9"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-old-locale" ,ghc-old-locale)
               ("ghc-text" ,ghc-text)
@@ -10061,7 +10061,8 @@ Haskell data types to and from HTTP API data.")
               ("ghc-silently" ,ghc-silently)
               ("ghc-fast-logger" ,ghc-fast-logger)
               ("ghc-scientific" ,ghc-scientific)
-              ("ghc-tagged" ,ghc-tagged)))
+              ("ghc-tagged" ,ghc-tagged)
+              ("ghc-void" ,ghc-void)))
     (native-inputs `(("ghc-hspec" ,ghc-hspec)))
     (home-page "https://www.yesodweb.com/book/persistent")
     (synopsis "Type-safe, multi-backend data serialization for Haskell")

From 47334ea099f3ed71cf0f9613d3f3e21d85834575 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:16:59 -0400
Subject: [PATCH 430/909] gnu: ghc-warp: Update to 3.2.23.

* gnu/packages/haskell-web.scm (ghc-warp): Update to 3.2.23.
[arguments]: Enable tests.
[inputs]: Remove ghc-blaze-builder, ghc-bytestring-builder, and
ghc-lifted-base; add ghc-bsb-http-chunked.
[native-inputs]: Remove ghc-auto-update and ghc-http; add curl,
ghc-lifted-base, and ghc-http-client.
---
 gnu/packages/haskell-web.scm | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index ed1e02f4aa..cf57e8fd96 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -23,6 +23,7 @@
 
 (define-module (gnu packages haskell-web)
   #:use-module (gnu packages)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-crypto)
@@ -551,7 +552,7 @@ transfers.")
 (define-public ghc-warp
   (package
     (name "ghc-warp")
-    (version "3.2.11.1")
+    (version "3.2.23")
     (source
      (origin
        (method url-fetch)
@@ -560,15 +561,12 @@ transfers.")
                            ".tar.gz"))
        (sha256
         (base32
-         "1zp5cy0bbj508vdvms1n5z80z37m253kwsqc5a83cfc990n6fgw5"))))
+         "12v9qhi4hyp0sb90yddsax16jj7x47nmqwn53sv7b5nszcxgzam0"))))
     (build-system haskell-build-system)
-    (arguments
-     `(#:tests? #f)) ; FIXME: Test-Suite `spec` fails.
     (inputs
      `(("ghc-async" ,ghc-async)
        ("ghc-auto-update" ,ghc-auto-update)
-       ("ghc-blaze-builder" ,ghc-blaze-builder)
-       ("ghc-bytestring-builder" ,ghc-bytestring-builder)
+       ("ghc-bsb-http-chunked" ,ghc-bsb-http-chunked)
        ("ghc-case-insensitive" ,ghc-case-insensitive)
        ("ghc-hashable" ,ghc-hashable)
        ("ghc-http-types" ,ghc-http-types)
@@ -581,18 +579,18 @@ transfers.")
        ("ghc-vault" ,ghc-vault)
        ("ghc-wai" ,ghc-wai)
        ("ghc-word8" ,ghc-word8)
-       ("ghc-lifted-base" ,ghc-lifted-base)
        ("ghc-http-date" ,ghc-http-date)
        ("ghc-simple-sendfile" ,ghc-simple-sendfile)
        ("ghc-http2" ,ghc-http2)))
     (native-inputs
-     `(("ghc-silently" ,ghc-silently)
+     `(("curl" ,curl)
+       ("ghc-silently" ,ghc-silently)
        ("ghc-hspec" ,ghc-hspec)
-       ("ghc-auto-update" ,ghc-auto-update)
        ("ghc-doctest" ,ghc-doctest)
+       ("ghc-lifted-base" ,ghc-lifted-base)
        ("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-hunit" ,ghc-hunit)
-       ("ghc-http" ,ghc-http)
+       ("ghc-http-client" ,ghc-http-client)
        ("hspec-discover" ,hspec-discover)))
     (home-page "http://github.com/yesodweb/wai")
     (synopsis "HTTP server library for Haskell's WAI")

From ccd4fd3f2a614996bff5436cc22e4715a7eb1f31 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:19:05 -0400
Subject: [PATCH 431/909] gnu: xmobar: Update to 0.28.

* gnu/packages/wm.scm (xmobar): Update to 0.28.
---
 gnu/packages/wm.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index db345cd2fd..4ec465f875 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -504,14 +504,14 @@ tiled on several screens.")
 (define-public xmobar
   (package
     (name "xmobar")
-    (version "0.27")
+    (version "0.28")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://hackage/package/xmobar/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0agx490q6sbmv3vfq33ys8dsrgwizj3bmha4i1pkxz5wp5q8cx3l"))))
+                "1xh87asg8y35srvp7d3gyyy4bkxsw122liihxgzgm8pqv2z3h4zd"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-hspec" ,ghc-hspec)

From 6dde5b8f974b306b7f60871877152224d82e3c2d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:20:38 -0400
Subject: [PATCH 432/909] gnu: ghc-chart: Update to 1.9.

* gnu/packages/haskell.scm (ghc-chart): Update to 1.9.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e07b3423fd..50956f43ed 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10526,7 +10526,7 @@ tools are not needed to actually run Gtk2Hs programs.")
 (define-public ghc-chart
   (package
     (name "ghc-chart")
-    (version "1.8.3")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
@@ -10534,7 +10534,7 @@ tools are not needed to actually run Gtk2Hs programs.")
                            "Chart-" version ".tar.gz"))
        (sha256
         (base32
-         "13s64fhb2pmkdmx5bkgbgcn25qjihs364fvr47a1dw25f804kiy1"))))
+         "1f5azj17y8xsb3gjhf7gg1gnnlq12rxkmfjmgcly314d7vghs05z"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-old-locale" ,ghc-old-locale)

From e4bc57c85bb3ec8bc8eef35f3ff0fd3d1cb4b267 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:23:48 -0400
Subject: [PATCH 433/909] gnu: ghc-persistent-template: Update to 2.5.4.

* gnu/packages/haskell.scm (ghc-persistent-template): Update to 2.5.4.
[arguments]: Update Cabal file to r2.
---
 gnu/packages/haskell.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 50956f43ed..7c1c4af8f2 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10109,7 +10109,7 @@ ghc-aeson.")
 (define-public ghc-persistent-template
   (package
     (name "ghc-persistent-template")
-    (version "2.5.3.1")
+    (version "2.5.4")
     (source
      (origin
        (method url-fetch)
@@ -10118,8 +10118,11 @@ ghc-aeson.")
                            "persistent-template-" version ".tar.gz"))
        (sha256
         (base32
-         "0449piw3n02q7dag7k1pakfmzmf3ms4wk1qmnagczpm1ckajinwd"))))
+         "008afcy7zbw7bzp9jww8gdldb51kfm0fg4p0x4xcp61gx4679bjc"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("2" "03qgwk32krldph3blw5agiqcpccr3649hajyn8wm9k71zz82dpn6")))
     (inputs `(("ghc-persistent" ,ghc-persistent)
               ("ghc-monad-control" ,ghc-monad-control)
               ("ghc-text" ,ghc-text)

From dc676afb8cf4b0a9b44d630c917dfdb996e597ee Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:24:07 -0400
Subject: [PATCH 434/909] gnu: ghc-trifecta: Update to 2.

* gnu/packages/haskell.scm (ghc-trifecta): Update to 2.
[inputs]: Remove ghc-doctest-0.13, ghc-doctest, and ghc-quickcheck.
[native-inputs]: Add ghc-doctest and ghc-quickcheck.
---
 gnu/packages/haskell.scm | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 7c1c4af8f2..aebe223193 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2944,7 +2944,7 @@ the parsers provided by @code{parsec}, @code{attoparsec} and @code{base}'s
 (define-public ghc-trifecta
   (package
     (name "ghc-trifecta")
-    (version "1.7.1.1")
+    (version "2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2952,11 +2952,10 @@ the parsers provided by @code{parsec}, @code{attoparsec} and @code{base}'s
                     "trifecta-" version ".tar.gz"))
               (sha256
                (base32
-                "13n6a3fdxngnzsjnhfrzigv1c2g0xm6lqkjcnirpc37sd0rpby31"))))
+                "0hznd8i65s81xy13i2qc7cvipw3lfb2yhkv53apbdsh6sbljz5sk"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-doctest" ,ghc-doctest-0.13)
-       ("ghc-reducers" ,ghc-reducers)
+     `(("ghc-reducers" ,ghc-reducers)
        ("ghc-semigroups" ,ghc-semigroups)
        ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
        ("ghc-ansi-terminal" ,ghc-ansi-terminal)
@@ -2965,17 +2964,17 @@ the parsers provided by @code{parsec}, @code{attoparsec} and @code{base}'s
        ("ghc-blaze-markup" ,ghc-blaze-markup)
        ("ghc-charset" ,ghc-charset)
        ("ghc-comonad" ,ghc-comonad)
-       ("ghc-doctest" ,ghc-doctest)
        ("ghc-fingertree" ,ghc-fingertree)
        ("ghc-hashable" ,ghc-hashable)
        ("ghc-lens" ,ghc-lens)
        ("ghc-parsers" ,ghc-parsers)
        ("ghc-profunctors" ,ghc-profunctors)
-       ("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-unordered-containers" ,ghc-unordered-containers)
        ("ghc-utf8-string" ,ghc-utf8-string)))
     (native-inputs
-     `(("cabal-doctest" ,cabal-doctest)))
+     `(("cabal-doctest" ,cabal-doctest)
+       ("ghc-doctest" ,ghc-doctest)
+       ("ghc-quickcheck" ,ghc-quickcheck)))
     (home-page "https://github.com/ekmett/trifecta/")
     (synopsis "Parser combinator library with convenient diagnostics")
     (description "Trifecta is a modern parser combinator library for Haskell,

From 8401d3aad04d4ed256c92e5c525f7c4130930b6f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Fri, 31 Aug 2018 23:58:50 -0400
Subject: [PATCH 435/909] gnu: Remove old versions of ghc-doctest.

* gnu/packages/haskell.scm (ghc-doctest-0.12, ghc-doctest-0.13): Remove.
---
 gnu/packages/haskell.scm | 31 -------------------------------
 1 file changed, 31 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index aebe223193..30f764339e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5366,37 +5366,6 @@ It is modeled after doctest for Python, see
 @uref{https://docs.python.org/library/doctest.html, the Doctest website}.")
     (license license:expat)))
 
-(define-public ghc-doctest-0.12
-  (package (inherit ghc-doctest)
-    (name "ghc-doctest")
-    (version "0.12.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://hackage.haskell.org/package/doctest/doctest-"
-             version
-             ".tar.gz"))
-       (sha256
-        (base32
-         "13h549cpgcvb7c54c7wif28g5wak84dxc3ais0hlqhzk1q6la91a"))))
-    (inputs
-     `(("ghc-code-page" ,ghc-code-page)
-       ,@(package-inputs ghc-doctest)))))
-
-(define-public ghc-doctest-0.13
-  (package (inherit ghc-doctest-0.12)
-    (name "ghc-doctest")
-    (version "0.13.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/"
-                           "doctest/doctest-" version ".tar.gz"))
-       (sha256
-        (base32
-         "08g3nmpqbnbkxc95d65hkhfabwax10qrq51vlynr342npn40mn2b"))))))
-
 (define-public ghc-lifted-base
   (package
     (name "ghc-lifted-base")

From 6ef07930743b1c2d81c9b3a026b5f66ce1b4f74b Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:24:28 -0400
Subject: [PATCH 436/909] gnu: ghc-warp-tls: Update to 3.2.4.3.

* gnu/packages/haskell-web.scm (ghc-warp-tls): Update to 3.2.4.3.
[inputs]: Add ghc-tls-session-manager.
---
 gnu/packages/haskell-web.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index cf57e8fd96..9f96727a86 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -627,7 +627,7 @@ limitation, automatic pruning, energy saving and replay resistance.")
 (define-public ghc-warp-tls
   (package
     (name "ghc-warp-tls")
-    (version "3.2.3")
+    (version "3.2.4.3")
     (source
      (origin
        (method url-fetch)
@@ -636,7 +636,7 @@ limitation, automatic pruning, energy saving and replay resistance.")
                            "warp-tls-" version ".tar.gz"))
        (sha256
         (base32
-         "14m2bzk5ivz9gdpxlcj6qnh46f2lycm1ybdjnfkj2876zrqwii7m"))))
+         "17gj295fr98l7mkz2gdz6kahdnmja0sql3kvy2zab6q168g53kc4"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-cryptonite" ,ghc-cryptonite)
@@ -644,6 +644,7 @@ limitation, automatic pruning, energy saving and replay resistance.")
        ("ghc-network" ,ghc-network)
        ("ghc-streaming-commons" ,ghc-streaming-commons)
        ("ghc-tls" ,ghc-tls)
+       ("ghc-tls-session-manager" ,ghc-tls-session-manager)
        ("ghc-wai" ,ghc-wai)
        ("ghc-warp" ,ghc-warp)))
     (home-page "http://github.com/yesodweb/wai")

From 12ce5d31d19bd40f71b1f7b865fe32dbf5f0848f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 22 Sep 2018 11:08:31 -0400
Subject: [PATCH 437/909] gnu: Add ghc-rio.

* gnu/packages/haskell.scm (ghc-rio): New variable.
---
 gnu/packages/haskell.scm | 52 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 30f764339e..a0ca08720f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10556,4 +10556,56 @@ widths to the Char type.")
        ("ghc-attoparsec" ,ghc-attoparsec-bootstrap)))
     (properties '(hidden? #t))))
 
+(define-public ghc-rio
+  (package
+    (name "ghc-rio")
+    (version "0.1.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/rio/rio-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "064h8a4hp53a479d3ak0vmqbx8hi0cpg7zn4wp23rjy26dka8p7g"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'add-setup-script
+           (lambda _
+             ;; The usual "Setup.hs" script is missing from the source.
+             (with-output-to-file "Setup.hs"
+               (lambda ()
+                 (format #t "import Distribution.Simple~%")
+                 (format #t "main = defaultMain~%"))))))))
+    (inputs
+     `(("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-microlens" ,ghc-microlens)
+       ("ghc-primitive" ,ghc-primitive)
+       ("ghc-text" ,ghc-text)
+       ("ghc-typed-process" ,ghc-typed-process)
+       ("ghc-unliftio" ,ghc-unliftio)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-vector" ,ghc-vector)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("hspec-discover" ,hspec-discover)))
+    (home-page "https://github.com/commercialhaskell/rio#readme")
+    (synopsis "A standard library for Haskell")
+    (description "This package works as a prelude replacement for Haskell,
+providing more functionality and types out of the box than the standard
+prelude (such as common data types like @code{ByteString} and
+@code{Text}), as well as removing common ``gotchas'', like partial
+functions and lazy I/O.  The guiding principle here is:
+@itemize
+@item If something is safe to use in general and has no expected naming
+conflicts, expose it.
+@item If something should not always be used, or has naming conflicts,
+expose it from another module in the hierarchy.
+@end itemize")
+    (license license:expat)))
+
 ;;; haskell.scm ends here

From 0ea695f67754c18a85d384dd32602f0a998549e0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:24:48 -0400
Subject: [PATCH 438/909] gnu: ghc-yesod-core: Update to 1.6.6.

* gnu/packages/haskell-web.scm (ghc-yesod-core): Update to 1.6.6.
[inputs]: Add ghc-unliftio and ghc-rio.
---
 gnu/packages/haskell-web.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 9f96727a86..2271e1e982 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -1069,7 +1069,7 @@ avoid any issues with characters.")
 (define-public ghc-yesod-core
   (package
     (name "ghc-yesod-core")
-    (version "1.4.37")
+    (version "1.6.6")
     (source
      (origin
        (method url-fetch)
@@ -1078,7 +1078,7 @@ avoid any issues with characters.")
                            "yesod-core-" version ".tar.gz"))
        (sha256
         (base32
-         "0ww8hl0cx2g58zrdx3j6d5m2xwhssbajdqws1xk6rzl7rpfm1b9j"))))
+         "0xahf6m5c7mkl74p0gimy4wb5w4s3lh92wwxmk517fbq666c92kb"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-wai" ,ghc-wai)
               ("ghc-extra" ,ghc-extra)
@@ -1089,6 +1089,7 @@ avoid any issues with characters.")
               ("ghc-random" ,ghc-random)
               ("ghc-cereal" ,ghc-cereal)
               ("ghc-old-locale" ,ghc-old-locale)
+              ("ghc-unliftio" ,ghc-unliftio)
               ("ghc-unordered-containers" ,ghc-unordered-containers)
               ("ghc-monad-control" ,ghc-monad-control)
               ("ghc-transformers-base" ,ghc-transformers-base)
@@ -1103,6 +1104,7 @@ avoid any issues with characters.")
               ("ghc-monad-logger" ,ghc-monad-logger)
               ("ghc-conduit" ,ghc-conduit)
               ("ghc-resourcet" ,ghc-resourcet)
+              ("ghc-rio" ,ghc-rio)
               ("ghc-lifted-base" ,ghc-lifted-base)
               ("ghc-blaze-html" ,ghc-blaze-html)
               ("ghc-blaze-markup" ,ghc-blaze-markup)

From 7eee87e65d9e2da183887ade425a29de1a1f024d Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:27:50 -0400
Subject: [PATCH 439/909] gnu: ghc-persistent-sqlite: Update to 2.8.2.

* gnu/packages/haskell.scm (ghc-persistent-sqlite): Update to 2.8.2.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a0ca08720f..a373de8ea4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10217,7 +10217,7 @@ working with it.")
 (define-public ghc-persistent-sqlite
   (package
     (name "ghc-persistent-sqlite")
-    (version "2.6.4")
+    (version "2.8.2")
     (source
      (origin
        (method url-fetch)
@@ -10226,7 +10226,7 @@ working with it.")
                            "persistent-sqlite-" version ".tar.gz"))
        (sha256
         (base32
-         "16mc2ra0hbyyc8ckjlxxc11bpskdymbr8c3g6ih6wzik639xprbm"))))
+         "1chbmvjz46smhgnzhha3bbkhys3fys6dip1jr4v7xp1jf78zbyp6"))))
     (build-system haskell-build-system)
     (inputs `(("ghc-persistent" ,ghc-persistent)
               ("ghc-unliftio-core" ,ghc-unliftio-core)

From c6cf0eb5fb7bd1a77164293b727d1bc0d678d64c Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 00:18:38 -0400
Subject: [PATCH 440/909] gnu: Add ghc-tree-diff.

* gnu/packages/haskell.scm (ghc-tree-diff): New variable.
---
 gnu/packages/haskell.scm | 60 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a373de8ea4..ed83ece155 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -872,6 +872,66 @@ and an alternative to newtype-th.")
 efficient memo functions using tries.")
     (license license:bsd-3)))
 
+(define-public ghc-tree-diff
+  (package
+    (name "ghc-tree-diff")
+    (version "0.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/tree-diff/tree-diff-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "049v44c520jy3icxlnrvbdblh3mjmvd7m6qmkzxbzkf02x63xqmz"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:cabal-revision
+       ("4" "1rqxxyj6hqllahs11693g855cxz8mgnb490s7j1ksd300i5xgjsp")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "tree-diff.cabal"
+               (("trifecta             >=1\\.7\\.1\\.1  && <1\\.8")
+                "trifecta             >=1.7.1.1  && <=2")))))))
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-generics-sop" ,ghc-generics-sop)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-memotrie" ,ghc-memotrie)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-parsers" ,ghc-parsers)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-scientific" ,ghc-scientific)
+       ("ghc-tagged" ,ghc-tagged)
+       ("ghc-text" ,ghc-text)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-uuid-types" ,ghc-uuid-types)
+       ("ghc-vector" ,ghc-vector)))
+    (native-inputs
+     `(("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-trifecta" ,ghc-trifecta)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-golden" ,ghc-tasty-golden)
+       ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)))
+    (home-page "https://github.com/phadej/tree-diff")
+    (synopsis "Compute difference between (expression) trees")
+    (description "This Haskell library provides a function for computing
+the difference bewteen (expression) trees.  It also provides a way to
+compute the difference between arbitrary abstract datatypes (ADTs) using
+@code{Generics}-derivable helpers.")
+    (license license:bsd-3)))
+
 (define-public ghc-haddock-library
   (package
     (name "ghc-haddock-library")

From 99daa2948810d6f738c8e133fec28f414c3e5db8 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:30:54 -0400
Subject: [PATCH 441/909] gnu: ghc-aws: Update to 0.20.

* gnu/packages/haskell.scm (ghc-aws): Update to 0.20.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ed83ece155..94fa666b86 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9656,14 +9656,14 @@ as well as a convenient Conduit module.")
 (define-public ghc-aws
   (package
     (name "ghc-aws")
-    (version "0.18")
+    (version "0.20")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://hackage.haskell.org/package/"
                            "aws-" version "/aws-" version ".tar.gz"))
        (sha256 (base32
-                "0h7473wkvc5xjzx5fd5k5fp70rjq5gqmn1cpy95mswvvfsq3irxj"))))
+                "0pwpabmypi1w8rni9qfwabgn95jks4h8dyw6889mn8xzsrhdhyf0"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; Tests require AWS credentials.
     (inputs

From 3b72e7e2d4bbdf024d3e6f5a083a0bfe54b65f37 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 23 Aug 2018 23:09:32 -0400
Subject: [PATCH 442/909] gnu: ghc-esqueleto: Update to commit b81e0d9.

* gnu/packages/haskell.scm (ghc-esqueleto): Update to commit b81e0d9.
[source]: Use git-fetch.
[arguments]: Disable Haddock and add phase to remove MySQL and PostgreSQL
test-suites.
[inputs]: Add ghc-unliftio.
[native-inputs]: Remove ghc-hunit, ghc-monad-control, and ghc-quickcheck.
---
 gnu/packages/haskell.scm | 91 ++++++++++++++++++++++++++--------------
 1 file changed, 59 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 94fa666b86..5f9c2a4b6e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8555,42 +8555,69 @@ JSON (JavaScript Object Notation) is a lightweight data-interchange format.")
     (license license:bsd-3)))
 
 (define-public ghc-esqueleto
-  (package
-    (name "ghc-esqueleto")
-    (version "2.5.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/"
-                           "esqueleto/esqueleto-" version ".tar.gz"))
-       (sha256
-        (base32
-         "10n49rzqmblky7pwjnysalyy6nacmxfms8dqbsdv6hlyzr8pb69x"))))
-    (build-system haskell-build-system)
-    (inputs
-     `(("ghc-blaze-html" ,ghc-blaze-html)
-       ("ghc-conduit" ,ghc-conduit)
-       ("ghc-monad-logger" ,ghc-monad-logger)
-       ("ghc-persistent" ,ghc-persistent)
-       ("ghc-resourcet" ,ghc-resourcet)
-       ("ghc-tagged" ,ghc-tagged)
-       ("ghc-text" ,ghc-text)
-       ("ghc-unordered-containers" ,ghc-unordered-containers)))
-    (native-inputs
-     `(("ghc-hspec" ,ghc-hspec)
-       ("ghc-hunit" ,ghc-hunit)
-       ("ghc-monad-control" ,ghc-monad-control)
-       ("ghc-persistent-sqlite" ,ghc-persistent-sqlite)
-       ("ghc-persistent-template" ,ghc-persistent-template)
-       ("ghc-quickcheck" ,ghc-quickcheck)))
-    (home-page "https://github.com/bitemyapp/esqueleto")
-    (synopsis "Type-safe embedded domain specific language for SQL queries")
-    (description "This library provides a type-safe embedded domain specific
+  (let ((version "2.5.3")
+        (revision "1")
+        (commit "b81e0d951e510ebffca03c5a58658ad884cc6fbd"))
+    (package
+      (name "ghc-esqueleto")
+      (version (git-version version revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/bitemyapp/esqueleto")
+               (commit commit)))
+         (sha256
+          (base32
+           "0lz1qxms7cfg5p3j37inlych0r2fwhm8xbarcys3df9m7jy9nixa"))))
+      (build-system haskell-build-system)
+      (arguments
+       `(#:haddock? #f  ; Haddock reports an internal error.
+         #:phases
+         (modify-phases %standard-phases
+           ;; This package normally runs tests for the MySQL, PostgreSQL, and
+           ;; SQLite backends.  Since we only have Haskell packages for
+           ;; SQLite, we remove the other two test suites.  FIXME: Add the
+           ;; other backends and run all three test suites.
+           (add-before 'configure 'remove-non-sqlite-test-suites
+             (lambda _
+               (use-modules (ice-9 rdelim))
+               (with-atomic-file-replacement "esqueleto.cabal"
+                 (lambda (in out)
+                   (let loop ((line (read-line in 'concat)) (deleting? #f))
+                     (cond
+                      ((eof-object? line) #t)
+                      ((string-every char-set:whitespace line)
+                       (unless deleting? (display line out))
+                       (loop (read-line in 'concat) #f))
+                      ((member line '("test-suite mysql\n"
+                                      "test-suite postgresql\n"))
+                       (loop (read-line in 'concat) #t))
+                      (else
+                       (unless deleting? (display line out))
+                       (loop (read-line in 'concat) deleting?)))))))))))
+      (inputs
+       `(("ghc-blaze-html" ,ghc-blaze-html)
+         ("ghc-conduit" ,ghc-conduit)
+         ("ghc-monad-logger" ,ghc-monad-logger)
+         ("ghc-persistent" ,ghc-persistent)
+         ("ghc-resourcet" ,ghc-resourcet)
+         ("ghc-tagged" ,ghc-tagged)
+         ("ghc-text" ,ghc-text)
+         ("ghc-unliftio" ,ghc-unliftio)
+         ("ghc-unordered-containers" ,ghc-unordered-containers)))
+      (native-inputs
+       `(("ghc-hspec" ,ghc-hspec)
+         ("ghc-persistent-sqlite" ,ghc-persistent-sqlite)
+         ("ghc-persistent-template" ,ghc-persistent-template)))
+      (home-page "https://github.com/bitemyapp/esqueleto")
+      (synopsis "Type-safe embedded domain specific language for SQL queries")
+      (description "This library provides a type-safe embedded domain specific
 language (EDSL) for SQL queries that works with SQL backends as provided by
 @code{ghc-persistent}.  Its language closely resembles SQL, so you don't have
 to learn new concepts, just new syntax, and it's fairly easy to predict the
 generated SQL and optimize it for your backend.")
-    (license license:bsd-3)))
+      (license license:bsd-3))))
 
 (define-public shellcheck
   (package

From 082d9383d1475b772f104f1a6b363e4c80d91cf9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:06:20 -0400
Subject: [PATCH 443/909] gnu: ghc-haddock-library: Update to 1.5.0.1.

* gnu/packages/patches/ghc-haddock-library-unbundle.patch: New file.
* gnu/packages/haskell.scm (ghc-haddock-library): Update to 1.5.0.1.
[source]: Add the patch; add a snippet to remove the bundled library.
[arguments]: Add a phase to relax test suite dependency constraints and
another to add a missing directory required for tests.
[native-inputs]: Add ghc-base-compat, ghc-optparse-applicative, and
ghc-tree-diff.
---
 gnu/packages/haskell.scm                      | 35 ++++++--
 .../ghc-haddock-library-unbundle.patch        | 86 +++++++++++++++++++
 2 files changed, 115 insertions(+), 6 deletions(-)
 create mode 100644 gnu/packages/patches/ghc-haddock-library-unbundle.patch

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5f9c2a4b6e..0e061a6b40 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -935,7 +935,7 @@ compute the difference between arbitrary abstract datatypes (ADTs) using
 (define-public ghc-haddock-library
   (package
     (name "ghc-haddock-library")
-    (version "1.4.3")
+    (version "1.5.0.1")
     (source
      (origin
        (method url-fetch)
@@ -945,14 +945,37 @@ compute the difference between arbitrary abstract datatypes (ADTs) using
              ".tar.gz"))
        (sha256
         (base32
-         "0ns4bpf6whmcfl0cm2gx2c73if416x4q3ac4l4qm8w84h0zpcr7p"))))
+         "1cmbg8l5xrwpliclwy3l057raypjqy0hsg1h1743ahaj8gq10b7z"))
+       (patches (search-patches
+                 "ghc-haddock-library-unbundle.patch"))
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   (delete-file-recursively "vendor")
+                   #t))))
     (build-system haskell-build-system)
-    (inputs
-     `(("ghc-base-compat" ,ghc-base-compat)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'relax-test-suite-dependencies
+           (lambda _
+             (substitute* "haddock-library.cabal"
+               (("base-compat\\s*\\^>= 0\\.9\\.3") "base-compat")
+               (("hspec\\s*\\^>= 2\\.4\\.4") "hspec"))))
+         ;; The release tarball does not contain the "fixtures/examples"
+         ;; directory, which is required for testing.  In the upstream
+         ;; repository, the directory exists and is populated.  Here, we
+         ;; create an empty directory to placate the tests.
+         (add-before 'check 'add-examples-directory
+           (lambda _
+             (mkdir "fixtures/examples")
+             #t)))))
     (native-inputs
-     `(("hspec-discover" ,hspec-discover)
+     `(("ghc-base-compat" ,ghc-base-compat)
        ("ghc-hspec" ,ghc-hspec)
-       ("ghc-quickcheck" ,ghc-quickcheck)))
+       ("ghc-optparse-applicative" ,ghc-optparse-applicative)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-tree-diff" ,ghc-tree-diff)
+       ("hspec-discover" ,hspec-discover)))
     (home-page "https://www.haskell.org/haddock/")
     (synopsis "Library exposing some functionality of Haddock")
     (description
diff --git a/gnu/packages/patches/ghc-haddock-library-unbundle.patch b/gnu/packages/patches/ghc-haddock-library-unbundle.patch
new file mode 100644
index 0000000000..0e8b548956
--- /dev/null
+++ b/gnu/packages/patches/ghc-haddock-library-unbundle.patch
@@ -0,0 +1,86 @@
+This patch (inspired by Debian) allows ghc-haddock-library to use our
+ghc-attoparsec package instead of using a bundled version.
+
+--- a/haddock-library.cabal	2018-09-01 01:22:18.676855884 -0400
++++ b/haddock-library.cabal	2018-09-01 01:25:10.501150260 -0400
+@@ -10,7 +10,6 @@
+                       itself, see the ‘haddock’ package.
+ license:              BSD3
+ license-files:        LICENSE
+-                      vendor/attoparsec-0.13.1.0/LICENSE
+ maintainer:           Alex Biehl <alexbiehl@gmail.com>, Simon Hengel <sol@typeful.net>, Mateusz Kowalczyk <fuuzetsu@fuuzetsu.co.uk>
+ homepage:             http://www.haskell.org/haddock/
+ bug-reports:          https://github.com/haskell/haddock/issues
+@@ -28,7 +27,6 @@
+     , containers   >= 0.4.2.1 && < 0.6
+     , transformers >= 0.3.0   && < 0.6
+ 
+-  -- internal sub-lib
+   build-depends:        attoparsec
+ 
+   hs-source-dirs:       src
+@@ -49,42 +47,6 @@
+   if impl(ghc >= 8.0)
+     ghc-options: -Wcompat -Wnoncanonical-monad-instances -Wnoncanonical-monadfail-instances
+ 
+-library attoparsec
+-  default-language:     Haskell2010
+-
+-  build-depends:
+-      base         >= 4.5     && < 4.12
+-    , bytestring   >= 0.9.2.1 && < 0.11
+-    , deepseq      >= 1.3     && < 1.5
+-
+-  hs-source-dirs:       vendor/attoparsec-0.13.1.0
+-
+-  -- NB: haddock-library needs only small part of lib:attoparsec
+-  --     internally, so we only bundle that subset here
+-  exposed-modules:
+-    Data.Attoparsec.ByteString
+-    Data.Attoparsec.ByteString.Char8
+-    Data.Attoparsec.Combinator
+-
+-  other-modules:
+-    Data.Attoparsec
+-    Data.Attoparsec.ByteString.Buffer
+-    Data.Attoparsec.ByteString.FastSet
+-    Data.Attoparsec.ByteString.Internal
+-    Data.Attoparsec.Internal
+-    Data.Attoparsec.Internal.Fhthagn
+-    Data.Attoparsec.Internal.Types
+-    Data.Attoparsec.Number
+-
+-  ghc-options:          -funbox-strict-fields -Wall -fwarn-tabs -O2
+-
+-  ghc-options: -Wall
+-  if impl(ghc >= 8.0)
+-    ghc-options: -Wcompat -Wnoncanonical-monad-instances -Wnoncanonical-monadfail-instances
+-  else
+-    build-depends: semigroups ^>= 0.18.3, fail ^>= 4.9.0.0
+-
+-
+ test-suite spec
+   type:             exitcode-stdio-1.0
+   default-language: Haskell2010
+@@ -115,11 +77,10 @@
+     , hspec         ^>= 2.4.4
+     , QuickCheck    ^>= 2.11
+ 
+-  -- internal sub-lib
+   build-depends: attoparsec
+ 
+   -- Versions for the dependencies below are transitively pinned by
+-  -- dependency on haddock-library:lib:attoparsec
++  -- dependency on attoparsec
+   build-depends:
+       base
+     , bytestring
+@@ -146,7 +107,7 @@
+     haddock-library
+ 
+   -- Versions for the dependencies below are transitively pinned by
+-  -- dependency on haddock-library:lib:attoparsec
++  -- dependency on attoparsec
+   build-depends:
+       base
+ 

From 1689d39cd264c7794189eea243ed0b147896610f Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:32:05 -0400
Subject: [PATCH 444/909] gnu: ghc-yesod-persistent: Update to 1.6.0.

* gnu/packages/haskell-web.scm (ghc-yesod-persistent): Update to 1.6.0.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 2271e1e982..0b8f287024 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -1140,7 +1140,7 @@ functions, widgets, etc.")
 (define-public ghc-yesod-persistent
   (package
     (name "ghc-yesod-persistent")
-    (version "1.4.3")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
@@ -1149,7 +1149,7 @@ functions, widgets, etc.")
                            "yesod-persistent-" version ".tar.gz"))
        (sha256
         (base32
-         "0kiksw46c8ww9yiwl28pkrppx8d6fhsasr0hvmsliqbrp16likj8"))))
+         "1gd59xf7b6v3cald58mzwnfbdzjr49cz60rm4wc5w9pvfx12pgj2"))))
     (build-system haskell-build-system)
     (arguments `(#:tests? #f)) ; FIXME: hspec-discover not available in PATH.
     (inputs `(("ghc-yesod-core" ,ghc-yesod-core)

From f548cd7254b696249a185972a55ff18dd0616b34 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:25:11 -0400
Subject: [PATCH 445/909] gnu: ghc-haddock-api: Update to 2.19.0.1.

* gnu/packages/haskell.scm (ghc-haddock-api): Update to 2.19.0.1.
[arguments]: Add a phase that patches the Cabal file to allow newer
versions of Cabal and hspec.
---
 gnu/packages/haskell.scm | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0e061a6b40..bcdb6fb609 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -989,8 +989,7 @@ the ‘haddock’ package.")
 (define-public ghc-haddock-api
   (package
     (name "ghc-haddock-api")
-    ;; This is the last version to be supported by Cabal < 2.0
-    (version "2.17.4")
+    (version "2.19.0.1")
     (source
      (origin
        (method url-fetch)
@@ -1000,8 +999,18 @@ the ‘haddock’ package.")
              ".tar.gz"))
        (sha256
         (base32
-         "00fn6pzgg8xjbaw12d76jdqh2dbc5xy7miyz0x6kidvvar7i35ss"))))
+         "0c6i7sljp7myz25d90gyw68a90i5jcrkajkxcciikp2hjirfaas3"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "haddock-api.cabal"
+               (("Cabal           \\^>= 2\\.0\\.0")
+                "Cabal           ^>= 2.2.0")
+               (("hspec           \\^>= 2\\.4\\.4")
+                "hspec            >= 2.4.4 && < 2.6")))))))
     (inputs
      `(("ghc-paths" ,ghc-paths)
        ("ghc-haddock-library" ,ghc-haddock-library)))

From 6a006a11fde6be270b2d35a9570544c9c70bb967 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Sat, 1 Sep 2018 10:55:48 -0400
Subject: [PATCH 446/909] gnu: ghc-pandoc: Adjust tests and test dependency
 constraints.

* gnu/packages/haskell.scm (ghc-pandoc)[arguments]: Add a phase to relax a
test suite dependency constraint and another to skip some failing tests.
---
 gnu/packages/haskell.scm | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index bcdb6fb609..8b2c157a71 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -6859,6 +6859,20 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
         (base32
          "1dqin92w513l7whg5wdgrngnxsj5mb8gppfvn7kjgyv2pdgpy0zy"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "pandoc.cabal"
+               (("tasty >= 0\\.11 && < 1\\.1")
+                "tasty >= 0.11 && < 1.1.1"))))
+         (add-before 'configure 'patch-tests
+           (lambda _
+             ;; These tests fail benignly and have been adjusted upstream:
+             ;; <https://github.com/commercialhaskell/stackage/issues/3719>.
+             (substitute* "test/Tests/Old.hs"
+               (("lhsWriterTests \"html\"") "[]")))))))
     (inputs
      `(("ghc-aeson" ,ghc-aeson)
        ("ghc-aeson-pretty" ,ghc-aeson-pretty)

From 69054c92854075ffc2027ef9a6459540571ef1f2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:33:31 -0400
Subject: [PATCH 447/909] gnu: ghc-yesod-form: Update to 1.6.2.

* gnu/packages/haskell-web.scm (ghc-yesod-form): Update to 1.6.2.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 0b8f287024..85b88aa72e 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -1173,7 +1173,7 @@ from Yesod.")
 (define-public ghc-yesod-form
     (package
     (name "ghc-yesod-form")
-    (version "1.4.16")
+    (version "1.6.2")
     (source
       (origin
         (method url-fetch)
@@ -1183,7 +1183,7 @@ from Yesod.")
                ".tar.gz"))
         (sha256
           (base32
-            "0lij3m5vn8nvh6y88r1dhk03xmmjwmjzazm307nc2wvc5fmx9p2j"))))
+            "1p1x1hffvarplc82ykdk7rm6p5isqgqf78bvxzpfhncxs4kwx057"))))
     (build-system haskell-build-system)
     (inputs
       `(("ghc-yesod-core" ,ghc-yesod-core)

From 1b29af3d16ef9f8636031c8136e50be8abeef5f0 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 00:31:02 -0400
Subject: [PATCH 448/909] gnu: ghc-haddock: Update to 2.19.0.1.

* gnu/packages/haskell.scm (ghc-haddock): Update to 2.19.0.1.
[arguments]: Add a phase that deletes four test suites to avoid a
dependency on haddock-test.
[native-inputs]: Remove ghc-haddock-test.
---
 gnu/packages/haskell.scm | 37 +++++++++++++++++++++++++++++--------
 1 file changed, 29 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 8b2c157a71..f153b48034 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -1049,7 +1049,7 @@ documentation-generation tool for Haskell libraries.")
 (define-public ghc-haddock
   (package
     (name "ghc-haddock")
-    (version "2.17.4")
+    (version "2.19.0.1")
     (source
      (origin
        (method url-fetch)
@@ -1059,16 +1059,37 @@ documentation-generation tool for Haskell libraries.")
              ".tar.gz"))
        (sha256
         (base32
-         "1z3h3v7w84dzsm47iavdppc2w899mr4c1agq9fzghgz902i0a655"))))
+         "1g1j9j0hf2yhyyh0gwz6bzbvfvliqz9x8a8hnkmwghm7w3xa6sb7"))))
     (build-system haskell-build-system)
-    ;; FIXME: Tests fail with this error:
-    ;; driver-test/Main.hs:4:1: error:
-    ;; Failed to load interface for ‘ResponseFileSpec’
-    (arguments `(#:tests? #f))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; There are four test suites that require the ghc-haddock-test
+         ;; package, which no longer builds with GHC 8.4.3.  This phase
+         ;; removes these four test suites from the Cabal file, so that we
+         ;; do not need ghc-haddock-test as an input.
+         (add-before 'configure 'remove-haddock-test-test-suites
+           (lambda _
+             (use-modules (ice-9 rdelim))
+             (with-atomic-file-replacement "haddock.cabal"
+               (lambda (in out)
+                 (let loop ((line (read-line in 'concat)) (deleting? #f))
+                   (cond
+                    ((eof-object? line) #t)
+                    ((string-every char-set:whitespace line)
+                     (unless deleting? (display line out))
+                     (loop (read-line in 'concat) #f))
+                    ((member line '("test-suite html-test\n"
+                                    "test-suite hypsrc-test\n"
+                                    "test-suite latex-test\n"
+                                    "test-suite hoogle-test\n"))
+                     (loop (read-line in 'concat) #t))
+                    (else
+                     (unless deleting? (display line out))
+                     (loop (read-line in 'concat) deleting?)))))))))))
     (inputs `(("ghc-haddock-api" ,ghc-haddock-api)))
     (native-inputs
-     `(("ghc-hspec" ,ghc-hspec)
-       ("ghc-haddock-test" ,ghc-haddock-test)))
+     `(("ghc-hspec" ,ghc-hspec)))
     (home-page "https://www.haskell.org/haddock/")
     (synopsis
      "Documentation-generation tool for Haskell libraries")

From 003ec2c8f08265b9e605268981e331e4b4fff6b2 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:23:22 -0400
Subject: [PATCH 449/909] gnu: ghc-pandoc-citeproc: Update to 0.14.3.1.

* gnu/packages/haskell.scm (ghc-pandoc-citeproc): Update to 0.14.3.1.
[arguments]: Add a phase to disable some failing YAML tests.
---
 gnu/packages/haskell.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index f153b48034..170d3bdc5d 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -7207,6 +7207,13 @@ the @code{conduit} package.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         ;; Many YAML tests (44) are failing do to changes in ghc-yaml:
+         ;; <https://github.com/jgm/pandoc-citeproc/issues/342>.
+         (add-before 'configure 'patch-tests
+           (lambda _
+             (substitute* "tests/test-pandoc-citeproc.hs"
+               (("let allTests = citeprocTests \\+\\+ biblio2yamlTests")
+                "let allTests = citeprocTests"))))
          ;; Tests need to be run after installation.
          (delete 'check)
          (add-after 'install 'post-install-check

From 662fd1a868ef11479030a00f5e485308c707da91 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Wed, 29 Aug 2018 01:35:00 -0400
Subject: [PATCH 450/909] gnu: ghc-yesod: Update to 1.6.0.

* gnu/packages/haskell-web.scm (ghc-yesod): Update to 1.6.0.
---
 gnu/packages/haskell-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 85b88aa72e..68dcd9e4b1 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -1216,7 +1216,7 @@ providing richtext field using Nic editor. ")
 (define-public ghc-yesod
   (package
     (name "ghc-yesod")
-    (version "1.4.5")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
@@ -1225,7 +1225,7 @@ providing richtext field using Nic editor. ")
              version ".tar.gz"))
        (sha256
         (base32
-         "1sg66nq8yaas2m5nqsdrxricvcizd1ik02zqk60sxh3wna08fz16"))))
+         "0wx77nbpzdh40p1bm527kimfj48vs9d2avpvvz2w42zi3pz2y94a"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-yesod-core" ,ghc-yesod-core)

From 8fe9ab95793c85f391613c789ee71515663f1b79 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Tue, 4 Sep 2018 23:52:09 -0400
Subject: [PATCH 451/909] gnu: Remove ghc-pandoc@1.

This old version of Pandoc no longer builds with GHC 8.4.3.

* gnu/packages/haskell-web.scm (ghc-aeson-for-pandoc-1): Remove variable.
* gnu/packages/haskell.scm (ghc-pandoc-types-for-pandoc-1,
ghc-texmath-for-pandoc-1, ghc-yaml-for-pandoc-1, ghc-hslua-for-pandoc-1,
ghc-skylighting-for-pandoc-1, ghc-doctemplates-for-pandoc-1, ghc-pandoc-1,
ghc-pandoc-citeproc-with-pandoc-1): Remove variables.
---
 gnu/packages/haskell-web.scm |  12 --
 gnu/packages/haskell.scm     | 212 -----------------------------------
 2 files changed, 224 deletions(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index 68dcd9e4b1..eaa7e6a9ec 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -852,18 +852,6 @@ for Haskell, optimized for ease of use and high performance.  (A note on
 naming: in Greek mythology, Aeson was the father of Jason.)")
     (license license:bsd-3)))
 
-(define-public ghc-aeson-for-pandoc-1
-  (package (inherit ghc-aeson)
-    (version "1.1.2.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/aeson/aeson-"
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "1zy5z8pzvh53qkjm0nm3f4rwqfqg3867ck8ncd6mrxpcyvxqqj1p"))))))
-
 (define-public ghc-aeson-pretty
   (package
     (name "ghc-aeson-pretty")
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 170d3bdc5d..e39c5e0b81 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -5757,25 +5757,6 @@ pandoc to represent structured documents.  It also provides functions for
 building up, manipulating and serialising @code{Pandoc} structures.")
     (license license:bsd-3)))
 
-(define-public ghc-pandoc-types-for-pandoc-1
-  (package (inherit ghc-pandoc-types)
-    (version "1.17.0.5")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://hackage.haskell.org/package/"
-                                  "pandoc-types/pandoc-types-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "1csipjdq00iiq77k2wlrg4i7afrzlh8nl585q785xzw7nn45b0n8"))))
-    (arguments
-     `(#:configure-flags (list "--allow-newer=QuickCheck"
-                               "--allow-newer=HUnit")))
-    (inputs
-     `(("ghc-syb" ,ghc-syb)
-       ("ghc-aeson" ,ghc-aeson-for-pandoc-1)
-       ("ghc-string-qq" ,ghc-string-qq)))))
-
 (define-public ghc-texmath
   (package
     (name "ghc-texmath")
@@ -5808,26 +5789,6 @@ markup formats).  The TeX reader supports basic LaTeX and AMS extensions, and
 it can parse and apply LaTeX macros.")
     (license license:gpl2+)))
 
-(define-public ghc-texmath-for-pandoc-1
-  (package (inherit ghc-texmath)
-    (version "0.9.4.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://hackage.haskell.org/package/"
-                                  "texmath/texmath-" version ".tar.gz"))
-              (sha256
-               (base32
-                "129q33m56diiv35kdwfb07838wrg0mm88kxdqxfyl1zvf9nzkqkd"))))
-    (inputs
-     `(("ghc-network-uri" ,ghc-network-uri)
-       ("ghc-pandoc-types" ,ghc-pandoc-types-for-pandoc-1)
-       ("ghc-parsec" ,ghc-parsec)
-       ("ghc-split" ,ghc-split)
-       ("ghc-syb" ,ghc-syb)
-       ("ghc-temporary" ,ghc-temporary)
-       ("ghc-utf8-string" ,ghc-utf8-string)
-       ("ghc-xml" ,ghc-xml)))))
-
 (define-public ghc-regex-pcre-builtin
   (package
     (name "ghc-regex-pcre-builtin")
@@ -6382,12 +6343,6 @@ back-ends.")
      "This package provides a library to parse and render YAML documents.")
     (license license:bsd-3)))
 
-(define-public ghc-yaml-for-pandoc-1
-  (package (inherit ghc-yaml)
-    (inputs
-     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
-       ,@(alist-delete "ghc-aeson" (package-inputs ghc-yaml))))))
-
 (define-public ghc-filemanip
   (package
     (name "ghc-filemanip")
@@ -6489,27 +6444,6 @@ TIFF and GIF formats.")
 described in @url{https://www.lua.org/}.")
     (license license:expat)))
 
-(define-public ghc-hslua-for-pandoc-1
-  (package (inherit ghc-hslua)
-    (version "0.4.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://hackage.haskell.org/package/"
-                                  "hslua/hslua-" version ".tar.gz"))
-              (sha256
-               (base32
-                "0gqp6qhp4v24kzv2j49kgk7bxqzw0w10x0zr0r2j9wkfavqb9wid"))))
-    (inputs
-     `(("lua" ,lua-5.1)
-       ("ghc-text" ,ghc-text)))
-    (native-inputs
-     `(("ghc-quickcheck" ,ghc-quickcheck)
-       ("ghc-quickcheck-instances" ,ghc-quickcheck-instances)
-       ("ghc-hspec" ,ghc-hspec)
-       ("ghc-hspec-contrib" ,ghc-hspec-contrib)
-       ("ghc-hunit" ,ghc-hunit)
-       ("hspec-discover" ,hspec-discover)))))
-
 (define-public ghc-hslua-module-text
   (package
     (name "ghc-hslua-module-text")
@@ -6763,56 +6697,6 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
      `(("ghc-skylighting-core" ,ghc-skylighting-core)
        ,@(package-inputs ghc-skylighting-core)))))
 
-(define-public ghc-skylighting-for-pandoc-1
-  (package (inherit ghc-skylighting)
-    (version "0.1.1.5")
-    (source (origin
-              (method git-fetch)
-              ;; We take the sources from Github, because the tarball on
-              ;; hackage does not include the XML files.
-              (uri (git-reference
-                    (url "https://github.com/jgm/skylighting.git")
-                    (commit version)))
-              (file-name (string-append "ghc-skylighting-" version "-checkout"))
-              (sha256
-               (base32
-                "0z3yv8v2fqqgv6lsf0ff3ld0h2vkg97b2jiry9wn2f1rizwdqmzl"))))
-    (arguments
-     `(#:configure-flags '("-fbootstrap")
-       #:phases
-       (modify-phases %standard-phases
-         ;; After building the skylighting-extract tool we use it to generate
-         ;; syntax source files from the included XML files.  These are then
-         ;; added to the skylighting.cabal file.
-         (add-after 'build 'extract-xml
-           (lambda _
-             (make-file-writable "skylighting.cabal")
-             (apply invoke "./dist/build/skylighting-extract/skylighting-extract"
-                    (find-files "xml" "\\.xml$"))
-             #t))
-         ;; Reconfigure without bootstrap flag
-         (add-after 'extract-xml 'configure-again
-           (lambda* (#:key outputs inputs tests? #:allow-other-keys)
-             ((assoc-ref %standard-phases 'configure)
-              #:outputs outputs
-              #:inputs inputs
-              #:tests? tests?
-              #:configure-flags '("-f-bootstrap"))))
-         (add-after 'configure-again 'build-again
-           (assoc-ref %standard-phases 'build)))))
-    (inputs
-     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
-       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
-       ("ghc-blaze-html" ,ghc-blaze-html)
-       ("ghc-case-insensitive" ,ghc-case-insensitive)
-       ("ghc-diff" ,ghc-diff)
-       ("ghc-hxt" ,ghc-hxt)
-       ("ghc-pretty-show" ,ghc-pretty-show)
-       ("ghc-regex-pcre-builtin" ,ghc-regex-pcre-builtin)
-       ("ghc-safe" ,ghc-safe)
-       ("ghc-text" ,ghc-text)
-       ("ghc-utf8-string" ,ghc-utf8-string)))))
-
 (define-public ghc-doctemplates
   (package
     (name "ghc-doctemplates")
@@ -6844,29 +6728,6 @@ provided.  Skylighting is intended to be the successor to highlighting-kate.")
      "This package provides a simple text templating system used by pandoc.")
     (license license:bsd-3)))
 
-(define-public ghc-doctemplates-for-pandoc-1
-  (package (inherit ghc-doctemplates)
-    (version "0.1.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/"
-                           "doctemplates/doctemplates-"
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "0swal6rjya1293mwvl63jch5fx9ghpsil7qs4v7rpansa0izalmp"))))
-    (build-system haskell-build-system)
-    (inputs
-     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
-       ("ghc-blaze-markup" ,ghc-blaze-markup)
-       ("ghc-blaze-html" ,ghc-blaze-html)
-       ("ghc-text" ,ghc-text)
-       ("ghc-vector" ,ghc-vector)
-       ("ghc-parsec" ,ghc-parsec)
-       ("ghc-unordered-containers" ,ghc-unordered-containers)
-       ("ghc-scientific" ,ghc-scientific)))))
-
 (define-public ghc-pandoc
   (package
     (name "ghc-pandoc")
@@ -6956,66 +6817,6 @@ definition lists, tables, and other features.  A compatibility mode is
 provided for those who need a drop-in replacement for Markdown.pl.")
     (license license:gpl2+)))
 
-;; This is the last version of Pandoc 1.x, which is preferred for Rmarkdown.
-(define-public ghc-pandoc-1
-  (package (inherit ghc-pandoc)
-    (version "1.19.2.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://hackage.haskell.org/package/pandoc/pandoc-"
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "0mim429mpakrcnm50csxyqk3ljcx2l26r5grk6w9isnggwgqrq5v"))))
-    (arguments
-     `(#:configure-flags (list "--allow-newer=skylighting")))
-    (inputs
-     `(("ghc-aeson" ,ghc-aeson-for-pandoc-1)
-       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
-       ("ghc-base64-bytestring" ,ghc-base64-bytestring)
-       ("ghc-blaze-html" ,ghc-blaze-html)
-       ("ghc-blaze-markup" ,ghc-blaze-markup)
-       ("ghc-cmark" ,ghc-cmark)
-       ("ghc-data-default" ,ghc-data-default)
-       ("ghc-deepseq-generics" ,ghc-deepseq-generics)
-       ("ghc-diff" ,ghc-diff)
-       ("ghc-doctemplates" ,ghc-doctemplates-for-pandoc-1)
-       ("ghc-executable-path" ,ghc-executable-path)
-       ("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
-       ("ghc-filemanip" ,ghc-filemanip)
-       ("ghc-haddock-library" ,ghc-haddock-library)
-       ("ghc-hslua" ,ghc-hslua-for-pandoc-1)
-       ("ghc-http" ,ghc-http)
-       ("ghc-http-client" ,ghc-http-client)
-       ("ghc-http-client-tls" ,ghc-http-client-tls)
-       ("ghc-http-types" ,ghc-http-types)
-       ("ghc-juicypixels" ,ghc-juicypixels)
-       ("ghc-network" ,ghc-network)
-       ("ghc-network-uri" ,ghc-network-uri)
-       ("ghc-old-time" ,ghc-old-time)
-       ("ghc-pandoc-types" ,ghc-pandoc-types-for-pandoc-1)
-       ("ghc-parsec" ,ghc-parsec)
-       ("ghc-random" ,ghc-random)
-       ("ghc-scientific" ,ghc-scientific)
-       ("ghc-sha" ,ghc-sha)
-       ("ghc-skylighting" ,ghc-skylighting-for-pandoc-1)
-       ("ghc-syb" ,ghc-syb)
-       ("ghc-tagsoup" ,ghc-tagsoup)
-       ("ghc-temporary" ,ghc-temporary)
-       ("ghc-texmath" ,ghc-texmath-for-pandoc-1)
-       ("ghc-text" ,ghc-text)
-       ("ghc-unordered-containers" ,ghc-unordered-containers)
-       ("ghc-vector" ,ghc-vector)
-       ("ghc-xml" ,ghc-xml)
-       ("ghc-yaml" ,ghc-yaml-for-pandoc-1)
-       ("ghc-zip-archive" ,ghc-zip-archive)
-       ("ghc-zlib" ,ghc-zlib)))
-    (native-inputs
-     `(("ghc-test-framework" ,ghc-test-framework)
-       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
-       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))))
-
 (define-public ghc-hs-bibutils
   (package
     (name "ghc-hs-bibutils")
@@ -7251,19 +7052,6 @@ and also has a mode for converting bibliographic databases a YAML format
 suitable for inclusion in pandoc YAML metadata.")
     (license license:bsd-3)))
 
-(define-public ghc-pandoc-citeproc-with-pandoc-1
-  (let ((for-pandoc-1
-         (package-input-rewriting
-          `((,ghc-aeson        . ,ghc-aeson-for-pandoc-1)
-            (,ghc-yaml         . ,ghc-yaml-for-pandoc-1)
-            (,ghc-texmath      . ,ghc-texmath-for-pandoc-1)
-            (,ghc-pandoc-types . ,ghc-pandoc-types-for-pandoc-1)
-            (,ghc-hslua        . ,ghc-hslua-for-pandoc-1)
-            (,ghc-skylighting  . ,ghc-skylighting-for-pandoc-1)
-            (,ghc-doctemplates . ,ghc-doctemplates-for-pandoc-1)
-            (,ghc-pandoc       . ,ghc-pandoc-1)))))
-    (for-pandoc-1 ghc-pandoc-citeproc)))
-
 (define-public ghc-union-find
   (package
     (name "ghc-union-find")

From 88c337177fbe99e8422a91e633713b4453279fe6 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 6 Sep 2018 23:58:30 -0400
Subject: [PATCH 452/909] gnu: ghc-base-compat: Update to 0.10.4.

* gnu/packages/haskell.scm (ghc-base-compat): Update to 0.10.4.
---
 gnu/packages/haskell.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index e39c5e0b81..bcf0b83a04 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -4547,7 +4547,7 @@ system.")
 (define-public ghc-base-compat
   (package
     (name "ghc-base-compat")
-    (version "0.9.3")
+    (version "0.10.4")
     (source
      (origin
        (method url-fetch)
@@ -4557,7 +4557,7 @@ system.")
              ".tar.gz"))
        (sha256
         (base32
-         "0452l6zf6fjhy4kxqwv6i6hhg6yfx4wcg450k3axpyj30l7jnq3x"))))
+         "0ksp990gxs731mq19rzbxrbs43nazfljjc8krlx5bjqblw3kfs8d"))))
     (build-system haskell-build-system)
     (native-inputs
      `(("ghc-quickcheck" ,ghc-quickcheck)

From 576b7dd5083827dd83b45749a6e9b983a20512c9 Mon Sep 17 00:00:00 2001
From: Timothy Sample <samplet@ngyro.com>
Date: Thu, 6 Sep 2018 23:59:34 -0400
Subject: [PATCH 453/909] gnu: ghc-tasty-golden: Update to 2.3.2.

* gnu/packages/haskell-check.scm (ghc-tasty-golden): Update to 2.3.2.
---
 gnu/packages/haskell-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell-check.scm b/gnu/packages/haskell-check.scm
index 42b7fd167b..0d4501df86 100644
--- a/gnu/packages/haskell-check.scm
+++ b/gnu/packages/haskell-check.scm
@@ -124,7 +124,7 @@ Haskell test framework.")
 (define-public ghc-tasty-golden
   (package
     (name "ghc-tasty-golden")
-    (version "2.3.1.1")
+    (version "2.3.2")
     (source
      (origin
        (method url-fetch)
@@ -134,7 +134,7 @@ Haskell test framework.")
              ".tar.gz"))
        (sha256
         (base32
-         "0pcf5hsyp5mmbqn7krdm49jxpkjm6rb4j83j28f76h7q55dzm1wy"))))
+         "0k3ibjhjc9vcwzrjnl4rnwvfm8l81q347nb7dgvcib6n5wm3s404"))))
     (build-system haskell-build-system)
     (inputs
      `(("ghc-temporary" ,ghc-temporary)

From 1d13003aa9ea35f506546e66fd26383aef3211bf Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 28 Sep 2018 08:30:19 +0200
Subject: [PATCH 454/909] gnu: Add ghc-weigh.

* gnu/packages/haskell.scm (ghc-weigh): New variable.
---
 gnu/packages/haskell.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index bcf0b83a04..4be0290825 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10557,4 +10557,26 @@ expose it from another module in the hierarchy.
 @end itemize")
     (license license:expat)))
 
+(define-public ghc-weigh
+  (package
+    (name "ghc-weigh")
+    (version "0.0.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/weigh/"
+                           "weigh-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0zw2a997gxgdzqmd7j730kxgynzmjvvlkw84dajmfzf1v9pbij7x"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-split" ,ghc-split)
+       ("ghc-temporary" ,ghc-temporary)))
+    (home-page "https://github.com/fpco/weigh#readme")
+    (synopsis "Measure allocations of a Haskell functions/values")
+    (description "This package provides tools to measure the memory usage of a
+Haskell value or function.")
+    (license license:bsd-3)))
+
 ;;; haskell.scm ends here

From d459e043c885811495088fb9d73b45b68db154de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 28 Sep 2018 08:30:42 +0200
Subject: [PATCH 455/909] gnu: Add ghc-linear.

* gnu/packages/haskell.scm (ghc-linear): New variable.
---
 gnu/packages/haskell.scm | 43 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4be0290825..8076838309 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10579,4 +10579,47 @@ expose it from another module in the hierarchy.
 Haskell value or function.")
     (license license:bsd-3)))
 
+(define-public ghc-linear
+  (package
+    (name "ghc-linear")
+    (version "1.20.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/linear/"
+                           "linear-" version ".tar.gz"))
+       (sha256
+        (base32
+         "046vkvxlb0s286qr55s0c6db0rlwbm1cmlmwhrrkqbkzhfcipgay"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-adjunctions" ,ghc-adjunctions)
+       ("ghc-base-orphans" ,ghc-base-orphans)
+       ("ghc-bytes" ,ghc-bytes)
+       ("ghc-cereal" ,ghc-cereal)
+       ("ghc-distributive" ,ghc-distributive)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-lens" ,ghc-lens)
+       ("ghc-reflection" ,ghc-reflection)
+       ("ghc-semigroups" ,ghc-semigroups)
+       ("ghc-semigroupoids" ,ghc-semigroupoids)
+       ("ghc-tagged" ,ghc-tagged)
+       ("ghc-transformers-compat" ,ghc-transformers-compat)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-void" ,ghc-void)))
+    (native-inputs
+     `(("cabal-doctest" ,cabal-doctest)
+       ("ghc-doctest" ,ghc-doctest)
+       ("ghc-simple-reflect" ,ghc-simple-reflect)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-hunit" ,ghc-hunit)))
+    (home-page "http://github.com/ekmett/linear/")
+    (synopsis "Linear algebra library for Haskell")
+    (description
+     "This package provides types and combinators for linear algebra on free
+vector spaces.")
+    (license license:bsd-3)))
+
 ;;; haskell.scm ends here

From 62dd7171d3fa3df964f34ebb1627704ea447cc21 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 28 Sep 2018 08:31:11 +0200
Subject: [PATCH 456/909] gnu: Add ghc-sdl2.

* gnu/packages/sdl.scm (ghc-sdl2): New variable.
---
 gnu/packages/sdl.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index 55ce45ce78..a50ed8cbcb 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -33,6 +33,7 @@
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system haskell)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages fcitx)
@@ -40,6 +41,7 @@
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages guile)
+  #:use-module (gnu packages haskell)
   #:use-module (gnu packages ibus)
   #:use-module (gnu packages image)
   #:use-module (gnu packages linux)
@@ -520,3 +522,40 @@ sound and device input (keyboards, joysticks, mice, etc.).")
 The bindings are written in pure Scheme using Guile's foreign function
 interface.")
     (license lgpl3+)))
+
+(define-public ghc-sdl2
+  (package
+    (name "ghc-sdl2")
+    (version "2.4.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "sdl2/sdl2-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0p4b12fmxps0sbnkqdfy0qw19s355yrkw7fgw6xz53wzq706k991"))))
+    (build-system haskell-build-system)
+    (arguments '(#:tests? #f)) ; tests require graphical environment
+    (inputs
+     `(("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-linear" ,ghc-linear)
+       ("ghc-statevar" ,ghc-statevar)
+       ("ghc-text" ,ghc-text)
+       ("ghc-vector" ,ghc-vector)
+       ("sdl2" ,sdl2)))
+    (native-inputs
+     `(("ghc-weigh" ,ghc-weigh)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://hackage.haskell.org/package/sdl2")
+    (synopsis "High- and low-level bindings to the SDL library")
+    (description
+     "This package contains bindings to the SDL 2 library, in both high- and
+low-level forms.  The @code{SDL} namespace contains high-level bindings, where
+enumerations are split into sum types, and we perform automatic
+error-checking.  The @code{SDL.Raw} namespace contains an almost 1-1
+translation of the C API into Haskell FFI calls.  As such, this does not
+contain sum types nor error checking.  Thus this namespace is suitable for
+building your own abstraction over SDL, but is not recommended for day-to-day
+programming.")
+    (license bsd-3)))

From d975534e856dc6c8426d9f28af3b5d30ead31ac3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 28 Sep 2018 08:31:25 +0200
Subject: [PATCH 457/909] gnu: Add ghc-sdl2-mixer.

* gnu/packages/sdl.scm (ghc-sdl2-mixer): New variable.
---
 gnu/packages/sdl.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index a50ed8cbcb..06f419f900 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -559,3 +559,31 @@ contain sum types nor error checking.  Thus this namespace is suitable for
 building your own abstraction over SDL, but is not recommended for day-to-day
 programming.")
     (license bsd-3)))
+
+(define-public ghc-sdl2-mixer
+  (package
+    (name "ghc-sdl2-mixer")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/sdl2-mixer/"
+                           "sdl2-mixer-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1k8avyccq5l9z7bwxigim312yaancxl1sr3q6a96bcm7pnhiak0g"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-data-default-class" ,ghc-data-default-class)
+       ("ghc-lifted-base" ,ghc-lifted-base)
+       ("ghc-monad-control" ,ghc-monad-control)
+       ("ghc-sdl2" ,ghc-sdl2)
+       ("ghc-vector" ,ghc-vector)
+       ("sdl2-mixer" ,sdl2-mixer)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://hackage.haskell.org/package/sdl2-mixer")
+    (synopsis "Bindings to SDL2 mixer")
+    (description "This package provides Haskell bindings to
+@code{SDL2_mixer}.")
+    (license bsd-3)))

From 21be24b74f1a0cac185637620d59a3764c539875 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 28 Sep 2018 08:31:36 +0200
Subject: [PATCH 458/909] gnu: Add ghc-sdl2-image.

* gnu/packages/sdl.scm (ghc-sdl2-image): New variable.
---
 gnu/packages/sdl.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index 06f419f900..caa1d6d1c1 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -587,3 +587,28 @@ programming.")
     (description "This package provides Haskell bindings to
 @code{SDL2_mixer}.")
     (license bsd-3)))
+
+(define-public ghc-sdl2-image
+  (package
+    (name "ghc-sdl2-image")
+    (version "2.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/sdl2-image/"
+                           "sdl2-image-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1pr6dkg73cy9z0w54lrkj9c5bhxj56nl92lxikjy8kz6nyr455rr"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-sdl2" ,ghc-sdl2)
+       ("ghc-text" ,ghc-text)
+       ("sdl2-image" ,sdl2-image)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://hackage.haskell.org/package/sdl2-image")
+    (synopsis "Bindings to SDL2_image")
+    (description "This package provides Haskell bindings to
+@code{SDL2_image}.")
+    (license expat)))

From 86eec9cf5c564f8782d78c0b992dbca07d5d5c8d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 28 Sep 2018 11:30:55 +0200
Subject: [PATCH 459/909] gnu: raincat: Update to 1.2.1.

* gnu/packages/games.scm (raincat): Update to 1.2.1.
[arguments]: Ensure raincat can find freeglut libraries at runtime.
[inputs]: Replace ghc-sdl, ghc-sdl-image, and ghc-sdl-mixer with ghc-sdl2,
ghc-sdl2-image, and ghc-sdl2-mixer, respectively.
---
 gnu/packages/games.scm | 27 ++++++++++++++++++---------
 1 file changed, 18 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 1fab9fe34a..86d6973a9a 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -2122,27 +2122,36 @@ on the screen and keyboard to display letters.")
 (define-public raincat
   (package
     (name "raincat")
-    (version "1.2")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "http://hackage.haskell.org/package/Raincat/Raincat-"
-             version
-             ".tar.gz"))
+       (uri (string-append "http://hackage.haskell.org/package/Raincat/"
+                           "Raincat-" version ".tar.gz"))
        (sha256
         (base32
-         "1zyxkvjxkadwakg03xnjii1hx0gs45ap9rfkpi4kxipzxppq1klk"))))
+         "10y9zi22m6hf13c9h8zd9vg7mljpwbw0r3djb6r80bna701fdf6c"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'wrap-executable
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/raincat")
+                 `("LD_LIBRARY_PATH" ":" =
+                   (,(string-append (assoc-ref inputs "freeglut")
+                                    "/lib"))))
+               #t))))))
     (inputs
      `(("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
        ("ghc-random" ,ghc-random)
        ("ghc-glut" ,ghc-glut)
        ("freeglut" ,freeglut)
        ("ghc-opengl" ,ghc-opengl)
-       ("ghc-sdl" ,ghc-sdl)
-       ("ghc-sdl-image" ,ghc-sdl-image)
-       ("ghc-sdl-mixer" ,ghc-sdl-mixer)))
+       ("ghc-sdl2" ,ghc-sdl2)
+       ("ghc-sdl2-image" ,ghc-sdl2-image)
+       ("ghc-sdl2-mixer" ,ghc-sdl2-mixer)))
     (home-page "http://www.bysusanlin.com/raincat/")
     (synopsis "Puzzle game with a cat in lead role")
     (description "Project Raincat is a game developed by Carnegie Mellon

From 6306ce727186d2f8d2be5632a9b5d92982841e95 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 30 Sep 2018 10:49:00 +0200
Subject: [PATCH 460/909] gnu: git-annex: Update to 6.20180926.

* gnu/packages/version-control.scm (git-annex): Update to 6.20180926.
---
 gnu/packages/version-control.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index c8ad067ff1..cc892b9c62 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -8,7 +8,7 @@
 ;;; Copyright © 2014, 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
-;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016, 2017, 2018 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -2103,7 +2103,7 @@ directory full of HOWTOs.")
 (define-public git-annex
   (package
     (name "git-annex")
-    (version "6.20180807")
+    (version "6.20180926")
     (source
      (origin
        (method url-fetch)
@@ -2111,7 +2111,7 @@ directory full of HOWTOs.")
                            "git-annex/git-annex-" version ".tar.gz"))
        (sha256
         (base32
-         "1wkqh1y58m0z1mf2j33qhndpxcjwv8mbv384kdk17vn0lp9zas1s"))))
+         "1251rj8h63y30sfqk0zh670yhz14p256y59n3590pg015pf3575d"))))
     (build-system haskell-build-system)
     (arguments
      `(#:configure-flags

From 787231e9570779892b2eb2e79563be4cfacc9b9d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 30 Sep 2018 12:23:59 +0200
Subject: [PATCH 461/909] gnu: agda: Fix build.

* gnu/packages/agda.scm (agda)[inputs]: Remove ghc-monadplus; add
ghc-filemanip.
[arguments]: Replace configure phase.
---
 gnu/packages/agda.scm | 46 +++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 44 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm
index 418025bc37..6bb38aac4d 100644
--- a/gnu/packages/agda.scm
+++ b/gnu/packages/agda.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Alex ter Weele <alex.ter.weele@gmail.com>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -51,13 +52,13 @@
        ("ghc-edisoncore" ,ghc-edisoncore)
        ("ghc-edit-distance" ,ghc-edit-distance)
        ("ghc-equivalence" ,ghc-equivalence)
+       ("ghc-filemanip" ,ghc-filemanip)
        ("ghc-geniplate-mirror" ,ghc-geniplate-mirror)
        ("ghc-gitrev" ,ghc-gitrev)
        ("ghc-happy" ,ghc-happy)
        ("ghc-hashable" ,ghc-hashable)
        ("ghc-hashtables" ,ghc-hashtables)
        ("ghc-ieee754" ,ghc-ieee754)
-       ("ghc-monadplus" ,ghc-monadplus)
        ("ghc-murmur-hash" ,ghc-murmur-hash)
        ("ghc-uri-encode" ,ghc-uri-encode)
        ("ghc-parallel" ,ghc-parallel)
@@ -70,9 +71,50 @@
     (arguments
      `(#:modules ((guix build haskell-build-system)
                   (guix build utils)
-                  (srfi srfi-26))
+                  (srfi srfi-26)
+                  (ice-9 match))
        #:phases
        (modify-phases %standard-phases
+         ;; FIXME: This is a copy of the standard configure phase with a tiny
+         ;; difference: this package needs the -package-db flag to be passed
+         ;; to "runhaskell" in addition to the "configure" action, because
+         ;; Setup.hs depends on filemanip.  Without this option the Setup.hs
+         ;; file cannot be evaluated.  The haskell-build-system should be
+         ;; changed to pass "-package-db" to "runhaskell" in any case.
+         (replace 'configure
+           (lambda* (#:key outputs inputs tests? (configure-flags '())
+                     #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (input-dirs (match inputs
+                                  (((_ . dir) ...)
+                                   dir)
+                                  (_ '())))
+                    (ghc-path (getenv "GHC_PACKAGE_PATH"))
+                    (params (append `(,(string-append "--prefix=" out))
+                                    `(,(string-append "--libdir=" out "/lib"))
+                                    `(,(string-append "--bindir=" out "/bin"))
+                                    `(,(string-append
+                                        "--docdir=" out
+                                        "/share/doc/" ((@@ (guix build haskell-build-system)
+                                                           package-name-version) out)))
+                                    '("--libsubdir=$compiler/$pkg-$version")
+                                    '("--package-db=../package.conf.d")
+                                    '("--global")
+                                    `(,@(map
+                                         (cut string-append "--extra-include-dirs=" <>)
+                                         (search-path-as-list '("include") input-dirs)))
+                                    `(,@(map
+                                         (cut string-append "--extra-lib-dirs=" <>)
+                                         (search-path-as-list '("lib") input-dirs)))
+                                    (if tests?
+                                        '("--enable-tests")
+                                        '())
+                                    configure-flags)))
+               (unsetenv "GHC_PACKAGE_PATH")
+               (apply invoke "runhaskell" "-package-db=../package.conf.d"
+                      "Setup.hs" "configure" params)
+               (setenv "GHC_PACKAGE_PATH" ghc-path)
+               #t)))
          (add-after 'compile 'agda-compile
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))

From c95908bb030bd80de47a0ef9fc7f1dde0b68d3a8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 30 Sep 2018 13:14:39 +0200
Subject: [PATCH 462/909] gnu: ghc-indents: Fix build.

* gnu/packages/haskell.scm (ghc-indents)[arguments]: Disable tests.
[native-inputs]: Add ghc-tasty and ghc-tasty-hunit.
---
 gnu/packages/haskell.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 8076838309..0e2dfd8817 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -2804,9 +2804,14 @@ isn't available, portable implementations are used.")
                (base32
                 "1ly3v41jacc6lrsvg4j3m5a6zs90gr8dyif5m6bf34hj1k5cgg0n"))))
     (build-system haskell-build-system)
+    ;; This package needs an older version of tasty.
+    (arguments '(#:tests? #f))
     (inputs
      `(("ghc-parsec" ,ghc-parsec)
        ("ghc-concatenative" ,ghc-concatenative)))
+    (native-inputs
+     `(("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)))
     (home-page "http://patch-tag.com/r/salazar/indents")
     (synopsis "Indentation sensitive parser-combinators for parsec")
     (description

From f0bce3a758a6cc66552f326e570b571e0155814a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Sun, 30 Sep 2018 19:44:25 +0800
Subject: [PATCH 463/909] gnu: ghc-xmonad-contrib: Fix build.

* gnu/packages/wm.scm (ghc-xmonad-contrib)[inputs]: Add ghc-semigroups.
---
 gnu/packages/wm.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 4ec465f875..7c58770de7 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -563,6 +563,7 @@ Haskell, no knowledge of the language is required to install and use it.")
        ("ghc-random" ,ghc-random)
        ("ghc-utf8-string" ,ghc-utf8-string)
        ("ghc-extensible-exceptions" ,ghc-extensible-exceptions)
+       ("ghc-semigroups", ghc-semigroups)
        ("ghc-x11" ,ghc-x11)
        ("ghc-x11-xft" ,ghc-x11-xft)
        ("xmonad" ,xmonad)))

From eaa1f873e69c64e5d7f7535e95f6ae0be75c3ac9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Sun, 30 Sep 2018 20:05:55 +0800
Subject: [PATCH 464/909] gnu: shellcheck: Update to 0.5.0.

* gnu/packages/haskell.scm (shellcheck): Update to 0.5.0.
[source]: Use tarball from hackage.
[inputs]: Add ghc-aeson.  Remove ghc-json.
---
 gnu/packages/haskell.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0e2dfd8817..df0190d591 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8489,20 +8489,21 @@ generated SQL and optimize it for your backend.")
 (define-public shellcheck
   (package
     (name "shellcheck")
-    (version "0.4.6")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/koalaman/shellcheck/archive/"
-                           "v" version ".tar.gz"))
+       (uri (string-append
+             "https://hackage.haskell.org/package/ShellCheck/ShellCheck-"
+             version ".tar.gz"))
        (sha256
         (base32
-         "1qkd69lc34n3l23ss9rq1azvx49bfq4hi4bmaj76rgxybscxhg0w"))
+         "0z1hscbr11hwkq8k1v0vaa947hb9m6k4cm831jk1gpj8dxrk151b"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system haskell-build-system)
     (inputs
-     `(("ghc-quickcheck" ,ghc-quickcheck)
-       ("ghc-json" ,ghc-json)
+     `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-quickcheck" ,ghc-quickcheck)
        ("ghc-parsec" ,ghc-parsec)
        ("ghc-regex-tdfa" ,ghc-regex-tdfa)))
     (home-page "https://github.com/koalaman/shellcheck")

From 70fa5899af8a2270c29e40035e6258865a4f4461 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Sun, 30 Sep 2018 20:33:46 +0800
Subject: [PATCH 465/909] gnu: ghc-wave: Fix build.

* gnu/packages/haskell.scm (ghc-wave)[arguments]: Add a phase to relax
dependency constraints.
---
 gnu/packages/haskell.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index df0190d591..4a915142c1 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8338,6 +8338,14 @@ Rust syntax.  It is intended to be useful for two different purposes:
         (base32
           "03zycmwrchhqvi37fdvlzz2d1vl4hy0i8xyys1zznw38qfq0h2i5"))))
     (build-system haskell-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'update-constraints
+           (lambda _
+             (substitute* "wave.cabal"
+               (("temporary.* < 1\\.3")
+                "temporary >= 1.1 && < 1.4")))))))
     (inputs
      `(("ghc-cereal" ,ghc-cereal)
        ("ghc-data-default-class"

From 1abdefe573d4928ce495d0dbd877d68df776df9a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Sun, 30 Sep 2018 20:52:07 +0800
Subject: [PATCH 466/909] gnu: ghc-gnuplot: Fix build.

* gnu/packages/haskell.scm (ghc-gnuplot)[inputs]: Add ghc-semigroups.
---
 gnu/packages/haskell.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4a915142c1..2dff323fce 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8134,6 +8134,7 @@ helper functions for Lists, Maybes, Tuples, Functions.")
        ("ghc-utility-ht" ,ghc-utility-ht)
        ("ghc-data-accessor-transformers" ,ghc-data-accessor-transformers)
        ("ghc-data-accessor" ,ghc-data-accessor)
+       ("ghc-semigroups" ,ghc-semigroups)
        ("gnuplot" ,gnuplot)))
     (arguments
      `(#:phases

From 456d76eaf6583e2439ff6df19427779a2d62848c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 30 Sep 2018 23:10:27 +0200
Subject: [PATCH 467/909] gnu: ghc-aws: Fix build.

* gnu/packages/haskell.scm (ghc-aws)[inputs]: Add ghc-lifted-base.
---
 gnu/packages/haskell.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 2dff323fce..205d2348d4 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9585,6 +9585,7 @@ as well as a convenient Conduit module.")
        ("ghc-data-default" ,ghc-data-default)
        ("ghc-http-conduit" ,ghc-http-conduit)
        ("ghc-http-types" ,ghc-http-types)
+       ("ghc-lifted-base" ,ghc-lifted-base)
        ("ghc-monad-control" ,ghc-monad-control)
        ("ghc-network" ,ghc-network)
        ("ghc-old-locale" ,ghc-old-locale)

From 52891580e1c83235c2bf3a8297b05662c3bc14e9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sun, 30 Sep 2018 23:18:09 +0200
Subject: [PATCH 468/909] gnu: ghc-statistics: Fix build.

* gnu/packages/haskell.scm (ghc-statistics)[arguments]: Add cabal revision.
---
 gnu/packages/haskell.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 205d2348d4..a140985eba 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8999,6 +8999,11 @@ that are much lighter weight than IO-threads.")
         (base32
          "0y27gafkib0x0fn39qfn2rkgsfrm09ng35sbb5dwr7rclhnxz59l"))))
     (build-system haskell-build-system)
+    (arguments
+     '(#:cabal-revision
+       ("2" "1bx70yqkn62ii17fjv3pig4hklrzkqd09zj67zzjiyjzmn04fir3")
+       ;; Two tests fail: "Discrete CDF is OK" and "Quantile is CDF inverse".
+       #:tests? #f))
     (inputs
      `(("ghc-aeson" ,ghc-aeson)
        ("ghc-base-orphans" ,ghc-base-orphans)
@@ -9018,8 +9023,6 @@ that are much lighter weight than IO-threads.")
        ("ghc-test-framework" ,ghc-test-framework)
        ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
-    (arguments
-     `(#:tests? #f)) ; FIXME: Test-Suite `spec` fails.
     (home-page "https://github.com/bos/mwc-random")
     (synopsis "Haskell library of statistical types, data, and functions")
     (description "This library provides a number of common functions

From b2bf43b22aad83c3d64391339f7c5f66c6d58789 Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 1 Oct 2018 08:30:14 -0400
Subject: [PATCH 469/909] gnu: Add r-pscl.

* gnu/packages/cran.scm (r-pscl): New variable.
---
 gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 58e9ad09c7..deb81f2430 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5895,3 +5895,29 @@ hemoglobin to reticulocytes (OFF-score), as well as example data.")
 based on entropy estimates from k-nearest neighbors distances and algorithms
 for the reconstruction of gene regulatory networks.")
     (license license:agpl3+)))
+
+(define-public r-pscl
+  (package
+    (name "r-pscl")
+    (version "1.5.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pscl" version))
+       (sha256
+        (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)))
+    (home-page "https://github.com/atahk/pscl/")
+    (synopsis "Political science computational laboratory")
+    (description
+     "The @code{pscl} is an R package providing classes and methods for:
+@enumerate
+@item Bayesian analysis of roll call data (item-response models);
+@item elementary Bayesian statistics;
+@item maximum likelihood estimation of zero-inflated and hurdle models for count
+data;
+@item utility functions.
+@end enumerate")
+    (license license:gpl2)))

From e710d1a4ffe0131d9a59eba1d1ad615f8448f50d Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 1 Oct 2018 08:30:37 -0400
Subject: [PATCH 470/909] gnu: Add r-accelmissing.

* gnu/packages/cran.scm (r-accelmissing): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index deb81f2430..a38c907cd5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5921,3 +5921,28 @@ data;
 @item utility functions.
 @end enumerate")
     (license license:gpl2)))
+
+(define-public r-accelmissing
+  (package
+    (name "r-accelmissing")
+    (version "1.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "accelmissing" version))
+       (sha256
+        (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mice" ,r-mice)
+       ("r-pscl" ,r-pscl)))
+    (home-page "https://cran.r-project.org/web/packages/accelmissing/")
+    (synopsis "Missing value imputation for accelerometer data")
+    (description
+     "This package provides a statistical method to impute the missing values in
+accelerometer data.  The methodology includes both parametric and
+semi-parametric multiple imputations under the zero-inflated Poisson lognormal
+model.  It also provides multiple functions to preprocess the accelerometer data
+previous to the missing data imputation.  These include detecting the wearing
+and the non-wearing time, selecting valid days and subjects, and creating plots.")
+    (license license:gpl2+)))

From 5ec20676d75a25c9163c6067d2e3eece84d08c2b Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 1 Oct 2018 14:54:46 +0200
Subject: [PATCH 471/909] gnu: wine-staging: Update to 3.17.

* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.17.
* gnu/packages/wine.scm (wine-staging): Update to 3.17.
---
 gnu/packages/wine.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index 782776606d..68839038b7 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -225,7 +225,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
    (name "wine-staging-patchset-data")
-   (version "3.16")
+   (version "3.17")
    (source
     (origin
       (method git-fetch)
@@ -235,7 +235,7 @@ integrate Windows applications into your desktop.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "0c1bs9qpxlvld6jkwjri2v8jaixxn1r5b0m9r5hnkfrnpl7z7cfv"))))
+        "1ds9q90xjg59ikic98kqkhmijnqx4yplvwsm6rav4mx72yci7d4w"))))
    (build-system trivial-build-system)
    (native-inputs
     `(("bash" ,bash)
@@ -281,7 +281,7 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0g55l41apiwgblfk9ihzd96003gd32w5ng79f96hmiwhyzwbqhxd"))))
+                "08fcziadw40153a9rv630m7iz6ipfzylms5y191z4sj2vvhy5vac"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("gtk+" ,gtk+)
               ("libva" ,libva)

From f359b115c74c9c5fdf482528a0480ed40f5a2446 Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 1 Oct 2018 08:49:21 -0400
Subject: [PATCH 472/909] gnu: Add r-mhsmm.

* gnu/packages/cran.scm (r-mhsmm): New variable.
---
 gnu/packages/cran.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a38c907cd5..82984548a2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5946,3 +5946,26 @@ model.  It also provides multiple functions to preprocess the accelerometer data
 previous to the missing data imputation.  These include detecting the wearing
 and the non-wearing time, selecting valid days and subjects, and creating plots.")
     (license license:gpl2+)))
+
+(define-public r-mhsmm
+  (package
+    (name "r-mhsmm")
+    (version "0.4.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "mhsmm" version))
+       (sha256
+        (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
+    (home-page "https://github.com/jaredo/mhsmm/")
+    (synopsis "Inference for hidden Markov and semi-Markov models")
+    (description
+     "The @code{r-mhsmm} package implements estimation and prediction methods for
+hidden Markov and semi-Markov models for multiple observation sequences.  Such
+techniques are of interest when observed data is thought to be dependent on some
+unobserved (or hidden) state.  Also, this package is suitable for equidistant
+time series data, with multivariate and/or missing data.  Allows user defined
+emission distributions.")
+    (license license:gpl2+)))

From 16c5285af40f66614cccfe3f916cfe78e49bae16 Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 1 Oct 2018 08:52:01 -0400
Subject: [PATCH 473/909] gnu: Add r-nleqslv.

* gnu/packages/cran.scm (r-nleqslv): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 82984548a2..b06d22bd51 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5969,3 +5969,25 @@ unobserved (or hidden) state.  Also, this package is suitable for equidistant
 time series data, with multivariate and/or missing data.  Allows user defined
 emission distributions.")
     (license license:gpl2+)))
+
+(define-public r-nleqslv
+  (package
+    (name "r-nleqslv")
+    (version "3.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "nleqslv" version))
+       (sha256
+        (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
+    (build-system r-build-system)
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/nleqslv/")
+    (synopsis "Solve systems of nonlinear equations")
+    (description
+     "The @code{r-nleqslv} package solves a system of nonlinear equations using a
+Broyden or a Newton method with a choice of global strategies such as line
+search and trust region.  There are options for using a numerical or user
+supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
+singular or ill-conditioned Jacobian.")
+    (license license:gpl2+)))

From 63ec2c505a29ee8c7c6a7633b054edc41dbc95fa Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 1 Oct 2018 08:52:34 -0400
Subject: [PATCH 474/909] gnu: Add r-physicalactivity.

* gnu/packages/cran.scm (r-physicalactivity): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b06d22bd51..932d7cb414 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -5991,3 +5991,36 @@ search and trust region.  There are options for using a numerical or user
 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
 singular or ill-conditioned Jacobian.")
     (license license:gpl2+)))
+
+(define-public r-physicalactivity
+  (package
+    (name "r-physicalactivity")
+    (version "0.2-2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "PhysicalActivity" version))
+       (sha256
+        (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
+    (properties
+     `((upstream-name . "PhysicalActivity")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
+    (synopsis "Procesing accelerometer data for physical activity measurement")
+    (description
+     "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
+for classification of monitor wear and nonwear time intervals in accelerometer
+data collected to assess physical activity.  The package also contains functions
+for making plots of accelerometer data and obtaining the summary of various
+information including daily monitor wear time and the mean monitor wear time
+during valid days.  The revised package version 0.2-1 improved the functions
+regarding speed, robustness and add better support for time zones and daylight
+saving.  In addition, several functions were added:
+@enumerate
+@item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
+@item the @code{markPAI} can categorize physical activity intensity level based
+on user-defined cut-points of accelerometer counts.
+@end enumerate
+  It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
+@code{queryActigraph} functions.")
+    (license license:gpl3+)))

From f95d45425152bda85950d2b8f9ead50bdce2e2cc Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 1 Oct 2018 08:53:00 -0400
Subject: [PATCH 475/909] gnu: Add r-acc.

* gnu/packages/cran.scm (r-acc): New variable.
---
 gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 932d7cb414..186a52a1f1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6024,3 +6024,36 @@ on user-defined cut-points of accelerometer counts.
   It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
 @code{queryActigraph} functions.")
     (license license:gpl3+)))
+
+(define-public r-acc
+  (package
+    (name "r-acc")
+    (version "1.3.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "acc" version))
+       (sha256
+        (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-circlize" ,r-circlize)
+       ("r-dbi" ,r-dbi)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iterators" ,r-iterators)
+       ("r-mhsmm" ,r-mhsmm)
+       ("r-nleqslv" ,r-nleqslv)
+       ("r-physicalactivity" ,r-physicalactivity)
+       ("r-plyr" ,r-plyr)
+       ("r-r-utils" ,r-r-utils)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://cran.r-project.org/web/packages/acc/")
+    (synopsis "Exploring accelerometer data")
+    (description
+     "This package processes accelerometer data from uni-axial and tri-axial devices
+and generates data summaries.  Also, includes functions to plot, analyze, and
+simulate accelerometer data.")
+    (license license:gpl2+)))

From 08cbd4f3b9ce0bc6aa052b22795a3a9b9f09b04c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 22:58:19 +0200
Subject: [PATCH 476/909] gnu: recode: Update to 3.7.1.

* gnu/packages/textutils.scm (recode): Update to 3.7.1.
---
 gnu/packages/textutils.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index ce34423713..7e26bdcf63 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -84,7 +84,7 @@ to DOS format and vice versa.")
 (define-public recode
   (package
     (name "recode")
-    (version "3.7")
+    (version "3.7.1")
     (source
      (origin
        (method url-fetch)
@@ -92,7 +92,7 @@ to DOS format and vice versa.")
                            "download/v" version "/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0r4yhf7i7zp2nl2apyzz7r3i2in12n385hmr8zcfr18ly0ly530q"))
+         "0215hfj0rhlh0grg91qfx75pp6z09bpv8211qdxqihniw7y9a4fs"))
        (modules '((guix build utils)))
        (snippet '(begin
                    (delete-file "tests/Recode.c")

From 538b71a967ed056e39318839f5c36ff201bd9320 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 22:12:45 +0200
Subject: [PATCH 477/909] gnu: perl-socket6: Update to 0.29.

* gnu/packages/networking.scm (perl-socket6): Update to 0.29.
---
 gnu/packages/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 0d6de040e5..e3486ffadc 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -927,7 +927,7 @@ private (reserved).")
 (define-public perl-socket6
  (package
   (name "perl-socket6")
-  (version "0.28")
+  (version "0.29")
   (source
     (origin
       (method url-fetch)
@@ -937,7 +937,7 @@ private (reserved).")
              ".tar.gz"))
       (sha256
         (base32
-          "11j5jzqbzmwlws9zals43ry2f1nw9qy6im7yhn9ck5rikywrmm5z"))))
+          "054izici8klfxs8hr5rljib28plijpsfymy99xbzdp047bx1b2a6"))))
   (build-system perl-build-system)
   (arguments
    `(#:phases

From 6c6c03fa00db33703002fa8845716f50f649d201 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 22:08:46 +0200
Subject: [PATCH 478/909] gnu: re2c: Update to 1.1.1.

* gnu/packages/re2c.scm (re2c): Update to 1.1.1.
---
 gnu/packages/re2c.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/re2c.scm b/gnu/packages/re2c.scm
index 2a35aa0cdb..e9668cba26 100644
--- a/gnu/packages/re2c.scm
+++ b/gnu/packages/re2c.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Sergei Trofimovich <slyfox@inbox.ru>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,7 +26,7 @@
 (define-public re2c
   (package
     (name "re2c")
-    (version "1.0.3")
+    (version "1.1.1")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/skvadrik/" name
@@ -33,7 +34,7 @@
                                  name "-" version ".tar.gz"))
              (sha256
               (base32
-               "0lnbj15hhgi3r40ipskmg178m18d8n5nph78sci6lprk7zgf0mng"))))
+               "1ksifjn18v6nra935dpqllmvkqgcdsggfjgmj77282x0gqrrfrc5"))))
     (build-system gnu-build-system)
     (home-page "http://re2c.org/")
     (synopsis "Lexer generator for C/C++")

From f8e710684e5c3f866413dff825ba17bdffceac5d Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Fri, 13 Jul 2018 20:39:46 +0100
Subject: [PATCH 479/909] services: Add Gitolite.

* gnu/services/version-control.scm (<gitolite-configuration>,
<gitolite-rc-file>): New record types.
(gitolite-accounts, gitolite-activation): New procedures.
(gitolite-service-type): New variables.
* gnu/tests/version-control.scm (%gitolite-test-admin-keypair, %gitolite-os,
%test-gitolite): New variables.
(run-gitolite-test): New procedure.
* doc/guix.texi (Version Control): Document the gitolite service.
---
 doc/guix.texi                    |  94 ++++++++++++++++
 gnu/services/version-control.scm | 180 ++++++++++++++++++++++++++++++-
 gnu/tests/version-control.scm    | 114 +++++++++++++++++++-
 3 files changed, 386 insertions(+), 2 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index e1046eb512..94bb0ec4e1 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -21028,6 +21028,100 @@ could instantiate a cgit service like this:
           (cgitrc "")))
 @end example
 
+@subsubheading Gitolite Service
+
+@cindex Gitolite service
+@cindex Git, hosting
+@uref{http://gitolite.com/gitolite/, Gitolite} is a tool for hosting Git
+repositories on a central server.
+
+Gitolite can handle multiple repositories and users, and supports flexible
+configuration of the permissions for the users on the repositories.
+
+The following example will configure Gitolite using the default @code{git}
+user, and the provided SSH public key.
+
+@example
+(service gitolite-service-type
+         (gitolite-configuration
+           (admin-pubkey (plain-file
+                           "yourname.pub"
+                           "ssh-rsa AAAA... guix@@example.com"))))
+@end example
+
+Gitolite is configured through a special admin repository which you can clone,
+for example, if you setup Gitolite on @code{example.com}, you would run the
+following command to clone the admin repository.
+
+@example
+git clone git@@example.com:gitolite-admin
+@end example
+
+When the Gitolite service is activated, the provided @code{admin-pubkey} will
+be inserted in to the @file{keydir} directory in the gitolite-admin
+repository.  If this results in a change in the repository, it will be
+committed using the message ``gitolite setup by GNU Guix''.
+
+@deftp {Data Type} gitolite-configuration
+Data type representing the configuration for @code{gitolite-service-type}.
+
+@table @asis
+@item @code{package} (default: @var{gitolite})
+Gitolite package to use.
+
+@item @code{user} (default: @var{git})
+User to use for Gitolite.  This will be user that you use when accessing
+Gitolite over SSH.
+
+@item @code{group} (default: @var{git})
+Group to use for Gitolite.
+
+@item @code{home-directory} (default: @var{"/var/lib/gitolite"})
+Directory in which to store the Gitolite configuration and repositories.
+
+@item @code{rc-file} (default: @var{(gitolite-rc-file)})
+A ``file-like'' object (@pxref{G-Expressions, file-like objects}),
+representing the configuration for Gitolite.
+
+@item @code{admin-pubkey} (default: @var{#f})
+A ``file-like'' object (@pxref{G-Expressions, file-like objects}) used to
+setup Gitolite.  This will be inserted in to the @file{keydir} directory
+within the gitolite-admin repository.
+
+To specify the SSH key as a string, use the @code{plain-file} function.
+
+@example
+(plain-file "yourname.pub" "ssh-rsa AAAA... guix@@example.com")
+@end example
+
+@end table
+@end deftp
+
+@deftp {Data Type} gitolite-rc-file
+Data type representing the Gitolite RC file.
+
+@table @asis
+@item @code{umask} (default: @code{#o0077})
+This controls the permissions Gitolite sets on the repositories and their
+contents.
+
+A value like @code{#o0027} will give read access to the group used by Gitolite
+(by default: @code{git}). This is necessary when using Gitolite with software
+like cgit or gitweb.
+
+@item @code{git-config-keys} (default: @code{""})
+Gitolite allows you to set git config values using the "config" keyword. This
+setting allows control over the config keys to accept.
+
+@item @code{roles} (default: @code{'(("READERS" . 1) ("WRITERS" . ))})
+Set the role names allowed to be used by users running the perms command.
+
+@item @code{enable} (default: @code{'("help" "desc" "info" "perms" "writable" "ssh-authkeys" "git-config" "daemon" "gitweb")})
+This setting controls the commands and features to enable within Gitolite.
+
+@end table
+@end deftp
+
 
 @node Game Services
 @subsubsection Game Services
diff --git a/gnu/services/version-control.scm b/gnu/services/version-control.scm
index 58274c8bee..13669925ab 100644
--- a/gnu/services/version-control.scm
+++ b/gnu/services/version-control.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,6 +33,7 @@
   #:use-module (guix store)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26)
+  #:use-module (ice-9 format)
   #:use-module (ice-9 match)
   #:export (git-daemon-service
             git-daemon-service-type
@@ -40,7 +42,23 @@
 
             git-http-configuration
             git-http-configuration?
-            git-http-nginx-location-configuration))
+            git-http-nginx-location-configuration
+
+            <gitolite-configuration>
+            gitolite-configuration
+            gitolite-configuration-package
+            gitolite-configuration-user
+            gitolite-configuration-rc-file
+            gitolite-configuration-admin-pubkey
+
+            <gitolite-rc-file>
+            gitolite-rc-file
+            gitolite-rc-file-umask
+            gitolite-rc-file-git-config-keys
+            gitolite-rc-file-roles
+            gitolite-rc-file-enable
+
+            gitolite-service-type))
 
 ;;; Commentary:
 ;;;
@@ -197,3 +215,163 @@ access to exported repositories under @file{/srv/git}."
             "")
         (list "fastcgi_param GIT_PROJECT_ROOT " git-root ";")
         "fastcgi_param PATH_INFO $1;"))))))
+
+
+;;;
+;;; Gitolite
+;;;
+
+(define-record-type* <gitolite-rc-file>
+  gitolite-rc-file make-gitolite-rc-file
+  gitolite-rc-file?
+  (umask           gitolite-rc-file-umask
+                   (default #o0077))
+  (git-config-keys gitolite-rc-file-git-config-keys
+                   (default ""))
+  (roles           gitolite-rc-file-roles
+                   (default '(("READERS" . 1)
+                              ("WRITERS" . 1))))
+  (enable          gitolite-rc-file-enable
+                   (default '("help"
+                              "desc"
+                              "info"
+                              "perms"
+                              "writable"
+                              "ssh-authkeys"
+                              "git-config"
+                              "daemon"
+                              "gitweb"))))
+
+(define-gexp-compiler (gitolite-rc-file-compiler
+                       (file <gitolite-rc-file>) system target)
+  (match file
+    (($ <gitolite-rc-file> umask git-config-keys roles enable)
+     (apply text-file* "gitolite.rc"
+      `("%RC = (\n"
+        "    UMASK => " ,(format #f "~4,'0o" umask) ",\n"
+        "    GIT_CONFIG_KEYS => '" ,git-config-keys "',\n"
+        "    ROLES => {\n"
+        ,@(map (match-lambda
+                 ((role . value)
+                  (simple-format #f "        ~A => ~A,\n" role value)))
+               roles)
+        "    },\n"
+        "\n"
+        "    ENABLE => [\n"
+        ,@(map (lambda (value)
+                 (simple-format #f "        '~A',\n" value))
+               enable)
+        "    ],\n"
+        ");\n"
+        "\n"
+        "1;\n")))))
+
+(define-record-type* <gitolite-configuration>
+  gitolite-configuration make-gitolite-configuration
+  gitolite-configuration?
+  (package        gitolite-configuration-package
+                  (default gitolite))
+  (user           gitolite-configuration-user
+                  (default "git"))
+  (group          gitolite-configuration-group
+                  (default "git"))
+  (home-directory gitolite-configuration-home-directory
+                  (default "/var/lib/gitolite"))
+  (rc-file        gitolite-configuration-rc-file
+                  (default (gitolite-rc-file)))
+  (admin-pubkey   gitolite-configuration-admin-pubkey))
+
+(define gitolite-accounts
+  (match-lambda
+    (($ <gitolite-configuration> package user group home-directory
+                                 rc-file admin-pubkey)
+     ;; User group and account to run Gitolite.
+     (list (user-group (name user) (system? #t))
+           (user-account
+            (name user)
+            (group group)
+            (system? #t)
+            (comment "Gitolite user")
+            (home-directory home-directory))))))
+
+(define gitolite-activation
+  (match-lambda
+    (($ <gitolite-configuration> package user group home
+                                 rc-file admin-pubkey)
+     #~(begin
+         (use-modules (ice-9 match)
+                      (guix build utils))
+
+         (let* ((user-info (getpwnam #$user))
+                (admin-pubkey #$admin-pubkey)
+                (pubkey-file (string-append
+                              #$home "/"
+                              (basename
+                               (strip-store-file-name admin-pubkey)))))
+
+           (simple-format #t "guix: gitolite: installing ~A\n" #$rc-file)
+           (copy-file #$rc-file #$(string-append home "/.gitolite.rc"))
+
+           ;; The key must be writable, so copy it from the store
+           (copy-file admin-pubkey pubkey-file)
+
+           (chmod pubkey-file #o500)
+           (chown pubkey-file
+                  (passwd:uid user-info)
+                  (passwd:gid user-info))
+
+           ;; Set the git configuration, to avoid gitolite trying to use
+           ;; the hostname command, as the network might not be up yet
+           (with-output-to-file #$(string-append home "/.gitconfig")
+             (lambda ()
+               (display "[user]
+        name = GNU Guix
+        email = guix@localhost
+")))
+           ;; Run Gitolite setup, as this updates the hooks and include the
+           ;; admin pubkey if specified. The admin pubkey is required for
+           ;; initial setup, and will replace the previous key if run after
+           ;; initial setup
+           (match (primitive-fork)
+             (0
+              ;; Exit with a non-zero status code if an exception is thrown.
+              (dynamic-wind
+                (const #t)
+                (lambda ()
+                  (setenv "HOME" (passwd:dir user-info))
+                  (setenv "USER" #$user)
+                  (setgid (passwd:gid user-info))
+                  (setuid (passwd:uid user-info))
+                  (primitive-exit
+                   (system* #$(file-append package "/bin/gitolite")
+                            "setup"
+                            "-m" "gitolite setup by GNU Guix"
+                            "-pk" pubkey-file)))
+                (lambda ()
+                  (primitive-exit 1))))
+             (pid (waitpid pid)))
+
+           (when (file-exists? pubkey-file)
+             (delete-file pubkey-file)))))))
+
+(define gitolite-service-type
+  (service-type
+   (name 'gitolite)
+   (extensions
+    (list (service-extension activation-service-type
+                             gitolite-activation)
+          (service-extension account-service-type
+                             gitolite-accounts)
+          (service-extension profile-service-type
+                             ;; The Gitolite package in Guix uses
+                             ;; gitolite-shell in the authorized_keys file, so
+                             ;; gitolite-shell needs to be on the PATH for
+                             ;; gitolite to work.
+                             (lambda (config)
+                               (list
+                                (gitolite-configuration-package config))))))
+   (description
+    "Setup @command{gitolite}, a Git hosting tool providing access over SSH..
+By default, the @code{git} user is used, but this is configurable.
+Additionally, Gitolite can integrate with with tools like gitweb or cgit to
+provide a web interface to view selected repositories.")))
diff --git a/gnu/tests/version-control.scm b/gnu/tests/version-control.scm
index 3b935a1b48..4409b8a12b 100644
--- a/gnu/tests/version-control.scm
+++ b/gnu/tests/version-control.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2017, 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,14 +28,17 @@
   #:use-module (gnu services)
   #:use-module (gnu services version-control)
   #:use-module (gnu services cgit)
+  #:use-module (gnu services ssh)
   #:use-module (gnu services web)
   #:use-module (gnu services networking)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages ssh)
   #:use-module (guix gexp)
   #:use-module (guix store)
   #:use-module (guix modules)
   #:export (%test-cgit
-            %test-git-http))
+            %test-git-http
+            %test-gitolite))
 
 (define README-contents
   "Hello!  This is what goes inside the 'README' file.")
@@ -300,3 +304,111 @@ HTTP-PORT."
    (name "git-http")
    (description "Connect to a running Git HTTP server.")
    (value (run-git-http-test))))
+
+
+;;;
+;;; Gitolite.
+;;;
+
+(define %gitolite-test-admin-keypair
+  (computed-file
+   "gitolite-test-admin-keypair"
+   (with-imported-modules (source-module-closure
+                           '((guix build utils)))
+     #~(begin
+         (use-modules (ice-9 match) (srfi srfi-26)
+                      (guix build utils))
+
+         (mkdir #$output)
+         (invoke #$(file-append openssh "/bin/ssh-keygen")
+                 "-f" (string-append #$output "/test-admin")
+                 "-t" "rsa"
+                 "-q"
+                 "-N" "")))))
+
+(define %gitolite-os
+  (simple-operating-system
+   (dhcp-client-service)
+   (service openssh-service-type)
+   (service gitolite-service-type
+            (gitolite-configuration
+             (admin-pubkey
+              (file-append %gitolite-test-admin-keypair "/test-admin.pub"))))))
+
+(define (run-gitolite-test)
+  (define os
+    (marionette-operating-system
+     %gitolite-os
+     #:imported-modules '((gnu services herd)
+                          (guix combinators))))
+
+  (define vm
+    (virtual-machine
+     (operating-system os)
+     (port-forwardings `((2222 . 22)))))
+
+  (define test
+    (with-imported-modules '((gnu build marionette)
+                             (guix build utils))
+      #~(begin
+          (use-modules (srfi srfi-64)
+                       (rnrs io ports)
+                       (gnu build marionette)
+                       (guix build utils))
+
+          (define marionette
+            (make-marionette (list #$vm)))
+
+          (mkdir #$output)
+          (chdir #$output)
+
+          (test-begin "gitolite")
+
+          ;; Wait for sshd to be up and running.
+          (test-assert "service running"
+            (marionette-eval
+             '(begin
+                (use-modules (gnu services herd))
+                (start-service 'ssh-daemon))
+             marionette))
+
+          (display #$%gitolite-test-admin-keypair)
+
+          (setenv "GIT_SSH_VARIANT" "ssh")
+          (setenv "GIT_SSH_COMMAND"
+                  (string-join
+                   '(#$(file-append openssh "/bin/ssh")
+                     "-i" #$(file-append %gitolite-test-admin-keypair
+                                         "/test-admin")
+                     "-o" "UserKnownHostsFile=/dev/null"
+                     "-o" "StrictHostKeyChecking=no")))
+
+          (test-assert "cloning the admin repository"
+            (invoke #$(file-append git "/bin/git")
+                    "clone" "-v"
+                    "ssh://git@localhost:2222/gitolite-admin"
+                    "/tmp/clone"))
+
+          (test-assert "admin key exists"
+            (file-exists? "/tmp/clone/keydir/test-admin.pub"))
+
+          (with-directory-excursion "/tmp/clone"
+            (invoke #$(file-append git "/bin/git")
+                    "-c" "user.name=Guix" "-c" "user.email=guix"
+                    "commit"
+                    "-m" "Test commit"
+                    "--allow-empty")
+
+            (test-assert "pushing, and the associated hooks"
+              (invoke #$(file-append git "/bin/git") "push")))
+
+          (test-end)
+          (exit (= (test-runner-fail-count (test-runner-current)) 0)))))
+
+  (gexp->derivation "gitolite" test))
+
+(define %test-gitolite
+  (system-test
+   (name "gitolite")
+   (description "Clone the Gitolite admin repository.")
+   (value (run-gitolite-test))))

From 75bb6e46eac90c95e910986ad8ae32927e879052 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Tue, 2 Oct 2018 13:19:44 +0200
Subject: [PATCH 480/909] gnu: cuirass: Update to fe2b73c.

* gnu/packages/ci.scm (cuirass): Update to fe2b73c.
---
 gnu/packages/ci.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index 067a288004..1cac8b9fb4 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -186,8 +186,8 @@ their dependencies.")
       (license l:gpl3+))))
 
 (define-public cuirass
-  (let ((commit "8d40c49170971ad7bbf8b97336934dbb3d949fc1")
-        (revision "19"))
+  (let ((commit "fe2b73c2353d106431ed0659345391f14ed64600")
+        (revision "20"))
     (package
       (name "cuirass")
       (version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -199,7 +199,7 @@ their dependencies.")
                 (file-name (string-append name "-" version))
                 (sha256
                  (base32
-                  "0xxcapf9ag3zx6131v128vhin5m2j3w2gjbjbpdwr0qkaysh0gvf"))))
+                  "00ldbig2p14qpwrl2i2hnhb9idgbbf0kqnlh4n79rmz96blm7463"))))
       (build-system gnu-build-system)
       (arguments
        '(#:modules ((guix build utils)

From f671c59555749161a5960a4c5c373297b60e4be8 Mon Sep 17 00:00:00 2001
From: Simon Josefsson <simon@josefsson.org>
Date: Mon, 1 Oct 2018 12:45:59 +0200
Subject: [PATCH 481/909] doc: Add static network example.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* doc/guix.texi (Networking Services): Add example for static-networking-service.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 doc/guix.texi | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/doc/guix.texi b/doc/guix.texi
index 94bb0ec4e1..3c116fc0be 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -11614,6 +11614,14 @@ This procedure can be called several times, one for each network
 interface of interest.  Behind the scenes what it does is extend
 @code{static-networking-service-type} with additional network interfaces
 to handle.
+
+For example:
+
+@example
+(static-networking-service "eno1" "192.168.1.82"
+                           #:gateway "192.168.1.2"
+                           #:name-servers '("192.168.1.2"))
+@end example
 @end deffn
 
 @cindex wicd

From 1df4abc7dcf03f0655fc2fa26de7a6c91bac8b4e Mon Sep 17 00:00:00 2001
From: Timo Eisenmann <eisenmann@fn.de>
Date: Mon, 1 Oct 2018 18:10:35 +0200
Subject: [PATCH 482/909] gnu: enlightenment: Fix keyboard switching
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/enlightenment.scm (enlightenment)[inputs]: Add 'setxkbmap'
[arguments]: Set absolute file name to 'setxkbmap'

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/enlightenment.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index c7812e8874..c0335016f8 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -269,6 +269,7 @@ Libraries with some extra bells and whistles.")
          (add-before 'configure 'set-system-actions
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((xkeyboard (assoc-ref inputs "xkeyboard-config"))
+                   (setxkbmap (assoc-ref inputs "setxkbmap"))
                    (utils     (assoc-ref inputs "util-linux"))
                    (libc      (assoc-ref inputs "libc")))
                ;; We need to patch the path to 'base.lst' to be able
@@ -278,6 +279,9 @@ Libraries with some extra bells and whistles.")
                  (("/usr/share/X11/xkb/rules/xorg.lst")
                   (string-append xkeyboard
                                  "/share/X11/xkb/rules/base.lst")))
+               (substitute* "src/bin/e_xkb.c"
+                 (("\"setxkbmap \"")
+                  (string-append "\"" setxkbmap "/bin/setxkbmap \"")))
                (substitute* (list "src/bin/e_intl.c"
                                   "src/modules/conf_intl/e_int_config_intl.c"
                                   "src/modules/wizard/page_010.c")
@@ -305,6 +309,7 @@ Libraries with some extra bells and whistles.")
        ("libxcb" ,libxcb)
        ("libxext" ,libxext)
        ("linux-pam" ,linux-pam)
+       ("setxkbmap" ,setxkbmap)
        ("xcb-util-keysyms" ,xcb-util-keysyms)
        ("xkeyboard-config" ,xkeyboard-config)))
     (home-page "https://www.enlightenment.org/about-enlightenment")

From a7b751965f8420c871ae24aee25f1eb7a217e608 Mon Sep 17 00:00:00 2001
From: Andy Patterson <ajpatter@uwaterloo.ca>
Date: Tue, 2 Oct 2018 04:57:31 -0400
Subject: [PATCH 483/909] build-system/asdf: Properly handle dependency
 specification casing.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* guix/build/lisp-utils.scm (normalize-dependency): Modify match
clauses to match the upper-case symbols that lisp produces.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 guix/build/lisp-utils.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/guix/build/lisp-utils.scm b/guix/build/lisp-utils.scm
index 6470cfec97..97bc6197a3 100644
--- a/guix/build/lisp-utils.scm
+++ b/guix/build/lisp-utils.scm
@@ -84,11 +84,12 @@
 (define (normalize-dependency dependency)
   "Normalize the name of DEPENDENCY.  Handles dependency definitions of the
 dependency-def form described by
-<https://common-lisp.net/project/asdf/asdf.html#The-defsystem-grammar>."
+<https://common-lisp.net/project/asdf/asdf.html#The-defsystem-grammar>.
+Assume that any symbols in DEPENDENCY will be in upper-case."
   (match dependency
-    ((':version name rest ...)
+    ((':VERSION name rest ...)
      `(:version ,(normalize-string name) ,@rest))
-    ((':feature feature-specification dependency-specification)
+    ((':FEATURE feature-specification dependency-specification)
      `(:feature
        ,feature-specification
        ,(normalize-dependency dependency-specification)))

From b0f43001195c69f730b49b0bf9de516edd53baed Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sun, 30 Sep 2018 12:59:01 -0400
Subject: [PATCH 484/909] gnu: Audacity: Use glib-or-gtk-build-system instead
 of a wrapper.

* gnu/packages/audio.scm (audacity)[build-system]: Use glib-or-gtk-build-system.
[arguments]: Remove the 'wrap-program' phase. Set #:out-of-source #f.
---
 gnu/packages/audio.scm | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 4465872732..8f100ce7a3 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -321,7 +321,7 @@ engineers, musicians, soundtrack editors and composers.")
               ;; "sbsms"
               ))
            #t))))
-    (build-system gnu-build-system)
+    (build-system glib-or-gtk-build-system)
     (inputs
      `(("wxwidgets" ,wxwidgets)
        ("gtk+" ,gtk+)
@@ -410,16 +410,12 @@ engineers, musicians, soundtrack editors and composers.")
                (("../lib-src/portmidi/porttime/porttime.h") "porttime.h"))
              (substitute* "src/prefs/MidiIOPrefs.cpp"
                (("../../lib-src/portmidi/pm_common/portmidi.h") "portmidi.h"))
-             #t))
-         (add-after 'install 'wrap-program
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (wrap-program (string-append (assoc-ref outputs "out")
-                                          "/bin/audacity")
-               ;; For GtkFileChooserDialog.
-               `("GSETTINGS_SCHEMA_DIR" =
-                 (,(string-append (assoc-ref inputs "gtk+")
-                                  "/share/glib-2.0/schemas"))))
              #t)))
+       ;; The translation Makefile generation is performed improperly for
+       ;; out-of-tree builds.
+       ;; XXX This can be removed if the glib-or-gkt-build-system
+       ;; switches to #:out-of-source? #t. See <https://bugs.gnu.org/32887>.
+       #:out-of-source? #f
        ;; The test suite is not "well exercised" according to the developers,
        ;; and fails with various errors.  See
        ;; <http://sourceforge.net/p/audacity/mailman/message/33524292/>.

From 994bccd9443032141accede0e403cbfb62f6c63e Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 28 Sep 2018 23:30:55 -0400
Subject: [PATCH 485/909] gnu: LibreOffice: Fix "File > Open" crash on foreign
 distros.

Fixes <https://bugs.gnu.org/30642>.

* gnu/packages/libreoffice.scm (libreoffice)[build-system]: Use
glib-or-gtk-build-system.
[arguments]: Set '#:out-of-source #f'.
---
 gnu/packages/libreoffice.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 68b4e265f3..881cf2008d 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -28,6 +28,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages libreoffice)
+  #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (guix download)
@@ -939,7 +940,7 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
          "149ziasibplihfxlzafzcm4737ns30hg9175967b43c81yv5f335"))
        (patches (search-patches "libreoffice-icu.patch"
                                 "libreoffice-glm.patch"))))
-    (build-system gnu-build-system)
+    (build-system glib-or-gtk-build-system)
     (native-inputs
      `(("bison" ,bison)
        ("cppunit" ,cppunit-1.14)
@@ -1017,6 +1018,9 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
     (arguments
      `(#:tests? #f ; Building the tests already fails.
        #:make-flags '("build-nocheck") ; Do not build unit tests, which fails.
+       ;; XXX Remove this if glib-or-gtk-build-system changes to in-source-tree
+       ;; builds by default.
+       #:out-of-source? #f
        #:phases
          (modify-phases %standard-phases
            (add-before 'configure 'prepare-src

From 712d01bbe9de285bb3007511c94957b13b74118e Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 29 Sep 2018 17:19:26 -0400
Subject: [PATCH 486/909] gnu: Add gopkg.in/asn1-ber.v1.

* gnu/packages/syncthing.scm (go-gopkg.in-asn1-ber.v1): New variable.
---
 gnu/packages/syncthing.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 29caaaf02e..61b45e111f 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1366,3 +1366,25 @@ Prometheus HTTP API.")
     (description "This is a union of Go Prometheus libraries")
     (home-page (package-home-page go-github-com-client-golang-prometheus))
     (license (package-license go-github-com-client-golang-prometheus))))
+
+(define-public go-gopkg.in-asn1-ber.v1
+  (package
+    (name "go-gopkg.in-asn1-ber.v1")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://gopkg.in/asn1-ber.v1")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1y8bvzbxpw0lfnn7pbcdwzqj4l90qj6xf88dvv9pxd9yl5g6cskx"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "gopkg.in/asn1-ber.v1"))
+    (synopsis "ASN.1 BER encoding and decoding in Go")
+    (description "This package provides ASN.1 BER encoding and decoding in the
+Go language.")
+    (home-page "https://gopkg.in/asn1-ber.v1")
+    (license expat)))

From 4cb2112d8f4aac799c756241bf27aaa99ff5a714 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 29 Sep 2018 17:19:58 -0400
Subject: [PATCH 487/909] gnu: Add gopkg.in/ldap.v2.

* gnu/packages/syncthing.scm (go-gopkg.in-ldap.v2): New variable.
---
 gnu/packages/syncthing.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index 61b45e111f..cfcfb74aae 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -1388,3 +1388,28 @@ Prometheus HTTP API.")
 Go language.")
     (home-page "https://gopkg.in/asn1-ber.v1")
     (license expat)))
+
+(define-public go-gopkg.in-ldap.v2
+  (package
+    (name "go-gopkg.in-ldap.v2")
+    (version "2.5.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://gopkg.in/ldap.v2")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1wf81wy04nhkqs0dg5zkivr4sh37r83bxrfwjz9vr4jq6vmljr3h"))))
+    (build-system go-build-system)
+    (arguments
+     '(#:import-path "gopkg.in/ldap.v2"
+       #:tests? #f)) ; the test suite requires network access
+    (propagated-inputs
+     `(("go-gopkg.in-asn1-ber.v1" ,go-gopkg.in-asn1-ber.v1)))
+    (synopsis "LDAP v3 functionality for Go")
+    (description "This package provides basic LDAP v3 functionality in the Go
+language.")
+    (home-page "https://gopkg.in/ldap.v2")
+    (license expat)))

From 5149857651299be32ee8dedd813b184ff1964099 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 29 Sep 2018 17:20:31 -0400
Subject: [PATCH 488/909] gnu: go-github-com-thejerf-suture: Update to
 3.0.0-0.bf6ee6a.

* gnu/packages/syncthing.scm (go-github-com-thejerf-suture): Update to
3.0.0-0.bf6ee6a.
---
 gnu/packages/syncthing.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index cfcfb74aae..bd7ff74b43 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -678,11 +678,11 @@ database in Go.")
       (license bsd-2))))
 
 (define-public go-github-com-thejerf-suture
-  (let ((commit "3f1fb62fe0a3cc6429122d7dc45588a8b59c5bb6")
+  (let ((commit "bf6ee6a0b047ebbe9ae07d847f750dd18c6a9276")
         (revision "0"))
     (package
       (name "go-github-com-thejerf-suture")
-      (version (git-version "2.0.3" revision commit))
+      (version (git-version "3.0.0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -691,7 +691,7 @@ database in Go.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0mp7gz6bp6xhggkgmbl33vpmrq3a6n2dkgcxbkb7csnpv4r4d59k"))))
+                  "0rzx9k408vaglwnnpgpcs6y7ff7p65915nbg33rvbaz13hxwkz3y"))))
       (build-system go-build-system)
       (arguments
        `(#:import-path "github.com/thejerf/suture"))

From 7d15490cd247c35aeac170e2cf002d1fd93b775a Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 29 Sep 2018 17:21:20 -0400
Subject: [PATCH 489/909] gnu: Syncthing: Update to 0.14.51.

* gnu/packages/syncthing.scm (syncthing): Update to 0.14.51.
[arguments]: Adjust the 'increase-test-timeout' phase.
[inputs]: Add go-gopkg.in-ldap.v2.
---
 gnu/packages/syncthing.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/syncthing.scm b/gnu/packages/syncthing.scm
index bd7ff74b43..2e936eef7d 100644
--- a/gnu/packages/syncthing.scm
+++ b/gnu/packages/syncthing.scm
@@ -30,7 +30,7 @@
 (define-public syncthing
   (package
     (name "syncthing")
-    (version "0.14.50")
+    (version "0.14.51")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/syncthing/syncthing"
@@ -38,7 +38,7 @@
                                   "/syncthing-source-v" version ".tar.gz"))
               (sha256
                (base32
-                "0yjj6zzivzw289bhwqjb4xcv8p39n5mcwwr5w6xf5ykzljc5pk55"))
+                "17phn8l2afhgzh0q9ambi28awj2m905sr1bicq2wc7ghypk5vgqh"))
               (modules '((guix build utils)))
               ;; Delete bundled ("vendored") free software source code.
               (snippet '(begin
@@ -59,7 +59,7 @@
          (add-before 'build 'increase-test-timeout
            (lambda _
              (substitute* "src/github.com/syncthing/syncthing/build.go"
-               (("60s") "999s"))
+               (("120s") "999s"))
              #t))
 
          (replace 'build
@@ -138,6 +138,7 @@
        ("go-github-com-pkg-errors" ,go-github-com-pkg-errors)
        ("go-github-com-rcrowley-go-metrics" ,go-github-com-rcrowley-go-metrics)
        ("go-github-com-sasha-s-go-deadlock" ,go-github-com-sasha-s-go-deadlock)
+       ("go-github-com-syncthing-notify" ,go-github-com-syncthing-notify)
        ("go-github-com-syndtr-goleveldb" ,go-github-com-syndtr-goleveldb)
        ("go-github-com-thejerf-suture" ,go-github-com-thejerf-suture)
        ("go-github-com-vitrun-qart" ,(go-github-com-vitrun-qart-union))
@@ -145,7 +146,7 @@
        ("go-golang-org-x-net-union" ,(go-golang-org-x-net-union))
        ("go-golang-org-x-text" ,(go-golang-org-x-text-union))
        ("go-golang-org-x-time-rate" ,go-golang-org-x-time-rate)
-       ("go-github-com-syncthing-notify" ,go-github-com-syncthing-notify)
+       ("go-gopkg.in-ldap.v2" ,go-gopkg.in-ldap.v2)
        ;; For tests
        ("go-github-com-d4l3k-messagediff" ,go-github-com-d4l3k-messagediff)))
     (synopsis "Decentralized continuous file system synchronization")

From f6890c08912c7b2a2b7f6c1cdeda412ff73e0b1d Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 11 Sep 2018 15:18:25 +0200
Subject: [PATCH 490/909] gnu: Add r-rbenchmark.

gnu/packages/cran.scm (r-rbenchmark): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 186a52a1f1..76c9c734f2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6057,3 +6057,28 @@ on user-defined cut-points of accelerometer counts.
 and generates data summaries.  Also, includes functions to plot, analyze, and
 simulate accelerometer data.")
     (license license:gpl2+)))
+
+(define-public r-rbenchmark
+  (package
+    (name "r-rbenchmark")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rbenchmark" version))
+       (sha256
+        (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
+    (synopsis "Benchmarking routine for R")
+    (description
+     "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
+and is intended to facilitate benchmarking of arbitrary R code.  The library
+consists of just one function, benchmark, which is a simple wrapper around
+system.time.  Given a specification of the benchmarking process (counts of
+replications, evaluation environment) and an arbitrary number of expressions,
+benchmark evaluates each of the expressions in the specified environment,
+replicating the evaluation as many times as specified, and returning the results
+conveniently wrapped into a data frame.")
+    (license license:gpl2+)))
+

From 7af2dd38268e8d043352a6f5845cce1ee8f2fe4f Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 11 Sep 2018 15:18:26 +0200
Subject: [PATCH 491/909] gnu: Add r-dvmisc.

gnu/packages/cran.scm (r-dvmisc): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 76c9c734f2..2db310b636 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6082,3 +6082,28 @@ replicating the evaluation as many times as specified, and returning the results
 conveniently wrapped into a data frame.")
     (license license:gpl2+)))
 
+(define-public r-dvmisc
+  (package
+    (name "r-dvmisc")
+    (version "1.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "dvmisc" version))
+       (sha256
+        (base32 "1dy0yykskwhkql19bhzmbwsgv028afc8jh9yqwbczj6f3vpv31zh"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-mass" ,r-mass)
+       ("r-rbenchmark" ,r-rbenchmark)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/dvmisc/")
+    (synopsis "Faster computation of common statistics and miscellaneous functions")
+    (description
+     "This package implements faster versions of base R functions (e.g. mean, standard
+deviation, covariance, weighted mean), mostly written in C++, along with
+miscellaneous functions for various purposes (e.g. create the histogram with
+fitted probability density function or probability mass function curve, create
+the body mass index groups, assess the linearity assumption in logistic
+regression).")
+    (license license:gpl2)))

From d8d8844ec12c017480e83cd541e98b55e18a17f4 Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 11 Sep 2018 15:18:27 +0200
Subject: [PATCH 492/909] gnu: Add r-accelerometry.

gnu/packages/cran.scm (r-accelerometry): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2db310b636..b567fdc0ce 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6107,3 +6107,27 @@ fitted probability density function or probability mass function curve, create
 the body mass index groups, assess the linearity assumption in logistic
 regression).")
     (license license:gpl2)))
+
+(define-public r-accelerometry
+  (package
+    (name "r-accelerometry")
+    (version "3.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "accelerometry" version))
+       (sha256
+        (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-dvmisc" ,r-dvmisc)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://cran.r-project.org/web/packages/accelerometry/")
+    (synopsis "Functions for processing accelerometer data")
+    (description
+     "This package provides a collection of functions that perform operations on
+time-series accelerometer data, such as identify the non-wear time, flag minutes
+that are part of an activity bout, and find the maximum 10-minute average count
+value.  The functions are generally very flexible, allowing for a variety of
+algorithms to be implemented.")
+    (license license:gpl3)))

From 3f0f49d70877df6c829b443830de99e0e1e1f6bc Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 2 Oct 2018 16:03:59 -0400
Subject: [PATCH 493/909] gnu: Add poretools.

* gnu/packages/bioinformatics.scm (poretools): New variable.
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b84498d042..172832d148 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13899,3 +13899,42 @@ adapters, even at low sequence identity.  Porechop also supports demultiplexing
 of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR
 Barcoding Kit or Rapid Barcoding Kit.")
       (license license:gpl3+))))
+
+(define-public poretools
+  ;; The latest release was in 2016 and the latest commit is from 2017
+  ;; the recommended way to install is to clone the git repository
+  ;; https://poretools.readthedocs.io/en/latest/content/installation.html
+  (let ((commit "e426b1f09e86ac259a00c261c79df91510777407")
+        (revision "1"))
+    (package
+      (name "poretools")
+      (version (git-version "0.6.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/arq5x/poretools.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"))))
+      (build-system python-build-system)
+      ;; requires python >=2.7, <3.0, and the same for python dependencies
+      (arguments `(#:python ,python-2))
+      (inputs
+       `(("hdf5" ,hdf5)))
+      (propagated-inputs
+       `(("python-dateutil" ,python2-dateutil)
+         ("python-h5py" ,python2-h5py)
+         ("python-matplotlib" ,python2-matplotlib)
+         ("python-pandas" ,python2-pandas)
+         ("python-seaborn" ,python2-seaborn)))
+      (home-page "https://poretools.readthedocs.io")
+      (synopsis "Toolkit for working with nanopore sequencing data")
+      (description
+       "The MinION from Oxford Nanopore Technologies is a nanopore sequencer.
+This @code{poretools} package is a flexible toolkit for exploring datasets
+generated by nanopore sequencing devices for the purposes of quality control and
+downstream analysis.  Poretools operates directly on the native FAST5, a variant
+of the Hierarchical Data Format (HDF5) standard.")
+      (license license:expat))))

From 1ddb2b5c1ca1e18924cbb969c974a0e8d8e54010 Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 2 Oct 2018 16:16:45 -0400
Subject: [PATCH 494/909] gnu: Add r-absim.

* gnu/packages/cran.scm (r-absim): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b567fdc0ce..4da1664c67 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6131,3 +6131,31 @@ that are part of an activity bout, and find the maximum 10-minute average count
 value.  The functions are generally very flexible, allowing for a variety of
 algorithms to be implemented.")
     (license license:gpl3)))
+
+(define-public r-absim
+  (package
+    (name "r-absim")
+    (version "0.2.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AbSim" version))
+       (sha256
+        (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
+    (properties `((upstream-name . "AbSim")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-ape" ,r-ape)
+       ("r-powerlaw" ,r-powerlaw)))
+    (home-page "https://cran.r-project.org/web/packages/AbSim/")
+    (synopsis "Time resolved simulations of antibody repertoires")
+    (description
+     "This package provides simulation methods for the evolution of antibody repertoires.
+  The heavy and light chain variable region of both human and C57BL/6 mice can
+be simulated in a time-dependent fashion.  Both single lineages using one set of
+V-, D-, and J-genes or full repertoires can be simulated.  The algorithm begins
+with an initial V-D-J recombination event, starting the first phylogenetic tree.
+  Upon completion, the main loop of the algorithm begins, with each iteration
+representing one simulated time step.  Various mutation events are possible at
+each time step, contributing to a diverse final repertoire.")
+    (license license:gpl2)))

From 0f1622220a39a620854b0a268793e262746d460a Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 2 Oct 2018 16:23:12 -0400
Subject: [PATCH 495/909] gnu: Add r-absfiltergsea.

* gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.
---
 gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 172832d148..b657bf6771 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13938,3 +13938,30 @@ generated by nanopore sequencing devices for the purposes of quality control and
 downstream analysis.  Poretools operates directly on the native FAST5, a variant
 of the Hierarchical Data Format (HDF5) standard.")
       (license license:expat))))
+
+(define-public r-absfiltergsea
+  (package
+    (name "r-absfiltergsea")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AbsFilterGSEA" version))
+       (sha256
+        (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
+    (properties `((upstream-name . "AbsFilterGSEA")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-deseq" ,r-deseq)
+       ("r-limma" ,r-limma)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
+    (synopsis "Improved false positive control of gene-permuting with absolute filtering")
+    (description
+     "This package provides a function that performs gene-permuting of a gene-set
+enrichment analysis (GSEA) calculation with or without the absolute filtering.
+  Without filtering, users can perform (original) two-tailed or one-tailed
+absolute GSEA.")
+    (license license:gpl2)))

From c2ffc4fb53a23c4db975a52f85686ed4b194cfcf Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 2 Oct 2018 16:26:10 -0400
Subject: [PATCH 496/909] gnu: Add r-ac3net.

* gnu/packages/cran.scm (r-ac3net): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4da1664c67..2486a48673 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6159,3 +6159,24 @@ with an initial V-D-J recombination event, starting the first phylogenetic tree.
 representing one simulated time step.  Various mutation events are possible at
 each time step, contributing to a diverse final repertoire.")
     (license license:gpl2)))
+
+(define-public r-ac3net
+  (package
+    (name "r-ac3net")
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "Ac3net" version))
+       (sha256
+        (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
+    (properties `((upstream-name . "Ac3net")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)))
+    (home-page "https://cran.r-project.org/web/packages/Ac3net/")
+    (synopsis "Inferring directional conservative causal core gene networks")
+    (description "This package infers directional Conservative causal core
+(gene) networks (C3NET).  This is a version of the algorithm C3NET with
+directional network.")
+    (license license:gpl3+)))

From da33385959502a3f897a2a6a1bf92dc5f02b3b9a Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 2 Oct 2018 16:27:12 -0400
Subject: [PATCH 497/909] gnu: Add r-aca.

* gnu/packages/cran.scm (r-aca): New variable.
---
 gnu/packages/cran.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2486a48673..26b3b0377b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6180,3 +6180,23 @@ each time step, contributing to a diverse final repertoire.")
 (gene) networks (C3NET).  This is a version of the algorithm C3NET with
 directional network.")
     (license license:gpl3+)))
+
+(define-public r-aca
+  (package
+    (name "r-aca")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACA" version))
+       (sha256
+        (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
+    (properties `((upstream-name . "ACA")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/ACA/")
+    (synopsis "Abrupt change-point or aberration detection in point series")
+    (description
+     "This package offers an interactive function for the detection of breakpoints in
+series.")
+    ;; Any version of the GPL
+    (license (list license:gpl2+ license:gpl3+))))

From 9c1c2108a5523015fd83e599b263dfb1ad348324 Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Tue, 2 Oct 2018 16:28:42 -0400
Subject: [PATCH 498/909] gnu: Add r-acceptancesampling.

* gnu/packages/cran.scm (r-acceptancesampling): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 26b3b0377b..52b3d52bac 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6200,3 +6200,31 @@ directional network.")
 series.")
     ;; Any version of the GPL
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-acceptancesampling
+  (package
+    (name "r-acceptancesampling")
+    (version "1.0-5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "AcceptanceSampling" version))
+       (sha256
+        (base32 "18krmmyn8pn11aqd81kbvka68lnd36mnpdh7p3pz9r4m4vjj007x"))))
+    (properties
+     `((upstream-name . "AcceptanceSampling")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
+    (synopsis "Creation and evaluation of acceptance sampling plans")
+    (description
+     "This @code{r-acceptancesampling} provides functionality for creating and evaluating
+acceptance sampling plans.  Acceptance sampling is a methodology commonly used
+in quality control and improvement.  International standards of acceptance
+sampling provide sampling plans for specific circumstances.  The aim of this
+package is to provide an easy-to-use interface to visualize single, double or
+multiple sampling plans.  In addition, methods have been provided to enable the
+user to assess sampling plans against pre-specified levels of performance, as
+measured by the probability of acceptance for a given level of quality in the
+lot.")
+    (license license:gpl3+)))
+

From 63781c5748b108db5ceab02ce2d201e901ff10a4 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 2 Oct 2018 16:29:25 -0400
Subject: [PATCH 499/909] gnu: Add r-acclma.

* gnu/packages/cran.scm (r-acclma): New variable.
---
 gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 52b3d52bac..a1bf750da6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6228,3 +6228,31 @@ measured by the probability of acceptance for a given level of quality in the
 lot.")
     (license license:gpl3+)))
 
+(define-public r-acclma
+  (package
+    (name "r-acclma")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "ACCLMA" version))
+       (sha256
+        (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
+    (properties `((upstream-name . "ACCLMA")))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
+    (synopsis "ACC & LMA graph plotting")
+    (description
+     "This package contains a function that imports data from a @acronym{Comma-Separated
+Values, @acronym{CSV}} file, or uses manually entered data from the format (x,
+y, weight) and plots the appropriate @acronym{Absolute Concentration Curve,
+@acronym{ACC}} vs @acronym{Line of Independence, @acronym{LOI}} graph and
+@acronym{@acronym{LOI} Minus @acronym{ACC}, @acronym{LMA}} graph.  The main
+function is plotLMA (source file, header) that takes a data set and plots the
+appropriate @acronym{LMA} and @acronym{ACC} graphs.  If no source file (a
+string) was passed, a manual data entry window is opened.  The header parameter
+indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
+a header row or not.  The dataset should contain only one independent variable
+(x) and one dependent variable (y) and can contain a weight for each
+observation.")
+    (license license:gpl2)))

From 2bc8b2af8947502d147fb3b67a0a40a5565c3707 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 2 Oct 2018 16:18:30 +0200
Subject: [PATCH 500/909] gnu: guile-cairo: Update to 1.10.0.

* gnu/packages/gtk.scm (guile-cairo): Update to 1.10.0.
[source]: Add 'snippet'.
[arguments]: Remove.
---
 gnu/packages/gtk.scm | 58 ++++++++++++--------------------------------
 1 file changed, 15 insertions(+), 43 deletions(-)

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index 76e64b36bc..8c25922c9e 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -777,54 +777,26 @@ application suites.")
 (define-public guile-cairo
   (package
     (name "guile-cairo")
-    (version "1.4.1")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "http://download.gna.org/guile-cairo/guile-cairo-"
-                    version
-                    ".tar.gz"))
+              (uri (string-append "mirror://savannah/guile-cairo/guile-cairo-"
+                                  version ".tar.gz"))
               (sha256
                (base32
-                "1f5nd9n46n6cwfl1byjml02q3y2hgn7nkx98km1czgwarxl7ws3x"))))
+                "0p6xrhf2k6n5dybn88050za7h90gnd7534n62l53vsca187pwgdf"))
+              (modules '((guix build utils)))
+              (snippet
+               (begin
+                 '(begin
+                    ;; Install Scheme files in …/guile/site/X.Y.
+                    (substitute* (find-files "." "^Makefile\\.in$")
+                      (("^(.*)dir = (.*)/guile/site(.*)" _ name prefix suffix)
+                       (string-append name "dir = " prefix
+                                      "/guile/site/@GUILE_EFFECTIVE_VERSION@"
+                                      suffix)))
+                    #t)))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:modules ((guix build utils)
-                  (guix build gnu-build-system)
-                  (ice-9 popen)
-                  (ice-9 rdelim))
-
-       #:phases (modify-phases %standard-phases
-                  (add-before 'configure 'set-module-directory
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      ;; Install modules under $out/share/guile/site/2.0.
-                      (let ((out (assoc-ref outputs "out"))
-                            (effective
-                             (read-line
-                              (open-pipe* OPEN_READ "guile" "-c"
-                                          "(display (effective-version))"))))
-                        (substitute* "Makefile.in"
-                          (("scmdir = ([[:graph:]]+).*" _ value)
-                           (string-append "scmdir = " value "/" effective "\n")))
-                        (substitute* "cairo/Makefile.in"
-                          (("moduledir = ([[:graph:]]+).*" _ value)
-                           (string-append "moduledir = "
-                                          "$(prefix)/share/guile/site/"
-                                          effective "/cairo\n'")))
-                        #t)))
-                  (add-after 'install 'install-missing-file
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      ;; By default 'vector-types.scm' is not installed, so do
-                      ;; it here.
-                      (let ((out (assoc-ref outputs "out"))
-                            (effective
-                             (read-line
-                              (open-pipe* OPEN_READ "guile" "-c"
-                                          "(display (effective-version))"))))
-                        (install-file "cairo/vector-types.scm"
-                                      (string-append out "/share/guile/site/"
-                                                     effective "/cairo"))
-                        #t))))))
     (inputs
      `(("guile-lib" ,guile-lib)
        ("expat" ,expat)

From 7eca7892014d173ff523417138b90aeff5b7dec1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 2 Oct 2018 22:53:47 +0200
Subject: [PATCH 501/909] daemon: Remove "case hack" for nars.

This code has never been of any use in Guix.

* nix/libutil/archive.cc (useCaseHack): Remove.
(parse): Keep only the alternate branch in "if (useCaseHack)".
---
 nix/libutil/archive.cc | 31 +------------------------------
 nix/libutil/archive.hh |  5 -----
 2 files changed, 1 insertion(+), 35 deletions(-)

diff --git a/nix/libutil/archive.cc b/nix/libutil/archive.cc
index 4e3d99356a..2599030454 100644
--- a/nix/libutil/archive.cc
+++ b/nix/libutil/archive.cc
@@ -21,14 +21,6 @@
 
 namespace nix {
 
-
-bool useCaseHack =
-#if __APPLE__
-    true;
-#else
-    false;
-#endif
-
 static string archiveVersion1 = "nix-archive-1";
 
 static string caseHackSuffix = "~nix~case~hack~";
@@ -85,19 +77,7 @@ static void dump(const Path & path, Sink & sink, PathFilter & filter)
            the case hack applied by restorePath(). */
         std::map<string, string> unhacked;
         for (auto & i : readDirectory(path))
-            if (useCaseHack) {
-                string name(i.name);
-                size_t pos = i.name.find(caseHackSuffix);
-                if (pos != string::npos) {
-                    printMsg(lvlDebug, format("removing case hack suffix from `%1%'") % (path + "/" + i.name));
-                    name.erase(pos);
-                }
-                if (unhacked.find(name) != unhacked.end())
-                    throw Error(format("file name collision in between `%1%' and `%2%'")
-                        % (path + "/" + unhacked[name]) % (path + "/" + i.name));
-                unhacked[name] = i.name;
-            } else
-                unhacked[i.name] = i.name;
+	    unhacked[i.name] = i.name;
 
         for (auto & i : unhacked)
             if (filter(path + "/" + i.first)) {
@@ -251,15 +231,6 @@ static void parse(ParseSink & sink, Source & source, const Path & path)
                     if (name <= prevName)
                         throw Error("NAR directory is not sorted");
                     prevName = name;
-                    if (useCaseHack) {
-                        auto i = names.find(name);
-                        if (i != names.end()) {
-                            printMsg(lvlDebug, format("case collision between `%1%' and `%2%'") % i->first % name);
-                            name += caseHackSuffix;
-                            name += std::to_string(++i->second);
-                        } else
-                            names[name] = 0;
-                    }
                 } else if (s == "node") {
                     if (s.empty()) throw badArchive("entry name missing");
                     parse(sink, source, path + "/" + name);
diff --git a/nix/libutil/archive.hh b/nix/libutil/archive.hh
index c216e9768f..9b83a5f288 100644
--- a/nix/libutil/archive.hh
+++ b/nix/libutil/archive.hh
@@ -71,9 +71,4 @@ void parseDump(ParseSink & sink, Source & source);
 
 void restorePath(const Path & path, Source & source);
 
-
-// FIXME: global variables are bad m'kay.
-extern bool useCaseHack;
-
-
 }

From c577ac194afb4c9df76f9955aeb6118aafac6c34 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 2 Oct 2018 22:57:13 +0200
Subject: [PATCH 502/909] daemon: Remove unused 'Settings' fields.

* nix/libstore/globals.hh (Settings)[sshSubstituterHosts]
[useSshSubstituter, logServers, enableImportNative]: Remove fields.
* nix/libstore/globals.cc (Settings::Settings, Settings::update): Remove
references to these.
---
 nix/libstore/globals.cc |  9 ---------
 nix/libstore/globals.hh | 12 ------------
 2 files changed, 21 deletions(-)

diff --git a/nix/libstore/globals.cc b/nix/libstore/globals.cc
index fcafac2df6..94c2e516f8 100644
--- a/nix/libstore/globals.cc
+++ b/nix/libstore/globals.cc
@@ -42,7 +42,6 @@ Settings::Settings()
     syncBeforeRegistering = false;
     useSubstitutes = true;
     useChroot = false;
-    useSshSubstituter = false;
     impersonateLinux26 = false;
     keepLog = true;
 #if HAVE_BZLIB_H
@@ -60,7 +59,6 @@ Settings::Settings()
     envKeepDerivations = false;
     lockCPU = getEnv("NIX_AFFINITY_HACK", "1") == "1";
     showTrace = false;
-    enableImportNative = false;
 }
 
 
@@ -142,11 +140,6 @@ void Settings::update()
     _get(gcKeepDerivations, "gc-keep-derivations");
     _get(autoOptimiseStore, "auto-optimise-store");
     _get(envKeepDerivations, "env-keep-derivations");
-    _get(sshSubstituterHosts, "ssh-substituter-hosts");
-    _get(useSshSubstituter, "use-ssh-substituter");
-    _get(logServers, "log-servers");
-    _get(enableImportNative, "allow-unsafe-native-code-during-evaluation");
-    _get(useCaseHack, "use-case-hack");
 
     string subs = getEnv("NIX_SUBSTITUTERS", "default");
     if (subs == "default") {
@@ -157,8 +150,6 @@ void Settings::update()
 #endif
         substituters.push_back(nixLibexecDir + "/nix/substituters/download-using-manifests.pl");
         substituters.push_back(nixLibexecDir + "/nix/substituters/download-from-binary-cache.pl");
-        if (useSshSubstituter)
-            substituters.push_back(nixLibexecDir + "/nix/substituters/download-via-ssh");
     } else
         substituters = tokenizeString<Strings>(subs, ":");
 }
diff --git a/nix/libstore/globals.hh b/nix/libstore/globals.hh
index 1293625e1f..4c142e6933 100644
--- a/nix/libstore/globals.hh
+++ b/nix/libstore/globals.hh
@@ -161,12 +161,6 @@ struct Settings {
     /* Whether to build in chroot. */
     bool useChroot;
 
-    /* Set of ssh connection strings for the ssh substituter */
-    Strings sshSubstituterHosts;
-
-    /* Whether to use the ssh substituter at all */
-    bool useSshSubstituter;
-
     /* Whether to impersonate a Linux 2.6 machine on newer kernels. */
     bool impersonateLinux26;
 
@@ -212,12 +206,6 @@ struct Settings {
     /* Whether to show a stack trace if Nix evaluation fails. */
     bool showTrace;
 
-    /* A list of URL prefixes that can return Nix build logs. */
-    Strings logServers;
-
-    /* Whether the importNative primop should be enabled */
-    bool enableImportNative;
-
 private:
     SettingsMap settings, overrides;
 

From 000b540791f082b8a8398dc2ed51fd1526d8357d Mon Sep 17 00:00:00 2001
From: Pierre-Antoine Rouby <contact@parouby.fr>
Date: Thu, 27 Sep 2018 21:01:25 +0200
Subject: [PATCH 503/909] gnu: grammalecte: Update source hash.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The zip file was modified in-place by the maintainers to push fixes to
the "server-side code", as discussed at <https://bugs.gnu.org/32856>.

* gnu/packages/dictionaries.scm (grammalecte): Update source hash.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/dictionaries.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/dictionaries.scm b/gnu/packages/dictionaries.scm
index 9f63223453..ce7ef1cf75 100644
--- a/gnu/packages/dictionaries.scm
+++ b/gnu/packages/dictionaries.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
 ;;; Copyright © 2017, 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Pierre-Antoine Rouby <contact@parouby.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -219,7 +220,7 @@ It comes with a German-English dictionary with approximately 270,000 entries.")
                            "Grammalecte-fr-v" version ".zip"))
        (sha256
         (base32
-         "1flsahqw2r0cmg0bixpl5w0acricmdh2cf4lf9zr66ydgmjnmv2s"))))
+         "11byjs3ggdhia5f4vyfqfvbbczsfqimll98h98g7hlsrm7vrifb0"))))
     (build-system python-build-system)
     (home-page "https://www.dicollecte.org")
     (synopsis  "French spelling and grammar checker")

From 68faa20e2d4511b43062f8279cc407aee735b275 Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@cray.com>
Date: Tue, 2 Oct 2018 13:53:13 -0500
Subject: [PATCH 504/909] quilt: Upgrade to 0.65.

* gnu/packages/patches/quilt-test-fix-regex.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/patchutils.scm (quilt)[version]: Upgrade to 0.65.
[source]: Use patch.
[arguments]: Adjust 'patch-tests' phase for new tests.  Re-enable "mail"
test.
---
 gnu/local.mk                                  |  1 +
 .../patches/quilt-test-fix-regex.patch        | 41 +++++++++++++++++++
 gnu/packages/patchutils.scm                   | 19 ++++++---
 3 files changed, 56 insertions(+), 5 deletions(-)
 create mode 100644 gnu/packages/patches/quilt-test-fix-regex.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 244c79d221..b2fda4ac69 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1101,6 +1101,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/qtscript-disable-tests.patch		\
   %D%/packages/patches/quagga-reproducible-build.patch          \
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
+  %D%/packages/patches/quilt-test-fix-regex.patch		\
   %D%/packages/patches/qtwebkit-pbutils-include.patch		\
   %D%/packages/patches/rapicorn-isnan.patch			\
   %D%/packages/patches/raptor2-heap-overflow.patch		\
diff --git a/gnu/packages/patches/quilt-test-fix-regex.patch b/gnu/packages/patches/quilt-test-fix-regex.patch
new file mode 100644
index 0000000000..2e249ac55b
--- /dev/null
+++ b/gnu/packages/patches/quilt-test-fix-regex.patch
@@ -0,0 +1,41 @@
+From 5193b137b5a9034ce79946edd40760df2f63a82a Mon Sep 17 00:00:00 2001
+From: Jean Delvare <jdelvare@suse.de>
+Date: Tue, 25 Apr 2017 15:17:53 +0200
+Subject: test: Escape curly braces in regex
+
+Curly braces in perl regex are supposed to be escaped, recent
+versions of perl complain when they aren't:
+
+Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/%{ <-- HERE (\w+)}/ at ./run line 114.
+Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/%{ <-- HERE \?}/ at ./run line 290.
+
+Signed-off-by: Jean Delvare <jdelvare@suse.de>
+---
+ test/run | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/test/run b/test/run
+index 942014e..03afc7a 100755
+--- a/test/run
++++ b/test/run
+@@ -112,7 +112,7 @@ sub flush_output()
+ sub substitute_vars($)
+ {
+ 	my ($line) = @_;
+-	$line =~ s[%{(\w+)}][defined $ENV{$1} ? $ENV{$1} : ""]eg;
++	$line =~ s[%\{(\w+)\}][defined $ENV{$1} ? $ENV{$1} : ""]eg;
+ 	return $line;
+ }
+ 
+@@ -288,7 +288,7 @@ while (defined(my $line = <SOURCE>)) {
+ 	# Parse the next command
+ 	if ($line =~ s/^\s*\$ ?//) {
+ 		# Substitute %{?} with the last command's status
+-		$line =~ s[%{\?}][$last_status]eg;
++		$line =~ s[%\{\?\}][$last_status]eg;
+ 
+ 		chomp($prog = substitute_vars($line));
+ 		$prog_line = $lineno;
+-- 
+cgit v1.0-41-gc330
+
diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm
index a68e369912..0cf111ac47 100644
--- a/gnu/packages/patchutils.scm
+++ b/gnu/packages/patchutils.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
@@ -92,7 +92,7 @@ listing the files modified by a patch.")
 (define-public quilt
   (package
     (name "quilt")
-    (version "0.61")
+    (version "0.65")
     (source
      (origin
       (method url-fetch)
@@ -100,7 +100,8 @@ listing the files modified by a patch.")
                           name "-" version ".tar.gz"))
       (sha256
        (base32
-        "1hwz58djkq9cv46sjwxbp2v5m8yjr41kd0nm1zm1xm6418khmv0y"))))
+        "06b816m2gz9jfif7k9v2hrm7fz76zjg5pavf7hd3ifybwn4cgjzn"))
+      (patches (search-patches "quilt-test-fix-regex.patch"))))
     (build-system gnu-build-system)
     (inputs `(("perl" ,perl)
               ("less" ,less)
@@ -116,8 +117,16 @@ listing the files modified by a patch.")
                  '("test/run"
                    "test/edit.test") 
                (("/bin/sh") (which "sh")))
-             ;; TODO: Run the mail tests once the mail feature can be supported.
-             (delete-file "test/mail.test")
+             (substitute* "test/create-delete.test"
+               ;; We'd rather use quilt's compat/getopt than declare a
+               ;; dependency on util-linux, but this test fails because of
+               ;; compat/getopt's handling of "---" in this test, so remove it
+               ;; for now.
+               ((" ---") ""))
+             (substitute* '("test/empty-files.test" "test/faildiff.test")
+               ;; compat/getopt seems not to handle splitting of short opts
+               ;; from its arguments.
+               (("-pab") "-p ab"))
              #t))
          (add-after 'install 'wrap-program
            ;; quilt's configure checks for the absolute path to the utilities it

From 24a80064ca7faf504563af33217e07372285fb2f Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@cray.com>
Date: Tue, 2 Oct 2018 14:01:55 -0500
Subject: [PATCH 505/909] quilt: Install translations.

* gnu/packages/patchutils.scm (quilt)[native-inputs]: New field.
---
 gnu/packages/patchutils.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm
index 0cf111ac47..767799768c 100644
--- a/gnu/packages/patchutils.scm
+++ b/gnu/packages/patchutils.scm
@@ -31,6 +31,7 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages file)
   #:use-module (gnu packages gawk)
+  #:use-module (gnu packages gettext)
   #:use-module (gnu packages less)
   #:use-module (gnu packages mail)
   #:use-module (gnu packages ncurses)
@@ -103,6 +104,8 @@ listing the files modified by a patch.")
         "06b816m2gz9jfif7k9v2hrm7fz76zjg5pavf7hd3ifybwn4cgjzn"))
       (patches (search-patches "quilt-test-fix-regex.patch"))))
     (build-system gnu-build-system)
+    (native-inputs
+     `(("gettext" ,gnu-gettext)))
     (inputs `(("perl" ,perl)
               ("less" ,less)
               ("file" ,file)

From d7d1fc821091de98d66dac71ceed390d82434e40 Mon Sep 17 00:00:00 2001
From: Eric Bavier <&lt;bavier@cray.com&gt>
Date: Tue, 2 Oct 2018 14:50:45 -0500
Subject: [PATCH 506/909] quilt: Add diffstat input.

* gnu/packages/patchutils.scm (quilt)[inputs]: Add diffstat.
[arguments]: Add it to wrapper.
---
 gnu/packages/patchutils.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm
index 767799768c..da20ae1c3f 100644
--- a/gnu/packages/patchutils.scm
+++ b/gnu/packages/patchutils.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages xml))
 
 (define-public patchutils
@@ -109,7 +110,8 @@ listing the files modified by a patch.")
     (inputs `(("perl" ,perl)
               ("less" ,less)
               ("file" ,file)
-              ("ed" ,ed)))
+              ("ed" ,ed)
+              ("diffstat" ,diffstat)))
     (arguments
      '(#:parallel-tests? #f
        #:phases
@@ -140,6 +142,7 @@ listing the files modified by a patch.")
                     (coreutils (assoc-ref inputs "coreutils"))
                     (diffutils (assoc-ref inputs "diffutils"))
                     (findutils (assoc-ref inputs "findutils"))
+                    (diffstat  (assoc-ref inputs "diffstat"))
                     (less      (assoc-ref inputs "less"))
                     (file      (assoc-ref inputs "file"))
                     (ed        (assoc-ref inputs "ed"))
@@ -151,7 +154,8 @@ listing the files modified by a patch.")
                    ,(map (lambda (dir)
                            (string-append dir "/bin"))
                          (list coreutils diffutils findutils
-                               less file ed sed bash grep)))))
+                               less file ed sed bash grep
+                               diffstat)))))
              #t)))))
     (home-page "https://savannah.nongnu.org/projects/quilt/")
     (synopsis "Script for managing patches to software")

From 944a3a8b8e36e1e1b9632a774c9ae4e63647d21c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 3 Oct 2018 15:22:44 +0200
Subject: [PATCH 507/909] gnu: recutils: Adjust Gnulib to libc 2.28.

Fixes <https://bugs.gnu.org/32776>.

* gnu/packages/databases.scm (recutils)[modules, snippet]: New fields.
---
 gnu/packages/databases.scm | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index b6e5012677..fecf661833 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -923,7 +923,23 @@ organized in a hash table or B+ tree.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0cdwa4094x3yx7vn98xykvnlp9rngvd58d19vs3vh5hrvggccg93"))))
+                "0cdwa4094x3yx7vn98xykvnlp9rngvd58d19vs3vh5hrvggccg93"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Adjust the bundled gnulib to work with glibc 2.28.  See e.g.
+                  ;; "m4-gnulib-libio.patch".  This is a phase rather than patch
+                  ;; or snippet to work around <https://bugs.gnu.org/32347>.
+                  (substitute* (find-files "lib" "\\.c$")
+                    (("#if defined _IO_ftrylockfile")
+                     "#if defined _IO_EOF_SEEN"))
+                  (substitute* "lib/stdio-impl.h"
+                    (("^/\\* BSD stdio derived implementations")
+                     (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
+                                    "# define _IO_IN_BACKUP 0x100\n"
+                                    "#endif\n\n"
+                                    "/* BSD stdio derived implementations")))
+                  #t))))
     (build-system gnu-build-system)
 
     ;; Running tests in parallel leads to test failures and crashes in

From d1022d68c25ab95ba789e02164326af47fd18a80 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Wed, 3 Oct 2018 21:32:49 +0800
Subject: [PATCH 508/909] gnu: guile-chickadee: Update to 0.3.0.

* gnu/packages/game-development.scm (guile-chickadee): Update to 0.3.0.
[arguments]: Add 'patch-godir' phase.
---
 gnu/packages/game-development.scm | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 86f2877f82..6bd72879c2 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1256,17 +1256,24 @@ a 2D editor view.")
 (define-public guile-chickadee
   (package
     (name "guile-chickadee")
-    (version "0.2.0")
+    (version "0.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://files.dthompson.us/chickadee/"
                                   "chickadee-" version ".tar.gz"))
               (sha256
                (base32
-                "10qx0ha5gsayybd186r1my7vc7rf5fbzp9jvmc4xg9a8wz8rqhah"))))
+                "0jl223dybsj5gvs7z4q60gnafj1b7kgi5mx0kj58m5knrp8qwg5h"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:make-flags '("GUILE_AUTO_COMPILE=0")))
+     '(#:make-flags '("GUILE_AUTO_COMPILE=0")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'patch-godir
+           (lambda _
+             ;; Install compiled '.go' files into the site directory.
+             (substitute* "Makefile.in"
+               (("/ccache") "/site-ccache")))))))
     (propagated-inputs
      `(("guile-opengl" ,guile-opengl)
        ("guile-sdl2" ,guile-sdl2)))

From 477dde6192bc795732be8643d66c98f89458fd68 Mon Sep 17 00:00:00 2001
From: Christopher Lemmer Webber <cwebber@dustycloud.org>
Date: Tue, 25 Sep 2018 21:09:32 -0400
Subject: [PATCH 509/909] gnu: emacs-racket-mode: Update to commit b977873.

* gnu/packages/emacs.scm (emacs-racket-mode): Update to commit b977873.
---
 gnu/packages/emacs.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 8da5add886..c10a80258e 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -10410,8 +10410,8 @@ perform regression test for packages that provide font-lock rules.")
       (license license:gpl3+))))
 
 (define-public emacs-racket-mode
-  (let ((commit "92c33487f6c707880ac3f6169e7ea65ddffd1463")
-        (revision "1"))
+  (let ((commit "b977873e6128f8399432dcd60cc39f6a6f803d9c")
+        (revision "2"))
     (package
       (name "emacs-racket-mode")
       (version (string-append "0.0.2" "-" revision "."
@@ -10425,7 +10425,7 @@ perform regression test for packages that provide font-lock rules.")
          (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
-           "19q6ym10gj2xdzzcgh3wdbq1xv8cv7nlrhv2b0bjvvdjzhiki472"))))
+           "0vp4bbbplqvmnhjpl6ajrlydmrhqzil56cfbs18m5c5fddx0zlh7"))))
       (build-system emacs-build-system)
       (arguments
        `(#:include '("\\.el$" "\\.rkt$")))

From 227ce488d7b899636e8e8635cbd2d08fb21c56a2 Mon Sep 17 00:00:00 2001
From: Katherine Cox-Buday <cox.katherine.e@gmail.com>
Date: Tue, 2 Oct 2018 16:38:52 -0500
Subject: [PATCH 510/909] gnu: Go 1.11: Update to 1.11.1

* gnu/packages/golang.scm (go-1.11): Update to 1.11.1.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/golang.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index bba03e77f2..7a049e39e1 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -504,7 +504,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
   (package
     (inherit go-1.10)
     (name "go")
-    (version "1.11")
+    (version "1.11.1")
     (source
      (origin
        (method url-fetch)
@@ -512,7 +512,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                            name version ".src.tar.gz"))
        (sha256
         (base32
-         "1ysj04jzds6xa8kdflkdsgyv3mg9fdn90zdf78g4g6p4bwpy3hdg"))))
+         "05qivf2f59pv4bfrmdr4m0xvswkmvvl9c5a2h5dy45g2k8b8r3sm"))))
     (arguments
      (substitute-keyword-arguments (package-arguments go-1.10)
        ((#:phases phases)

From 43eb42ef017aa4752503fb2913781bb446716c1e Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Wed, 3 Oct 2018 10:23:51 -0500
Subject: [PATCH 511/909] quilt: Remove test workarounds.

* gnu/packages/patches/quilt-compat-getopt-fix-second-separator.patch,
gnu/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch:
New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/patchutils.scm (quilt)[source]: Use them.
[arguments]: Remove workarounds in 'patch-tests' phase.
---
 gnu/local.mk                                  |  2 +
 ...etopt-fix-option-with-nondigit-param.patch | 45 ++++++++++++++
 ...t-compat-getopt-fix-second-separator.patch | 58 +++++++++++++++++++
 gnu/packages/patchutils.scm                   | 14 +----
 4 files changed, 108 insertions(+), 11 deletions(-)
 create mode 100644 gnu/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch
 create mode 100644 gnu/packages/patches/quilt-compat-getopt-fix-second-separator.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index b2fda4ac69..61e5913a01 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1102,6 +1102,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/quagga-reproducible-build.patch          \
   %D%/packages/patches/quickswitch-fix-dmenu-check.patch	\
   %D%/packages/patches/quilt-test-fix-regex.patch		\
+  %D%/packages/patches/quilt-compat-getopt-fix-second-separator.patch	\
+  %D%/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch	\
   %D%/packages/patches/qtwebkit-pbutils-include.patch		\
   %D%/packages/patches/rapicorn-isnan.patch			\
   %D%/packages/patches/raptor2-heap-overflow.patch		\
diff --git a/gnu/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch b/gnu/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch
new file mode 100644
index 0000000000..6bbec67e75
--- /dev/null
+++ b/gnu/packages/patches/quilt-compat-getopt-fix-option-with-nondigit-param.patch
@@ -0,0 +1,45 @@
+From: Jean Delvare <jdelvare@suse.de>
+Subject: compat/getopt: Allow non-digit parameter embedded in short option
+
+The compatibility getopt script allows only digit parameters to be
+embedded in short options. Util-linux's getopt implementation does
+not have such a restriction and allows any parameter to be embedded
+in short options. As a consequence, using the compatibility getopt
+script would choke for example on "-pab", which is a legal option
+of the "quilt refresh" command.
+
+Remove the limitation on digits so that the compatibility getopt
+script allows what util-linux allows. This fixes the second half
+of bug #54772:
+https://savannah.nongnu.org/bugs/index.php?54772
+
+As a side note, this feature of the compatibility script was broken
+anyway, as it would output the digits in reverse order.
+
+Signed-off-by: Jean Delvare <jdelvare@suse.de>
+---
+ compat/getopt.in |   13 ++++---------
+ 1 file changed, 4 insertions(+), 9 deletions(-)
+
+--- quilt.orig/compat/getopt.in	2018-10-03 16:05:56.818667040 +0200
++++ quilt/compat/getopt.in	2018-10-03 16:12:17.624841732 +0200
+@@ -108,15 +108,10 @@ foreach my $word (@words) {
+ 				if (scalar(@letters) == 0) {
+ 					$need_param = $letter;
+ 				} else {
+-					# short options can have numerical args
+-					# embedded in the short option list: -UO
+-					die "unexpected character after option $letter"
+-						if ($letters[$#letters] !~ /[0-9]/);
+-					my @digits;
+-					while (scalar(@letters) && ($letters[$#letters] =~ /[0-9]/)) {
+-						push @digits, pop @letters;
+-					}
+-					push @options, quote_word(join('', reverse @digits));
++					# short options can have args
++					# embedded in the short option list
++					push @options, quote_word(join('', reverse @letters));
++					@letters = ();
+ 				}
+ 			}
+ 		}
diff --git a/gnu/packages/patches/quilt-compat-getopt-fix-second-separator.patch b/gnu/packages/patches/quilt-compat-getopt-fix-second-separator.patch
new file mode 100644
index 0000000000..cde2c8d41c
--- /dev/null
+++ b/gnu/packages/patches/quilt-compat-getopt-fix-second-separator.patch
@@ -0,0 +1,58 @@
+From: Jean Delvare <jdelvare@suse.de>
+Subject: compat/getopt: Handle a second separator
+
+getopt can be passed 2 '--' separators. The first one tells that
+getopt options are over and target program options start. The second
+one tells that the target program's options are over and following
+arguments should be treated as non-options even if they look like
+options.
+
+This second separator was not handled, causing the compatibility
+getopt script to treat the following arguments as options, eventually
+failing one way or another.
+
+Properly detect and handle the second separator. This fixes the first
+half of bug #54772:
+https://savannah.nongnu.org/bugs/index.php?54772
+
+Signed-off-by: Jean Delvare <jdelvare@suse.de>
+---
+ compat/getopt.in |   13 ++++++++++---
+ 1 file changed, 10 insertions(+), 3 deletions(-)
+
+--- quilt.orig/compat/getopt.in	2018-10-03 15:23:21.147620172 +0200
++++ quilt/compat/getopt.in	2018-10-03 16:05:56.818667040 +0200
+@@ -8,12 +8,12 @@
+ 
+ use strict;
+ 
+-my $opts;
++my $opts = '';
+ my @words;
+ my $found_sep = 0;
+ 
+ foreach my $arg (@ARGV) {
+-  if ($arg eq '--') {
++  if (!$found_sep && $arg eq '--') {
+     $found_sep = 1;
+   }
+   else {
+@@ -62,10 +62,17 @@ sub quote_word
+ 	return "'$word'";
+ }
+ 
++# there can be a second separator, to inhibit processing following arguments
++# as options
++$found_sep = 0;
+ foreach my $word (@words) {
++	if ($word eq '--') {
++		$found_sep = 1;
++		next;
++	}
+ 
+ 	# allow '-' to be an option value
+-	if (!$need_param && $word !~ /^-./) {
++	if ($found_sep || (!$need_param && $word !~ /^-./)) {
+ 		push @barewords, quote_word($word);
+ 		next;
+ 	}
diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm
index da20ae1c3f..688e62cdc8 100644
--- a/gnu/packages/patchutils.scm
+++ b/gnu/packages/patchutils.scm
@@ -103,7 +103,9 @@ listing the files modified by a patch.")
       (sha256
        (base32
         "06b816m2gz9jfif7k9v2hrm7fz76zjg5pavf7hd3ifybwn4cgjzn"))
-      (patches (search-patches "quilt-test-fix-regex.patch"))))
+      (patches (search-patches "quilt-test-fix-regex.patch"
+                               "quilt-compat-getopt-fix-second-separator.patch"
+                               "quilt-compat-getopt-fix-option-with-nondigit-param.patch"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("gettext" ,gnu-gettext)))
@@ -122,16 +124,6 @@ listing the files modified by a patch.")
                  '("test/run"
                    "test/edit.test") 
                (("/bin/sh") (which "sh")))
-             (substitute* "test/create-delete.test"
-               ;; We'd rather use quilt's compat/getopt than declare a
-               ;; dependency on util-linux, but this test fails because of
-               ;; compat/getopt's handling of "---" in this test, so remove it
-               ;; for now.
-               ((" ---") ""))
-             (substitute* '("test/empty-files.test" "test/faildiff.test")
-               ;; compat/getopt seems not to handle splitting of short opts
-               ;; from its arguments.
-               (("-pab") "-p ab"))
              #t))
          (add-after 'install 'wrap-program
            ;; quilt's configure checks for the absolute path to the utilities it

From 6f2a2bd66d5f7e5e8d7d2fd6f6cfdf3e5006b567 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Wed, 26 Sep 2018 23:15:59 +0200
Subject: [PATCH 512/909] gnu: Add emacs-all-the-icons.

* gnu/packages/emacs.scm (emacs-all-the-icons): New variable.
---
 gnu/packages/emacs.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index c10a80258e..b25358718c 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -12262,3 +12262,42 @@ execute its commands and resize images.")
       (description "Synosaurus is a thesaurus fontend for Emacs with pluggable
 backends, including the @command{wordnet} offline backend.")
       (license license:gpl3+))))
+
+(define-public emacs-all-the-icons
+  (package
+    (name "emacs-all-the-icons")
+    (version "3.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/domtronn/all-the-icons.el.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1sdl33117lccznj38021lwcdnpi9nxmym295q6y460y4dm4lx0jn"))))
+    (build-system emacs-build-system)
+    (arguments
+     `(#:include '("\\.el$" "^data/" "^fonts/")
+       ;; Compiling "test/" fails with "Symbol’s value as variable is void:
+       ;; all-the-icons--root-code".  Ignoring tests.
+       #:exclude '("^test/")
+       #:tests? #f))
+    (propagated-inputs
+     `(("f" ,emacs-f)
+       ("memoize" ,emacs-memoize)))
+    (home-page "https://github.com/domtronn/all-the-icons.el")
+    (synopsis "Collect icon fonts and propertize them within Emacs")
+    (description "All-the-icons is a utility package to collect various icon
+fonts and propertize them within Emacs.  Icon fonts allow you to propertize
+and format icons the same way you would normal text.  This enables things such
+as better scaling of and anti aliasing of the icons.")
+    ;; Package is released under Expat license.  Elisp files are licensed
+    ;; under GPL3+.  Fonts come with various licenses: Expat for
+    ;; "all-the-icons.ttf" and "file-icons.ttf", Apache License 2.0 for
+    ;; "material-design-icons.ttf", and SIL OFL 1.1 for "fontawesome.ttf",
+    ;; "ocitcons.ttf" and "weathericons.ttf".
+    (license
+     (list license:expat license:gpl3+ license:silofl1.1 license:asl2.0))))
+

From d406dcc046b140de616d3ea83a7591865c7eb5be Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Wed, 26 Sep 2018 23:25:24 +0200
Subject: [PATCH 513/909] gnu: Add emacs-powerline.

* gnu/packages/emacs.scm (emacs-powerline): New variable.
---
 gnu/packages/emacs.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index b25358718c..b9f3d678e0 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -12301,3 +12301,25 @@ as better scaling of and anti aliasing of the icons.")
     (license
      (list license:expat license:gpl3+ license:silofl1.1 license:asl2.0))))
 
+(define-public emacs-powerline
+  (package
+    (name "emacs-powerline")
+    (version "2.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/milkypostman/powerline.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1hp3xp18943n0rlggz55150020ivw8gvi1vyxkr4z8xhpwq4gaar"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/milkypostman/powerline/")
+    (synopsis "Mode-line plugin for Emacs")
+    (description "Powerline is a utility plugin which allows you to create
+a better-looking, more functional Emacs mode-line.  A collection of predefined
+themes comes with the package.")
+    (license license:gpl3+)))
+

From 0c1fd6f8ade5c30e12985f7bd29ea4bf49559741 Mon Sep 17 00:00:00 2001
From: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date: Wed, 26 Sep 2018 23:27:06 +0200
Subject: [PATCH 514/909] gnu: Add emacs-spaceline.

* gnu/packages/emacs.scm (emacs-spaceline): New variable.
---
 gnu/packages/emacs.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index b9f3d678e0..1df3456e4a 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -12323,3 +12323,35 @@ a better-looking, more functional Emacs mode-line.  A collection of predefined
 themes comes with the package.")
     (license license:gpl3+)))
 
+(define-public emacs-spaceline
+  (package
+    (name "emacs-spaceline")
+    (version "2.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/TheBB/spaceline.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1q8r95zfrh0vxna5ml2pq9b9f66clfqcl4d2qy2aizkvzyxg6skl"))))
+    (build-system emacs-build-system)
+    (propagated-inputs
+     `(("dash" ,emacs-dash)
+       ("powerline" ,emacs-powerline)
+       ("s" ,emacs-s)))
+    (home-page "https://github.com/TheBB/spaceline")
+    (synopsis "Powerline theme from Spacemacs")
+    (description "Spaceline provides Spacemacs' mode-line theme.
+This package provides features for three kinds of users.
+
+@itemize
+@item You just want to use the Spacemacs mode-line theme and forget about it.
+@item You want to use something similar to the Spacemacs mode-line theme, but
+with a handful of easy tweaks.
+@item You want an easy-to-use library for building your own mode-line from
+scratch, and you think the Spacemacs theme looks good.
+@end itemize")
+    (license license:gpl3+)))

From 7d99f015acb2611bca9f42f2d04cae68ef52aba3 Mon Sep 17 00:00:00 2001
From: David Thompson <davet@gnu.org>
Date: Wed, 3 Oct 2018 14:28:11 -0400
Subject: [PATCH 515/909] gnu: tiled: Update to 1.2.0.

* gnu/packages/game-development.scm (tiled): Update to 1.2.0.
---
 gnu/packages/game-development.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 6bd72879c2..bfebcc433e 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -397,7 +397,7 @@ support.")
 (define-public tiled
   (package
     (name "tiled")
-    (version "1.1.6")
+    (version "1.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/bjorn/tiled/archive/v"
@@ -405,7 +405,7 @@ support.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "194ciw8688mikndvxivzb8ql5vm405pkwnn4srzm7ymwfc4xygb0"))))
+                "13dlf5kzvhhjkhy19118x3diakmraz4m9kxrsdam8dms6xivb6lp"))))
     (build-system gnu-build-system)
     (inputs
      `(("qtbase" ,qtbase)

From ef1f9acf470e1871395daf18ce5d1c58d87f2ab0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 3 Oct 2018 23:04:32 +0200
Subject: [PATCH 516/909] gnu: azr3: Fix build.

Fixes <https://bugs.gnu.org/32698>.

* gnu/packages/audio.scm (azr3)[arguments]: Add build phase to reset timestamp
of man page source.
---
 gnu/packages/audio.scm | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 8f100ce7a3..95cc2ed68c 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -449,7 +449,14 @@ tools.")
              "CXXFLAGS=-std=gnu++11"
              "CFLAGS=-std=gnu++11"
              (string-append "prefix=" %output)
-             (string-append "pkgdatadir=" %output "/share/azr3-jack"))))
+             (string-append "pkgdatadir=" %output "/share/azr3-jack"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'fix-timestamp
+           (lambda _
+             (let ((early-1980 315619200)) ; 1980-01-02 UTC
+               (utime "azr3.1" early-1980 early-1980))
+             #t)))))
     (inputs
      `(("gtkmm" ,gtkmm-2)
        ("lvtk" ,lvtk)

From 46f9022c9919e647e62a39e0dacf51e31457e6f8 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Wed, 3 Oct 2018 23:56:44 +0200
Subject: [PATCH 517/909] gnu: Add java-commons-exec.

* gnu/packages/java.scm (java-commons-exec-1.1): New variable.
(java-commons-exec): New variable.
---
 gnu/packages/java.scm | 79 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index d2f4c9d05b..5207c6cc64 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -4288,6 +4288,85 @@ setter and getter method.")
 file filters and endian classes.")
     (license license:asl2.0)))
 
+(define-public java-commons-exec-1.1
+  (package
+    (name "java-commons-exec")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://apache/commons/exec/source/"
+                           "commons-exec-" version "-src.tar.gz"))
+       (sha256
+        (base32
+         "025dk8xgj10lxwwwqp0hng2rn7fr4vcirxzydqzx9k4dim667alk"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:make-flags
+       (list (string-append "-Dmaven.junit.jar="
+                            (assoc-ref %build-inputs "java-junit")
+                            "/share/java/junit.jar"))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'delete-network-tests
+           (lambda _
+             (delete-file "src/test/java/org/apache/commons/exec/DefaultExecutorTest.java")
+             (substitute* "src/test/java/org/apache/commons/exec/TestRunner.java"
+              (("suite\\.addTestSuite\\(DefaultExecutorTest\\.class\\);") ""))
+             #t))
+         ;; The "build" phase automatically tests.
+         (delete 'check)
+         (replace 'install (install-jars "target")))))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (home-page "http://commons.apache.org/proper/commons-exec/")
+    (synopsis "Common program execution related classes")
+    (description "Commons-Exec simplifies executing external processes.")
+    (license license:asl2.0)))
+
+(define-public java-commons-exec
+  (package
+    (inherit java-commons-exec-1.1)
+    (version "1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://apache/commons/exec/source/"
+                           "commons-exec-" version "-src.tar.gz"))
+       (sha256
+        (base32
+         "17yb4h6f8l49c5iyyvda4z2nmw0bxrx857nrwmsr7mmpb7x441yv"))))
+    (arguments
+     `(#:test-target "test"
+       #:make-flags
+       (list (string-append "-Dmaven.junit.jar="
+                            (assoc-ref %build-inputs "java-junit")
+                            "/share/java/junit.jar")
+             "-Dmaven.compiler.source=1.7"
+             "-Dmaven.compiler.target=1.7")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'delete-network-tests
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; This test hangs indefinitely.
+             (delete-file "src/test/java/org/apache/commons/exec/issues/Exec60Test.java")
+             (substitute* "src/test/java/org/apache/commons/exec/issues/Exec41Test.java"
+              (("ping -c 10 127.0.0.1") "sleep 10"))
+             (substitute* "src/test/java/org/apache/commons/exec/issues/Exec49Test.java"
+              (("/bin/ls") "ls"))
+             (call-with-output-file "src/test/scripts/ping.sh"
+               (lambda (port)
+                 (format port "#!~a/bin/sh\nsleep $1\n"
+                              (assoc-ref inputs "bash"))))
+             #t))
+         ;; The "build" phase automatically tests.
+         (delete 'check)
+         (replace 'install (install-jars "target")))))
+    (native-inputs
+     `(("java-junit" ,java-junit)
+       ("java-hamcrest-core" ,java-hamcrest-core)))))
+
 (define-public java-commons-lang
   (package
     (name "java-commons-lang")

From 615a7eec567f313e1e421ee081c502201932fcd3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Tue, 2 Oct 2018 16:32:03 +0200
Subject: [PATCH 518/909] gnu: Add stlink.

* gnu/packages/embedded.scm (stlink): New variable.
---
 gnu/packages/embedded.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index 0174224616..38c76cd737 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,6 +28,7 @@
   #:use-module (guix svn-download)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
   #:use-module (guix build utils)
@@ -1104,3 +1106,40 @@ and displaying decoded target responses.
 @end enumerate")
     (home-page "https://www.freecalypso.org/")
     (license license:public-domain)))
+
+(define-public stlink
+  (package
+    (name "stlink")
+    (version "1.5.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/texane/stlink/archive/v"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "01z1cz1a5xbbhd163qrqcgp4bi1k145pb80jmwdz50g7sfzmy570"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f                      ;no tests
+       #:configure-flags
+       (let* ((out (assoc-ref %outputs "out"))
+              (etc (in-vicinity out "etc"))
+              (modprobe (in-vicinity etc "modprobe.d"))
+              (udev-rules (in-vicinity etc "udev/rules.d")))
+         (list (string-append "-DSTLINK_UDEV_RULES_DIR=" udev-rules)
+               (string-append "-DSTLINK_MODPROBED_DIR=" modprobe)))))
+    (inputs
+     `(("libusb" ,libusb)))
+    (synopsis "Programmer for STM32 Discovery boards")
+    (description "This package provides a firmware programmer for the STM32
+Discovery boards.  It supports two versions of the chip: ST-LINK/V1 (on
+STM32VL discovery kits) and ST-LINK/V2 (on STM32L discovery and later kits).
+Two different transport layers are used: ST-LINK/V1 uses SCSI passthru
+commands over USB, and ST-LINK/V2 and ST-LINK/V2-1 (seen on Nucleo boards) use
+raw USB commands.")
+    (home-page "https://github.com/texane/stlink")
+    ;; The flashloaders/stm32l0x.s and flashloaders/stm32lx.s source files are
+    ;; licensed under the GPLv2+.
+    (license (list license:bsd-3 license:gpl2+))))

From 5165fb40f4a730b36cddeab6ae894d360e727639 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Thu, 4 Oct 2018 03:02:30 +0200
Subject: [PATCH 519/909] gnu: Add java-fasterxml-jackson-modules-base-mrbean.

* gnu/packages/java.scm (java-fasterxml-jackson-modules-base-mrbean): New
variable.
---
 gnu/packages/java.scm | 49 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 5207c6cc64..96da495c29 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -7664,6 +7664,55 @@ configuration.")
     (description "This package is the jaxb annotations module for jackson.")
     (license license:asl2.0))); found on wiki.fasterxml.com/JacksonLicensing
 
+(define-public java-fasterxml-jackson-modules-base-mrbean
+  (package
+    (name "java-fasterxml-jackson-modules-base-mrbean")
+    (version "2.9.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/FasterXML/"
+                                  "jackson-modules-base/archive/"
+                                  "jackson-modules-base-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1wws95xi8sppp6b0k2vvjdjyynl20r1a4dwrhai08lzlria6blp5"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "jackson-modules-base-mrbean.jar"
+       #:source-dir "mrbean/src/main/java"
+       #:test-dir "mrbean/src/test"
+       #:test-exclude
+       ;; Base class for tests
+       (list "**/BaseTest.java")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'generate-PackageVersion.java
+           (lambda _
+             (let* ((out (string-append "mrbean/src/main/java/com/fasterxml/"
+                                        "jackson/module/mrbean/PackageVersion.java"))
+                    (in (string-append out ".in")))
+               (copy-file in out)
+               (substitute* out
+                 (("@package@") "com.fasterxml.jackson.module.mrbean")
+                 (("@projectversion@") ,version)
+                 (("@projectgroupid@") "com.fasterxml.jackson.module.mrbean")
+                 (("@projectartifactid@") "jackson-module-mrbean")))
+             #t)))))
+    (inputs
+     `(("java-asm" ,java-asm)
+       ("java-fasterxml-jackson-annotations"
+        ,java-fasterxml-jackson-annotations)
+       ("java-fasterxml-jackson-core" ,java-fasterxml-jackson-core)
+       ("java-fasterxml-jackson-databind" ,java-fasterxml-jackson-databind)))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (home-page "https://github.com/FasterXML/jackson-modules-base")
+    (synopsis "POJO type materialization for Java")
+    (description "This package implements POJO type materialization.
+Databinders can construct implementation classes for Java interfaces as part
+of deserialization.")
+    (license license:asl2.0)))
+
 (define-public java-snakeyaml
   (package
     (name "java-snakeyaml")

From 84ae0e29fd4fea418db450aa42b611b6d90d962e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 3 Oct 2018 22:31:03 +0200
Subject: [PATCH 520/909] gnu: rtags: Don't use unstable tarball.

* gnu/packages/code.scm (rtags)[source]: Use GIT-FETCH and GIT-FILE-NAME.
---
 gnu/packages/code.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 4264e292bd..98a86b763f 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -403,13 +403,13 @@ functionality such as HTML output.")
   (package
     (name "rtags")
     (version "2.18")
-    (home-page "https://github.com/Andersbakken/rtags")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append home-page "/archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Andersbakken/rtags.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (patches (search-patches "rtags-separate-rct.patch"))
        (modules '((guix build utils)))
        (snippet
@@ -424,7 +424,7 @@ functionality such as HTML output.")
              #t)))
        (sha256
         (base32
-         "0scjbp1z201q8njvrxqz7lk2m9b6k2rxd5q1shrng6532r7ndif2"))))
+         "0raqjbkl1ykga4ahgl9xw49cgh3cyqcf42z36z7d6fz1fw192kg0"))))
     (build-system cmake-build-system)
     (arguments
      '(#:build-type "RelWithDebInfo"
@@ -442,6 +442,7 @@ functionality such as HTML output.")
        ("lua" ,lua)
        ("rct" ,rct)
        ("selene" ,selene)))
+    (home-page "https://github.com/Andersbakken/rtags")
     (synopsis "Indexer for the C language family with Emacs integration")
     (description
      "RTags is a client/server application that indexes C/C++ code and keeps a

From 5eff43804eaed5744967f83edbaeb7ffdb77aec1 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 12:36:50 +0200
Subject: [PATCH 521/909] gnu: Add memtest86+.

* gnu/packages/hardware.scm (memtest86+): New public variable.
---
 gnu/packages/hardware.scm | 61 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)

diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm
index f77336e504..62f6316bca 100644
--- a/gnu/packages/hardware.scm
+++ b/gnu/packages/hardware.scm
@@ -18,6 +18,7 @@
 
 (define-module (gnu packages hardware)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages linux)
@@ -74,6 +75,66 @@ calibrated, and restored when the calibration is applied.")
     (license (list license:bsd-3        ; FindDDCUtil.cmake
                    license:gpl2+))))    ; everything else
 
+;; Distinct from memtest86, which is obsolete.
+(define-public memtest86+
+  (package
+    (name "memtest86+")
+    ;; Update the description when/if UEFI support is released.
+    (version "5.01")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://www.memtest.org/download/5.01/memtest86+-"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "0fch1l55753y6jkk0hj8f6vw4h1kinkn9ysp22dq5g9zjnvjf88l"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:system "i686-linux"            ; the result runs outside of any OS
+       #:tests? #f                      ; no way to test this
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ; no configure script
+         (replace 'build
+           ;; The default 'make all' does wonderful things, like scp(1) a file to
+           ;; 192.168.0.12. Build the bootable images and nothing more.
+           (lambda _
+             (invoke "make"
+                     "memtest"          ; ELF executable
+                     "memtest.bin")))   ; DOS/MBR boot sector
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (lib (string-append out "/lib/memtest86+"))
+                    (doc (string-append out "/share/doc/memtest86+-" ,version)))
+               (for-each
+                (lambda (file)
+                  (install-file file lib))
+                (list "memtest"
+                      "memtest.bin"))
+               (for-each
+                (lambda (file)
+                  (install-file file doc))
+                (list "FAQ"
+                      "README"))))))))
+    (native-inputs
+     ;; Newer GCCs fail with a deluge of "multiple definition of `__foo'" errors.
+     `(("gcc" ,gcc-4.9)))
+    (supported-systems (list "i686-linux" "x86_64-linux"))
+    (home-page "https://www.memtest.org/")
+    (synopsis "Thorough real-mode memory tester")
+    (description
+     "Memtest86+ is a thorough, stand-alone memory test for x86 systems.  It
+repeatedly writes different patterns to all memory locations, reads them back
+again, and verifies whether the result is the same as what was written.  This
+can help debug even intermittent and non-deterministic errors.
+
+It runs independently of any operating system, at computer boot-up, so that it
+can scan as much of your RAM as possible for hardware defects.
+
+Memtest86+ cannot currently be used on computers booted with UEFI.")
+    (license license:gpl2)))
+
 (define-public msr-tools
   (package
     (name "msr-tools")

From fb5412511479c19b3e4c884e9cc65e652ea923e2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 16:11:22 +0200
Subject: [PATCH 522/909] gnu: Add memtester.

* gnu/packages/hardware.scm (memtester): New public variable.
---
 gnu/packages/hardware.scm | 51 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm
index 62f6316bca..02ab9e2e00 100644
--- a/gnu/packages/hardware.scm
+++ b/gnu/packages/hardware.scm
@@ -116,7 +116,8 @@ calibrated, and restored when the calibration is applied.")
                 (lambda (file)
                   (install-file file doc))
                 (list "FAQ"
-                      "README"))))))))
+                      "README"))
+               #t))))))
     (native-inputs
      ;; Newer GCCs fail with a deluge of "multiple definition of `__foo'" errors.
      `(("gcc" ,gcc-4.9)))
@@ -135,6 +136,54 @@ can scan as much of your RAM as possible for hardware defects.
 Memtest86+ cannot currently be used on computers booted with UEFI.")
     (license license:gpl2)))
 
+(define-public memtester
+  (package
+    (name "memtester")
+    (version "4.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       ;; Even the latest release is available under 'old-versions/'.
+       (uri (string-append "http://pyropus.ca/software/memtester/old-versions/"
+                           "memtester-" version ".tar.gz"))
+       (sha256
+        (base32 "127xymmyzb9r6dxqrwd69v7gf8csv8kv7fjvagbglf3wfgyy5pzr"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (list "CC=gcc")
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           ;; This is a home-brewed configuration system where the cc/ld command
+           ;; lines are stored in one-line files.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out")))
+               (substitute* (list "conf-cc" "conf-ld")
+                 (("^cc") "gcc"))
+               (substitute* "Makefile"
+                 (("(INSTALLPATH.*=).*" _ assignment)
+                  (string-append assignment out)))
+               #t)))
+         (replace 'check
+           ;; There is no test suite. Test some RAM for a single iteration.
+           (lambda _
+             (invoke "./memtester" "64K" "1"))))))
+    (home-page "http://pyropus.ca/software/memtester/")
+    (synopsis "User-space memory subsystem tester")
+    (description
+     "Memtester stress-tests the memory subsystem of your operating system and
+computer.  It repeatedly writes different patterns to all memory locations,
+reads them back again, and verifies whether the result is the same as what was
+written.  This can help debug even intermittent and non-deterministic errors.
+
+Memtester runs entirely in user space.  This means that you don't need to reboot
+to test your memory, but also that it's not possible to test all of the RAM
+installed in the system.
+
+It can also be told to test memory starting at a particular physical address.")
+    (license license:gpl2)))
+
 (define-public msr-tools
   (package
     (name "msr-tools")

From 20377e4a99d7855685f29433059d53fca2761ce9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 3 Oct 2018 02:48:01 +0200
Subject: [PATCH 523/909] gnu: rubberband: Use HTTPS home page.

* gnu/packages/audio.scm (rubberband)[home-page]: Use HTTPS.
---
 gnu/packages/audio.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 95cc2ed68c..c92b5056d1 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2245,7 +2245,7 @@ aimed at audio/musical applications.")
        ("vamp" ,vamp)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-    (home-page "http://breakfastquay.com/rubberband/")
+    (home-page "https://breakfastquay.com/rubberband/")
     (synopsis "Audio time-stretching and pitch-shifting library")
     (description
      "Rubber Band is a library and utility program that permits changing the

From 8d54e7ff221f2679cd2677bf483bdfb057b0a35e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 00:14:21 +0200
Subject: [PATCH 524/909] gnu: wpa-supplicant-gui: Remove redundant code.

* gnu/packages/admin.scm (wpa-supplicant-gui)[arguments]: Remove
substitution already handled by the build system.
---
 gnu/packages/admin.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index a0ab431ddd..fa60cadd01 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1194,9 +1194,6 @@ This package provides the 'wpa_supplicant' daemon and the 'wpa_cli' command.")
                     (lambda* (#:key inputs outputs #:allow-other-keys)
                       (let ((out (assoc-ref outputs "out"))
                             (qt '("qtbase" "qtsvg")))
-                        (substitute* "wpa_gui.desktop"
-                          (("Exec=wpa_gui")
-                           (string-append "Exec=" out "/bin/wpa_gui")))
                         (install-file "wpa_gui" (string-append out "/bin"))
                         (install-file "wpa_gui.desktop"
                                       (string-append out "/share/applications"))

From 18995af2cdb8101af099ff8e62c185425096ec7a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 24 Sep 2018 20:32:07 +0200
Subject: [PATCH 525/909] gnu: Add freedroidrpg.

* gnu/packages/games.scm (freedroidrpg): New public variable.
---
 gnu/packages/games.scm | 53 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 86d6973a9a..ec92f508bc 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -364,6 +364,59 @@ played.  Freedoom complements the Doom engine with free levels, artwork, sound
 effects and music to make a completely free game.")
    (license license:bsd-3)))
 
+(define-public freedroidrpg
+  (package
+    (name "freedroidrpg")
+    (version "0.16.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://ftp.osuosl.org/pub/freedroid/"
+                           "freedroidRPG-" (version-major+minor version) "/"
+                           "freedroidRPG-" version ".tar.gz"))
+       (sha256
+        (base32 "0n4kn38ncmcy3lrxmq8fjry6c1z50z4q1zcqfig0j4jb0dsz2va2"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list
+        (string-append "CFLAGS="
+                       "-I" (assoc-ref %build-inputs "sdl-gfx") "/include/SDL "
+                       "-I" (assoc-ref %build-inputs "sdl-image") "/include/SDL "
+                       "-I" (assoc-ref %build-inputs "sdl-mixer") "/include/SDL")
+        "--enable-opengl")
+       ;; FIXME: the test suite fails with the following error output:
+       ;;   4586 Segmentation fault      env SDL_VIDEODRIVER=dummy \
+       ;;   SDL_AUDIODRIVER=dummy ./src/freedroidRPG -nb text
+       #:tests? #f))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("glu" ,glu)
+       ("libjpeg" ,libjpeg)
+       ("libogg" ,libogg)
+       ("libpng" ,libpng)
+       ("libvorbis" ,libvorbis)
+       ("mesa" ,mesa)
+       ("python" ,python-wrapper)
+       ("sdl" ,sdl)
+       ("sdl-gfx" ,sdl-gfx)
+       ("sdl-image" ,sdl-image)
+       ("sdl-mixer" ,sdl-mixer)
+       ("zlib" ,zlib)))
+    (home-page "http://www.freedroid.org/")
+    (synopsis "Isometric role-playing game against killer robots")
+    (description
+     "Freedroid RPG is an @dfn{RPG} (Role-Playing Game) with isometric graphics.
+The game tells the story of a world destroyed by a conflict between robots and
+their human masters.  To restore peace to humankind, the player must complete
+numerous quests while fighting off rebelling robots---either by taking control
+of them, or by simply blasting them to pieces with melee and ranged weapons in
+real-time combat.")
+    (license (list license:expat        ; lua/
+                   license:gpl3         ; src/gen_savestruct.py
+                   license:gpl2+))))    ; the rest
+
 (define-public golly
   (package
     (name "golly")

From 99f97a775244d932e55e0546ee90d43a8110c4b7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 23:19:45 +0200
Subject: [PATCH 526/909] gnu: packagekit: Update to 1.1.11.

* gnu/packages/freedesktop.scm (packagekit): Update to 1.1.11.
---
 gnu/packages/freedesktop.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 626d883648..5cc2699ad8 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -349,7 +349,7 @@ of a the system to know what users are logged in, and where.")
 (define-public packagekit
   (package
     (name "packagekit")
-    (version "1.1.10")
+    (version "1.1.11")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -358,7 +358,7 @@ of a the system to know what users are logged in, and where.")
                    "PackageKit-" version ".tar.xz"))
              (sha256
               (base32
-               "1msfmb22cm4s3l6vsbr86b8s0v897sy6gcga3qg87z7640a0di2b"))))
+               "0fi6wn54y03zh5sn92nmmxkh4cd8yn44cyk0l8phw60ivfwmkh1q"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f

From 7f12d8134e43eda122d47e11ef9c5d6879ebb32d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 23:22:11 +0200
Subject: [PATCH 527/909] gnu: disorderfs: Update to 0.5.4.

* gnu/packages/file-systems.scm (disorderfs): Update to 0.5.4.
---
 gnu/packages/file-systems.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/file-systems.scm b/gnu/packages/file-systems.scm
index 3c9d7d49c1..b195019866 100644
--- a/gnu/packages/file-systems.scm
+++ b/gnu/packages/file-systems.scm
@@ -107,7 +107,7 @@ single file can be mounted.")
 (define-public disorderfs
   (package
     (name "disorderfs")
-    (version "0.5.3")
+    (version "0.5.4")
     (source
      (origin
        (method git-fetch)
@@ -117,7 +117,7 @@ single file can be mounted.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1nmhfvxpvz3xsfxl9wqnh6r2l5m7hjq6n0vpblsl5xdcvwaqcf50"))))
+         "1mw4ix9h17ikki8p2rxdvzp87rcm1c7by5lvfn5gxlxr7hlj9f8g"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

From a926109d623b0faa0f09855e7647a629a45f979a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 23:29:04 +0200
Subject: [PATCH 528/909] gnu: ndctl: Return #t from phases.

* gnu/packages/disk (ndctl)[arguments]: Rename inaccurately named
'autogen' phase to 'patch-FHS-file-names'. Explicitly return #t.
---
 gnu/packages/disk.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 58c867d765..fa3a0431a5 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -630,14 +630,15 @@ passphrases.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
+         (add-after 'unpack 'patch-FHS-file-names
            (lambda _
              (substitute* "autogen.sh"
                (("/bin/sh") (which "sh")))
              (substitute* "git-version-gen"
                (("/bin/sh") (which "sh")))
              (substitute* "git-version"
-               (("/bin/bash") (which "bash"))))))
+               (("/bin/bash") (which "bash")))
+             #t)))
        #:make-flags
        (let ((out (assoc-ref %outputs "out")))
          (list (string-append "BASH_COMPLETION_DIR=" out

From 9e783d0bf22a7ff965105eb45f6c179a832bbabf Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 1 Oct 2018 23:11:08 +0200
Subject: [PATCH 529/909] gnu: ddcutil: Update to 0.9.2.

* gnu/packages/hardware.scm (ddcutil): Update to 0.9.2.
---
 gnu/packages/hardware.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm
index 02ab9e2e00..52bc3d0527 100644
--- a/gnu/packages/hardware.scm
+++ b/gnu/packages/hardware.scm
@@ -36,14 +36,14 @@
 (define-public ddcutil
   (package
     (name "ddcutil")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://www.ddcutil.com/tarballs/"
                            name "-" version ".tar.gz"))
        (sha256
-        (base32 "1b4bm3zhk5vnad6fxf0mn8nrlj3fngifl7nzxgxw0n56hlv7ccv0"))))
+        (base32 "0nhi261vf2n3jpi0a0n6659911kxi3lj7a4h7cmv0ip6sbb8rk88"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))

From 1f2cf5d9db2d9991822064cf1a3c3a7082bab5da Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 06:12:18 +0200
Subject: [PATCH 530/909] gnu: nickle: Update to 2.82.

* gnu/packages/nickle.scm (nickle): Update to 2.82.
---
 gnu/packages/nickle.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/nickle.scm b/gnu/packages/nickle.scm
index 860c111f43..c8179419bb 100644
--- a/gnu/packages/nickle.scm
+++ b/gnu/packages/nickle.scm
@@ -28,14 +28,14 @@
 (define-public nickle
   (package
     (name "nickle")
-    (version "2.81")
+    (version "2.82")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://nickle.org/release/nickle-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1daqsflnqqgfkq6w6dknbm42avz70f5qxn7qidvgp472i4a37acr"))))
+                "0jy96z01qbrnmsrywn5mfa14615qdix6b8520qd65c6yjyrk8gs0"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("readline" ,readline)))

From b1d30f46c10123fc5e38ac6aff8a1b2b3773b72a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 06:04:02 +0200
Subject: [PATCH 531/909] gnu: imapfilter: Don't use unstable tarball.

* gnu/packages/mail.scm (imapfilter)[source]: Use GIT-FETCH and GIT-FILE-NAME.
---
 gnu/packages/mail.scm | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 5435f89c42..048218cc57 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -2559,14 +2559,13 @@ PGP handling, multiple servers, and secure connections.")
     (version "2.6.11")
     (source
      (origin
-       (method url-fetch)
-       (uri
-        (string-append "https://github.com/lefcha/imapfilter/archive/"
-                       "v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/lefcha/imapfilter.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "1yslvwr3w5fnl06gfrp0lim8zdlasx3cvgd2fsqi0695xnb9bsms"))))
+        (base32 "0cjnp7vqmgqym2zswabkmwlbj21r063vw7wkwxglj08z5qyjl5ps"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f

From 88abd73eeb81a6b77069345252a7138583a1fda4 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 06:05:31 +0200
Subject: [PATCH 532/909] gnu: imapfilter: Update to 2.6.12.

* gnu/packages/mail.scm (imapfilter): Update to 2.6.12.
---
 gnu/packages/mail.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 048218cc57..7348719ede 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -2556,7 +2556,7 @@ PGP handling, multiple servers, and secure connections.")
 (define-public imapfilter
   (package
     (name "imapfilter")
-    (version "2.6.11")
+    (version "2.6.12")
     (source
      (origin
        (method git-fetch)
@@ -2565,7 +2565,7 @@ PGP handling, multiple servers, and secure connections.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0cjnp7vqmgqym2zswabkmwlbj21r063vw7wkwxglj08z5qyjl5ps"))))
+        (base32 "0vzpc54fjf5vb5vx5w0fl20xvx1k9cg6a3hbl86mm8kwsqf3wrab"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f

From 91a3c8005d5d28afa7821db2f942fede9b9cf99e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 06:25:53 +0200
Subject: [PATCH 533/909] gnu: rpm: Update to 4.14.2.

* gnu/packages/package-management.scm (rpm): Update to 4.14.2.
[arguments]: Rename 'set-nspr-search-path' phase to
'set-nss-library-path' and remove CPATH work-around.
Remove obsolete 'fix-rpm-symlinks' phase.
[home-page]: Drop www.
---
 gnu/packages/package-management.scm | 32 ++++++-----------------------
 1 file changed, 6 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 69788c9463..42172d8242 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -495,7 +495,7 @@ symlinks to the files in a common directory such as /usr/local.")
 (define-public rpm
   (package
     (name "rpm")
-    (version "4.13.0.2")
+    (version "4.14.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://ftp.rpm.org/releases/rpm-"
@@ -503,40 +503,20 @@ symlinks to the files in a common directory such as /usr/local.")
                                   version ".tar.bz2"))
               (sha256
                (base32
-                "1521y4ghjns449kzpwkjn9cksh686383xnfx0linzlalqc3jqgig"))))
+                "0armd7dqr8bl0isx8l4xlylm7dikasmxhhcbz336fkp2x30w5jw0"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--with-external-db"   ;use the system's bdb
                            "--enable-python"
                            "--without-lua")
        #:phases (modify-phases %standard-phases
-                  (add-before 'configure 'set-nspr-search-path
+                  (add-before 'configure 'set-nss-library-path
                     (lambda* (#:key inputs #:allow-other-keys)
-                      ;; nspr.pc contains the right -I flag pointing to
-                      ;; 'include/nspr', but unfortunately 'configure' doesn't
-                      ;; use 'pkg-config'.  Thus, augment CPATH.
-                      ;; Likewise for NSS.
-                      (let ((nspr (assoc-ref inputs "nspr"))
-                            (nss  (assoc-ref inputs "nss")))
-                        (setenv "CPATH"
-                                (string-append (getenv "C_INCLUDE_PATH") ":"
-                                               nspr "/include/nspr:"
-                                               nss "/include/nss"))
+                      (let ((nss (assoc-ref inputs "nss")))
                         (setenv "LIBRARY_PATH"
                                 (string-append (getenv "LIBRARY_PATH") ":"
                                                nss "/lib/nss"))
-                        #t)))
-                  (add-after 'install 'fix-rpm-symlinks
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      ;; 'make install' gets these symlinks wrong.  Fix them.
-                      (let* ((out (assoc-ref outputs "out"))
-                             (bin (string-append out "/bin")))
-                        (with-directory-excursion bin
-                          (for-each (lambda (file)
-                                      (delete-file file)
-                                      (symlink "rpm" file))
-                                    '("rpmquery" "rpmverify"))
-                          #t)))))))
+                        #t))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)))
     (inputs
@@ -552,7 +532,7 @@ symlinks to the files in a common directory such as /usr/local.")
        ("bzip2" ,bzip2)
        ("zlib" ,zlib)
        ("cpio" ,cpio)))
-    (home-page "http://www.rpm.org/")
+    (home-page "http://rpm.org/")
     (synopsis "The RPM Package Manager")
     (description
      "The RPM Package Manager (RPM) is a command-line driven package

From 104f475f9b95953a67640a82127ade689931a6e7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 05:58:52 +0200
Subject: [PATCH 534/909] gnu: perl-string-copyright: Update to 0.003006.

* gnu/packages/license.scm (perl-string-copyright): Update to 0.003006.
---
 gnu/packages/license.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/license.scm b/gnu/packages/license.scm
index 44c7a1bb2a..e50ce831b1 100644
--- a/gnu/packages/license.scm
+++ b/gnu/packages/license.scm
@@ -61,7 +61,7 @@ Regexp::Pattern is a convention for organizing reusable regex patterns.")
 (define-public perl-string-copyright
   (package
     (name "perl-string-copyright")
-    (version "0.003005")
+    (version "0.003006")
     (source
      (origin
        (method url-fetch)
@@ -70,7 +70,7 @@ Regexp::Pattern is a convention for organizing reusable regex patterns.")
              version ".tar.gz"))
        (sha256
         (base32
-         "12c6x4c10gr46ryc3dpwgfi6wggmgy4a1ls2hwhcpdm3wvzy5619"))))
+         "0fzymv065nn3glwnw34nkyadzw2dh4rcz8avmki4zrnk4k45m01a"))))
     (build-system perl-build-system)
     (native-inputs
      `(("perl-number-range" ,perl-number-range)))

From fe30eb6d24dd750a124cb0c1f6300fc3d5518d7f Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 05:50:49 +0200
Subject: [PATCH 535/909] gnu: ephoto: Fix typos in description.

* gnu/packages/enlightenment.scm (ephoto)[description]: Fix typos.
Wrap at 80 columns.
---
 gnu/packages/enlightenment.scm | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index c0335016f8..1a0ebba304 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -464,19 +464,22 @@ and in creating applications based on the Enlightenment Foundation Library suite
     (home-page "http://smhouston.us/ephoto/")
     (synopsis "EFL image viewer/editor/manipulator/slideshow creator")
     (description "Ephoto is an image viewer and editor written using the
-@dfn{Enlightenment Foundation Libraries} (EFL).  It focuses on simplicity and ease
-of use, while taking advantage of the speed and small footprint the EFL provide.
+@dfn{Enlightenment Foundation Libraries} (EFL).  It focuses on simplicity and
+ease of use, while taking advantage of the speed and small footprint the EFL
+provide.
 
 Ephoto’s features include:
 @enumerate
-@item Browsing the filesystem and displaying images in an easy to use grid view.
+@item Browsing the file system and displaying images in an easy-to-use grid view.
 @item Browsing images in a single image view format.
 @item Viewing images in a slideshow.
 @item Editing your image with features such as cropping, auto enhance,
 blurring, sharpening, brightness/contrast/gamma adjustments, hue/saturation/value
 adjustments, and color level adjustment.
-@item Applying artistic filters to your image such as black and white and old photo.
-@item Drag And Drop along with file operations to easy maintain your photo directories.
+@item Applying artistic filters to your image such as black and white and old
+photo.
+@item Drag And Drop along with file operations to easily maintain your photo
+directories.
 @end enumerate\n")
     (license (list
                license:bsd-2 ; Ephoto's thumbnailing code

From 1fc346de4eb6881c087eae2c603a761b510e28f2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 05:45:02 +0200
Subject: [PATCH 536/909] gnu: retroarch: Don't use unstable tarball.

* gnu/packages/emulators.scm (retroarch)[source]: Use GIT-FETCH and GIT-FILE-NAME.
---
 gnu/packages/emulators.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index 443137f141..a07ce29243 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -1058,12 +1058,13 @@ emulation community.  It provides highly accurate emulation.")
     (version "1.7.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/libretro/RetroArch/archive/v"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/libretro/RetroArch.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0h6y2hpjg4b470jvn9ghwp0k3a527sbb6xhia17frlm9w9v5028w"))))
+        (base32 "1gagdwydj6kl3gzi9z1rjgrbjvi325f8159fdaryzf5gjj8avp8m"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests

From 689ca9ba23e8c5003cba5163235e9c5fb1206f16 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 05:56:12 +0200
Subject: [PATCH 537/909] gnu: retroarch: Update to 1.7.5.

* gnu/packages/emulators.scm (retroarch): Update to 1.7.5.
---
 gnu/packages/emulators.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm
index a07ce29243..438e9df1fc 100644
--- a/gnu/packages/emulators.scm
+++ b/gnu/packages/emulators.scm
@@ -1055,7 +1055,7 @@ emulation community.  It provides highly accurate emulation.")
 (define-public retroarch
   (package
     (name "retroarch")
-    (version "1.7.4")
+    (version "1.7.5")
     (source
      (origin
        (method git-fetch)
@@ -1064,7 +1064,7 @@ emulation community.  It provides highly accurate emulation.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1gagdwydj6kl3gzi9z1rjgrbjvi325f8159fdaryzf5gjj8avp8m"))))
+        (base32 "1jfpgl34jjxn3dvxd1kd564swkw7v98hnn562v998b7vllz3dxdm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests

From cd81c9e2a76f825534b1c48e722926d5c70fca8f Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Thu, 4 Oct 2018 08:12:39 +0200
Subject: [PATCH 538/909] gnu: mpv: Update to 0.29.1.

* gnu/packages/video.scm (mpv): Update to 0.29.1.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 54ffef86de..2f6a89e14d 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1121,7 +1121,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.")
 (define-public mpv
   (package
     (name "mpv")
-    (version "0.29.0")
+    (version "0.29.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1129,7 +1129,7 @@ SVCD, DVD, 3ivx, DivX 3/4/5, WMV and H.264 movies.")
                     ".tar.gz"))
               (sha256
                (base32
-                "06bk8836brzik1qmq8kycwg5n35r438sd2176k6msjg5rrwghakp"))
+                "08x63hlpj6s8xixmdbx6raff5p5mih7cnk0bcql9f3wrs5hx9ygr"))
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system waf-build-system)
     (native-inputs

From 89fdd9ee0cc8817283449b33a8c1a2604c575c7e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 3 Oct 2018 22:44:11 +0200
Subject: [PATCH 539/909] services: rottlog: Use command strings in the mcron
 jobs.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/services/admin.scm (default-jobs): Remove the lambda around
"/…/bin/rottlog" to make "herd schedule mcron" more
transparent (otherwise it just says "Lambda function").
---
 gnu/services/admin.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/gnu/services/admin.scm b/gnu/services/admin.scm
index f08c896334..d7bda61ed7 100644
--- a/gnu/services/admin.scm
+++ b/gnu/services/admin.scm
@@ -125,11 +125,9 @@ for ROTATION."
 
 (define (default-jobs rottlog)
   (list #~(job '(next-hour '(0))                  ;midnight
-               (lambda ()
-                 (system* #$(file-append rottlog "/sbin/rottlog"))))
+               #$(file-append rottlog "/sbin/rottlog"))
         #~(job '(next-hour '(12))                 ;noon
-               (lambda ()
-                 (system* #$(file-append rottlog "/sbin/rottlog"))))))
+               #$(file-append rottlog "/sbin/rottlog"))))
 
 (define-record-type* <rottlog-configuration>
   rottlog-configuration make-rottlog-configuration

From 666fb2884ab487ae69ed3541c4adaf0b4fb6ef41 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 4 Oct 2018 09:46:43 +0200
Subject: [PATCH 540/909] gnu: r-acclma: Fix uses of @acronym in description.

* gnu/packages/cran.scm (r-acclma)[description]: Fix order of arguments
to @acronym.  The wrong order was causing 'stexi->shtml' to fail (match
error).
---
 gnu/packages/cran.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index a1bf750da6..efcc2dccb5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -6243,12 +6243,12 @@ lot.")
     (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
     (synopsis "ACC & LMA graph plotting")
     (description
-     "This package contains a function that imports data from a @acronym{Comma-Separated
-Values, @acronym{CSV}} file, or uses manually entered data from the format (x,
-y, weight) and plots the appropriate @acronym{Absolute Concentration Curve,
-@acronym{ACC}} vs @acronym{Line of Independence, @acronym{LOI}} graph and
-@acronym{@acronym{LOI} Minus @acronym{ACC}, @acronym{LMA}} graph.  The main
-function is plotLMA (source file, header) that takes a data set and plots the
+     "This package contains a function that imports data from a @acronym{CSV,
+Comma-Separated Values} file, or uses manually entered data from the format (x,
+y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
+Curve} vs @acronym{LOI, Line of Independence} graph and
+@acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph.  The main
+function is @code{plotLMA} (source file, header) that takes a data set and plots the
 appropriate @acronym{LMA} and @acronym{ACC} graphs.  If no source file (a
 string) was passed, a manual data entry window is opened.  The header parameter
 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has

From 63856931dbe1e72311b472347331ce1c16b0de0b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20H=C3=B6fling?=
 <bjoern.hoefling@bjoernhoefling.de>
Date: Wed, 3 Oct 2018 22:28:19 +0200
Subject: [PATCH 541/909] gnu: opencv: Update to 3.4.3.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

[[PGP Signed Part:Good signature from BF286CB6593E5FFD Björn Höfling <bjoern.hoefling@bjoernhoefling.de> (trust undefined) created at 2018-10-03T22:28:20+0200 using DSA]]

* gnu/packages/image-processing.scm (opencv): Update to 3.4.3.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/image-processing.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 8f80b75af4..0901dc429f 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -200,7 +200,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
 (define-public opencv
   (package
     (name "opencv")
-    (version "3.4.1")
+    (version "3.4.3")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/opencv/opencv/archive/"
@@ -208,7 +208,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
               (file-name (string-append name "-" version ".zip"))
               (sha256
                (base32
-                "1g8pvnlkzzp50amd89149hqsbvsc2hq3vk1d6a9fksdcx8ra9g94"))
+                "0pycx1pz8lj794q32mlalyc3ijqxwsyin65r26nh4yc0p71xiirp"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -345,7 +345,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
                                "opencv/opencv_extra/zip/" version))
            (file-name (string-append "opencv-extra-" version ".zip"))
            (sha256
-            (base32 "0wfh3pvfxqydf7hsccp50npcsg37sf6fqi6cd3zkc4qil9zhpbps"))))
+            (base32 "0yd1vidzbg6himxyh4yzivywijg8548kfmcn421khabnipm7l74y"))))
        ("opencv-contrib"
         ,(origin
            (method url-fetch)
@@ -353,7 +353,7 @@ integrates with various databases on GUI toolkits such as Qt and Tk.")
                                "opencv/opencv_contrib/zip/" version))
            (file-name (string-append "opencv-contrib-" version ".zip"))
            (sha256
-           (base32 "18zm0qmjcdvg90c33gzv0ws0xdaid1xpqzz2xa9l2x12qkr6zj3p"))))))
+           (base32 "0j0ci6ia1qwklp9hq07ypl0vkngj1wrgh6n98n657m5d0pyp4m0g"))))))
     (inputs `(("libjpeg" ,libjpeg)
               ("libpng" ,libpng)
               ("jasper" ,jasper)

From ff30bb010bdce50f92eea0ad64280c9701a2687d Mon Sep 17 00:00:00 2001
From: Diego Nicola Barbato <dnbarbato@posteo.de>
Date: Wed, 3 Oct 2018 22:39:34 +0200
Subject: [PATCH 542/909] gnu: escpr: Update to 1.6.30.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/cups.scm (escpr): Update to 1.6.30.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/cups.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index 986280f4cb..81e442eef1 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -656,7 +656,7 @@ HP@tie{}LaserJet, and possibly other printers.  See @file{README} for details.")
 (define-public escpr
   (package
     (name "escpr")
-    (version "1.6.20")
+    (version "1.6.30")
     ;; XXX: This currently works.  But it will break as soon as a newer
     ;; version is available since the URLs for older versions are not
     ;; preserved.  An alternative source will be added as soon as
@@ -664,12 +664,12 @@ HP@tie{}LaserJet, and possibly other printers.  See @file{README} for details.")
     (source (origin
               (method url-fetch)
               ;; The uri has to be chopped up in order to satisfy guix lint.
-              (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/07/16/23/"
-                                  "804253d188a31ae6a0f2722648248ef952afedfb/"
-                                  "epson-inkjet-printer-escpr-1.6.20-1lsb3.2.tar.gz"))
+              (uri (string-append "https://download3.ebz.epson.net/dsc/f/03/00/08/18/20/"
+                                  "e94de600e28e510c1cfa158929d8b2c0aadc8aa0/"
+                                  "epson-inkjet-printer-escpr-1.6.30-1lsb3.2.tar.gz"))
               (sha256
                (base32
-                "19800pl7kbbgdzbsy9ijmd7dm3ly4kr2h1dxypqpd075g6n0i770"))))
+                "0m8pyfkixisp0vclwxj340isn15zzisal0v2xvv66kxfd68dzf12"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

From 1d0be47ab680db938ac8da1ee65e1de91e198f67 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 4 Oct 2018 10:24:34 +0200
Subject: [PATCH 543/909] progress: Generate valid 'download-progress' traces
 when the size is unknown.

Fixes <https://bugs.gnu.org/32895>.
Reported by Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>.

* guix/progress.scm (progress-reporter/trace): In 'stop', make sure SIZE
is an integer.  Previously we'd generate a "@ download-progress" trace
with #f for the 'transferred' number when downloading files whose size
is not known in advance.
---
 guix/progress.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/guix/progress.scm b/guix/progress.scm
index 3b9ff408cd..f846944952 100644
--- a/guix/progress.scm
+++ b/guix/progress.scm
@@ -304,12 +304,12 @@ progress reports, write \"build trace\" lines to be processed elsewhere."
                      log-port)))
    (report (rate-limited report-progress %progress-interval))
    (stop (lambda ()
-           (report-progress size)
-           (display (format #f "@ download-succeeded ~a ~a ~a~%"
-                            file url
-                            (or (and=> (stat file #f) stat:size)
-                                size))
-                    log-port)))))
+           (let ((size (or (and=> (stat file #f) stat:size)
+                           size)))
+             (report-progress size)
+             (display (format #f "@ download-succeeded ~a ~a ~a~%"
+                              file url size)
+                      log-port))))))
 
 ;; TODO: replace '(@ (guix build utils) dump-port))'.
 (define* (dump-port* in out

From ca91d3522540851a327f0be22dc33cce1749e8d5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 4 Oct 2018 11:21:37 +0200
Subject: [PATCH 544/909] gnu: guix: Update to 1d0be47.

* gnu/packages/package-management.scm (guix): Update to 1d0be47.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 42172d8242..500abd5125 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -101,8 +101,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "0.15.0")
-        (commit "7fed9353ece5974ff431fa666a530da237a12085")
-        (revision 4))
+        (commit "1d0be47ab680db938ac8da1ee65e1de91e198f67")
+        (revision 5))
     (package
       (name "guix")
 
@@ -118,7 +118,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "11j13xszjcrf3barf38bixx3hbrfj5w81fskjp8gn6m42knx1yal"))
+                  "19cn4ndmr9cqd7qh6w3nchbmdpaawdl9kc6g0v6g680vzcja417k"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

From ddf72f505939e34dc2a287170174e7e4cfe4f829 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 15:54:57 +0200
Subject: [PATCH 545/909] gnu: perl-xml-feed: Update to 0.54.

* gnu/packages/xml.scm (perl-xml-feed): Update to 0.54.
---
 gnu/packages/xml.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 2bf5ea3569..b5f44a4258 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -770,17 +770,17 @@ server, collect the answer, and finally decoding the XML to Perl.")
 (define-public perl-xml-feed
   (package
     (name "perl-xml-feed")
-    (version "0.53")
+    (version "0.54")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/D/DA/DAVECROSS/"
                                   "XML-Feed-" version ".tar.gz"))
               (sha256
                (base32
-                "07b165g6wk8kqwpl49r3n0kag6p2nrkyp3ch0h8qyxb6nrnkkq7c"))))
+                "0ydyi7wdhv8325h7j27vrlwiqxll56sn8zy5nbzhpma3nrf61bci"))))
     (build-system perl-build-system)
     (arguments
-     `(#:tests? #f)) ; Tests require internet connection
+     `(#:tests? #f))                    ; tests require internet connection
     (native-inputs
      `(("perl-module-build" ,perl-module-build)
        ("perl-uri" ,perl-uri)

From 4fab0da09651344959803015edf01adc2473354e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 15:46:01 +0200
Subject: [PATCH 546/909] gnu: html-xml-utils: Update to 7.7.

* gnu/packages/xml.scm (html-xml-utils): Update to 7.7.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index b5f44a4258..e14524a684 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -1120,7 +1120,7 @@ XSLT and EXSLT.")
 (define-public html-xml-utils
  (package
    (name "html-xml-utils")
-   (version "7.6")
+   (version "7.7")
    (source
     (origin
       (method url-fetch)
@@ -1129,7 +1129,7 @@ XSLT and EXSLT.")
             version ".tar.gz"))
       (sha256
        (base32
-        "0l97ps089byy62838wf2jwvvc465iw29z9r5kwmwcq7f3bn11y3m"))))
+        "1vwqp5q276j8di9zql3kygf31z2frp2c59yjqlrvvwcvccvkcdwr"))))
    (build-system gnu-build-system)
    (home-page "https://www.w3.org/Tools/HTML-XML-utils/")
    (synopsis "Command line utilities to manipulate HTML and XML files")

From 0136fbd167c38ef476baf1fea9354da5248c4a69 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 15:42:03 +0200
Subject: [PATCH 547/909] gnu: hexedit: Update to 1.4.2.

* gnu/packages/hexedit.scm (hexedit): Update to 1.4.2.
[source]: Use the author's more up-to-date git repository.
[native-inputs]: Add autoconf and automake.
---
 gnu/packages/hexedit.scm | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/hexedit.scm b/gnu/packages/hexedit.scm
index 88dbfb234d..9aea8e8700 100644
--- a/gnu/packages/hexedit.scm
+++ b/gnu/packages/hexedit.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2017 Gábor Boskovits <boskovits@gmail.com>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,25 +22,33 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages ncurses)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu))
 
 (define-public hexedit
   (package
     (name "hexedit")
-    (version "1.2.13")
+    (version "1.4.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "http://rigaux.org/"
-                                  name "-" version ".src.tgz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pixel/hexedit.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1mwdp1ikk64cqmagnrrps5jkn3li3n47maiqh2qc1xbp1ains4ka"))))
+                "1xsxa5mip892jkvz9jshj73y6c7j3mgp8y393ciihqlyf2nmfs67"))))
     (build-system gnu-build-system)
-    (arguments '(#:tests? #f)) ; no check target
-    (inputs `(("ncurses" ,ncurses)))
+    (arguments '(#:tests? #f))          ; no check target
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (inputs
+     `(("ncurses" ,ncurses)))
     (synopsis "View and edit files or devices in hexadecimal or ASCII")
     (description "hexedit shows a file both in ASCII and in hexadecimal.  The
 file can be a device as the file is read a piece at a time.  You can modify

From 68c0a6260fde80a5b11e286e1c964fe8eccb1d41 Mon Sep 17 00:00:00 2001
From: Arun Isaac <arunisaac@systemreboot.net>
Date: Thu, 4 Oct 2018 19:59:35 +0530
Subject: [PATCH 548/909] gnu: geos: Update to 3.7.0.

* gnu/packages/geo.scm (geos): Update to 3.7.0.
---
 gnu/packages/geo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 4275476e34..4481e21ddf 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -62,7 +62,7 @@
 (define-public geos
   (package
     (name "geos")
-    (version "3.6.2")
+    (version "3.7.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.osgeo.org/geos/geos-"
@@ -70,7 +70,7 @@
                                   ".tar.bz2"))
               (sha256
                (base32
-                "0ak5szby29l9l0vy43dm5z2g92xzdky20q1gc1kah1fnhkgi6nh4"))))
+                "1mrz778m6bd1x9k6sha5kld43kalhq79h2lynlx2jx7xjakl3gsg"))))
     (build-system gnu-build-system)
     (arguments `(#:phases
                  (modify-phases %standard-phases

From 38a9bf805d7ea476dce2a271bd93c36afb6ba3ae Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 16:09:53 +0200
Subject: [PATCH 549/909] gnu: mbedtls-apache: Update to 2.13.0 [security
 fixes].

* gnu/packages/tls.scm (mbedtls-apache): Update to 2.13.0.
[native-inputs]: Add python.
---
 gnu/packages/tls.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index bf462981ee..f92a36b6e2 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -842,7 +842,7 @@ then ported to the GNU / Linux environment.")
 (define-public mbedtls-apache
   (package
     (name "mbedtls-apache")
-    (version "2.7.6")
+    (version "2.13.0")
     (source
      (origin
        (method url-fetch)
@@ -852,13 +852,14 @@ then ported to the GNU / Linux environment.")
                            version "-apache.tgz"))
        (sha256
         (base32
-         "0fl2nrxvlgx9ja7yy3kd1zadpr98fxbvn3f6fl2mj87gryhkfqlk"))))
+         "1nh6xfyxs3mnnpgc6pancvdhv6ihz9lhsxdlg90gqa8n5r6lwfsr"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags
        (list "-DUSE_SHARED_MBEDTLS_LIBRARY=ON")))
     (native-inputs
-     `(("perl" ,perl)))
+     `(("perl" ,perl)
+       ("python" ,python)))
     (synopsis "Small TLS library")
     (description
      "@code{mbed TLS}, formerly known as PolarSSL, makes it trivially easy

From 8e87aa04979dae66a1e45b54c0f92da07745e1e6 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 17:26:57 +0200
Subject: [PATCH 550/909] gnu: hiawatha: Update to 10.8.3.

* gnu/packages/web.scm (hiawatha): Update to 10.8.3.
[source]: Also delete bundled copy of nghttp2.
[inputs]: Use mbedtls-for-hiawatha instead of vanilla mbedtls-apache.
* gnu/packages/tls.scm (mbedtls-for-hiawatha): New public variable.
---
 gnu/packages/tls.scm | 18 ++++++++++++++++++
 gnu/packages/web.scm | 15 ++++++++-------
 2 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index f92a36b6e2..715148c432 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -869,6 +869,24 @@ coding footprint.")
     (home-page "https://tls.mbed.org")
     (license license:asl2.0)))
 
+;; The Hiawatha Web server requires some specific features to be enabled.
+(define-public mbedtls-for-hiawatha
+  (hidden-package
+   (package
+     (inherit mbedtls-apache)
+     (arguments
+      (substitute-keyword-arguments
+          `(#:phases
+            (modify-phases %standard-phases
+              (add-after 'configure 'configure-extra-features
+                (lambda _
+                  (for-each (lambda (feature)
+                              (invoke "scripts/config.pl" "set" feature))
+                            (list "MBEDTLS_THREADING_C"
+                                  "MBEDTLS_THREADING_PTHREAD"))
+                  #t)))
+            ,@(package-arguments mbedtls-apache)))))))
+
 (define-public ghc-tls
   (package
     (name "ghc-tls")
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 8e776258b3..401711928d 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5173,7 +5173,7 @@ functions of Tidy.")
 (define-public hiawatha
   (package
     (name "hiawatha")
-    (version "10.7")
+    (version "10.8.3")
     (source
      (origin
        (method url-fetch)
@@ -5181,15 +5181,16 @@ functions of Tidy.")
                            "hiawatha-" version ".tar.gz"))
        (modules '((guix build utils)))
        (snippet '(begin
-                   ;; We use our packaged mbedtls, so delete the included copy.
-                   (delete-file-recursively "mbedtls")
+                   ;; We use packaged libraries, so delete the bundled copies.
+                   (for-each delete-file-recursively
+                             (list "nghttp2" "mbedtls"))
                    #t))
        (sha256
         (base32
-         "0x2zfc8kc6c7rl4gwymwmg13w1c60biv6c6c9fvzpnl59bc9jgin"))))
+         "0w7047pwijhsbvvv1qjynp7gvn0nil56w82f7ax0gabrg7ddzk6s"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f ; No tests included
+     `(#:tests? #f                      ; no tests included
        #:configure-flags (list (string-append "-DUSE_SYSTEM_MBEDTLS=on")
                                (string-append "-DENABLE_TOMAHAWK=on")
                                (string-append "-DWEBROOT_DIR="
@@ -5212,8 +5213,8 @@ functions of Tidy.")
                (wrap-program (string-append sbin "/hiawatha")
                  `("PATH" ":" prefix (,mbed)))))))))
     (inputs
-     ;; TODO: package "hiawatha-monitor", an optional dependency of "hiawatha"
-     `(("mbedtls-apache" ,mbedtls-apache) ;Hiawatha includes this version.
+     ;; TODO: package "hiawatha-monitor", an optional dependency of "hiawatha".
+     `(("mbedtls-apache" ,mbedtls-for-hiawatha)
        ("zlib" ,zlib)
        ("libxslt" ,libxslt)
        ("libxml2" ,libxml2)))

From aff91b0d0bc4c4459625558dc547af3567b6e5f3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 19:04:37 +0200
Subject: [PATCH 551/909] gnu: hiawatha: Support HTTP/2.

* gnu/packages/web.sck (hiawatha)[arguments]: USE_SYSTEM_NGHTTP2
to ENABLE_HTTP2.
[inputs]: Add nghttp2:lib.
---
 gnu/packages/web.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 401711928d..01db03e79d 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5192,6 +5192,8 @@ functions of Tidy.")
     (arguments
      `(#:tests? #f                      ; no tests included
        #:configure-flags (list (string-append "-DUSE_SYSTEM_MBEDTLS=on")
+                               (string-append "-DENABLE_HTTP2=on")
+                               (string-append "-DUSE_SYSTEM_NGHTTP2=on")
                                (string-append "-DENABLE_TOMAHAWK=on")
                                (string-append "-DWEBROOT_DIR="
                                               (assoc-ref %outputs "out")
@@ -5214,10 +5216,11 @@ functions of Tidy.")
                  `("PATH" ":" prefix (,mbed)))))))))
     (inputs
      ;; TODO: package "hiawatha-monitor", an optional dependency of "hiawatha".
-     `(("mbedtls-apache" ,mbedtls-for-hiawatha)
-       ("zlib" ,zlib)
-       ("libxslt" ,libxslt)
-       ("libxml2" ,libxml2)))
+     `(("libxslt" ,libxslt)
+       ("libxml2" ,libxml2)
+       ("mbedtls-apache" ,mbedtls-for-hiawatha)
+       ("nghttp2" ,nghttp2 "lib")
+       ("zlib" ,zlib)))
     (home-page "https://www.hiawatha-webserver.org")
     (synopsis "Webserver with focus on security")
     (description

From e14b3067e324f05a852d216aec5432cc285dfcec Mon Sep 17 00:00:00 2001
From: David Thompson <davet@gnu.org>
Date: Thu, 4 Oct 2018 11:05:06 -0400
Subject: [PATCH 552/909] gnu: guile-next: Add the correct native search paths.

* gnu/packages/guile.scm (guile-next): Add native search paths for version 3.0.
---
 gnu/packages/guile.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 6d8ab71c78..04625827c5 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -355,7 +355,15 @@ without requiring the source code to be rewritten.")
                (lambda _
                  ;; Remove this test that's bound to fail.
                  (delete-file "test-suite/tests/version.test")
-                 #t)))))))))
+                 #t))))))
+      (native-search-paths
+       (list (search-path-specification
+              (variable "GUILE_LOAD_PATH")
+              (files '("share/guile/site/3.0")))
+             (search-path-specification
+              (variable "GUILE_LOAD_COMPILED_PATH")
+              (files '("lib/guile/3.0/site-ccache"
+                       "share/guile/site/3.0"))))))))
 
 (define (make-guile-readline guile)
   (package

From 55b616fd15769c0d2f90eb8b1d0a1af6a9474a48 Mon Sep 17 00:00:00 2001
From: David Thompson <davet@gnu.org>
Date: Thu, 4 Oct 2018 12:09:55 -0400
Subject: [PATCH 553/909] gnu: guile-next: Update to commit
 6f3357b0df64c4be17e72079864c09a542f1c779.

* gnu/packages/guile.scm (guile-next): Update to commit
6f3357b0df64c4be17e72079864c09a542f1c779.
---
 gnu/packages/guile.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 04625827c5..1d330668a7 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -318,8 +318,8 @@ without requiring the source code to be rewritten.")
 
 (define-public guile-next
   ;; This is the upcoming Guile 3.0, with JIT support.
-  (let ((commit "a74b4a45fab1a78e34954bce5f031e8a9765f827")
-        (revision "0"))
+  (let ((commit "6f3357b0df64c4be17e72079864c09a542f1c779")
+        (revision "1"))
     (package
       (inherit guile-2.2)
       (name "guile-next")
@@ -331,7 +331,7 @@ without requiring the source code to be rewritten.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "0kq6mabv7j4gdlwmpz3iaddv98sc7awkl2358sg8j50sg10yw8nx"))
+                  "1c2xy5cflg0hws48914rz3z8mdmf8w3lblfic0kxnymcmdv9cbhv"))
                 (file-name (git-file-name name version))))
       (native-inputs
        `(("autoconf", autoconf)

From 7382ecd81859de878b22a6510b8262abe69d38bf Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 7 Mar 2018 16:54:43 +0100
Subject: [PATCH 554/909] gnu: Add nsd.

* gnu/packages/dns.scm (nsd): New public variable.
---
 gnu/packages/dns.scm | 71 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)

diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index 4fc1c25229..ad1a8638bc 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -289,6 +289,77 @@ asynchronous fashion.")
                    (license:non-copyleft "file://LICENSE") ; includes.h
                    license:openssl))))
 
+(define-public nsd
+  (package
+    (name "nsd")
+    (version "4.1.25")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://www.nlnetlabs.nl/downloads/nsd/nsd-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0zyzjd3wmq258jiry62ci1z23qfd0rc5ggnpmybc60xvpddgynwg"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list "--enable-pie"             ; fully benefit from ASLR
+             "--enable-ratelimit"
+             "--enable-recvmmsg"
+             "--enable-relro-now"       ; protect GOT and .dtor areas
+             "--disable-radix-tree"
+             (string-append "--with-libevent="
+                            (assoc-ref %build-inputs "libevent"))
+             (string-append "--with-ssl="
+                            (assoc-ref %build-inputs "openssl"))
+             "--with-configdir=/etc"
+             "--with-nsd_conf_file=/etc/nsd/nsd.conf"
+             "--with-logfile=/var/log/nsd.log"
+             "--with-pidfile=/var/db/nsd/nsd.pid"
+             "--with-dbfile=/var/db/nsd/nsd.db"
+             "--with-zonesdir=/etc/nsd"
+             "--with-xfrdfile=/var/db/nsd/xfrd.state"
+             "--with-zonelistfile=/var/db/nsd/zone.list")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'patch-installation-paths
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (doc (string-append out "/share/doc/" ,name "-" ,version)))
+               ;; The ‘make install’ target tries to create the parent
+               ;; directories of run-time things like ‘pidfile’ above, and
+               ;; useless empty directories like 'configdir'.  Remove such
+               ;; '$(INSTALL)' lines and install the example configuration file
+               ;; in an appropriate location.
+               (substitute* "Makefile.in"
+                 ((".*INSTALL.*\\$\\((config|pid|xfr|db)dir" command)
+                  (string-append "#" command))
+                 (("\\$\\(nsdconfigfile\\)\\.sample" file-name)
+                  (string-append doc "/examples/" file-name)))
+               #t))))
+       #:tests? #f))                    ; no tests
+    (inputs
+     `(("libevent" ,libevent)
+       ("openssl" ,openssl)))
+    (home-page "https://www.nlnetlabs.nl/projects/nsd/about/")
+    (synopsis "Authoritative DNS name server")
+    (description "@dfn{NSD}, short for Name Server Daemon, is an authoritative
+name server for the Domain Name System (@dfn{DNS}).  It aims to be a fast and
+RFC-compliant nameserver.
+
+NSD uses zone information compiled via @command{zonec} into a binary database
+file (@file{nsd.db}).  This allows fast startup of the name service daemon and
+allows syntax-structural errors in zone files to be flagged at compile time,
+before being made available to NSD service itself.  However, most traditional
+BIND-style zone files can be directly imported into NSD without modification.
+
+The collection of programs and processes that make up NSD are designed so that
+the daemon itself runs as a non-privileged user and can be easily configured to
+run in a @code{chroot} jail, thus making any security flaws in NSD less likely
+to result in system-wide compromise.")
+    (license (list license:bsd-3))))
+
 (define-public unbound
   (package
     (name "unbound")

From b9b53fb4ffa188a2dad2b3062a552877f1124750 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 21:26:38 +0200
Subject: [PATCH 555/909] gnu: hwloc: Update to 2.0.2.

* gnu/packages/mpi.scm (hwloc): Update to 2.0.2.
---
 gnu/packages/mpi.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 7dfec16fc7..fc8aadef29 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -125,7 +126,7 @@ bind processes, and much more.")
   ;; Note: 2.0 isn't the default yet, see above.
   (package
     (inherit hwloc)
-    (version "2.0.1")
+    (version "2.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.open-mpi.org/software/hwloc/v"
@@ -133,7 +134,7 @@ bind processes, and much more.")
                                   "/downloads/hwloc-" version ".tar.bz2"))
               (sha256
                (base32
-                "0jf0krj1h95flmb784ifv9vnkdnajjz00p4zbhmja7vm4v67axdr"))))
+                "1phc863d5b2fvwpyyq4mlh4rkjdslh6h0h197zmyk3prwrq7si8l"))))
 
     ;; libnuma is no longer needed.
     (inputs (alist-delete "numactl" (package-inputs hwloc)))

From d8b042326dda505c8e65789572e3dd65311ba8e3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 19:52:03 +0200
Subject: [PATCH 556/909] gnu: hiawatha: Set sane run-time directory defaults.

* gnu/packages/web.scm (hiawatha)[arguments]: Set sane default
directories. Replace the 'remove-empty-dirs' phase with a
'install-no-empty-directories' one.
---
 gnu/packages/web.scm | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 01db03e79d..c3b06b05bc 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -5195,17 +5195,20 @@ functions of Tidy.")
                                (string-append "-DENABLE_HTTP2=on")
                                (string-append "-DUSE_SYSTEM_NGHTTP2=on")
                                (string-append "-DENABLE_TOMAHAWK=on")
+                               (string-append "-DLOG_DIR=/var/log/hiawatha")
+                               (string-append "-DPID_DIR=/run")
                                (string-append "-DWEBROOT_DIR="
                                               (assoc-ref %outputs "out")
-                                              "/share/hiawatha/html"))
+                                              "/share/hiawatha/html")
+                               (string-append "-DWORK_DIR=/var/lib/hiawatha"))
        #:phases
        (modify-phases %standard-phases
-         (add-after 'install 'remove-empty-dirs
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out")))
-               ;; The directories in "var" are empty, remove them.
-               (delete-file-recursively (string-append out "/var"))
-               #t)))
+         (add-after 'unpack 'install-no-empty-directories
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("install\\(DIRECTORY DESTINATION" match)
+                (string-append "#" match)))
+             #t))
          (add-after 'install 'wrap
            (lambda* (#:key inputs outputs #:allow-other-keys)
              ;; Make sure 'hiawatha' finds 'mbedtls'.

From 9e2aa70bad8c06cdf9a44065a31f12b3205e92e0 Mon Sep 17 00:00:00 2001
From: Paul Garlick <pgarlick@tourbillion-technology.com>
Date: Wed, 26 Sep 2018 12:59:54 +0100
Subject: [PATCH 557/909] gnu: petsc-openmpi: Configure with support for MUMPS
 solver.

* gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add metis,
mumps-openmpi, scalapack and pt-scotch.
[arguments]: Add "--with-PACKAGENAME=1" flags.  Move 'mpi-setup' phase
ahead of 'configure' phase.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/maths.scm | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b7d669ccea..766c6e920f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1702,13 +1702,21 @@ scientific applications modeled by partial differential equations.")
   (package (inherit petsc)
     (name "petsc-openmpi")
     (inputs
-     `(("openmpi" ,openmpi)
-       ("hdf5" ,hdf5-parallel-openmpi)
+     `(("hdf5" ,hdf5-parallel-openmpi)
+       ("metis" ,metis)
+       ("mumps" ,mumps-openmpi)
+       ("openmpi" ,openmpi)
+       ("scalapack" ,scalapack)
+       ("scotch" ,pt-scotch)
        ,@(package-inputs petsc)))
     (arguments
      (substitute-keyword-arguments (package-arguments petsc)
        ((#:configure-flags cf)
         ``("--with-mpiexec=mpirun"
+           "--with-metis=1"
+           "--with-mumps=1"
+           "--with-scalapack=1"
+           "--with-ptscotch=1"
            ,(string-append "--with-mpi-dir="
                            (assoc-ref %build-inputs "openmpi"))
            ,(string-append "--with-hdf5-include="
@@ -1718,9 +1726,9 @@ scientific applications modeled by partial differential equations.")
            ,@(delete "--with-mpi=0" ,cf)))
        ((#:phases phases)
         `(modify-phases ,phases
-           (add-before 'check 'mpi-setup
+           (add-before 'configure 'mpi-setup
              ,%openmpi-setup)))))
-    (synopsis "Library to solve PDEs (with MPI support)")))
+    (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
 
 (define-public petsc-complex-openmpi
   (package (inherit petsc-complex)
@@ -1737,7 +1745,6 @@ scientific applications modeled by partial differential equations.")
            ,@(delete "--with-mpi=0" ,cf)))))
     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
 
-
 (define-public python-kiwisolver
   (package
     (name "python-kiwisolver")

From 45f4ddd7c017ebfc8096f702c72a1fdac67787ed Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 4 Oct 2018 20:34:08 -0400
Subject: [PATCH 558/909] gnu: linux-libre@4.9: Update to 4.9.131.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.131.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index ec2520cdff..2b36d8b93c 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.130"
-                    "1l3ra1pbgz0wbpp1ci90sj9x9iamvagx1vdbdfbmpjsgh1cfnpmq"
+  (make-linux-libre "4.9.131"
+                    "11pxwl7dmisbf2szg9qzkvhlpk68clh5l478n7b62q7hd8j3hxlv"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 2195636cc185b38aa66abc5a4de2b7965c18fa02 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 4 Oct 2018 20:34:50 -0400
Subject: [PATCH 559/909] gnu: linux-libre@4.14: Update to 4.14.74.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.74.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 2b36d8b93c..2a7e1d846f 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.73")
-(define %linux-libre-4.14-hash "0s2aphqgasx0lnprb2hzaqgbcd5i9774gfyhz5a6sqj6dygr00xy")
+(define %linux-libre-4.14-version "4.14.74")
+(define %linux-libre-4.14-hash "0cxyx2yinnc8q0hmhb0swjgdz3s0ry7wxzyqss9f2i74xjjz4rm0")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From 2e073dc23c27e9fc2e255ee47d2025d044df7c8e Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 4 Oct 2018 20:35:38 -0400
Subject: [PATCH 560/909] gnu: linux-libre: Update to 4.18.12.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.12.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 2a7e1d846f..d52e8d7d19 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.11")
-(define %linux-libre-hash "1r4yf7gr7rf8igkg5jv781wa8vn6ii7fsdnffyshin1slnxbd79k")
+(define %linux-libre-version "4.18.12")
+(define %linux-libre-hash "1mcnb1mm7m6i9s591c3kx0f1vbzhbl3w92w137swcm9zifqpci5r")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch

From 4a5e2a90d8595885ecda1e577df4a6a0d294d643 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 4 Oct 2018 19:24:39 -0400
Subject: [PATCH 561/909] gnu: icecat: Add fixes from mozilla-esr60 [security
 fixes].

Includes fixes for CVE-2018-12386 and CVE-2018-12387.

* gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the
upstream mozilla-esr60 repository.
---
 gnu/packages/gnuzilla.scm | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index ea3b61c231..d2110f3290 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -502,7 +502,23 @@ security standards.")
         (search-patch  "icecat-use-system-media-libs.patch")
         (mozilla-patch "icecat-CVE-2018-12385.patch"      "80a4a7ef2813" "1vgcbimpnfjqj934v0cryq1g13xac3wfmd4jyhcb5s60x8xyssf5")
         (search-patch  "icecat-CVE-2018-12383.patch")
-        (mozilla-patch "icecat-bug-1489744.patch"         "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")))
+        (mozilla-patch "icecat-bug-1489744.patch"         "6546ee839d30" "11mhvj77r789b428bfxqq5wdx8yr7lbrdjzr8qjj6fw197pldn51")
+        (mozilla-patch "icecat-CVE-2018-12386.patch"      "4808fcb2e6ca" "05sc881l7sh8bag8whd2ggdn198lskqcxq8f41scfpqscw6xs5d5")
+        (mozilla-patch "icecat-CVE-2018-12387.patch"      "b8f5c37486e1" "0lvmbh126m695kgdbasy1y5xh9n1j08cwdhn071mgvj6yn8cns5z")
+        (mozilla-patch "icecat-bug-1464751.patch"         "d5d00faf0465" "1mj7dbb06brwrk0mvap0z4lfl2hwz1cj6dwjvdrisxm046pdw98i")
+        (mozilla-patch "icecat-bug-1472538.patch"         "11462f2b98f2" "1nxgh0plzilylx8r73r7d74pv66qwjqxmd7nqii33p0snl2jjfzs")
+        (mozilla-patch "icecat-bug-1478685.patch"         "098585dc86fc" "1b0x4qdh6isvffmibvc8ad8z62m3iky9q6jq0z6gyvn8q252cqal")
+        (mozilla-patch "icecat-bug-1486080.patch"         "3f8d57d936ea" "0pz2c18wcgj44v0j8my9xbm90m4bsjcvzmavj569fi8bh6s6zz8p")
+        (mozilla-patch "icecat-bug-1423278.patch"         "878ceaee5634" "0i47s5nvrx9vqbnj6s9y9f4ffww20p8nviqa6frg676y1188xlyl")
+        (mozilla-patch "icecat-bug-1442010.patch"         "87be1b98ec9a" "15f4l18c7hz9aqn89gg3dwmdidfwgn10dywgpzydm8mps45amx7j")
+        (mozilla-patch "icecat-bug-1484559.patch"         "99e58b5307ce" "02fdgbliwzi2r2376wg6k1rky1isfka0smac4ii2cll01jhpfrn6")
+        (mozilla-patch "icecat-bug-1487098.patch"         "f25ce451a492" "18nzg39iyxza1686180qk9cc88l5j2hf1h35d62lrqmdgd9vcj33")
+        (mozilla-patch "icecat-bug-1484905.patch"         "35c26bc231df" "0qh8d4z6y03h5xh7djci26a01l6zq667lg2k11f6zzg7z2j0h67x")
+        (mozilla-patch "icecat-bug-1488061.patch"         "050d0cfa8e3d" "05ql798ynbyz5pvyri4b95j4ixmgnny3zl7sd2ckfrrbm9mxh627")
+        (mozilla-patch "icecat-bug-1434963-pt1.patch"     "1e6dad87efed" "1v00a6cmgswjk54041jyv1ib129fxshpzwk6mn6lr0v5hylk3bx9")
+        (mozilla-patch "icecat-bug-1434963-pt2.patch"     "6558c46df9ea" "0vdy9dm9w5k1flhcfxwvvff0aa415b5mgmmq5r37i83686768xfb")
+        (mozilla-patch "icecat-bug-1434963-pt3.patch"     "686fcfa8abd6" "0ihqr11aq4b0y7mx7bwn8yzn25mv3k2gdphm951mj1g85qg35ann")
+        (mozilla-patch "icecat-bug-1491132.patch"         "14120e0c74d6" "188c5fbhqqhmlk88p70l6d97skh7xy4jhqdby1ri3h9ix967515j")))
       (modules '((guix build utils)))
       (snippet
        '(begin

From bd5f5eece9fc208de01190cd25dce9c281acddd6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Oct 2018 21:14:43 +0200
Subject: [PATCH 562/909] gnu: htslib: Update to 1.9.

* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b657bf6771..64d7e1c869 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3512,7 +3512,7 @@ performance.")
 (define-public htslib
   (package
     (name "htslib")
-    (version "1.8")
+    (version "1.9")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3520,7 +3520,7 @@ performance.")
                     version "/htslib-" version ".tar.bz2"))
               (sha256
                (base32
-                "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
+                "16ljv43sc3fxmv63w7b2ff8m1s7h89xhazwmbm1bicz8axq8fjz0"))))
     (build-system gnu-build-system)
     (inputs
      `(("openssl" ,openssl)

From 4ae4a15232bff0e93cbfc5d48e49a29a23a73cd6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Oct 2018 21:15:47 +0200
Subject: [PATCH 563/909] gnu: samtools: Update to 1.9.

* gnu/packages/bioinformatics.scm (samtools): Update to 1.9.
[origin]: Remove bundled htslib sources.
[arguments]: Remove obsolete make-flags.
---
 gnu/packages/bioinformatics.scm | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 64d7e1c869..996e3731f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4997,7 +4997,7 @@ to the user's query of interest.")
 (define-public samtools
   (package
     (name "samtools")
-    (version "1.8")
+    (version "1.9")
     (source
      (origin
        (method url-fetch)
@@ -5006,15 +5006,19 @@ to the user's query of interest.")
                        version "/samtools-" version ".tar.bz2"))
        (sha256
         (base32
-         "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
+         "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"))
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   ;; Delete bundled htslib.
+                   (delete-file-recursively "htslib-1.9")
+                   #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((ice-9 ftw)
                   (ice-9 regex)
                   (guix build gnu-build-system)
                   (guix build utils))
-       #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
-       #:configure-flags (list "--with-ncurses" "--with-htslib=system")
+       #:configure-flags (list "--with-ncurses")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-tests

From f79b59e3114af8fcd598427655f3ab9512d58164 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Oct 2018 21:18:34 +0200
Subject: [PATCH 564/909] gnu: bcftools: Update to 1.9.

* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9.
[arguments]: Remove obsolete make flags.
---
 gnu/packages/bioinformatics.scm | 27 +++++++++------------------
 1 file changed, 9 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 996e3731f3..8a79f66823 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -288,34 +288,25 @@ BAM files.")
 (define-public bcftools
   (package
     (name "bcftools")
-    (version "1.8")
+    (version "1.9")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://github.com/samtools/bcftools/releases/download/"
-                    version "/bcftools-" version ".tar.bz2"))
+              (uri (string-append "https://github.com/samtools/bcftools/"
+                                  "releases/download/"
+                                  version "/bcftools-" version ".tar.bz2"))
               (sha256
                (base32
-                "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
+                "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Delete bundled htslib.
-                          (delete-file-recursively "htslib-1.8")
+                          (delete-file-recursively "htslib-1.9")
                           #t))))
     (build-system gnu-build-system)
     (arguments
-     `(#:test-target "test"
-       #:configure-flags (list "--with-htslib=system")
-       #:make-flags
-       (list
-        "USE_GPL=1"
-        "LIBS=-lgsl -lgslcblas"
-        (string-append "prefix=" (assoc-ref %outputs "out"))
-        (string-append "HTSDIR=" (assoc-ref %build-inputs "htslib") "/include")
-        (string-append "HTSLIB=" (assoc-ref %build-inputs "htslib") "/lib/libhts.so")
-        (string-append "BGZIP=" (assoc-ref %build-inputs "htslib") "/bin/bgzip")
-        (string-append "TABIX=" (assoc-ref %build-inputs "htslib") "/bin/tabix")
-        (string-append "PACKAGE_VERSION=" ,version))
+     `(#:configure-flags
+       (list "--enable-libgsl")
+       #:test-target "test"
        #:phases
        (modify-phases %standard-phases
          (add-before 'check 'patch-tests

From 1a28b9ab55b36f420ed24acd4c957b7fc0fe33b2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Oct 2018 21:31:24 +0200
Subject: [PATCH 565/909] gnu: python-plotly: Add python-pandas to inputs.

* gnu/packages/graph.scm (python-plotly)[propagated-inputs]: Add
python-pandas.
---
 gnu/packages/graph.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 245ee8f956..cb314719b7 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -224,6 +224,7 @@ lines.")
     (propagated-inputs
      `(("python-decorator" ,python-decorator)
        ("python-nbformat" ,python-nbformat)
+       ("python-pandas" ,python-pandas)
        ("python-pytz" ,python-pytz)
        ("python-requests" ,python-requests)
        ("python-six" ,python-six)))

From 939882f73430ae7644b3c7913cb389cf00c234e0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Oct 2018 21:32:06 +0200
Subject: [PATCH 566/909] gnu: python-pysam: Update to 0.15.1.

* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.15.1.
[source]: Fetch from git.
[arguments]: Delete tests requiring internet access; use "invoke".
[inputs]: Add curl.
---
 gnu/packages/bioinformatics.scm | 51 +++++++++++++++++----------------
 1 file changed, 27 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8a79f66823..4c1739f1b1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1436,17 +1436,17 @@ multiple sequence alignments.")
 (define-public python-pysam
   (package
     (name "python-pysam")
-    (version "0.13.0")
+    (version "0.15.1")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
               ;; Test data is missing on PyPi.
-              (uri (string-append
-                    "https://github.com/pysam-developers/pysam/archive/v"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (git-reference
+                    (url "https://github.com/pysam-developers/pysam.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp"))
+                "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; Drop bundled htslib. TODO: Also remove samtools
@@ -1473,6 +1473,11 @@ multiple sequence alignments.")
              #t))
          (replace 'check
            (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; This file contains tests that require a connection to the
+             ;; internet.
+             (delete-file "tests/tabix_test.py")
+             ;; FIXME: This test fails
+             (delete-file "tests/AlignmentFile_test.py")
              ;; Add first subdirectory of "build" directory to PYTHONPATH.
              (setenv "PYTHONPATH"
                      (string-append
@@ -1483,28 +1488,26 @@ multiple sequence alignments.")
              ;; Step out of source dir so python does not import from CWD.
              (with-directory-excursion "tests"
                (setenv "HOME" "/tmp")
-               (and (zero? (system* "make" "-C" "pysam_data"))
-                    (zero? (system* "make" "-C" "cbcf_data"))
-                    ;; Running nosetests without explicitly asking for a
-                    ;; single process leads to a crash.  Running with multiple
-                    ;; processes fails because the tests are not designed to
-                    ;; run in parallel.
+               (invoke "make" "-C" "pysam_data")
+               (invoke "make" "-C" "cbcf_data")
+               ;; Running nosetests without explicitly asking for a single
+               ;; process leads to a crash.  Running with multiple processes
+               ;; fails because the tests are not designed to run in parallel.
 
-                    ;; FIXME: tests keep timing out on some systems.
-                    ;; (zero? (system* "nosetests" "-v"
-                    ;;                 "--processes" "1"))
-                    )))))))
+               ;; FIXME: tests keep timing out on some systems.
+               (invoke "nosetests" "-v" "--processes" "1")))))))
     (propagated-inputs
-     `(("htslib"            ,htslib))) ; Included from installed header files.
+     `(("htslib" ,htslib))) ; Included from installed header files.
     (inputs
-     `(("ncurses"           ,ncurses)
-       ("zlib"              ,zlib)))
+     `(("ncurses" ,ncurses)
+       ("curl" ,curl)
+       ("zlib" ,zlib)))
     (native-inputs
-     `(("python-cython"     ,python-cython)
+     `(("python-cython" ,python-cython)
        ;; Dependencies below are are for tests only.
-       ("samtools"          ,samtools)
-       ("bcftools"          ,bcftools)
-       ("python-nose"       ,python-nose)))
+       ("samtools" ,samtools)
+       ("bcftools" ,bcftools)
+       ("python-nose" ,python-nose)))
     (home-page "https://github.com/pysam-developers/pysam")
     (synopsis "Python bindings to the SAMtools C API")
     (description

From 8e72f0f3190443935c03264037c83099ed68445f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Oct 2018 21:34:16 +0200
Subject: [PATCH 567/909] gnu: deeptools: Update to 3.1.2.

* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2.
[source]: Fetch from git.
[arguments]: Delete reset-gzip-timestamps phase.
[inputs]: Add python-plotly.
---
 gnu/packages/bioinformatics.scm | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4c1739f1b1..39c84bf4c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2006,18 +2006,25 @@ with Python.")
 (define-public deeptools
   (package
     (name "deeptools")
-    (version "2.5.1")
+    (version "3.1.2")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/deeptools/deepTools/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/deeptools/deepTools.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540"))))
+                "06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This phase fails, but it's not needed.
+         (delete 'reset-gzip-timestamps))))
     (inputs
-     `(("python-scipy" ,python-scipy)
+     `(("python-plotly" ,python-plotly)
+       ("python-scipy" ,python-scipy)
        ("python-numpy" ,python-numpy)
        ("python-numpydoc" ,python-numpydoc)
        ("python-matplotlib" ,python-matplotlib)

From a6798218bea0d6b2df598042d1ced29f74bb4250 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Oct 2018 22:49:49 +0200
Subject: [PATCH 568/909] gnu: samtools-0.1: Adjust to match changes in
 samtools.

* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make
flags.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 39c84bf4c8..d48f484e03 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5073,9 +5073,9 @@ viewer.")
         (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
     (arguments
      `(#:tests? #f ;no "check" target
+       #:make-flags
+       (list "LIBCURSES=-lncurses")
        ,@(substitute-keyword-arguments (package-arguments samtools)
-           ((#:make-flags flags)
-            `(cons "LIBCURSES=-lncurses" ,flags))
            ((#:phases phases)
             `(modify-phases ,phases
                (replace 'install

From e65b2181e8b436278e3dd0b405602a400fbd0a75 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 5 Oct 2018 19:05:39 +0200
Subject: [PATCH 569/909] gnu: icu4c: Skip tests on i686.

* gnu/packages/icu4c.scm (icu4c)[arguments]: On i686-linux, set #:tests? #f.
---
 gnu/packages/icu4c.scm | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/gnu/packages/icu4c.scm b/gnu/packages/icu4c.scm
index cbba9aa42a..2d28107e81 100644
--- a/gnu/packages/icu4c.scm
+++ b/gnu/packages/icu4c.scm
@@ -55,6 +55,12 @@
                     (string-prefix? "mips" s)))
               '("--with-data-packaging=archive")
               '()))
+        ,@(if (string-prefix? "i686" (or (%current-target-system)
+                                         (%current-system)))
+              ;; FIXME: Some tests are failing on i686:
+              ;; <https://unicode-org.atlassian.net/browse/ICU-20080>.
+              '(#:tests? #f)
+              '())
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'chdir-to-source

From 38aca674c3bcd2ace1c6ec79c8b58343c8eea403 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 5 Oct 2018 15:22:55 +0200
Subject: [PATCH 570/909] gnu: libfilezilla: Update to 0.14.0.

* gnu/packages/ftp.scm (libfilezilla): Update to 0.14.0.
---
 gnu/packages/ftp.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index faf9f5dd10..6d89626fe0 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -170,7 +170,7 @@ as required.")
 (define-public libfilezilla
   (package
     (name "libfilezilla")
-    (version "0.13.2")
+    (version "0.14.0")
     (source
      (origin
        (method url-fetch)
@@ -178,7 +178,7 @@ as required.")
                            name "/" name "-" version ".tar.bz2"))
        (sha256
         (base32
-         "0z9cqscca4w94j9npgcknrrw8gfwn5ids903042fczlr977j0i19"))))
+         "15cfz98asypf9rfybv4c6kx8nk3wak7qlm1azldc0gd1nqm4xqvz"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("cppunit" ,cppunit)

From 3f904456923d6ba658ccf5f164511478f430afa5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Fri, 5 Oct 2018 19:11:28 +0200
Subject: [PATCH 571/909] gnu: filezilla: Update to 3.37.4.

* gnu/packages/ftp.scm (filezilla): Update to 3.37.4.
---
 gnu/packages/ftp.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index 6d89626fe0..b9c6d209b8 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -207,14 +207,14 @@ output.
 (define-public filezilla
   (package
     (name "filezilla")
-    (version "3.37.1")
+    (version "3.37.4")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.filezilla-project.org/client/"
                            "FileZilla_" version "_src.tar.bz2"))
        (sha256
-        (base32 "1bbxlm8gc0r5jing8xmkdbhj5a1qfbjn8varhny3mrk1am4m7s7l"))))
+        (base32 "169wy7ilsh518mcinkjmr6m0kzxbzchmc9mivf5c9b4zp1w4gg3i"))))
     (build-system gnu-build-system)
     (arguments
       ;; Don't let filezilla phone home to check for updates.

From 8713c03e557114c576c796400300d0dbab4f06c8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 22:16:36 +0200
Subject: [PATCH 572/909] gnu: audacity: Don't use unstable tarball.

* gnu/packages/audio.scm (audacity)[source]: Use GIT-FETCH and GIT-FILE-NAME.
---
 gnu/packages/audio.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index c92b5056d1..434efab953 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -291,12 +291,14 @@ engineers, musicians, soundtrack editors and composers.")
     (version "2.2.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/audacity/audacity/archive"
-                           "/Audacity-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/audacity/audacity.git")
+             (commit (string-append "Audacity-" version))))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "18q7i77ynihx7xp45lz2lv0k0wrh6736pcrivlpwrxjgbvyqx7km"))
+         "10maxmjxbmjybj7n4m7a9bbm7g8xxw8f8vbsf7c9ih5j2gr15ihs"))
        (patches (search-patches "audacity-build-with-system-portaudio.patch"))
        (modules '((guix build utils)))
        (snippet

From b008a12ae78b533c14dd7e88f29df091eca3c0d7 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 21:59:55 +0200
Subject: [PATCH 573/909] gnu: fdroidserver: Update to 1.0.10.

* gnu/packages/android.scm (fdroidserver): Update to 1.0.10.
---
 gnu/packages/android.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index 53d7d8d441..9f8d850ff5 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -863,14 +863,14 @@ useful for reverse engineering, analysis of Android applications and more.")
 (define-public fdroidserver
   (package
     (name "fdroidserver")
-    (version "1.0.9")
+    (version "1.0.10")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "fdroidserver" version))
         (sha256
          (base32
-          "0cwb1fmindw6v9jkiim9yn3496rk1pvnk94s1r0vz2hxgz16xp7n"))))
+          "0n6kkby65qzqdx1jn72grfffvr1w1j1rby5pwm9z8rymmsh8s0pm"))))
     (build-system python-build-system)
     (arguments
      `(#:phases

From fc4738149f5cbaffc8e0b37bfb61e25fac0ecd67 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 00:30:53 +0200
Subject: [PATCH 574/909] gnu: Add bastet.

* gnu/packages/games.scm (bastet): New public variable.
* gnu/packages/patches/bastet-change-source-of-unordered_set.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                  |  1 +
 gnu/packages/games.scm                        | 64 +++++++++++++++++++
 ...astet-change-source-of-unordered_set.patch | 40 ++++++++++++
 3 files changed, 105 insertions(+)
 create mode 100644 gnu/packages/patches/bastet-change-source-of-unordered_set.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 61e5913a01..8c6579b03f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -591,6 +591,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/awesome-reproducible-png.patch		\
   %D%/packages/patches/azr3.patch				\
   %D%/packages/patches/bash-completion-directories.patch	\
+  %D%/packages/patches/bastet-change-source-of-unordered_set.patch	\
   %D%/packages/patches/bazaar-CVE-2017-14176.patch		\
   %D%/packages/patches/beignet-correct-file-names.patch		\
   %D%/packages/patches/binutils-aarch64-symbol-relocation.patch	\
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index ec92f508bc..7365a7f5d8 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -181,6 +181,70 @@ more advanced player there are new game modes and a wide variety of physics
 settings to tweak as well.")
     (license license:gpl2+)))
 
+(define-public bastet
+  (package
+    (name "bastet")
+    (version "0.43.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/fph/bastet.git")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "09kamxapm9jw9przpsgjfg33n9k94bccv65w95dakj0br33a75wn"))
+       (patches
+        (search-patches "bastet-change-source-of-unordered_set.patch"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (list (string-append "CXXFLAGS=-I"
+                            (assoc-ref %build-inputs "boost") "/include"))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ; no configure script
+         (replace 'check
+           ;; The 'Test' target builds the tests, but doesn't actually run them.
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (apply invoke "make" "Test" make-flags)
+             (setenv "HOME" ".")
+             (invoke "./Test")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out     (assoc-ref outputs "out"))
+                    (share   (string-append out "/share"))
+                    (hicolor (string-append share "/icons/hicolor")))
+               (install-file "bastet"
+                             (string-append out "/bin"))
+
+               (install-file "bastet.desktop"
+                             (string-append share "/applications"))
+               (install-file "bastet.svg"
+                             (string-append hicolor "/scalable/apps"))
+
+               (install-file "bastet.appdata.xml"
+                             (string-append share "/appdata"))
+
+               (install-file "bastet.6"
+                             (string-append out "/share/man/man6"))
+               #t))))))
+    (native-inputs
+     `(("hicolor-icon-theme" ,hicolor-icon-theme)))
+    (inputs
+     `(("boost" ,boost)
+       ("ncurses" ,ncurses)))
+    (home-page "http://fph.altervista.org/prog/bastet.html")
+    (synopsis "Antagonistic Tetris-style falling brick game for text terminals")
+    (description
+     "Bastet (short for Bastard Tetris) is a simple ncurses-based falling brick
+game.  Unlike normal Tetris, Bastet does not choose the next brick at random.
+Instead, it uses a special algorithm to choose the worst brick possible.
+
+Playing bastet can be a painful experience, especially if you usually make
+canyons and wait for the long I-shaped block to clear four rows at a time.")
+    (license license:gpl3+)))
+
 (define-public cataclysm-dda
   (let ((commit "ad3b0c3d521292d119f97a83390e7acfe9e9e7f7")
         (revision "1"))
diff --git a/gnu/packages/patches/bastet-change-source-of-unordered_set.patch b/gnu/packages/patches/bastet-change-source-of-unordered_set.patch
new file mode 100644
index 0000000000..ef3970a3e2
--- /dev/null
+++ b/gnu/packages/patches/bastet-change-source-of-unordered_set.patch
@@ -0,0 +1,40 @@
+From: Tobias Geerinckx-Rice <me@tobias.gr>
+Date: Wed, 3 Oct 2018 23:30:42 +0200
+Subject: [PATCH] bastet: Change source of unordered_set.
+
+This allows building bastet 0.43.2 with boost >=1.66.
+It was backported verbatim from the upstream master branch.
+
+From 0e03f8d4d6bc6949cf1c447e632ce0d1b98c4be1 Mon Sep 17 00:00:00 2001
+From: Federico Poloni <fpoloni@di.unipi.it>
+Date: Wed, 4 Oct 2017 19:35:01 +0200
+Subject: [PATCH] Changed source of unordered_set (should hopefully fix #6
+ without reopening #1)
+
+---
+ BastetBlockChooser.hpp | 5 ++---
+ 1 file changed, 2 insertions(+), 3 deletions(-)
+
+diff --git a/BastetBlockChooser.hpp b/BastetBlockChooser.hpp
+index 992e556..7ee3b7c 100644
+--- a/BastetBlockChooser.hpp
++++ b/BastetBlockChooser.hpp
+@@ -23,8 +23,7 @@
+ 
+ #include "Well.hpp"
+ 
+-#include <boost/tr1/tr1/unordered_set>
+-#include <set>
++#include <boost/unordered_set.hpp>
+ #include <boost/functional/hash.hpp>
+ 
+ namespace Bastet{
+@@ -75,7 +74,7 @@ namespace Bastet{
+   public:
+     Searcher(BlockType b, const Well *well, Vertex v, WellVisitor *visitor);
+   private:
+-    std::tr1::unordered_set<Vertex> _visited;
++    boost::unordered_set<Vertex> _visited;
+     //std::set<Vertex> _visited; ^^ the above is more efficient, we need to do many inserts
+     BlockType _block;
+     const Well *_well;

From 73ca145a7eee5a4613469956d214880850e63a40 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sun, 16 Sep 2018 22:13:41 -0400
Subject: [PATCH 575/909] gnu: gnucash: Update to 3.3.

* gnu/packages/patches/gnucash-disable-failing-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/gnucash.scm (gnucash): Update to 3.3.
[source]: Add patch.
[arguments]: Add 'set-env-vars', 'glib-or-gtk-compile-schemas', and
'glib-or-gtk-wrap' phases.
---
 gnu/local.mk                                  |  1 +
 gnu/packages/gnucash.scm                      | 49 ++++++++++++++-----
 .../gnucash-disable-failing-tests.patch       | 39 +++++++++++++++
 .../patches/gnucash-price-quotes-perl.patch   |  5 +-
 4 files changed, 81 insertions(+), 13 deletions(-)
 create mode 100644 gnu/packages/patches/gnucash-disable-failing-tests.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 8c6579b03f..8f854e98b5 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -762,6 +762,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gnome-todo-libical-compat.patch		\
   %D%/packages/patches/gnome-tweak-tool-search-paths.patch	\
   %D%/packages/patches/gnucash-price-quotes-perl.patch		\
+  %D%/packages/patches/gnucash-disable-failing-tests.patch	\
   %D%/packages/patches/gnutls-skip-trust-store-test.patch	\
   %D%/packages/patches/gnutls-skip-pkgconfig-test.patch		\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm
index fc8a9b6bfc..45720df9a4 100644
--- a/gnu/packages/gnucash.scm
+++ b/gnu/packages/gnucash.scm
@@ -28,6 +28,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
@@ -50,7 +51,7 @@
 (define-public gnucash
   (package
     (name "gnucash")
-    (version "3.0")
+    (version "3.3")
     (source
      (origin
       (method url-fetch)
@@ -58,11 +59,9 @@
                           version "/gnucash-" version ".tar.bz2"))
       (sha256
        (base32
-        "1ffvf1rryg5yin86fnf1zvy6hnpwzrjarbdfmjmrf2mqlmv48xac"))
-
-      ;; TODO: rebase this patch
-;      (patches (search-patches "gnucash-price-quotes-perl.patch"))
-      ))
+        "0grr5qi5rn1xvr7qx5d7mcxa2mcgycy2b325ry73bb485a6yv5l3"))
+      (patches (search-patches "gnucash-price-quotes-perl.patch"
+                               "gnucash-disable-failing-tests.patch"))))
     (build-system cmake-build-system)
     (inputs
      `(("guile" ,guile-2.2)
@@ -76,7 +75,8 @@
        ("webkitgtk" ,webkitgtk)
        ("aqbanking" ,aqbanking)
        ("perl-date-manip" ,perl-date-manip)
-       ("perl-finance-quote" ,perl-finance-quote)))
+       ("perl-finance-quote" ,perl-finance-quote)
+       ("tzdata" ,tzdata-for-tests)))
     (native-inputs
      `(("glib" ,glib "bin") ; glib-compile-schemas, etc.
        ("intltool" ,intltool)
@@ -90,6 +90,13 @@
        #:configure-flags
        (list "-DWITH_OFX=OFF"  ; libofx is not available yet
              "-DWITH_SQL=OFF") ; without dbi.h
+       #:make-flags '("GUILE_AUTO_COMPILE=0")
+       #:modules ((guix build cmake-build-system)
+                  ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
+                  (guix build utils))
+       #:imported-modules (,@%gnu-build-system-modules
+                           (guix build cmake-build-system)
+                           (guix build glib-or-gtk-build-system))
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'unpack-gmock
@@ -99,14 +106,28 @@
                      "-C" "gmock" "--strip-components=1")
              (setenv "GMOCK_ROOT" (string-append (getcwd) "/gmock/googlemock"))
              #t))
+         (add-after 'unpack 'set-env-vars
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((tzdata (assoc-ref inputs "tzdata")))
+               ;; At least one test is time-related and requires this
+               ;; environment variable.
+               (setenv "TZDIR"
+                       (string-append tzdata
+                                      "/share/zoneinfo"))
+               (substitute* "CMakeLists.txt"
+                 (("set\\(SHELL /bin/bash\\)")
+                  (string-append "set(SHELL " (which "bash") ")")))
+               #t)))
          ;; There are about 100 megabytes of documentation.
          (add-after
           'install 'install-docs
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let ((docs (assoc-ref inputs "gnucash-docs"))
                   (doc-output (assoc-ref outputs "doc")))
+              (mkdir-p (string-append doc-output "/share"))
               (symlink (string-append docs "/share/gnome")
-                       (string-append doc-output "/share/gnome")))))
+                       (string-append doc-output "/share/gnome"))
+              #t)))
          (add-after
           'install-docs 'wrap-programs
           (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -134,7 +155,11 @@
                       '("gnucash"
                         "gnc-fq-check"
                         "gnc-fq-helper"
-                        "gnc-fq-dump")))))))
+                        "gnc-fq-dump"))))
+         (add-after 'install 'glib-or-gtk-compile-schemas
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-compile-schemas))
+         (add-after 'install 'glib-or-gtk-wrap
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
     (home-page "https://www.gnucash.org/")
     (synopsis "Personal and small business financial accounting software")
     (description
@@ -150,7 +175,9 @@ financial calculations or scheduled transactions.")
 (define gnucash-docs
   (package
     (name "gnucash-docs")
-    (version (package-version gnucash))
+    ;;(version (package-version gnucash))
+    ;; The current version of gnucash-docs is not available at the moment.
+    (version "3.2")
     (source
      (origin
        (method url-fetch)
@@ -158,7 +185,7 @@ financial calculations or scheduled transactions.")
                            version "/gnucash-docs-" version ".tar.gz"))
        (sha256
         (base32
-         "0yq65s3z3dwdwdf2nq1d1w9ckdjdyjwkfpmvhzyib54b66q65xh5"))))
+         "1763m6d8gkhllwb9rnr9ifch39brmh7kr2m6icqfbc53a91m56j6"))))
     (build-system gnu-build-system)
     ;; These are native-inputs because they are only required for building the
     ;; documentation.
diff --git a/gnu/packages/patches/gnucash-disable-failing-tests.patch b/gnu/packages/patches/gnucash-disable-failing-tests.patch
new file mode 100644
index 0000000000..e0fdd86b5d
--- /dev/null
+++ b/gnu/packages/patches/gnucash-disable-failing-tests.patch
@@ -0,0 +1,39 @@
+test-stress-options.scm does not exist, and test-qof passes when run in the
+build directory after the gnucash build.
+
+diff -ur gnucash-3.3.old/gnucash/report/standard-reports/test/CMakeLists.txt gnucash-3.3/gnucash/report/standard-reports/test/CMakeLists.txt
+--- gnucash-3.3.old/gnucash/report/standard-reports/test/CMakeLists.txt	2018-10-04 09:29:00.916641417 -0400
++++ gnucash-3.3/gnucash/report/standard-reports/test/CMakeLists.txt	2018-10-04 09:30:52.962504860 -0400
+@@ -13,10 +13,6 @@
+   test-income-gst.scm
+ )
+ 
+-set(scm_test_with_textual_ports_SOURCES
+-    test-stress-options.scm
+-)
+-
+ set(GUILE_DEPENDS
+   scm-gnc-module
+   scm-app-utils
+@@ -31,9 +27,6 @@
+ 
+ if (HAVE_SRFI64)
+   gnc_add_scheme_tests("${scm_test_with_srfi64_SOURCES}")
+-  if (HAVE_TEXT_PORTS)
+-    gnc_add_scheme_tests("${scm_test_with_textual_ports_SOURCES}")
+-  endif (HAVE_TEXT_PORTS)
+ endif (HAVE_SRFI64)
+ 
+ gnc_add_scheme_tests("${scm_test_standard_reports_SOURCES}")
+diff -ur gnucash-3.3.old/libgnucash/engine/test/CMakeLists.txt gnucash-3.3/libgnucash/engine/test/CMakeLists.txt
+--- gnucash-3.3.old/libgnucash/engine/test/CMakeLists.txt	2018-10-04 09:29:00.876640751 -0400
++++ gnucash-3.3/libgnucash/engine/test/CMakeLists.txt	2018-10-05 10:46:22.542962546 -0400
+@@ -54,8 +54,6 @@
+ # This test does not run on Win32
+ if (NOT WIN32)
+   set(SOURCES ${test_qof_SOURCES} ${CMAKE_SOURCE_DIR}/common/test-core/unittest-support.c)
+-  add_engine_test(test-qof "${SOURCES}")
+-  target_compile_definitions(test-qof PRIVATE TESTPROG=test_qof)
+ 
+   set(SOURCES ${test_engine_SOURCES} ${CMAKE_SOURCE_DIR}/common/test-core/unittest-support.c)
+   add_engine_test(test-engine "${SOURCES}")
diff --git a/gnu/packages/patches/gnucash-price-quotes-perl.patch b/gnu/packages/patches/gnucash-price-quotes-perl.patch
index 982763f0ec..3101ddb007 100644
--- a/gnu/packages/patches/gnucash-price-quotes-perl.patch
+++ b/gnu/packages/patches/gnucash-price-quotes-perl.patch
@@ -1,8 +1,9 @@
 After wrapping gnc-fq-check and gnc-fq-helper we can no longer execute them
 with perl, so execute them directly instead.
 
---- gnucash-2.6.6/src/scm/price-quotes.scm.orig	2014-04-27 17:42:28.000000000 -0500
-+++ gnucash-2.6.6/src/scm/price-quotes.scm	2015-07-09 16:12:11.196218472 -0500
+diff -ur gnucash-3.2.old/libgnucash/scm/price-quotes.scm gnucash-3.2/libgnucash/scm/price-quotes.scm
+--- gnucash-3.2.old/libgnucash/scm/price-quotes.scm	2018-09-15 00:48:33.718389646 -0400
++++ gnucash-3.2/libgnucash/scm/price-quotes.scm	2018-09-15 13:51:49.249862724 -0400
 @@ -74,7 +74,7 @@
      (define (start-program)
        (if (not (string-null? gnc:*finance-quote-check*))

From b0e829c632c8b0d0d9173c8b0fa457bbc2f92a0f Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Fri, 5 Oct 2018 13:55:21 -0400
Subject: [PATCH 576/909] gnu: gnucash-docs: Update to 3.3.

The documentation on SourceForge is now located in the same directory as the
source code.

* gnu/packages/gnucash.scm (gnucash-docs): Update to 3.3.
---
 gnu/packages/gnucash.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/gnucash.scm b/gnu/packages/gnucash.scm
index 45720df9a4..4e68f20866 100644
--- a/gnu/packages/gnucash.scm
+++ b/gnu/packages/gnucash.scm
@@ -175,17 +175,15 @@ financial calculations or scheduled transactions.")
 (define gnucash-docs
   (package
     (name "gnucash-docs")
-    ;;(version (package-version gnucash))
-    ;; The current version of gnucash-docs is not available at the moment.
-    (version "3.2")
+    (version (package-version gnucash))
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "mirror://sourceforge/gnucash/gnucash-docs/"
+       (uri (string-append "mirror://sourceforge/gnucash/gnucash%20%28stable%29/"
                            version "/gnucash-docs-" version ".tar.gz"))
        (sha256
         (base32
-         "1763m6d8gkhllwb9rnr9ifch39brmh7kr2m6icqfbc53a91m56j6"))))
+         "10v4hw4lh888r8yv473pqrvzfjg8dwamk62sghs93rn88ndwm16c"))))
     (build-system gnu-build-system)
     ;; These are native-inputs because they are only required for building the
     ;; documentation.

From 357450dca0933a36a59a23c0e2be5d646f123706 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sat, 29 Sep 2018 11:14:51 +0100
Subject: [PATCH 577/909] gnu: bioruby: Update to 1.5.2.

This works with Ruby 2.5.

* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d48f484e03..43220d22fe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6863,14 +6863,14 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
 (define-public bioruby
   (package
     (name "bioruby")
-    (version "1.5.1")
+    (version "1.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (rubygems-uri "bio" version))
        (sha256
         (base32
-         "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"))))
+         "1d56amdsjv1mag7m6gv2w0xij8hqx1v5xbdjsix8sp3yp36m7938"))))
     (build-system ruby-build-system)
     (propagated-inputs
      `(("ruby-libxml" ,ruby-libxml)))

From 0b060e3486afdefdf5a5f474518b2a6bfae405d9 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sat, 29 Sep 2018 11:15:36 +0100
Subject: [PATCH 578/909] gnu: ruby-shindo: Remove -rubygems flags.

These have been removed in Ruby 2.5.

* gnu/packages/ruby.scm (ruby-shindo)[arguments]: Change fix-tests phase to
also remove the -rubygems flags.
---
 gnu/packages/ruby.scm | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 3673bf2346..b216f3f48b 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1211,12 +1211,15 @@ standard output stream.")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'fix-tests
-          (lambda _
-            (substitute* "Rakefile"
-              (("system \"shindo") "system \"./bin/shindo")
-              ;; This test doesn't work, so we disable it.
-              (("fail \"The build_error test should fail") "#"))
-            #t)))))
+           (lambda _
+             (substitute* "tests/tests_helper.rb"
+               (("-rubygems") ""))
+             (substitute* "Rakefile"
+               (("system \"shindo") "system \"./bin/shindo")
+               ;; This test doesn't work, so we disable it.
+               (("fail \"The build_error test should fail") "#")
+               ((" -rubygems") ""))
+             #t)))))
     (propagated-inputs
      `(("ruby-formatador" ,ruby-formatador)))
     (synopsis "Simple depth first Ruby testing")

From 39ecb977d3e097ffe9c46390090bd197581ac072 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sat, 29 Sep 2018 11:17:02 +0100
Subject: [PATCH 579/909] gnu: ruby-term-ansicolor: Fix test for Ruby 2.5.

* gnu/packages/ruby.scm (ruby-term-ansicolor)[arguments]: Add new fix-test
phase to fix a test that fails under Ruby 2.5.
---
 gnu/packages/ruby.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index b216f3f48b..c039df1559 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2914,6 +2914,11 @@ Ruby's large and slower test/unit.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'fix-test
+           (lambda -
+             (substitute* "tests/hsl_triple_test.rb"
+               (("0\\\\\\.0%")
+                "0\\.?0?%"))))
          (replace 'build
           (lambda _
             (invoke "gem" "build" "term-ansicolor.gemspec"))))))

From 2c7cb711e938ff9e358ffb274ea2f96ae84fc1e9 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sat, 29 Sep 2018 11:18:54 +0100
Subject: [PATCH 580/909] gnu: ruby-sass-spec: Fix spec expectation.

This fixes building ruby-sass with Ruby 2.5.

* gnu/packages/ruby.scm (ruby-sass-spec)[arguments]: Add patch-test phase to
fix the expectation of one of the tests. Also change the comment regarding the
tests not being run.
---
 gnu/packages/ruby.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index c039df1559..a0fe0c2e98 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -5456,8 +5456,16 @@ strings or files.")
        ("ruby-diffy" ,ruby-diffy)
        ("ruby-terminfo" ,ruby-terminfo)))
     (arguments
-     ;; No Rakefile
-     `(#:tests? #f))
+     `(;; This package contains tests for a sass implementation, and the to
+       ;; avoid any circular dependencies, the tests are not run here
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-test
+           (lambda _
+             (delete-file "spec/values/colors/alpha_hex-3.5/error")
+             (substitute* "spec/values/colors/alpha_hex-3.5/expected_output.css"
+               (("string") "color")))))))
     (home-page "https://github.com/sass/sass-spec")
     (synopsis "Test suite for Sass")
     (description "Sass Spec is a test suite for Sass.  Test cases are all in

From 4d372cb9a27b57664112b76e6a209b713abd1d10 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sat, 29 Sep 2018 11:28:28 +0100
Subject: [PATCH 581/909] gnu: Add ruby-mathn.

* gnu/packages/ruby.scm (ruby-mathn): New variable.
---
 gnu/packages/ruby.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index a0fe0c2e98..e54b1a0f69 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -5108,6 +5108,29 @@ are doing, you can fiddle with every last bit of your email directly.")
     (home-page "https://github.com/mikel/mail")
     (license license:expat)))
 
+(define-public ruby-mathn
+  (package
+    (name "ruby-mathn")
+    (version "0.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "mathn" version))
+       (sha256
+        (base32
+         "1wn812llln9jzgybz2d7536q39z3gi99i6fi0j1dapcpzvhgrr0p"))))
+    (build-system ruby-build-system)
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rake-compiler" ,ruby-rake-compiler)))
+    (synopsis "Extends math operations for increased precision")
+    (description
+     "This gem makes mathematical operations more precise in Ruby and
+integrates other mathematical standard libraries.  Prior to Ruby 2.5,
+@code{mathn} was part of the Ruby standard library.")
+    (home-page "https://github.com/ruby/mathn")
+    (license license:bsd-2)))
+
 (define-public ruby-code-statistics
   (package
     (name "ruby-code-statistics")

From 11ff2adc74f3c168cadb6cc5bf7f4be08442b9ea Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sat, 29 Sep 2018 11:29:30 +0100
Subject: [PATCH 582/909] gnu: ruby-sass: Update to 3.6.0.

* gnu/packages/ruby.scm (ruby-sass)[version]: Update to 3.6.0.
[source]: Update sha256.
[native-inputs]: Add ruby-mathn, as this is needed when using Ruby 2.5.
---
 gnu/packages/ruby.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index e54b1a0f69..2080944cae 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -5498,18 +5498,19 @@ the @file{spec} directory.")
 (define-public ruby-sass
   (package
     (name "ruby-sass")
-    (version "3.5.7")
+    (version "3.6.0")
     (source (origin
               (method url-fetch)
               (uri (rubygems-uri "sass" version))
               (sha256
                (base32
-                "1sy7xsbgpcy90j5ynbq967yplffp74pvph3r8ivn2sv2b44q6i61"))))
+                "18c6prbw9wl8bqhb2435pd9s0lzarl3g7xf8pmyla28zblvwxmyh"))))
     (build-system ruby-build-system)
     (propagated-inputs
      `(("ruby-sass-listen" ,ruby-sass-listen)))
     (native-inputs
-     `(("ruby-sass-spec" ,ruby-sass-spec)))
+     `(("ruby-sass-spec" ,ruby-sass-spec)
+       ("ruby-mathn" ,ruby-mathn)))
     (home-page "http://sass-lang.com/")
     (synopsis "CSS extension language")
     (description "Sass is a CSS extension language.  It extends CSS with

From 42384b517ed5352bb50fb9c0c5f49b168c198004 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 5 Oct 2018 23:05:19 +0200
Subject: [PATCH 583/909] progress: Fix total size in "@ download-succeeded"
 traces.

Fixes a regression introduced in
1d0be47ab680db938ac8da1ee65e1de91e198f67 whereby the total size for
directories (coming from substitutes) would be 4KiB.  This led the
progress bar to go back to the start, typically.

* guix/progress.scm (progress-reporter/trace): Add 'total'.  In 'start',
initialize it.  Adjust 'report' to update it.  Adjust 'stop' to prefer
SIZE as the actual size and then TOTAL.  Do not use the size of FILE as
the total since that could be 4KiB when FILE is a directory.
---
 guix/progress.scm | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/guix/progress.scm b/guix/progress.scm
index f846944952..9da667a027 100644
--- a/guix/progress.scm
+++ b/guix/progress.scm
@@ -289,6 +289,8 @@ tasks is performed.  Write PREFIX at the beginning of the line."
                                   #:optional (log-port (current-output-port)))
   "Like 'progress-reporter/file', but instead of returning human-readable
 progress reports, write \"build trace\" lines to be processed elsewhere."
+  (define total 0)                                ;bytes transferred
+
   (define (report-progress transferred)
     (define message
       (format #f "@ download-progress ~a ~a ~a ~a~%"
@@ -299,13 +301,16 @@ progress reports, write \"build trace\" lines to be processed elsewhere."
 
   (progress-reporter
    (start (lambda ()
+            (set! total 0)
             (display (format #f "@ download-started ~a ~a ~a~%"
                              file url (or size "-"))
                      log-port)))
-   (report (rate-limited report-progress %progress-interval))
+   (report (let ((report (rate-limited report-progress %progress-interval)))
+             (lambda (transferred)
+               (set! total transferred)
+               (report transferred))))
    (stop (lambda ()
-           (let ((size (or (and=> (stat file #f) stat:size)
-                           size)))
+           (let ((size (or size total)))
              (report-progress size)
              (display (format #f "@ download-succeeded ~a ~a ~a~%"
                               file url size)

From a45c64701b5599bb527fd8cf2070174f9e866d3d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:28:49 +0200
Subject: [PATCH 584/909] gnu: ghc-http-conduit: Remove ghc-http-client from
 native-inputs.

* gnu/packages/haskell-web.scm (ghc-http-conduit)[native-inputs]: Remove
ghc-http-client.
---
 gnu/packages/haskell-web.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/haskell-web.scm b/gnu/packages/haskell-web.scm
index eaa7e6a9ec..2e404e2fcf 100644
--- a/gnu/packages/haskell-web.scm
+++ b/gnu/packages/haskell-web.scm
@@ -369,7 +369,6 @@ and HPACK.  Currently HTTP/2 16 framing and HPACK 10 is supported.")
        ("ghc-warp" ,ghc-warp)
        ("ghc-wai-conduit" ,ghc-wai-conduit)
        ("ghc-http-types" ,ghc-http-types)
-       ("ghc-http-client" ,ghc-http-client)
        ("ghc-cookie" ,ghc-cookie)
        ("ghc-conduit-extra" ,ghc-conduit-extra)
        ("ghc-streaming-commons" ,ghc-streaming-commons)

From 279c97dba8ceecab9d1c7a5c8b5503d1c2e605a3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:28:50 +0200
Subject: [PATCH 585/909] gnu: ghc-regex: Fix build.

* gnu/packages/haskell.scm (ghc-regex)[arguments]: Add build phase to relax
version checks.
---
 gnu/packages/haskell.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a140985eba..c8e4523ebd 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3003,6 +3003,17 @@ Haskell library @code{regex-base}.")
         (base32
          "1sjkpkgv4phy5b5v2lr89x4vx4dh44pj0sbvlsp6n86w9v6v4jwb"))))
     (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'relax-dependencies
+           (lambda _
+             (substitute* "regex.cabal"
+               (("base-compat.*>=.*0.6.*")
+                "base-compat >= 0.6\n")
+               (("template-haskell.*>=.*2.7.*")
+                "template-haskell >= 2.7\n"))
+             #t)))))
     (inputs
      `(("ghc-base-compat" ,ghc-base-compat)
        ("ghc-hashable" ,ghc-hashable)

From 7df25c77c5d57d127e556b6527b69abce82ef814 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:28:51 +0200
Subject: [PATCH 586/909] gnu: Add ghc-cairo.

* gnu/packages/haskell.scm (ghc-cairo): New variable.
---
 gnu/packages/haskell.scm | 77 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c8e4523ebd..964b14749f 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -43,6 +43,7 @@
   #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages haskell-check)
   #:use-module (gnu packages haskell-crypto)
   #:use-module (gnu packages haskell-web)
@@ -10587,6 +10588,82 @@ expose it from another module in the hierarchy.
 @end itemize")
     (license license:expat)))
 
+(define-public ghc-cairo
+  (package
+    (name "ghc-cairo")
+    (version "0.13.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/cairo/"
+                           "cairo-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1wxylv4d8120ri0vgar168ikqa9m6533ipdwi38qlmxmw20ws2j2"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:modules ((guix build haskell-build-system)
+                  (guix build utils)
+                  (ice-9 match)
+                  (srfi srfi-26))
+       #:phases
+       (modify-phases %standard-phases
+         ;; FIXME: This is a copy of the standard configure phase with a tiny
+         ;; difference: this package needs the -package-db flag to be passed
+         ;; to "runhaskell" in addition to the "configure" action, because it
+         ;; depends on gtk2hs-buildtools, which provide setup hooks.  Without
+         ;; this option the Setup.hs file cannot be evaluated.  The
+         ;; haskell-build-system should be changed to pass "-package-db" to
+         ;; "runhaskell" in any case.
+         (replace 'configure
+           (lambda* (#:key outputs inputs tests? (configure-flags '())
+                     #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (input-dirs (match inputs
+                                  (((_ . dir) ...)
+                                   dir)
+                                  (_ '())))
+                    (ghc-path (getenv "GHC_PACKAGE_PATH"))
+                    (params (append `(,(string-append "--prefix=" out))
+                                    `(,(string-append "--libdir=" out "/lib"))
+                                    `(,(string-append "--bindir=" out "/bin"))
+                                    `(,(string-append
+                                        "--docdir=" out
+                                        "/share/doc/" ((@@ (guix build haskell-build-system)
+                                                           package-name-version) out)))
+                                    '("--libsubdir=$compiler/$pkg-$version")
+                                    '("--package-db=../package.conf.d")
+                                    '("--global")
+                                    `(,@(map
+                                         (cut string-append "--extra-include-dirs=" <>)
+                                         (search-path-as-list '("include") input-dirs)))
+                                    `(,@(map
+                                         (cut string-append "--extra-lib-dirs=" <>)
+                                         (search-path-as-list '("lib") input-dirs)))
+                                    (if tests?
+                                        '("--enable-tests")
+                                        '())
+                                    configure-flags)))
+               (unsetenv "GHC_PACKAGE_PATH")
+               (apply invoke "runhaskell" "-package-db=../package.conf.d"
+                      "Setup.hs" "configure" params)
+               (setenv "GHC_PACKAGE_PATH" ghc-path)
+               #t))))))
+    (inputs
+     `(("ghc-utf8-string" ,ghc-utf8-string)
+       ("ghc-text" ,ghc-text)
+       ("cairo" ,cairo)))
+    (native-inputs
+     `(("ghc-gtk2hs-buildtools" ,ghc-gtk2hs-buildtools)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://projects.haskell.org/gtk2hs/")
+    (synopsis "Haskell bindings to the Cairo vector graphics library")
+    (description
+     "Cairo is a library to render high quality vector graphics.  There exist
+various backends that allows rendering to Gtk windows, PDF, PS, PNG and SVG
+documents, amongst others.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 562cfae330e2b8382ab106478514d833187c7d15 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:28:52 +0200
Subject: [PATCH 587/909] gnu: Add ghc-chart-cairo.

* gnu/packages/haskell.scm (ghc-chart-cairo): New variable.
---
 gnu/packages/haskell.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 964b14749f..c040965e92 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10664,6 +10664,33 @@ various backends that allows rendering to Gtk windows, PDF, PS, PNG and SVG
 documents, amongst others.")
     (license license:bsd-3)))
 
+(define-public ghc-chart-cairo
+  (package
+    (name "ghc-chart-cairo")
+    (version "1.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/Chart-cairo/"
+                           "Chart-cairo-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0iany6lfyfb1cw0pxfs5aw5k0a6x41m6ql9ad9w59biwdckbsyqr"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-old-locale" ,ghc-old-locale)
+       ("ghc-cairo" ,ghc-cairo)
+       ("ghc-colour" ,ghc-colour)
+       ("ghc-data-default-class" ,ghc-data-default-class)
+       ("ghc-operational" ,ghc-operational)
+       ("ghc-lens" ,ghc-lens)
+       ("ghc-chart" ,ghc-chart)))
+    (home-page "https://github.com/timbod7/haskell-chart/wiki")
+    (synopsis "Cairo backend for Charts")
+    (description "This package provides a Cairo vector graphics rendering
+backend for the Charts library.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 6c8197783dca26159a669202a0635af0338d4992 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:10:15 +0200
Subject: [PATCH 588/909] gnu: Add ghc-atomic-write.

* gnu/packages/haskell.scm (ghc-atomic-write): New variable.
---
 gnu/packages/haskell.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c040965e92..c1815c60da 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10691,6 +10691,41 @@ documents, amongst others.")
 backend for the Charts library.")
     (license license:bsd-3)))
 
+(define-public ghc-atomic-write
+  (package
+    (name "ghc-atomic-write")
+    (version "0.2.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://hackage.haskell.org/package/atomic-write/atomic-write-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1iaq0hprxcv0sl1sgwcgmm87zraf738va1bciwnx2jkk3k1v9iyv"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-temporary" ,ghc-temporary)
+       ("ghc-unix-compat" ,ghc-unix-compat)
+       ("ghc-text" ,ghc-text)))
+    (native-inputs
+     `(("ghc-temporary" ,ghc-temporary)
+       ("ghc-unix-compat" ,ghc-unix-compat)
+       ("ghc-text" ,ghc-text)
+       ("ghc-hspec" ,ghc-hspec)
+       ("hspec-discover" ,hspec-discover)))
+    (home-page "https://github.com/stackbuilders/atomic-write")
+    (synopsis "Atomically write to a file")
+    (description
+     "Atomically write to a file on POSIX-compliant systems while preserving
+permissions.  @code{mv} is an atomic operation.  This makes it simple to write
+to a file atomically just by using the @code{mv} operation.  However, this
+will destroy the permissions on the original file.  This library preserves
+permissions while atomically writing to a file.")
+    (license license:expat)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From d05ed20ef12e5c9520252f2da230c54f46de703d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:38 +0200
Subject: [PATCH 589/909] gnu: Add ghc-cereal-conduit.

* gnu/packages/haskell.scm (ghc-cereal-conduit): New variable.
---
 gnu/packages/haskell.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index c1815c60da..a8d22a682a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10726,6 +10726,33 @@ will destroy the permissions on the original file.  This library preserves
 permissions while atomically writing to a file.")
     (license license:expat)))
 
+(define-public ghc-cereal-conduit
+  (package
+    (name "ghc-cereal-conduit")
+    (version "0.8.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "cereal-conduit/cereal-conduit-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1srr7agvgfw78q5s1npjq5sgynvhjgllpihiv37ylkwqm4c4ap6r"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-conduit" ,ghc-conduit)
+       ("ghc-resourcet" ,ghc-resourcet)
+       ("ghc-cereal" ,ghc-cereal)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)))
+    (home-page "https://github.com/snoyberg/conduit")
+    (synopsis "Turn Data.Serialize Gets and Puts into Sources, Sinks, and Conduits")
+    (description
+     "This package turn @code{Data.Serialize} @code{Gets} and @code{Puts} into
+@code{Sources}, @code{Sinks}, and @code{Conduits}.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 36ec599e785ba3563ede377e05e8172c4323a2aa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:40 +0200
Subject: [PATCH 590/909] gnu: Add ghc-lzma.

* gnu/packages/haskell.scm (ghc-lzma): New variable.
---
 gnu/packages/haskell.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index a8d22a682a..3e10398966 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10753,6 +10753,37 @@ permissions while atomically writing to a file.")
 @code{Sources}, @code{Sinks}, and @code{Conduits}.")
     (license license:bsd-3)))
 
+(define-public ghc-lzma
+  (package
+    (name "ghc-lzma")
+    (version "0.0.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/lzma/"
+                           "lzma-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0i416gqi8j55nd1pqbkxvf3f6hn6fjys6gq98lkkxphva71j30xg"))))
+    (build-system haskell-build-system)
+    (arguments
+     '(#:tests? #f ; requires older versions of QuickCheck and tasty.
+       #:cabal-revision
+       ("3" "1sify6gnsalyp6dakfzi0mdy5jcz2kcp9jsdsgkmxd40nfzgd44m")))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-tasty" ,ghc-tasty)
+       ("ghc-tasty-hunit" ,ghc-tasty-hunit)
+       ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)))
+    (home-page "https://github.com/hvr/lzma")
+    (synopsis "LZMA/XZ compression and decompression")
+    (description
+     "This package provides a pure interface for compressing and
+decompressing LZMA streams of data represented as lazy @code{ByteString}s.  A
+monadic incremental interface is provided as well.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 80588cfccfd193d70491bb2a386667bf538dbb5d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:42 +0200
Subject: [PATCH 591/909] gnu: Add ghc-stm-conduit.

* gnu/packages/haskell.scm (ghc-stm-conduit): New variable.
---
 gnu/packages/haskell.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 3e10398966..d2f6a8b237 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10784,6 +10784,45 @@ decompressing LZMA streams of data represented as lazy @code{ByteString}s.  A
 monadic incremental interface is provided as well.")
     (license license:bsd-3)))
 
+(define-public ghc-stm-conduit
+  (package
+    (name "ghc-stm-conduit")
+    (version "4.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/stm-conduit/"
+                           "stm-conduit-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0paapljn7nqfzrx889y0n8sszci38mdiaxkgr0bb00ph9246rr7z"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-stm" ,ghc-stm)
+       ("ghc-stm-chans" ,ghc-stm-chans)
+       ("ghc-cereal" ,ghc-cereal)
+       ("ghc-cereal-conduit" ,ghc-cereal-conduit)
+       ("ghc-conduit" ,ghc-conduit)
+       ("ghc-conduit-extra" ,ghc-conduit-extra)
+       ("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-resourcet" ,ghc-resourcet)
+       ("ghc-async" ,ghc-async)
+       ("ghc-monad-loops" ,ghc-monad-loops)
+       ("ghc-unliftio" ,ghc-unliftio)))
+    (native-inputs
+     `(("ghc-doctest" ,ghc-doctest)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)))
+    (home-page "https://github.com/cgaebel/stm-conduit")
+    (synopsis "Introduces conduits to channels and promotes using conduits concurrently")
+    (description
+     "This package provides two simple conduit wrappers around STM channels: a
+source and a sink.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 38757d610eedad4dfa4030841132c028460b6c84 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:44 +0200
Subject: [PATCH 592/909] gnu: Add ghc-bindings-dsl.

* gnu/packages/haskell.scm (ghc-bindings-dsl): New variable.
---
 gnu/packages/haskell.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d2f6a8b237..41b1146040 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10823,6 +10823,31 @@ monadic incremental interface is provided as well.")
 source and a sink.")
     (license license:bsd-3)))
 
+(define-public ghc-bindings-dsl
+  (package
+    (name "ghc-bindings-dsl")
+    (version "1.0.25")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/bindings-DSL/"
+                           "bindings-DSL-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0kqrd78nspl3lk4a0fqn47d8dirjg3b24dkvkigcrlb81hw35pk3"))))
+    (build-system haskell-build-system)
+    (home-page "https://github.com/jwiegley/bindings-dsl/wiki")
+    (synopsis "FFI domain specific language, on top of hsc2hs")
+    (description
+     "This is a set of macros to be used when writing Haskell FFI.  They were
+designed to be able to fully describe C interfaces, so that @code{hsc2hs} can
+extract from them all Haskell code needed to mimic such interfaces.  All
+Haskell names used are automatically derived from C names, structures are
+mapped to Haskell instances of @code{Storable}, and there are also macros you
+can use with C code to help write bindings to inline functions or macro
+functions.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 44c6180b3fc76f5e015a1b7097eb7a3196210be8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:46 +0200
Subject: [PATCH 593/909] gnu: Add ghc-lzma-conduit.

* gnu/packages/haskell.scm (ghc-lzma-conduit): New variable.
---
 gnu/packages/haskell.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 41b1146040..4ebaecbd86 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10848,6 +10848,37 @@ can use with C code to help write bindings to inline functions or macro
 functions.")
     (license license:bsd-3)))
 
+(define-public ghc-lzma-conduit
+  (package
+    (name "ghc-lzma-conduit")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/lzma-conduit/"
+                           "lzma-conduit-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0hm72da7xk9l3zxjh274yg444vf405djxqbkf3q3p2qhicmxlmg9"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-conduit" ,ghc-conduit)
+       ("ghc-lzma" ,ghc-lzma)
+       ("ghc-resourcet" ,ghc-resourcet)))
+    (native-inputs
+     `(("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-quickcheck" ,ghc-quickcheck)))
+    (home-page "https://github.com/alphaHeavy/lzma-conduit")
+    (synopsis "Conduit interface for lzma/xz compression")
+    (description
+     "This package provides a @code{Conduit} interface for the LZMA
+compression algorithm used in the @code{.xz} file format.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 4fc161b9c60163f8353648a8e6e00d8229362ff4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:48 +0200
Subject: [PATCH 594/909] gnu: Add ghc-bzlib-conduit.

* gnu/packages/haskell.scm (ghc-bzlib-conduit): New variable.
---
 gnu/packages/haskell.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 4ebaecbd86..d79329f686 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10879,6 +10879,34 @@ functions.")
 compression algorithm used in the @code{.xz} file format.")
     (license license:bsd-3)))
 
+(define-public ghc-bzlib-conduit
+  (package
+    (name "ghc-bzlib-conduit")
+    (version "0.3.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/bzlib-conduit/"
+                           "bzlib-conduit-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0fd2hnr782s7qgipazg2yxwia9qqhkvm9bcm90773c3zkxa13n23"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-bindings-dsl" ,ghc-bindings-dsl)
+       ("ghc-conduit" ,ghc-conduit)
+       ("ghc-data-default-class" ,ghc-data-default-class)
+       ("ghc-resourcet" ,ghc-resourcet)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-random" ,ghc-random)))
+    (home-page "https://github.com/snoyberg/bzlib-conduit")
+    (synopsis "Streaming compression/decompression via conduits")
+    (description
+     "This package provides Haskell bindings to bzlib and Conduit support for
+streaming compression and decompression.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 71c2e3e1a1a0416e6d09eee2691cf4c0decd9be5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:50 +0200
Subject: [PATCH 595/909] gnu: Add ghc-pqueue.

* gnu/packages/haskell.scm (ghc-pqueue): New variable.
---
 gnu/packages/haskell.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d79329f686..80d331c466 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10907,6 +10907,28 @@ compression algorithm used in the @code{.xz} file format.")
 streaming compression and decompression.")
     (license license:bsd-3)))
 
+(define-public ghc-pqueue
+  (package
+    (name "ghc-pqueue")
+    (version "1.4.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "pqueue/pqueue-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1zvwm1zcqqq5n101s1brjhgbay8rf9fviq6gxbplf40i63m57p1x"))))
+    (build-system haskell-build-system)
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)))
+    (home-page "https://hackage.haskell.org/package/pqueue")
+    (synopsis "Reliable, persistent, fast priority queues")
+    (description
+     "This package provides a fast, reliable priority queue implementation
+based on a binomial heap.")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From a933cbfb617d84d37e270b4dd89f2de92013834d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:52 +0200
Subject: [PATCH 596/909] gnu: Add ghc-conduit-algorithms.

* gnu/packages/haskell.scm (ghc-conduit-algorithms): New variable.
---
 gnu/packages/haskell.scm | 42 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 80d331c466..befb1baae5 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10929,6 +10929,48 @@ streaming compression and decompression.")
 based on a binomial heap.")
     (license license:bsd-3)))
 
+(define-public ghc-conduit-algorithms
+  (package
+    (name "ghc-conduit-algorithms")
+    (version "0.0.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "conduit-algorithms/conduit-algorithms-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "07gx2q3d1bbfw14q41rmqg0i4m018pci10lswc0k1ij6lw7sb9fd"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-async" ,ghc-async)
+       ("ghc-bzlib-conduit" ,ghc-bzlib-conduit)
+       ("ghc-conduit" ,ghc-conduit)
+       ("ghc-conduit-combinators" ,ghc-conduit-combinators)
+       ("ghc-conduit-extra" ,ghc-conduit-extra)
+       ("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-lzma-conduit" ,ghc-lzma-conduit)
+       ("ghc-monad-control" ,ghc-monad-control)
+       ("ghc-pqueue" ,ghc-pqueue)
+       ("ghc-resourcet" ,ghc-resourcet)
+       ("ghc-stm" ,ghc-stm)
+       ("ghc-stm-conduit" ,ghc-stm-conduit)
+       ("ghc-streaming-commons" ,ghc-streaming-commons)
+       ("ghc-unliftio-core" ,ghc-unliftio-core)
+       ("ghc-vector" ,ghc-vector)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-th" ,ghc-test-framework-th)))
+    (home-page "https://github.com/luispedro/conduit-algorithms#readme")
+    (synopsis "Conduit-based algorithms")
+    (description
+     "This package provides algorithms on @code{Conduits}, including higher
+level asynchronous processing and some other utilities.")
+    (license license:expat)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 320323141f697483277918f411ecc62a8a7ab85d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:32:54 +0200
Subject: [PATCH 597/909] gnu: Add ghc-interpolate.

* gnu/packages/haskell.scm (ghc-interpolate): New variable.
---
 gnu/packages/haskell.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index befb1baae5..8a33cbd6b2 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10971,6 +10971,34 @@ based on a binomial heap.")
 level asynchronous processing and some other utilities.")
     (license license:expat)))
 
+(define-public ghc-interpolate
+  (package
+    (name "ghc-interpolate")
+    (version "0.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/interpolate/"
+                           "interpolate-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1gkaj98yz363v38fv78sqby236mp8yqwqcilx7kr2b9z0w3204bf"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-haskell-src-meta" ,ghc-haskell-src-meta)))
+    (native-inputs
+     `(("ghc-base-compat" ,ghc-base-compat)
+       ("ghc-hspec" ,ghc-hspec)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-quickcheck-instances" ,ghc-quickcheck-instances)
+       ("ghc-text" ,ghc-text)
+       ("hspec-discover" ,hspec-discover)))
+    (home-page "https://github.com/sol/interpolate")
+    (synopsis "String interpolation library")
+    (description "This package provides a string interpolation library for
+Haskell.")
+    (license license:expat)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 5e6bf3e2da6934daeadc36afeb8e09f105754efe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:15:04 +0200
Subject: [PATCH 598/909] gnu: Add ghc-hpack.

* gnu/packages/haskell.scm (ghc-hpack): New variable.
---
 gnu/packages/haskell.scm | 45 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 8a33cbd6b2..9a5f7c9746 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10999,6 +10999,51 @@ level asynchronous processing and some other utilities.")
 Haskell.")
     (license license:expat)))
 
+(define-public ghc-hpack
+  (package
+    (name "ghc-hpack")
+    (version "0.28.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/hpack/"
+                           "hpack-" version ".tar.gz"))
+       (sha256
+        (base32
+         "18w0h76jdp3mk9vin8da9iz3cwhcxmw787xy8wlh8bxcpcr16q5r"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-bifunctors" ,ghc-bifunctors)
+       ("ghc-cryptonite" ,ghc-cryptonite)
+       ("ghc-glob" ,ghc-glob)
+       ("ghc-http-client" ,ghc-http-client)
+       ("ghc-http-client-tls" ,ghc-http-client-tls)
+       ("ghc-http-types" ,ghc-http-types)
+       ("ghc-scientific" ,ghc-scientific)
+       ("ghc-text" ,ghc-text)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-yaml" ,ghc-yaml)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-hunit" ,ghc-hunit)
+       ("ghc-interpolate" ,ghc-interpolate)
+       ("ghc-mockery" ,ghc-mockery)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-temporary" ,ghc-temporary)
+       ("hspec-discover" ,hspec-discover)))
+    (home-page "https://github.com/sol/hpack")
+    (synopsis "Tools for an alternative Haskell package format")
+    (description
+     "Hpack is a format for Haskell packages.  It is an alternative to the
+Cabal package format and follows different design principles.  Hpack packages
+are described in a file named @code{package.yaml}.  Both @code{cabal2nix} and
+@code{stack} support @code{package.yaml} natively.  For other build tools the
+@code{hpack} executable can be used to generate a @code{.cabal} file from
+@code{package.yaml}.")
+    (license license:expat)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 52f5114d016688fb143079056a64b8abfb319507 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:37:58 +0200
Subject: [PATCH 599/909] gnu: Add ghc-raw-string-qq.

* gnu/packages/haskell.scm (ghc-raw-string-qq): New variable.
---
 gnu/packages/haskell.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9a5f7c9746..6b8a4ee3fc 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11044,6 +11044,31 @@ are described in a file named @code{package.yaml}.  Both @code{cabal2nix} and
 @code{package.yaml}.")
     (license license:expat)))
 
+(define-public ghc-raw-strings-qq
+  (package
+    (name "ghc-raw-strings-qq")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "raw-strings-qq/raw-strings-qq-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1lxy1wy3awf52968iy5y9r5z4qgnn2sxkdrh7js3m9gadb11w09f"))))
+    (build-system haskell-build-system)
+    (native-inputs `(("ghc-hunit" ,ghc-hunit)))
+    (home-page "https://github.com/23Skidoo/raw-strings-qq")
+    (synopsis "Raw string literals for Haskell")
+    (description
+     "This package provides a quasiquoter for raw string literals, i.e. string
+literals that don't recognise the standard escape sequences.  Basically, they
+make your code more readable by freeing you from the responsibility to escape
+backslashes.  They are useful when working with regular expressions,
+DOS/Windows paths and markup languages (such as XML).")
+    (license license:bsd-3)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 88189099dff99ecb4912c9c01adb920868049bec Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:00 +0200
Subject: [PATCH 600/909] gnu: Add ghc-inline-c.

* gnu/packages/haskell.scm (ghc-inline-c): New variable.
---
 gnu/packages/haskell.scm | 46 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 6b8a4ee3fc..9bc86bfbd3 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11069,6 +11069,52 @@ backslashes.  They are useful when working with regular expressions,
 DOS/Windows paths and markup languages (such as XML).")
     (license license:bsd-3)))
 
+(define-public ghc-inline-c
+  (package
+    (name "ghc-inline-c")
+    (version "0.6.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/inline-c/"
+                           "inline-c-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0vbfrsqsi7mdziqsnj68bsqlwbqxxhvrmy9rv6w8z18d1m8w3n6h"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'create-Setup.hs
+           (lambda _
+             (with-output-to-file "Setup.hs"
+               (lambda _
+                 (display "\
+import Distribution.Simple
+main = defaultMain")))
+             #t)))))
+    (inputs
+     `(("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)
+       ("ghc-cryptohash" ,ghc-cryptohash)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-parsers" ,ghc-parsers)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)
+       ("ghc-vector" ,ghc-vector)))
+    (native-inputs
+     `(("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-hspec" ,ghc-hspec)
+       ("ghc-raw-strings-qq" ,ghc-raw-strings-qq)
+       ("ghc-regex-posix" ,ghc-regex-posix)))
+    (home-page "http://hackage.haskell.org/package/inline-c")
+    (synopsis "Write Haskell source files including C code inline")
+    (description
+     "inline-c lets you seamlessly call C libraries and embed high-performance
+inline C code in Haskell modules.  Haskell and C can be freely intermixed in
+the same source file, and data passed to and from code in either language with
+minimal overhead.  No FFI required.")
+    (license license:expat)))
+
 (define-public ghc-weigh
   (package
     (name "ghc-weigh")

From 9ef95a196f5144506eb92e3870de96a180454643 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:02 +0200
Subject: [PATCH 601/909] gnu: Add ghc-safe-exceptions.

* gnu/packages/haskell.scm (ghc-safe-exceptions): New variable.
---
 gnu/packages/haskell.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9bc86bfbd3..5d68ddcada 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11180,4 +11180,37 @@ Haskell value or function.")
 vector spaces.")
     (license license:bsd-3)))
 
+(define-public ghc-safe-exceptions
+  (package
+    (name "ghc-safe-exceptions")
+    (version "0.1.7.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "safe-exceptions/safe-exceptions-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0sd0zfsm9pcll5bzzj523rbn45adjrnavdkz52hgmdjjgdcdrk8q"))))
+    (build-system haskell-build-system)
+    (arguments
+     '(#:cabal-revision
+       ("4" "0fid41gishzsyb47wzxhd5falandfirqcp760hcja81qjpfmqd32")))
+    (inputs `(("ghc-exceptions" ,ghc-exceptions)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)
+       ("ghc-void" ,ghc-void)
+       ("hspec-discover" ,hspec-discover)))
+    (home-page "https://github.com/fpco/safe-exceptions")
+    (synopsis "Safe, consistent, and easy exception handling")
+    (description "Runtime exceptions - as exposed in @code{base} by the
+@code{Control.Exception} module - have long been an intimidating part of the
+Haskell ecosystem.  This package is intended to overcome this.  It provides a
+safe and simple API on top of the existing exception handling machinery.  The
+API is equivalent to the underlying implementation in terms of power but
+encourages best practices to minimize the chances of getting the exception
+handling wrong.")
+    (license license:expat)))
+
 ;;; haskell.scm ends here

From d9ee3e375ca54bb6f4fd6bbc5b3646e27a0c25d0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:04 +0200
Subject: [PATCH 602/909] gnu: Add ghc-inline-c-cpp.

* gnu/packages/haskell.scm (ghc-inline-c-cpp): New variable.
---
 gnu/packages/haskell.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 5d68ddcada..9e47c4cbfc 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11213,4 +11213,40 @@ encourages best practices to minimize the chances of getting the exception
 handling wrong.")
     (license license:expat)))
 
+(define-public ghc-inline-c-cpp
+  (package
+    (name "ghc-inline-c-cpp")
+    (version "0.2.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/inline-c-cpp/"
+                           "inline-c-cpp-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1rk7fmpkmxw9hhwr8df29kadnf0ybnwj64ggdbnsdrpfyhnkisci"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'create-Setup.hs
+           (lambda _
+             (with-output-to-file "Setup.hs"
+               (lambda _
+                 (display "\
+import Distribution.Simple
+main = defaultMain")))
+             #t)))))
+    (inputs
+     `(("ghc-inline-c" ,ghc-inline-c)
+       ("ghc-safe-exceptions" ,ghc-safe-exceptions)))
+    (native-inputs
+     `(("ghc-hspec" ,ghc-hspec)))
+    (home-page "https://hackage.haskell.org/package/inline-c-cpp")
+    (synopsis "Lets you embed C++ code into Haskell")
+    (description
+     "This package provides utilities to inline C++ code into Haskell using
+@code{inline-c}.")
+    (license license:expat)))
+
 ;;; haskell.scm ends here

From d453b899448bd1dc909e7ef279d52940a95031e0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:06 +0200
Subject: [PATCH 603/909] gnu: Add ghc-bytestring-lexing.

* gnu/packages/haskell.scm (ghc-bytestring-lexing): New variable.
---
 gnu/packages/haskell.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 9e47c4cbfc..33354e883b 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11249,4 +11249,25 @@ main = defaultMain")))
 @code{inline-c}.")
     (license license:expat)))
 
+(define-public ghc-bytestring-lexing
+  (package
+    (name "ghc-bytestring-lexing")
+    (version "0.5.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "bytestring-lexing/bytestring-lexing-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0wrzniawhgpphc6yx1v972gyqxdbv0pizaz9bafahrshyb9svy81"))))
+    (build-system haskell-build-system)
+    (home-page "http://code.haskell.org/~wren/")
+    (synopsis "Parse and produce literals from strict or lazy bytestrings")
+    (description
+     "This package provides tools to parse and produce literals efficiently
+from strict or lazy bytestrings.")
+    (license license:bsd-2)))
+
 ;;; haskell.scm ends here

From c7e400b1eefd627e634a9624f4f68f217d55715d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:08 +0200
Subject: [PATCH 604/909] gnu: Add ghc-configurator.

* gnu/packages/haskell.scm (ghc-configurator): New variable.
---
 gnu/packages/haskell.scm | 43 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 33354e883b..af44232cee 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11270,4 +11270,47 @@ main = defaultMain")))
 from strict or lazy bytestrings.")
     (license license:bsd-2)))
 
+(define-public ghc-configurator
+  (package
+    (name "ghc-configurator")
+    (version "0.3.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/"
+                           "configurator/configurator-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1d1iq1knwiq6ia5g64rw5hqm6dakz912qj13r89737rfcxmrkfbf"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-attoparsec" ,ghc-attoparsec)
+       ("ghc-hashable" ,ghc-hashable)
+       ("ghc-text" ,ghc-text)
+       ("ghc-unix-compat" ,ghc-unix-compat)
+       ("ghc-unordered-containers" ,ghc-unordered-containers)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)))
+    (home-page "http://github.com/bos/configurator")
+    (synopsis "Configuration management")
+    (description
+     "This package provides a configuration management library for programs
+and daemons.  The features include:
+
+@enumerate
+@item Automatic, dynamic reloading in response to modifications to
+  configuration files.
+@item A simple, but flexible, configuration language, supporting several of
+  the most commonly needed types of data, along with interpolation of strings
+  from the configuration or the system environment (e.g. @code{$(HOME)}).
+@item Subscription-based notification of changes to configuration properties.
+@item An @code{import} directive allows the configuration of a complex
+  application to be split across several smaller files, or common configuration
+  data to be shared across several applications.
+@end enumerate\n")
+    (license license:bsd-3)))
+
 ;;; haskell.scm ends here

From ea202046fa66028463df9cf23399d4adc39f5c36 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:10 +0200
Subject: [PATCH 605/909] gnu: Add ghc-file-embed.

* gnu/packages/haskell.scm (ghc-file-embed): New variable.
---
 gnu/packages/haskell.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index af44232cee..28f5bdffe6 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11313,4 +11313,25 @@ and daemons.  The features include:
 @end enumerate\n")
     (license license:bsd-3)))
 
+(define-public ghc-file-embed
+  (package
+    (name "ghc-file-embed")
+    (version "0.0.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/file-embed/"
+                           "file-embed-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0lj164cnzqyd487mli91nnr7137a4h4qsasfwsnsh77sx12fpk9k"))))
+    (build-system haskell-build-system)
+    (home-page "https://github.com/snoyberg/file-embed")
+    (synopsis "Use Template Haskell to embed file contents directly")
+    (description
+     "This package allows you to use Template Haskell to read a file or all
+the files in a directory, and turn them into @code{(path, bytestring)} pairs
+embedded in your Haskell code.")
+    (license license:bsd-3)))
+
 ;;; haskell.scm ends here

From b1f9cc88c4e371e39aae4a6dee8fcc775c2ac9a5 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:12 +0200
Subject: [PATCH 606/909] gnu: Add ghc-safeio.

* gnu/packages/haskell.scm (ghc-safeio): New variable.
---
 gnu/packages/haskell.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 28f5bdffe6..0a90ac523c 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -11334,4 +11334,34 @@ the files in a directory, and turn them into @code{(path, bytestring)} pairs
 embedded in your Haskell code.")
     (license license:bsd-3)))
 
+(define-public ghc-safeio
+  (package
+    (name "ghc-safeio")
+    (version "0.0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://hackage.haskell.org/package/safeio/"
+                           "safeio-" version ".tar.gz"))
+       (sha256
+        (base32
+         "04g3070cbjdqj0h9l9ii6470xcbn40xfv4fr89a8yvnkdim9nyfm"))))
+    (build-system haskell-build-system)
+    (inputs
+     `(("ghc-conduit" ,ghc-conduit)
+       ("ghc-conduit-combinators" ,ghc-conduit-combinators)
+       ("ghc-exceptions" ,ghc-exceptions)
+       ("ghc-resourcet" ,ghc-resourcet)))
+    (native-inputs
+     `(("ghc-hunit" ,ghc-hunit)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit" ,ghc-test-framework-hunit)
+       ("ghc-test-framework-th" ,ghc-test-framework-th)))
+    (home-page "https://github.com/luispedro/safeio")
+    (synopsis "Write output to disk atomically")
+    (description
+     "This package implements utilities to perform atomic output so as to
+avoid the problem of partial intermediate files.")
+    (license license:expat)))
+
 ;;; haskell.scm ends here

From d71078bc75d149c70dc573a259986f1731145693 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Oct 2018 18:38:14 +0200
Subject: [PATCH 607/909] gnu: Add ngless.

* gnu/packages/bioinformatics.scm (ngless): New variable.
---
 gnu/packages/bioinformatics.scm | 87 +++++++++++++++++++++++++++++++++
 1 file changed, 87 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 43220d22fe..ab9dc185a3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -38,6 +38,7 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system haskell)
   #:use-module (guix build-system ocaml)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system python)
@@ -72,6 +73,8 @@
   #:use-module (gnu packages groff)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages haskell)
+  #:use-module (gnu packages haskell-check)
+  #:use-module (gnu packages haskell-web)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
@@ -13970,3 +13973,87 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
   Without filtering, users can perform (original) two-tailed or one-tailed
 absolute GSEA.")
     (license license:gpl2)))
+
+(define-public ngless
+  (package
+    (name "ngless")
+    (version "0.9.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/ngless/ngless.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117"))))
+    (build-system haskell-build-system)
+    (arguments
+     `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
+                     ; error: parse error on input import
+                     ; import Options.Applicative
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'create-cabal-file
+           (lambda _ (invoke "hpack") #t)))))
+    (inputs
+     `(("ghc-aeson" ,ghc-aeson)
+       ("ghc-ansi-terminal" ,ghc-ansi-terminal)
+       ("ghc-async" ,ghc-async)
+       ("ghc-atomic-write" ,ghc-atomic-write)
+       ("ghc-bytestring-lexing" ,ghc-bytestring-lexing)
+       ("ghc-chart" ,ghc-chart)
+       ("ghc-chart-cairo" ,ghc-chart-cairo)
+       ("ghc-conduit" ,ghc-conduit)
+       ("ghc-conduit-algorithms" ,ghc-conduit-algorithms)
+       ("ghc-conduit-combinators" ,ghc-conduit-combinators)
+       ("ghc-conduit-extra" ,ghc-conduit-extra)
+       ("ghc-configurator" ,ghc-configurator)
+       ("ghc-convertible" ,ghc-convertible)
+       ("ghc-data-default" ,ghc-data-default)
+       ("ghc-double-conversion" ,ghc-double-conversion)
+       ("ghc-edit-distance" ,ghc-edit-distance)
+       ("ghc-either" ,ghc-either)
+       ("ghc-errors" ,ghc-errors)
+       ("ghc-extra" ,ghc-extra)
+       ("ghc-filemanip" ,ghc-filemanip)
+       ("ghc-file-embed" ,ghc-file-embed)
+       ("ghc-gitrev" ,ghc-gitrev)
+       ("ghc-hashtables" ,ghc-hashtables)
+       ("ghc-http-conduit" ,ghc-http-conduit)
+       ("ghc-inline-c" ,ghc-inline-c)
+       ("ghc-inline-c-cpp" ,ghc-inline-c-cpp)
+       ("ghc-intervalmap" ,ghc-intervalmap)
+       ("ghc-missingh" ,ghc-missingh)
+       ("ghc-optparse-applicative" ,ghc-optparse-applicative)
+       ("ghc-parsec" ,ghc-parsec)
+       ("ghc-regex" ,ghc-regex)
+       ("ghc-safe" ,ghc-safe)
+       ("ghc-safeio" ,ghc-safeio)
+       ("ghc-strict" ,ghc-strict)
+       ("ghc-tar" ,ghc-tar)
+       ("ghc-text" ,ghc-text)
+       ("ghc-unliftio" ,ghc-unliftio)
+       ("ghc-unliftio-core" ,ghc-unliftio-core)
+       ("ghc-vector" ,ghc-vector)
+       ("ghc-yaml" ,ghc-yaml)
+       ("ghc-zlib" ,ghc-zlib)))
+    (propagated-inputs
+     `(("r-r6" ,r-r6)
+       ("r-hdf5r" ,r-hdf5r)
+       ("r-iterators" ,r-iterators)
+       ("r-itertools" ,r-itertools)
+       ("r-matrix" ,r-matrix)))
+    (native-inputs
+     `(("ghc-hpack" ,ghc-hpack)
+       ("ghc-quickcheck" ,ghc-quickcheck)
+       ("ghc-test-framework" ,ghc-test-framework)
+       ("ghc-test-framework-hunit",ghc-test-framework-hunit)
+       ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
+       ("ghc-test-framework-th" ,ghc-test-framework-th)))
+    (home-page "https://gitlab.com/ngless/ngless")
+    (synopsis "DSL for processing next-generation sequencing data")
+    (description "Ngless is a domain-specific language for
+@dfn{next-generation sequencing} (NGS) data processing.")
+    (license license:expat)))

From e90ce1157794bfecfe93f7c31dc4bd631dd710fb Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 6 Oct 2018 03:32:12 -0400
Subject: [PATCH 608/909] gnu: git: Update to 2.19.1 [fixes CVE-2018-17456].

* gnu/packages/version-control.scm (git): Update to 2.19.1.
---
 gnu/packages/version-control.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index cc892b9c62..00d7e1f189 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -146,14 +146,14 @@ as well as the classic centralized workflow.")
    (name "git")
    ;; XXX When updating Git, check if the special 'git-source' input to cgit
    ;; needs to be updated as well.
-   (version "2.19.0")
+   (version "2.19.1")
    (source (origin
             (method url-fetch)
             (uri (string-append "mirror://kernel.org/software/scm/git/git-"
                                 version ".tar.xz"))
             (sha256
              (base32
-              "1x1y5z3awabmfg7hk6zb331jxngad4nal4507v96bnf0izsyy3qq"))))
+              "1dfv43lmdnxz42504jc89sihbv1d4d6kgqcz3c5ji140kfm5cl1l"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("native-perl" ,perl)
@@ -166,7 +166,7 @@ as well as the classic centralized workflow.")
                 version ".tar.xz"))
           (sha256
            (base32
-            "1jvxiqvp9q4is3np063ny7rnmk5hm36d34bhi3cgv89njqdh8laf"))))))
+            "1vn6pi9yvw7rnb9dvi1yjrvv39fqd1m9mwbaffqwizs3gaf91br7"))))))
    (inputs
     `(("curl" ,curl)
       ("expat" ,expat)

From ccfac015bfb9eb3fa50590517f01fdb20c810750 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sat, 6 Oct 2018 18:18:22 +0200
Subject: [PATCH 609/909] gnu: wcslib: Update to 5.20.

* gnu/packages/astronomy.scm (wcslib): Update to 5.20.
[arguments]: Build parallelly.
---
 gnu/packages/astronomy.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index 88e3723a1f..3c8b9cc8df 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -68,7 +68,7 @@ in FITS files.")
 (define-public wcslib
   (package
     (name "wcslib")
-    (version "5.18")
+    (version "5.20")
     (source
      (origin
        (method url-fetch)
@@ -76,7 +76,7 @@ in FITS files.")
              "ftp://ftp.atnf.csiro.au/pub/software/wcslib/" name "-" version
              ".tar.bz2"))
        (sha256
-        (base32 "16jh568k99c9p0y3qzcgps2rii933x9wlay7q1xm0lr59zqzp4xn"))))
+        (base32 "1c8g9kv4dxrnawnqi4spi2p10s2xs7x75pdfxhbqxgcc97dkgh0b"))))
     (inputs
      `(("cfitsio" ,cfitsio)))
     (build-system gnu-build-system)
@@ -89,8 +89,7 @@ in FITS files.")
                (("/bin/sh") "sh"))
              #t))
          (delete 'install-license-files)) ; installed by ‘make install’
-       ;; Both the build and tests fail randomly when run in parallel.
-       #:parallel-build? #f
+       ;; Parallel execution of the test suite is not supported.
        #:parallel-tests? #f))
     (home-page "https://www.atnf.csiro.au/people/mcalabre/WCS")
     (synopsis "Library which implements the FITS WCS standard")

From 96808b39e76aae65a0ed3149780f23d91326b6c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Sun, 7 Oct 2018 14:55:55 +0800
Subject: [PATCH 610/909] gnu: pd: Update to 0.49-0.

* gnu/packages/music.scm (pd): Update to 0.49-0.
---
 gnu/packages/music.scm | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 2d834d8c1f..3163e6a8f6 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1726,7 +1726,7 @@ export.")
 (define-public pd
   (package
     (name "pd")
-    (version "0.47-1")
+    (version "0.49-0")
     (source (origin
               (method url-fetch)
               (uri
@@ -1734,16 +1734,20 @@ export.")
                               version ".src.tar.gz"))
               (sha256
                (base32
-                "0k5s949kqd7yw97h3m8z81bjz32bis9m4ih8df1z0ymipnafca67"))))
+                "18rzqbpgnnvyslap7k0ly87aw1bbxkb0rk5agpr423ibs9slxq6j"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no "check" target
+       #:configure-flags
+       (list
+        "--enable-jack"
+        (string-append "--with-wish=" (string-append
+                                       (assoc-ref %build-inputs "tk")
+                                       "/bin/wish8.6")))
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'fix-wish-path
+         (add-before 'configure 'fix-with-path
            (lambda _
-             (substitute* "src/s_inter.c"
-               (("  wish ") (string-append "  " (which "wish8.6") " ")))
              (substitute* "tcl/pd-gui.tcl"
                (("exec wish ") (string-append "exec " (which "wish8.6") " ")))
              #t))

From c8a99ab9112b6a671b15766301f03e428108c4eb Mon Sep 17 00:00:00 2001
From: fis trivial <ybbs.daans@hotmail.com>
Date: Sun, 7 Oct 2018 09:03:40 +0000
Subject: [PATCH 611/909] gnu: mercurial: Update to 4.6.2.

* gnu/packages/version-control.scm (mercurial): Update to 4.6.2.
---
 gnu/packages/version-control.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 00d7e1f189..528d117e29 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1119,14 +1119,14 @@ control to Git repositories.")
 (define-public mercurial
   (package
     (name "mercurial")
-    (version "4.4.1")
+    (version "4.6.2")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://www.mercurial-scm.org/"
                                  "release/mercurial-" version ".tar.gz"))
              (sha256
               (base32
-               "0ik2ypzxjr6vpcghxvn39a73gw52629n7vwak04gnbycsq95aalg"))))
+               "1bv6wgcdx8glihjjfg22khhc52mclsn4kwfqvzbzlg0b42h4xl0w"))))
     (build-system python-build-system)
     (arguments
      `(;; Restrict to Python 2, as Python 3 would require

From 2c4be1add077bf30f949282edcc2ea507ba44497 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:14:13 +0200
Subject: [PATCH 612/909] gnu: Add java-w3c-smil.

* gnu/packages/batik.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
---
 gnu/local.mk           |  1 +
 gnu/packages/batik.scm | 90 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 91 insertions(+)
 create mode 100644 gnu/packages/batik.scm

diff --git a/gnu/local.mk b/gnu/local.mk
index 8f854e98b5..f1ce800dd5 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -77,6 +77,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/backup.scm			\
   %D%/packages/base.scm				\
   %D%/packages/bash.scm				\
+  %D%/packages/batik.scm			\
   %D%/packages/bdw-gc.scm			\
   %D%/packages/benchmark.scm			\
   %D%/packages/bioconductor.scm			\
diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
new file mode 100644
index 0000000000..91eb8f01d5
--- /dev/null
+++ b/gnu/packages/batik.scm
@@ -0,0 +1,90 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages batik)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system ant)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages textutils))
+
+(define-public java-w3c-smil-3.0
+  (package
+    (name "java-w3c-smil")
+    (version "3.0")
+    (source #f)
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "w3c-smil.jar"
+       #:source-dir "."
+       #:tests? #f ; No tests exist.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             ;; https://www.w3.org/TR/SMIL3/smil-timing.html#q142
+             (mkdir-p "org/w3c/dom/smil")
+             (call-with-output-file "org/w3c/dom/smil/ElementTimeControl.java"
+               (lambda (port)
+                 (format port "
+package org.w3c.dom.smil;
+
+import org.w3c.dom.DOMException;
+
+public interface ElementTimeControl {
+    public boolean  beginElement();
+
+    public boolean  beginElementAt(float offset);
+
+    public boolean endElement();
+
+    public boolean endElementAt(float offset);
+}
+")))
+             (call-with-output-file "org/w3c/dom/smil/TimeEvent.java"
+               (lambda (port)
+                 (format port "
+package org.w3c.dom.smil;
+
+import org.w3c.dom.events.Event;
+import org.w3c.dom.views.AbstractView;
+
+public interface TimeEvent extends Event {
+    public AbstractView getView();
+
+    public int getDetail();
+
+    public void initTimeEvent(String typeArg,
+                              AbstractView viewArg,
+                              int detailArg);
+
+}
+")))
+             #t)))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://www.w3.org/Style/CSS/SAC/")
+    (synopsis "W3C SAC interface for CSS parsers in Java")
+    (description "This package provides a SAC interface by the W3C.
+SAC is an interface for CSS parsers.")
+    (license license:w3c)))

From da99c46f63d13cd42b871f3e180be830061cc8b3 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:15:21 +0200
Subject: [PATCH 613/909] gnu: Add java-w3c-svg.

* gnu/packages/batik.scm (java-w3c-svg-1.0, java-w3c-svg): New variables.
---
 gnu/packages/batik.scm | 68 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index 91eb8f01d5..b3361d9092 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -88,3 +88,71 @@ public interface TimeEvent extends Event {
     (description "This package provides a SAC interface by the W3C.
 SAC is an interface for CSS parsers.")
     (license license:w3c)))
+
+(define-public java-w3c-svg-1.0
+  (package
+    (name "java-w3c-svg")
+    (version "20010904")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://www.w3.org/TR/2001/REC-SVG-" version
+                            "/java-binding.zip"))
+        (sha256
+         (base32
+          "0gnxvx51bg6ijplf6l2q0i1m07101f7fickawshfygnsdjqfdnbp"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "w3c-svg.jar"
+       #:source-dir "."
+       #:tests? #f ; No tests exist.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             (invoke "unzip" source)))
+         (add-after 'unpack 'patch-interface
+           (lambda _
+             ;; Make it compatible with batik.
+             ;; This is equivalent to usingxml commons externals'
+             ;; "externals" part from https://xerces.apache.org/mirrors.cgi
+             (substitute* "SVGFEConvolveMatrixElement.java"
+              (("public SVGAnimatedLength[ ]*getKernelUnitLength")
+               "public SVGAnimatedNumber getKernelUnitLength"))
+             (substitute* "SVGFEMorphologyElement.java"
+              (("public SVGAnimatedLength[ ]*getRadius")
+               "public SVGAnimatedNumber getRadius"))
+             (call-with-output-file "EventListenerInitializer.java"
+               (lambda (port)
+                 (format port "
+// License: http://www.apache.org/licenses/LICENSE-2.0
+package org.w3c.dom.svg;
+public interface EventListenerInitializer {
+    public void initializeEventListeners(SVGDocument doc);
+}
+
+")))
+             #t)))))
+    (propagated-inputs
+     `(("java-w3c-smil" ,java-w3c-smil-3.0)))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://www.w3.org/Style/CSS/SAC/")
+    (synopsis "W3C SVG interface")
+    (description "This package provides a SVG interface.")
+    (license license:w3c)))
+
+(define-public java-w3c-svg
+  (package
+    (inherit java-w3c-svg-1.0)
+    (version "20110816")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "http://www.w3.org/TR/2011/REC-SVG11-" version
+                            "/java-binding.zip"))
+        (sha256
+         (base32
+          "0jicqcrxav8ggs37amgvvwgc2f0qp1c5wns4rb2i3si83s2m09ns"))))
+    (propagated-inputs
+     `())))

From 283f57d8fa3dc2a9a6798dbea6b6b87319fda1ad Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:16:01 +0200
Subject: [PATCH 614/909] gnu: Add java-w3c-sac.

* gnu/packages/batik.scm (java-w3c-sac): New variable.
---
 gnu/packages/batik.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index b3361d9092..cf946e570e 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -156,3 +156,33 @@ public interface EventListenerInitializer {
           "0jicqcrxav8ggs37amgvvwgc2f0qp1c5wns4rb2i3si83s2m09ns"))))
     (propagated-inputs
      `())))
+
+(define-public java-w3c-sac
+  (package
+    (name "java-w3c-sac")
+    (version "1.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append "https://www.w3.org/2002/06/sacjava-" version
+                            ".zip"))
+        (sha256
+         (base32
+          "1djp2nnzf8jchnwz1ij9i5jfx4cg1ryf3lbw133yzjy0wkhcla52"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "w3c-sac.jar"
+       #:source-dir "sac-1.3"
+       #:tests? #f ; No tests exist.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'unpack
+           (lambda* (#:key source #:allow-other-keys)
+             (invoke "unzip" source))))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://www.w3.org/Style/CSS/SAC/")
+    (synopsis "W3C SAC interface for CSS parsers in Java")
+    (description "This package provides a SAC interface by the W3C.
+SAC is an interface for CSS parsers.")
+    (license license:w3c)))

From 52d2725ab126a98f170482d483ef4ddd71ba8edf Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:32:05 +0200
Subject: [PATCH 615/909] gnu: Add java-xmlgraphics-commons.

* gnu/packages/batik.scm (java-xmlgraphics-commons): New variable.
---
 gnu/packages/batik.scm | 45 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index cf946e570e..d45600f7b9 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -186,3 +186,48 @@ public interface EventListenerInitializer {
     (description "This package provides a SAC interface by the W3C.
 SAC is an interface for CSS parsers.")
     (license license:w3c)))
+
+(define-public java-xmlgraphics-commons
+  (package
+    (name "java-xmlgraphics-commons")
+    (version "2.3")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append
+              "mirror://apache/xmlgraphics/commons/source/xmlgraphics-commons-"
+              version "-src.tar.gz"))
+        (sha256
+         (base32
+          "0a432a4ca3vgnbada5cy9mlmfzmq6hi4i176drfxrp17q2d43w23"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:build-target "jar-main"
+       ;; TODO: More detailed tests are available--but they need
+       ;; commons-xml-resolver.
+       ;; TODO: Provide commons-xml-resolver.
+       #:test-target "junit-basic"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-reproducible
+           (lambda _
+             (substitute* "build.xml"
+              (("<attribute name=\"Build-Id\" value=\"[^\"]*\"")
+               "<attribute name=\"Build-Id\" value=\"\""))
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (out-share (string-append out "/share/java")))
+               (for-each (lambda (name)
+                           (install-file name out-share))
+                         (find-files "build"
+                                     "xmlgraphics-commons.*\\.jar$"))
+               #t))))))
+    (native-inputs
+     `(("java-junit" ,java-junit)))
+    (home-page "https://xmlgraphics.apache.org/commons/")
+    (synopsis "XMLGraphics constants")
+    (description "This package provides XMLGraphics constants (originally
+from @code{batik}).")
+    (license license:asl2.0)))

From 02803fdf45541584d0341786d5dfbfb76f17d317 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:42:15 +0200
Subject: [PATCH 616/909] gnu: java-xmlgraphics-commons: Remove bundled
 dependencies.

* gnu/packages/batik.scm (java-xmlgraphics-commons): Remove bundled
dependencies.
---
 gnu/packages/batik.scm | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index d45600f7b9..9449e565f1 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -26,7 +26,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages java)
-  #:use-module (gnu packages textutils))
+  #:use-module (gnu packages textutils)
+  #:use-module (gnu packages xml))
 
 (define-public java-w3c-smil-3.0
   (package
@@ -199,13 +200,16 @@ SAC is an interface for CSS parsers.")
               version "-src.tar.gz"))
         (sha256
          (base32
-          "0a432a4ca3vgnbada5cy9mlmfzmq6hi4i176drfxrp17q2d43w23"))))
+          "0a432a4ca3vgnbada5cy9mlmfzmq6hi4i176drfxrp17q2d43w23"))
+        (modules '((guix build utils)))
+        (snippet
+         `(begin
+            (delete-file-recursively "lib")
+            #t))))
     (build-system ant-build-system)
     (arguments
      `(#:build-target "jar-main"
-       ;; TODO: More detailed tests are available--but they need
-       ;; commons-xml-resolver.
-       ;; TODO: Provide commons-xml-resolver.
+       ;; TODO: More detailed tests are available.
        #:test-target "junit-basic"
        #:phases
        (modify-phases %standard-phases
@@ -215,6 +219,11 @@ SAC is an interface for CSS parsers.")
               (("<attribute name=\"Build-Id\" value=\"[^\"]*\"")
                "<attribute name=\"Build-Id\" value=\"\""))
              #t))
+         (add-before 'build 'prepare-build-directories
+           (lambda _
+             (mkdir "lib")
+             (mkdir "lib/build")
+             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -225,7 +234,14 @@ SAC is an interface for CSS parsers.")
                                      "xmlgraphics-commons.*\\.jar$"))
                #t))))))
     (native-inputs
-     `(("java-junit" ,java-junit)))
+     `(("java-apache-xml-commons-resolver" ,java-apache-xml-commons-resolver)
+       ("java-hamcrest" ,java-hamcrest-core)
+       ("java-junit" ,java-junit)
+       ("java-mockito" ,java-mockito-1)
+       ("java-objenesis" ,java-objenesis)))
+    (propagated-inputs
+     `(("java-commons-io" ,java-commons-io)
+       ("java-commons-logging-minimal" ,java-commons-logging-minimal)))
     (home-page "https://xmlgraphics.apache.org/commons/")
     (synopsis "XMLGraphics constants")
     (description "This package provides XMLGraphics constants (originally

From 05dae4030225d604fd3c8562ce23dbbe597d5de9 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:43:47 +0200
Subject: [PATCH 617/909] gnu: java-xmlgraphics-commons: Make error in tests
 fail the "check" phase.

* gnu/packages/batik.scm (java-xmlgraphics-commons)[arguments]<#:test-target>:
Use "junit" test target.
---
 gnu/packages/batik.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index 9449e565f1..5bba859370 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -209,8 +209,7 @@ SAC is an interface for CSS parsers.")
     (build-system ant-build-system)
     (arguments
      `(#:build-target "jar-main"
-       ;; TODO: More detailed tests are available.
-       #:test-target "junit-basic"
+       #:test-target "junit"
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'make-reproducible

From 3158425eb85419bc8bf787fe1b00af30133bdaa3 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:46:26 +0200
Subject: [PATCH 618/909] gnu: java-xmlgraphics-commons: Add dependency to
 java-cglib.

* gnu/packages/batik.scm (java-xmlgraphics-commons)[native-inputs]: Add
java-cglib.
---
 gnu/packages/batik.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index 5bba859370..5a74d7cc35 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -234,6 +234,7 @@ SAC is an interface for CSS parsers.")
                #t))))))
     (native-inputs
      `(("java-apache-xml-commons-resolver" ,java-apache-xml-commons-resolver)
+       ("java-cglib" ,java-cglib)
        ("java-hamcrest" ,java-hamcrest-core)
        ("java-junit" ,java-junit)
        ("java-mockito" ,java-mockito-1)

From 12a0b38ce6f93913ead590bb7ebc35db66a6e7b2 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 14:47:36 +0200
Subject: [PATCH 619/909] gnu: java-xmlgraphics-commons: Add dependency to
 java-asm.

* gnu/packages/batik.scm (java-xmlgraphics-commons)[native-inputs]: Add
java-asm.
---
 gnu/packages/batik.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index 5a74d7cc35..cdd1e44713 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -234,6 +234,7 @@ SAC is an interface for CSS parsers.")
                #t))))))
     (native-inputs
      `(("java-apache-xml-commons-resolver" ,java-apache-xml-commons-resolver)
+       ("java-asm" ,java-asm)
        ("java-cglib" ,java-cglib)
        ("java-hamcrest" ,java-hamcrest-core)
        ("java-junit" ,java-junit)

From ae6922ed148b6bde06e37a2c244c67a4f5e6dc00 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Sun, 7 Oct 2018 15:28:37 +0200
Subject: [PATCH 620/909] gnu: Add java-jakarta-regexp.

* gnu/packages/java.scm (java-jakarta-regexp): New variable.
---
 gnu/packages/java.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 96da495c29..93f5bb6aff 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -9634,6 +9634,39 @@ Candidate Recommendation, and will correctly serialize XML 1.1 documents if
 the DOM level 3 load/save API's are in use.")
     (license license:asl2.0)))
 
+(define-public java-jakarta-regexp
+  (package
+    (name "java-jakarta-regexp")
+    (version "1.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (string-append
+              "https://archive.apache.org/dist/jakarta/regexp/jakarta-regexp-"
+              version ".tar.gz"))
+        (sha256
+         (base32
+          "0zg9rmyif48dck0cv6ynpxv23mmcsx265am1fnnxss7brgw0ms3r"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:test-target "test"
+       #:phases
+       (modify-phases %standard-phases
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (out-share (string-append out "/share/java")))
+                (mkdir-p out-share)
+                (for-each (lambda (name)
+                            (install-file name out-share))
+                          (find-files "build" "^jakarta-regexp-.*\\.jar$"))
+                #t))))))
+    (home-page "https://attic.apache.org/projects/jakarta-regexp.html")
+    (synopsis "Regular expression parser generator for Java.")
+    (description "@code{jakarta-regexp} is an old regular expression parser
+generator for Java.")
+    (license license:asl2.0)))
+
 (define-public java-jline
   (package
     (name "java-jline")

From 236fadf52868d3ced233b144f9d560b51dcecec1 Mon Sep 17 00:00:00 2001
From: Jan Nieuwenhuizen <janneke@gnu.org>
Date: Sun, 7 Oct 2018 00:35:23 +0200
Subject: [PATCH 621/909] gnu: mes: Update to 0.18.

* gnu/packages/patches/mes-nyacc-0.86.0.patch: Removef file.
* gnu/local.mk (dist_patch_DATA): Remove entry.
* gnu/packages/mes.scm (mes): Update to 0.18.
---
 gnu/local.mk                                |   1 -
 gnu/packages/mes.scm                        |   5 +-
 gnu/packages/patches/mes-nyacc-0.86.0.patch | 197 --------------------
 3 files changed, 2 insertions(+), 201 deletions(-)
 delete mode 100644 gnu/packages/patches/mes-nyacc-0.86.0.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index f1ce800dd5..8be91c3708 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -956,7 +956,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/mcrypt-CVE-2012-4409.patch			\
   %D%/packages/patches/mcrypt-CVE-2012-4426.patch			\
   %D%/packages/patches/mcrypt-CVE-2012-4527.patch			\
-  %D%/packages/patches/mes-nyacc-0.86.0.patch			\
   %D%/packages/patches/mesa-skip-disk-cache-test.patch		\
   %D%/packages/patches/meson-for-build-rpath.patch		\
   %D%/packages/patches/metabat-fix-compilation.patch		\
diff --git a/gnu/packages/mes.scm b/gnu/packages/mes.scm
index 880e140b80..6dc6dfb4cb 100644
--- a/gnu/packages/mes.scm
+++ b/gnu/packages/mes.scm
@@ -63,15 +63,14 @@ extensive examples, including parsers for the Javascript and C99 languages.")
   (let ((triplet "i686-unknown-linux-gnu"))
     (package
       (name "mes")
-      (version "0.17.1")
+      (version "0.18")
       (source (origin
                 (method url-fetch)
                 (uri (string-append "mirror://gnu/mes/"
                                     "mes-" version ".tar.gz"))
-                (patches (search-patches "mes-nyacc-0.86.0.patch"))
                 (sha256
                  (base32
-                  "02g8zig53ffd0ai8kqhv2zj7bj2366a8hr6ydkwakmi2d1amyrna"))))
+                  "1dsaaqyanzsq9m5wrcd2bjhb3qd6928c9q97rg5r730pyqjwxyxf"))))
       (build-system gnu-build-system)
       (supported-systems '("i686-linux" "x86_64-linux"))
       (propagated-inputs
diff --git a/gnu/packages/patches/mes-nyacc-0.86.0.patch b/gnu/packages/patches/mes-nyacc-0.86.0.patch
deleted file mode 100644
index 58dfc5a46b..0000000000
--- a/gnu/packages/patches/mes-nyacc-0.86.0.patch
+++ /dev/null
@@ -1,197 +0,0 @@
-From 9e610736bf779f3295c1192e748cd19cbbe3be28 Mon Sep 17 00:00:00 2001
-From: Jan Nieuwenhuizen <janneke@gnu.org>
-Date: Wed, 5 Sep 2018 20:28:06 +0200
-Subject: [PATCH 1/2] mes: Support Nyacc 0.85.3: Add char-set-copy.
-
-* mes/module/srfi/srfi-14.mes (char-set-copy): New function>
----
- mes/module/srfi/srfi-14.mes | 3 +++
- 1 file changed, 3 insertions(+)
-
-diff --git a/mes/module/srfi/srfi-14.mes b/mes/module/srfi/srfi-14.mes
-index 0be39b1e..a16d16ce 100644
---- a/mes/module/srfi/srfi-14.mes
-+++ b/mes/module/srfi/srfi-14.mes
-@@ -52,3 +52,6 @@
- 
- (define (char-whitespace? c)
-   (char-set-contains? char-set:whitespace c))
-+
-+(define (char-set-copy cs)
-+  (map identity cs))
--- 
-2.18.0
-
-From b952bdf44f11edbfc277600dc35236aae1769b54 Mon Sep 17 00:00:00 2001
-From: Jan Nieuwenhuizen <janneke@gnu.org>
-Date: Wed, 5 Sep 2018 22:14:34 +0200
-Subject: [PATCH 2/2] mes: Support Nyacc 0.85.3: Integrate progress.
-
-* mes/module/nyacc/lang/sx-util.mes: New file.
-* mes/module/nyacc/version.mes: New file.
-* mes/module/nyacc/lang/c99/cpp.mes (nyacc): Include them.
-* mes/module/nyacc/lang/c99/parser.mes (nyacc): Include them.
-* module/mescc/preprocess.scm (need-progress): New function.
-(progress): New function.
-(insert-progress-monitors): Use them to Integrate progress.
----
- mes/module/mescc/preprocess.mes      |  1 +
- mes/module/nyacc/lang/c99/cpp.mes    |  1 +
- mes/module/nyacc/lang/c99/parser.mes |  1 +
- mes/module/nyacc/lang/sx-util.mes    | 27 +++++++++++++++++++++
- mes/module/nyacc/version.mes         | 26 +++++++++++++++++++++
- module/mescc/preprocess.scm          | 35 ++++++++++++++++++++++++++++
- 6 files changed, 91 insertions(+)
- create mode 100644 mes/module/nyacc/lang/sx-util.mes
- create mode 100644 mes/module/nyacc/version.mes
-
-diff --git a/mes/module/mescc/preprocess.mes b/mes/module/mescc/preprocess.mes
-index c7c5fcaa..022a372c 100644
---- a/mes/module/mescc/preprocess.mes
-+++ b/mes/module/mescc/preprocess.mes
-@@ -24,4 +24,5 @@
- (mes-use-module (srfi srfi-13))
- (mes-use-module (srfi srfi-26))
- (mes-use-module (nyacc lang c99 parser))
-+(mes-use-module (nyacc version))
- (include-from-path "mescc/preprocess.scm")
-diff --git a/mes/module/nyacc/lang/c99/cpp.mes b/mes/module/nyacc/lang/c99/cpp.mes
-index fad1dc55..b25c4a93 100644
---- a/mes/module/nyacc/lang/c99/cpp.mes
-+++ b/mes/module/nyacc/lang/c99/cpp.mes
-@@ -28,5 +28,6 @@
- 
- (mes-use-module (nyacc parse))
- (mes-use-module (nyacc lex))
-+(mes-use-module (nyacc lang sx-util))
- (mes-use-module (nyacc lang util))
- (include-from-path "nyacc/lang/c99/cpp.scm")
-diff --git a/mes/module/nyacc/lang/c99/parser.mes b/mes/module/nyacc/lang/c99/parser.mes
-index c51552d6..1a9aaf73 100644
---- a/mes/module/nyacc/lang/c99/parser.mes
-+++ b/mes/module/nyacc/lang/c99/parser.mes
-@@ -32,6 +32,7 @@
- 
- (mes-use-module (nyacc lex))
- (mes-use-module (nyacc parse))
-+(mes-use-module (nyacc lang sx-util))
- (mes-use-module (nyacc lang util))
- (mes-use-module (nyacc lang c99 cpp))
- 
-diff --git a/mes/module/nyacc/lang/sx-util.mes b/mes/module/nyacc/lang/sx-util.mes
-new file mode 100644
-index 00000000..41ac5b4a
---- /dev/null
-+++ b/mes/module/nyacc/lang/sx-util.mes
-@@ -0,0 +1,27 @@
-+;;; -*-scheme-*-
-+
-+;;; GNU Mes --- Maxwell Equations of Software
-+;;; Copyright © 2018 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
-+;;;
-+;;; This file is part of GNU Mes.
-+;;;
-+;;; GNU Mes is free software; you can redistribute it and/or modify it
-+;;; under the terms of the GNU General Public License as published by
-+;;; the Free Software Foundation; either version 3 of the License, or (at
-+;;; your option) any later version.
-+;;;
-+;;; GNU Mes is distributed in the hope that it will be useful, but
-+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-+;;; GNU General Public License for more details.
-+;;;
-+;;; You should have received a copy of the GNU General Public License
-+;;; along with GNU Mes.  If not, see <http://www.gnu.org/licenses/>.
-+
-+;;; Commentary:
-+
-+;;; Code:
-+
-+(mes-use-module (srfi srfi-1))
-+(mes-use-module (srfi srfi-16))
-+(include-from-path "nyacc/lang/sx-util.scm")
-diff --git a/mes/module/nyacc/version.mes b/mes/module/nyacc/version.mes
-new file mode 100644
-index 00000000..b9db628e
---- /dev/null
-+++ b/mes/module/nyacc/version.mes
-@@ -0,0 +1,26 @@
-+;;; -*-scheme-*-
-+
-+;;; GNU Mes --- Maxwell Equations of Software
-+;;; Copyright © 2018 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
-+;;;
-+;;; This file is part of GNU Mes.
-+;;;
-+;;; GNU Mes is free software; you can redistribute it and/or modify it
-+;;; under the terms of the GNU General Public License as published by
-+;;; the Free Software Foundation; either version 3 of the License, or (at
-+;;; your option) any later version.
-+;;;
-+;;; GNU Mes is distributed in the hope that it will be useful, but
-+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-+;;; GNU General Public License for more details.
-+;;;
-+;;; You should have received a copy of the GNU General Public License
-+;;; along with GNU Mes.  If not, see <http://www.gnu.org/licenses/>.
-+
-+;;; Commentary:
-+
-+;;; Code:
-+
-+(include-from-path "nyacc/version.scm")
-+(display "nyacc version\n")
-diff --git a/module/mescc/preprocess.scm b/module/mescc/preprocess.scm
-index 9e341cba..c2efb32c 100644
---- a/module/mescc/preprocess.scm
-+++ b/module/mescc/preprocess.scm
-@@ -26,9 +26,44 @@
-   #:use-module (srfi srfi-1)
-   #:use-module (srfi srfi-26)
-   #:use-module (nyacc lang c99 parser)
-+  #:use-module (nyacc lang c99 parser)
-+  #:use-module (nyacc version)
-   #:use-module (mes guile)
-   #:export (c99-input->ast))
- 
-+(format (current-error-port) "*nyacc-version*=~a\n" *nyacc-version*)
-+;; list of which rules you want progress reported
-+(define need-progress
-+  (assoc-ref
-+   '(("0.85.3" (1 2 3))
-+     ("0.86.0" (1 2 3)))
-+   *nyacc-version*))
-+
-+(define (progress o)
-+  (when (and o (getenv "NYACC_DEBUG"))
-+    (display "    :" (current-error-port))
-+    (display o (current-error-port))
-+    (display "\n" (current-error-port))))
-+
-+(define (insert-progress-monitors act-v len-v)
-+  (let ((n (vector-length act-v)))
-+    (let loop ((ix 0))
-+      (when (< ix n)
-+	(if (memq ix need-progress)
-+	    (vector-set
-+	     act-v ix
-+	     (lambda args
-+	       (progress (list-ref args (1- (vector-ref len-v ix))))
-+	       (apply (vector-ref act-v ix) args))))
-+        (loop (1+ ix))))))
-+
-+(cond-expand
-+ (guile
-+  (insert-progress-monitors (@@ (nyacc lang c99 parser) c99-act-v)
-+                            (@@ (nyacc lang c99 parser) c99-len-v)))
-+ (mes
-+  (insert-progress-monitors c99-act-v c99-len-v)))
-+
- (define (logf port string . rest)
-   (apply format (cons* port string rest))
-   (force-output port)
--- 
-2.18.0
-

From 247537da81095d3bc03dc210954910d1008bafd3 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 6 Oct 2018 22:43:35 -0400
Subject: [PATCH 622/909] gnu: borg: The backup client cannot override the
 server-side storage quota.

* gnu/packages/patches/borg-respect-storage-quota.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/backup.scm (borg)[source]: Use it.
---
 gnu/local.mk                                  |  1 +
 gnu/packages/backup.scm                       |  1 +
 .../patches/borg-respect-storage-quota.patch  | 32 +++++++++++++++++++
 3 files changed, 34 insertions(+)
 create mode 100644 gnu/packages/patches/borg-respect-storage-quota.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 8be91c3708..ea2d650e28 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -599,6 +599,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/binutils-loongson-workaround.patch	\
   %D%/packages/patches/blast+-fix-makefile.patch		\
   %D%/packages/patches/boost-fix-icu-build.patch		\
+  %D%/packages/patches/borg-respect-storage-quota.patch		\
   %D%/packages/patches/byobu-writable-status.patch		\
   %D%/packages/patches/cairo-CVE-2016-9082.patch			\
   %D%/packages/patches/calibre-no-updates-dialog.patch		\
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index ea5bc8e398..408b64b48d 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -498,6 +498,7 @@ detection, and lossless compression.")
      (origin
        (method url-fetch)
        (uri (pypi-uri "borgbackup" version))
+       (patches (search-patches "borg-respect-storage-quota.patch"))
        (sha256
         (base32
          "1p3zia62vyg9vadkdjzzkzbj4dmgijr7ix5lmhfbxpwy5q9imdgp"))
diff --git a/gnu/packages/patches/borg-respect-storage-quota.patch b/gnu/packages/patches/borg-respect-storage-quota.patch
new file mode 100644
index 0000000000..d23d1ffc01
--- /dev/null
+++ b/gnu/packages/patches/borg-respect-storage-quota.patch
@@ -0,0 +1,32 @@
+Make sure the client respects the storage quota set by the server:
+
+https://github.com/borgbackup/borg/issues/4093
+
+Patch copied from upstream source repository:
+
+https://github.com/borgbackup/borg/commit/975cc33206e0e3644626fb7204c34d2157715b61
+
+From 975cc33206e0e3644626fb7204c34d2157715b61 Mon Sep 17 00:00:00 2001
+From: Manu <manu@snapdragon.cc>
+Date: Wed, 3 Oct 2018 23:47:36 +0800
+Subject: [PATCH] Add storage_quota for forced_result if set by serve command.
+
+---
+ src/borg/archiver.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/src/borg/archiver.py b/src/borg/archiver.py
+index 916725e7..279194c1 100644
+--- a/src/borg/archiver.py
++++ b/src/borg/archiver.py
+@@ -4276,6 +4276,7 @@ def get_args(self, argv, cmd):
+             result.restrict_to_paths = forced_result.restrict_to_paths
+             result.restrict_to_repositories = forced_result.restrict_to_repositories
+             result.append_only = forced_result.append_only
++            result.storage_quota = forced_result.storage_quota
+         return result
+ 
+     def parse_args(self, args=None):
+-- 
+2.19.1
+

From cd220e60da3add3884aef7cc0ab8f4b9e8fb2e3c Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sun, 7 Oct 2018 15:08:46 -0400
Subject: [PATCH 623/909] gnu: ncmpc: Update to 0.32.

* gnu/packages/mpd.scm (ncmpc): Update to 0.32.
[inputs]: Add boost, pcre, and python-sphinx. Remove glib.
[arguments]: Install the man pages correctly. Remove unnecessary configure flag.
---
 gnu/packages/mpd.scm | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm
index c024152dda..3e69ddba69 100644
--- a/gnu/packages/mpd.scm
+++ b/gnu/packages/mpd.scm
@@ -47,6 +47,7 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages pcre)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages pulseaudio)
@@ -186,7 +187,7 @@ player daemon.")
 (define-public ncmpc
   (package
     (name "ncmpc")
-    (version "0.30")
+    (version "0.32")
     (source (origin
               (method url-fetch)
               (uri
@@ -195,11 +196,14 @@ player daemon.")
                               "/ncmpc-" version ".tar.xz"))
               (sha256
                (base32
-                "18qj3cgqczgfk334x0ywxwa1ckrk9fbjyp34n4zzcxwaifshrzp3"))))
+                "1b01q1pcaw5yyhvmlffc3h0r3w8qy7rhn55a7xj4qkcfqvs8ap08"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags
-       (list "-Dcurses=ncurses")
+       ;; Otherwise, they are installed incorrectly, in
+       ;; '$out/share/man/man/man1'.
+       (list (string-append "-Dmandir=" (assoc-ref %outputs "out")
+                            "/share"))
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'expand-C++-include-path
@@ -211,11 +215,13 @@ player daemon.")
                (setenv path (string-append c++ ":" (getenv path)))
                #t))))))
     (inputs `(("gcc", gcc-8)            ; for its C++14 support
-              ("glib" ,glib)
+              ("boost" ,boost)
+              ("pcre" ,pcre)
               ("libmpdclient" ,libmpdclient)
               ("ncurses" ,ncurses)))
     (native-inputs `(("gettext" ,gettext-minimal) ; for xgettext
-                     ("pkg-config" ,pkg-config)))
+                     ("pkg-config" ,pkg-config)
+                     ("python-sphinx" ,python-sphinx)))
     (synopsis "Curses Music Player Daemon client")
     (description "ncmpc is a fully featured MPD client, which runs in a
 terminal using ncurses.")

From 68afb9dccf91cc1a58b6db405befa176b191d809 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 4 Oct 2018 11:30:23 -0400
Subject: [PATCH 624/909] build-system/glib-or-gtk: Build 'in-source' by
 default.

* guix/build-system/glib-or-gtk.scm (glib-or-gtk-build): Change to
'out-of-source? #f'.
* gnu/packages/audio.scm (audacity)[arguments]: Use the default 'out-of-source?'
setting.
* gnu/packages/libreoffice.scm (libreoffice): Likewise.
---
 gnu/packages/audio.scm            | 5 -----
 gnu/packages/libreoffice.scm      | 3 ---
 guix/build-system/glib-or-gtk.scm | 2 +-
 3 files changed, 1 insertion(+), 9 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 434efab953..17b6363f7c 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -413,11 +413,6 @@ engineers, musicians, soundtrack editors and composers.")
              (substitute* "src/prefs/MidiIOPrefs.cpp"
                (("../../lib-src/portmidi/pm_common/portmidi.h") "portmidi.h"))
              #t)))
-       ;; The translation Makefile generation is performed improperly for
-       ;; out-of-tree builds.
-       ;; XXX This can be removed if the glib-or-gkt-build-system
-       ;; switches to #:out-of-source? #t. See <https://bugs.gnu.org/32887>.
-       #:out-of-source? #f
        ;; The test suite is not "well exercised" according to the developers,
        ;; and fails with various errors.  See
        ;; <http://sourceforge.net/p/audacity/mailman/message/33524292/>.
diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm
index 881cf2008d..e5ab5c5071 100644
--- a/gnu/packages/libreoffice.scm
+++ b/gnu/packages/libreoffice.scm
@@ -1018,9 +1018,6 @@ converting QuarkXPress file format.  It supports versions 3.1 to 4.1.")
     (arguments
      `(#:tests? #f ; Building the tests already fails.
        #:make-flags '("build-nocheck") ; Do not build unit tests, which fails.
-       ;; XXX Remove this if glib-or-gtk-build-system changes to in-source-tree
-       ;; builds by default.
-       #:out-of-source? #f
        #:phases
          (modify-phases %standard-phases
            (add-before 'configure 'prepare-src
diff --git a/guix/build-system/glib-or-gtk.scm b/guix/build-system/glib-or-gtk.scm
index 621e68e0ab..fcd92f2334 100644
--- a/guix/build-system/glib-or-gtk.scm
+++ b/guix/build-system/glib-or-gtk.scm
@@ -112,7 +112,7 @@
                             (configure-flags ''())
                             ;; Disable icon theme cache generation.
                             (make-flags ''("gtk_update_icon_cache=true"))
-                            (out-of-source? #t)
+                            (out-of-source? #f)
                             (tests? #t)
                             (test-target "check")
                             (parallel-build? #t)

From a18accba468beecf0200383f56d02894caf6f41a Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sun, 7 Oct 2018 20:15:31 -0400
Subject: [PATCH 625/909] gnu: Remove Go 1.10.

* gnu/packages/golang.scm (go-1.10): Remove variable.
(go-1.11)[arguments]: Remove unnecessary environment variable from
'set-bootstrap-variables' phase.
---
 gnu/packages/golang.scm | 128 ++++------------------------------------
 1 file changed, 10 insertions(+), 118 deletions(-)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 7a049e39e1..7f26fbdab6 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -386,123 +386,9 @@ in the style of communicating sequential processes (@dfn{CSP}).")
        ,@(package-native-inputs go-1.4)))
     (supported-systems %supported-systems)))
 
-(define-public go-1.10
-  (package
-    (inherit go-1.9)
-    (name "go")
-    (version "1.10.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://storage.googleapis.com/golang/"
-                           name version ".src.tar.gz"))
-       (sha256
-        (base32
-         "10ap5pan71y2hdwzv4cg8wx4sy8fkcz5520rm1ldjg25xmjlkr3g"))))
-    (arguments
-     (substitute-keyword-arguments (package-arguments go-1.9)
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (replace 'prebuild
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (let* ((gcclib (string-append (assoc-ref inputs "gcc:lib") "/lib"))
-                      (ld (string-append (assoc-ref inputs "libc") "/lib"))
-                      (loader (car (find-files ld "^ld-linux.+")))
-                      (net-base (assoc-ref inputs "net-base"))
-                      (tzdata-path
-                       (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo"))
-                      (output (assoc-ref outputs "out")))
-
-                 ;; Removing net/ tests, which fail when attempting to access
-                 ;; network resources not present in the build container.
-                 (for-each delete-file
-                           '("net/listen_test.go"
-                             "net/parse_test.go"
-                             "net/cgo_unix_test.go"))
-
-                 (substitute* "os/os_test.go"
-                   (("/usr/bin") (getcwd))
-                   (("/bin/pwd") (which "pwd"))
-                   (("/bin/sh") (which "sh")))
-
-                 ;; Add libgcc to runpath
-                 (substitute* "cmd/link/internal/ld/lib.go"
-                   (("!rpath.set") "true"))
-                 (substitute* "cmd/go/internal/work/gccgo.go"
-                   (("cgoldflags := \\[\\]string\\{\\}")
-                    (string-append "cgoldflags := []string{"
-                                   "\"-rpath=" gcclib "\""
-                                   "}"))
-                   (("\"-lgcc_s\", ")
-                    (string-append
-                     "\"-Wl,-rpath=" gcclib "\", \"-lgcc_s\", ")))
-                 (substitute* "cmd/go/internal/work/gc.go"
-                   (("ldflags = setextld\\(ldflags, compiler\\)")
-                    (string-append
-                     "ldflags = setextld(ldflags, compiler)\n"
-                     "ldflags = append(ldflags, \"-r\")\n"
-                     "ldflags = append(ldflags, \"" gcclib "\")\n")))
-
-                 ;; Disable failing tests: these tests attempt to access
-                 ;; commands or network resources which are neither available
-                 ;; nor necessary for the build to succeed.
-                 (for-each
-                  (match-lambda
-                    ((file regex)
-                     (substitute* file
-                       ((regex all before test_name)
-                        (string-append before "Disabled" test_name)))))
-                  '(("net/net_test.go" "(.+)(TestShutdownUnix.+)")
-                    ("net/dial_test.go" "(.+)(TestDialTimeout.+)")
-                    ("os/os_test.go" "(.+)(TestHostname.+)")
-                    ("time/format_test.go" "(.+)(TestParseInSydney.+)")
-                    ("time/format_test.go" "(.+)(TestParseInLocation.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestEcho.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestCommandRelativeName.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestCatStdin.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestCatGoodAndBadFile.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestExitStatus.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestPipes.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestStdinClose.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestIgnorePipeErrorOnSuccess.+)")
-                    ("syscall/syscall_unix_test.go" "(.+)(TestPassFD\\(.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestExtraFiles/areturn.+)")
-                    ("cmd/go/go_test.go" "(.+)(TestCoverageWithCgo.+)")
-                    ("cmd/go/go_test.go" "(.+)(TestTwoPkgConfigs.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestOutputStderrCapture.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestExtraFiles.+)")
-                    ("os/exec/exec_test.go" "(.+)(TestExtraFilesRace.+)")
-                    ("net/lookup_test.go" "(.+)(TestLookupPort.+)")
-                    ("syscall/exec_linux_test.go"
-                     "(.+)(TestCloneNEWUSERAndRemapNoRootDisableSetgroups.+)")))
-
-                 ;; fix shebang for testar script
-                 ;; note the target script is generated at build time.
-                 (substitute* "../misc/cgo/testcarchive/carchive_test.go"
-                   (("#!/usr/bin/env") (string-append "#!" (which "env"))))
-
-                 (substitute* "net/lookup_unix.go"
-                   (("/etc/protocols") (string-append net-base "/etc/protocols")))
-                 (substitute* "net/port_unix.go"
-                   (("/etc/services") (string-append net-base "/etc/services")))
-                 (substitute* "time/zoneinfo_unix.go"
-                   (("/usr/share/zoneinfo/") tzdata-path))
-                 (substitute* (find-files "cmd" "\\.go")
-                   (("/lib(64)?/ld-linux.*\\.so\\.[0-9]") loader))
-                 #t)))
-           (replace 'set-bootstrap-variables
-             (lambda* (#:key outputs inputs #:allow-other-keys)
-               ;; Tell the build system where to find the bootstrap Go.
-               (let ((go  (assoc-ref inputs "go")))
-                 (setenv "GOROOT_BOOTSTRAP" go)
-                 (setenv "GOGC" "400")
-                 ;; Go 1.10 tries to write to $HOME in a test
-                 (setenv "HOME" "/tmp")
-                 #t)))))))))
-
 (define-public go-1.11
   (package
-    (inherit go-1.10)
+    (inherit go-1.9)
     (name "go")
     (version "1.11.1")
     (source
@@ -514,7 +400,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
         (base32
          "05qivf2f59pv4bfrmdr4m0xvswkmvvl9c5a2h5dy45g2k8b8r3sm"))))
     (arguments
-     (substitute-keyword-arguments (package-arguments go-1.10)
+     (substitute-keyword-arguments (package-arguments go-1.9)
        ((#:phases phases)
         `(modify-phases ,phases
            (replace 'prebuild
@@ -533,7 +419,7 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                            '("net/listen_test.go"
                              "net/parse_test.go"
                              "net/cgo_unix_test.go"
-                             ;; A side affect of these test scripts is testing
+                             ;; A side effect of these test scripts is testing
                              ;; cgo. Attempts at using cgo flags and
                              ;; directives with these scripts as specified
                              ;; here (https://golang.org/cmd/cgo/) have not
@@ -616,7 +502,13 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                    (("/usr/share/zoneinfo/") tzdata-path))
                  (substitute* (find-files "cmd" "\\.go")
                    (("/lib(64)?/ld-linux.*\\.so\\.[0-9]") loader))
-                 #t)))))))))
+                 #t)))
+           (replace 'set-bootstrap-variables
+             (lambda* (#:key outputs inputs #:allow-other-keys)
+               ;; Tell the build system where to find the bootstrap Go.
+               (let ((go  (assoc-ref inputs "go")))
+                 (setenv "GOROOT_BOOTSTRAP" go)
+                 (setenv "GOGC" "400"))))))))))
 
 (define-public go go-1.9)
 

From 0a3e9bf62171b051656f24b81094064b479ebf2e Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sun, 7 Oct 2018 21:08:38 -0400
Subject: [PATCH 626/909] gnu: Go 1.9: Fix test failure with binutils >= 2.31.

* gnu/packages/golang.scm (go-1.9)[arguments]: Add a substitution to the
prebuild phase.
---
 gnu/packages/golang.scm | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 7f26fbdab6..1ce06a47b6 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -273,6 +273,15 @@ in the style of communicating sequential processes (@dfn{CSP}).")
                     (string-append
                      "\"-Wl,-rpath=" gcclib "\", \"-lgcc_s\", ")))
 
+                 ;; XXX Commit 65fa2b615b72c1fa61a7 in the Go repo.  We do this
+                 ;; without a patch because ((guix packages) patch-and-repack)
+                 ;; resets file mtimes, and parts of Go's test suite rely on
+                 ;; those timestamps.
+                 ;; <https://github.com/golang/go/issues/26369>
+                 (substitute* "cmd/internal/objfile/elf.go"
+                   (("PT_LOAD")
+                     "PT_LOAD && p.Flags&elf.PF_X != 0"))
+
                  ;; Disable failing tests: these tests attempt to access
                  ;; commands or network resources which are neither available
                  ;; nor necessary for the build to succeed.

From a0410663743eaa3bdbf3727baaa9fbc615db2549 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sun, 7 Oct 2018 20:14:02 -0400
Subject: [PATCH 627/909] gnu: crawl, crawl-tiles: Update to 0.22.1.

* gnu/packages/games.scm (crawl, crawl-tiles): Update to 0.22.1.
* gnu/packages/patches/crawl-upgrade-saves.patch: Update accordingly.
---
 gnu/packages/games.scm                        |  4 +--
 .../patches/crawl-upgrade-saves.patch         | 25 ++++++++++---------
 2 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 7365a7f5d8..2547c72c23 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -4397,7 +4397,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
 (define-public crawl
   (package
     (name "crawl")
-    (version "0.21.0")
+    (version "0.22.1")
     (source
      (origin
        (method url-fetch)
@@ -4411,7 +4411,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
                             version "-nodeps.tar.xz")))
        (sha256
         (base32
-         "0mmnkch8s9l7dh136yjvcyjr0vmyzv7z370rlcyir91qz6gg82n1"))
+         "1qc90wwbxvjzqq66n8kfr0a2ny7sfvv2n84si67jiv2887d0ws6k"))
        (patches (search-patches "crawl-upgrade-saves.patch"))))
     (build-system gnu-build-system)
     (inputs
diff --git a/gnu/packages/patches/crawl-upgrade-saves.patch b/gnu/packages/patches/crawl-upgrade-saves.patch
index 301942dc30..4c0b3a427b 100644
--- a/gnu/packages/patches/crawl-upgrade-saves.patch
+++ b/gnu/packages/patches/crawl-upgrade-saves.patch
@@ -5,8 +5,9 @@ By default crawl checks for a mtime difference on files in DATADIR to see if an
 upgrade is required, but guix nulls all file dates,
 and crawl would never upgrade saves.
 
---- a/source/database.cc	2016-05-31 09:56:08.000000000 +0200
-+++ a/source/database.cc	2017-06-05 03:00:19.270632107 +0200
+diff -ur a/source/database.cc b/source/database.cc
+--- a/source/database.cc	2018-08-09 21:49:26.000000000 -0400
++++ b/source/database.cc	2018-10-07 18:06:41.022445789 -0400
 @@ -25,6 +25,7 @@
  #include "syscalls.h"
  #include "threads.h"
@@ -23,16 +24,16 @@ and crawl would never upgrade saves.
      TextDB *_parent;
      const char* lang() { return _parent ? Options.lang_name : 0; }
  public:
-@@ -165,7 +167,7 @@
+@@ -163,7 +165,7 @@
  
- TextDB::TextDB(const char* db_name, const char* dir, ...)
-     : _db_name(db_name), _directory(dir),
+ TextDB::TextDB(const char* db_name, const char* dir, vector<string> files)
+     : _db_name(db_name), _directory(dir), _input_files(files),
 -      _db(nullptr), timestamp(""), _parent(0), translation(0)
 +      _db(nullptr), timestamp(""), version(""),  _parent(0), translation(0)
  {
-     va_list args;
-     va_start(args, dir);
-@@ -187,7 +189,7 @@
+ }
+ 
+@@ -171,7 +173,7 @@
      : _db_name(parent->_db_name),
        _directory(parent->_directory + Options.lang_name + "/"),
        _input_files(parent->_input_files), // FIXME: pointless copy
@@ -41,7 +42,7 @@ and crawl would never upgrade saves.
  {
  }
  
-@@ -202,6 +204,9 @@
+@@ -186,6 +188,9 @@
          return false;
  
      timestamp = _query_database(*this, "TIMESTAMP", false, false, true);
@@ -51,7 +52,7 @@ and crawl would never upgrade saves.
      if (timestamp.empty())
          return false;
  
-@@ -245,6 +250,9 @@
+@@ -229,6 +234,9 @@
      string ts;
      bool no_files = true;
  
@@ -61,7 +62,7 @@ and crawl would never upgrade saves.
      for (const string &file : _input_files)
      {
          string full_input_path = _directory + file;
-@@ -261,7 +269,7 @@
+@@ -245,7 +253,7 @@
          ts += buf;
      }
  
@@ -70,7 +71,7 @@ and crawl would never upgrade saves.
      {
          // No point in empty databases, although for simplicity keep ones
          // for disappeared translations for now.
-@@ -321,7 +329,10 @@
+@@ -313,7 +321,10 @@
              _store_text_db(full_input_path, _db);
          }
      }

From 5103c98f68490d32e71fe7208161450de4fb6f43 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 8 Oct 2018 08:23:10 +0200
Subject: [PATCH 628/909] gnu: c-toxcore: Update to 0.2.8.

* gnu/packages/messaging.scm (c-toxcore): Update to 0.2.8.
---
 gnu/packages/messaging.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index af67c922b4..8ac86a852f 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -873,7 +873,7 @@ protocols.")
 (define-public c-toxcore
   (package
     (name "c-toxcore")
-    (version "0.2.7")
+    (version "0.2.8")
     (source
      (origin
        (method url-fetch)
@@ -882,7 +882,7 @@ protocols.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1lcw979zakyb5kzy8yfk87js3bzfz3k2jxidda6ga6ljdnqdpxmy"))))
+         "0qlkimlvbd24nlj7w9b5rpz1r807magqxmfylc1mlxsqhmfi5zj7"))))
     (arguments
      `(#:tests? #f)) ; FIXME: Testsuite seems to stay stuck on test 3. Disable
                      ; for now.

From 402561ccefd5367ec878461cc088b533993ba0b7 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Thu, 4 Oct 2018 15:48:04 +1000
Subject: [PATCH 629/909] gnu: python2-backports-functools-lru-cache: Update to
 1.5.

* gnu/packages/python.scm (python2-backports-functools-lru-cache): Update to 1.5.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 4703d95a2d..6a2bd6e8f5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -11418,7 +11418,7 @@ editors.")
 (define-public python2-backports-functools-lru-cache
   (package
     (name "python2-backports-functools-lru-cache")
-    (version "1.3")
+    (version "1.5")
     (source
      (origin
        (method url-fetch)
@@ -11426,7 +11426,7 @@ editors.")
        (uri (pypi-uri "backports.functools_lru_cache" version))
        (sha256
         (base32
-         "158ysf2hb0q4p4695abfiym9x1ywg0dgh8a3apd7gqaaxjy22jj4"))))
+         "06jgv8gib4fhky0p5cmxdghvsgjyzcdgk48k8pxb1ccf11znk64x"))))
     (build-system python-build-system)
     (native-inputs
      `(("python2-setuptools-scm" ,python2-setuptools-scm)))

From 1deab8cbf6d93fec3b119de71374488087427ba8 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 7 Oct 2018 16:32:27 +0100
Subject: [PATCH 630/909] gnu: Add picard.

* gnu/packages/music.scm (picard): New variable.
---
 gnu/packages/music.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 3163e6a8f6..e1bac6f51e 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2429,6 +2429,47 @@ and managing stations, can be controlled remotely via fifo, and can run
 event-based scripts for scrobbling, notifications, etc.")
     (license license:expat)))
 
+(define-public picard
+  (package
+    (name "picard")
+    (version "2.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://musicbrainz.osuosl.org/pub/musicbrainz/"
+                    "picard/picard-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0ds3ylpqn717fnzcjrfn05v5xram01bj6n3hwn9igmkd1jgf8vhc"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-source
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "picard/const/__init__.py"
+               (("pyfpcalc")
+                (string-append
+                 "pyfpcalc', '"
+                 (assoc-ref inputs "chromaprint") "/bin/fpcalc")))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (invoke "python" "setup.py" "install"
+                     (string-append "--prefix=" (assoc-ref outputs "out"))
+                     "--root=/"))))))
+    (native-inputs
+     `(("gettext" ,gettext-minimal)))
+    (inputs
+     `(("chromaprint" ,chromaprint)
+       ("python-pyqt" ,python-pyqt)
+       ("python-mutagen" ,python-mutagen)))
+    (home-page "https://picard.musicbrainz.org/")
+    (synopsis "Graphical music tagging application")
+    (description
+     "MusicBrainz Picard is a music tagging application, supporting multiple
+formats, looking up tracks through metadata and audio fingerprints.")
+    (license license:gpl2+)))
+
 (define-public python-mutagen
   (package
     (name "python-mutagen")

From f6e9976393c80d12b5f3235bf7fe593077cbc9d1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 8 Oct 2018 14:18:48 +0200
Subject: [PATCH 631/909] gnu: Add r-dnabarcodes.

* gnu/packages/bioconductor.scm (r-dnabarcodes): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 108f3c398f..1b779855b2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -886,3 +886,30 @@ Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
 order to evaluate synthesis, processing and degradation rates and assess via
 modeling the rates that determines changes in mature mRNA levels.")
     (license license:gpl2)))
+
+(define-public r-dnabarcodes
+  (package
+    (name "r-dnabarcodes")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DNABarcodes" version))
+       (sha256
+        (base32
+         "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x"))))
+    (properties `((upstream-name . "DNABarcodes")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://bioconductor.org/packages/DNABarcodes")
+    (synopsis "Create and analyze DNA barcodes")
+    (description
+     "This package offers tools to create DNA barcode sets capable of
+correcting insertion, deletion, and substitution errors.  Existing barcodes
+can be analyzed regarding their minimal, maximal and average distances between
+barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
+demultiplexed, i.e. assigned to their original reference barcode.")
+    (license license:gpl2)))

From 1d6417340d6c6a80e24b9cd7e9c357b87c8da309 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 8 Oct 2018 17:29:34 +0200
Subject: [PATCH 632/909] gnu: Add font-sil-gentium.

* gnu/packages/fonts.scm (font-sil-gentium): New variable.
---
 gnu/packages/fonts.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 6d4abc637b..7fdcda4eee 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1302,3 +1302,29 @@ Kannada, Malayalam, Manipuri, Oriya, Punjabi, Tamil and Telugu scripts.")
      "Inria Sans and Inria Serif are the two members of a type family designed
 for Inria, a public research institute in computer science and mathematics.")
     (license license:silofl1.1)))
+
+(define-public font-sil-gentium
+  (package
+    (name "font-sil-gentium")
+    (version "5.000")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://software.sil.org/downloads/r/gentium/GentiumPlus-"
+                    version ".zip"))
+              (sha256
+               (base32
+                "0m7189870hha217n1vgpmf89mwggrxkh679ffi1lxpnjggqi2n9k"))))
+    ;; Note: The zip file provides TTF files only, but the developer release,
+    ;; which contains additional files, has a 'SOURCES.txt' file that says
+    ;; that "the primary source files for the fonts are the fonts themselves".
+    ;; Thus it looks like the TTF can be considered source.
+    (build-system font-build-system)
+    (synopsis "Serif font for the Cyrillic, Greek, and Latin alphabets")
+    (description
+     "Gentium is a typeface family designed to enable the diverse ethnic
+groups around the world who use the Latin, Cyrillic and Greek scripts to
+produce readable, high-quality publications.  The font comes with regular and
+italics shapes.  This package provides only TrueType files (TTF).")
+    (home-page "https://software.sil.org/gentium/")
+    (license license:silofl1.1)))

From 46e78707a3d72d1fd08432cba8886415c79ebacc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 8 Oct 2018 17:35:22 +0200
Subject: [PATCH 633/909] gnu: Add font-sil-charis.

* gnu/packages/fonts.scm (font-sil-charis): New variable.
---
 gnu/packages/fonts.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 7fdcda4eee..1195695d7a 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1328,3 +1328,27 @@ produce readable, high-quality publications.  The font comes with regular and
 italics shapes.  This package provides only TrueType files (TTF).")
     (home-page "https://software.sil.org/gentium/")
     (license license:silofl1.1)))
+
+(define-public font-sil-charis
+  (package
+    (name "font-sil-charis")
+    (version "5.000")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://software.sil.org/downloads/r/charis/CharisSIL-"
+                    version ".zip"))
+              (sha256
+               (base32
+                "1zcvw37f1a7gkml3yfm6hxh93844llm7xj4w52600qq3ndrm8gjy"))))
+    ;; As for Gentium (see above), the TTF files are considered source.
+    (build-system font-build-system)
+    (synopsis "Serif font for the Cyrillic and Latin alphabets")
+    (description
+     "Charis SIL is a Unicode-based font family that supports the wide range
+of languages that use the Latin and Cyrillic scripts.  It is specially
+designed to make long texts pleasant and easy to read, even in less than ideal
+reproduction and display environments.  This package provides only TrueType
+files (TTF).")
+    (home-page "https://software.sil.org/charis/")
+    (license license:silofl1.1)))

From f8e0d27c5c2f338012f00cd3c4620ca76751495c Mon Sep 17 00:00:00 2001
From: Mathieu Lirzin <mthl@gnu.org>
Date: Sun, 7 Oct 2018 17:53:04 +0200
Subject: [PATCH 634/909] gnu: emacs-google-translate: Update to 0.11.15.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/emacs.scm (emacs-google-translate): Update to 0.11.15.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/emacs.scm | 38 ++++++++++++++++++--------------------
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 1df3456e4a..aad698da0e 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -11344,27 +11344,25 @@ the GIF result.")
       (license license:gpl3+))))
 
 (define-public emacs-google-translate
-  (let ((commit "d8b84a8359fcc697114d1298840e9a45b111c974"))
-    (package
-      (name "emacs-google-translate")
-      (version (git-version "0.11.14" "1" commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/atykhonov/google-translate")
-               (commit commit)))
-         (file-name (string-append name "-" version "-checkout"))
-         (sha256
-          (base32
-           "1qs4hcg1i2m487z50nnwgs0sa2xj4lpgizbrvi2yda0mf3m75fgc"))))
-      (build-system emacs-build-system)
-      (home-page "https://github.com/atykhonov/google-translate")
-      (synopsis "Emacs interface to Google Translate")
-      (description
-       "This packages provides an Emacs interface to the Google Translate
+  (package
+    (name "emacs-google-translate")
+    (version "0.11.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/atykhonov/google-translate/"
+                           "archive/v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1zxvfagbaf5mxi528mz33c8vxdk86wj0xx5y2jfy97wi8dzrwn3g"))))
+    (build-system emacs-build-system)
+    (home-page "https://github.com/atykhonov/google-translate")
+    (synopsis "Emacs interface to Google Translate")
+    (description
+     "This packages provides an Emacs interface to the Google Translate
 on-line service.")
-      (license license:gpl3+))))
+    (license license:gpl3+)))
 
 (define-public emacs-helm-company
   (let ((commit "acc9c7901e094c1591327a0db1ec7a439f67a84d"))

From b6bd8b108a4ad53e89d6b83edc57df18935f131c Mon Sep 17 00:00:00 2001
From: pimi <madalinionel.patrascu@mdc-berlin.de>
Date: Mon, 8 Oct 2018 11:17:41 +0200
Subject: [PATCH 635/909] gnu: Add filtlong.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/bioinformatics.scm (filtlong): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab9dc185a3..ed713cd144 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14057,3 +14057,63 @@ absolute GSEA.")
     (description "Ngless is a domain-specific language for
 @dfn{next-generation sequencing} (NGS) data processing.")
     (license license:expat)))
+
+(define-public filtlong
+  ;; The recommended way to install is to clone the git repository
+  ;; https://github.com/rrwick/Filtlong#installation
+  ;; and the lastest release is more than nine months old
+  (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab")
+        (revision "1"))
+    (package
+      (name "filtlong")
+      (version (git-version "0.2.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rrwick/Filtlong.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f                    ; no check target
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (bin (string-append out "/bin"))
+                      (scripts (string-append out "/share/filtlong/scripts")))
+                 (install-file "bin/filtlong" bin)
+                 (install-file "scripts/histogram.py" scripts)
+                 (install-file "scripts/read_info_histograms.sh" scripts))
+               #t))
+           (add-after 'install 'wrap-program
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (path (getenv "PYTHONPATH")))
+                 (wrap-program (string-append out
+                                              "/share/filtlong/scripts/histogram.py")
+                   `("PYTHONPATH" ":" prefix (,path))))
+               #t))
+           (add-before 'check 'patch-tests
+             (lambda _
+               (substitute* "scripts/read_info_histograms.sh"
+                 (("awk") (which "gawk")))
+               #t)))))
+      (inputs
+       `(("gawk" ,gawk)                 ;for read_info_histograms.sh
+         ("python" ,python-2)           ;required for histogram.py
+         ("zlib" ,zlib)))
+      (home-page "https://github.com/rrwick/Filtlong/")
+      (synopsis "Tool for quality filtering of Nanopore and PacBio data")
+      (description
+       "The Filtlong package is a tool for filtering long reads by quality.
+It can take a set of long reads and produce a smaller, better subset.  It uses
+both read length (longer is better) and read identity (higher is better) when
+choosing which reads pass the filter.")
+      (license (list license:gpl3       ;filtlong
+                     license:asl2.0))))) ;histogram.py

From df2d77c45ff357a25fee5f96478b1b65dc93f507 Mon Sep 17 00:00:00 2001
From: Thorsten Wilms <t_w_@freenet.de>
Date: Mon, 8 Oct 2018 21:12:54 +0200
Subject: [PATCH 636/909] gnu: Add emacs-colum-marker.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/emacs.scm (emacs-colum-marker): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/emacs.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index aad698da0e..c9493dabd4 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -39,6 +39,7 @@
 ;;; Copyright © 2018 Jack Hill <jackhill@jackhill.us>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Alex Branham <alex.branham@gmail.com>
+;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -12353,3 +12354,24 @@ with a handful of easy tweaks.
 scratch, and you think the Spacemacs theme looks good.
 @end itemize")
     (license license:gpl3+)))
+
+(define-public emacs-column-marker
+  (package
+    (name "emacs-column-marker")
+    (version "9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri "https://www.emacswiki.org/emacs/download/column-marker.el")
+       (sha256 (base32 "05bv198zhqw5hqq6cr11mhz02dpca74hhp1ycwq369m0yb2naxy9"))))
+    (build-system emacs-build-system)
+    (home-page "https://www.emacswiki.org/emacs/ColumnMarker")
+    (synopsis "Emacs mode for highlighting columns")
+    (description
+     "With @code{column-marker.el} you can highlight any number of text columns.
+Three such highlight column markers are provided by default.  This is
+especially useful for languages like COBOL or Fortran where certain columns
+have special meaning.  It is also handy for aligning text across long vertical
+distances.  Multi-column characters, such as @kbd{TAB} are treated
+correctly.")
+    (license license:gpl2+)))

From 65b8d610739065671af288836d74e5ffbf382c8f Mon Sep 17 00:00:00 2001
From: Thorsten Wilms <t_w_@freenet.de>
Date: Mon, 8 Oct 2018 21:11:10 +0200
Subject: [PATCH 637/909] gnu: Add gimp-resynthesizer.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/gimp.scm (gimp-resynthesizer): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/gimp.scm | 65 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm
index df8f242c7a..cd0deac158 100644
--- a/gnu/packages/gimp.scm
+++ b/gnu/packages/gimp.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2018 Thorsten Wilms <t_w_@freenet.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -305,3 +306,67 @@ brushstrokes which is used by MyPaint and GIMP.")
 MyPaint.")
     (home-page "https://github.com/Jehan/mypaint-brushes")
     (license license:cc0)))
+
+(define-public gimp-resynthesizer
+  ;; GIMP does not respect any plugin search path environment variable, so after
+  ;; installation users have to edit their GIMP settings to include
+  ;; "$HOME/.guix-profile/lib/gimp/2.0/plug-ins/" in
+  ;; “Edit->Preferences->Folders->Plug Ins”.
+  (package
+    (name "gimp-resynthesizer")
+    (version "2.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/bootchk/resynthesizer/archive/v"
+			   version ".tar.gz"))
+       (sha256
+        (base32
+         "0l3404w6rqny7h3djskxf149gzx6x4qhndgbh3403c9lbh4pi1kr"))
+       (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system gnu-build-system)
+    (arguments
+     `( ;; Turn off tests to avoid:
+       ;; make[1]: *** No rule to make target '../src/resynth-gui.c', needed by 'resynthesizer.pot'.  Stop.
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+	 (add-after 'unpack 'set-env
+	   (lambda _
+	     (setenv "CONFIG_SHELL" (which "sh"))
+	     #t))
+	 (add-after 'configure 'set-prefix
+           ;; Install plugin under $prefix, not under GIMP's libdir.
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((target (string-append (assoc-ref outputs "out")
+                                          "/lib/gimp/"
+                                          ,(version-major
+                                            (package-version gimp))
+                                          ".0")))
+               (substitute* (list "src/resynthesizer/Makefile"
+				  "src/resynthesizer-gui/Makefile")
+		 (("GIMP_LIBDIR = .*")
+                  (string-append "GIMP_LIBDIR = " target "\n")))
+               (mkdir-p target)
+               #t))))))
+    (native-inputs
+     `(("autoconf" ,autoconf-wrapper)
+       ("automake" ,automake)
+       ("glib" ,glib "bin")                       ; glib-gettextize
+       ("intltool" ,intltool)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("gimp" ,gimp)
+       ("gdk-pixbuf" ,gdk-pixbuf)                 ; needed by gimp-2.0.pc
+       ("cairo" ,cairo)
+       ("gegl" ,gegl)
+       ("gtk+" ,gtk+-2)                           ; needed by gimpui-2.0.pc
+       ("glib" ,glib)))
+    (home-page "https://github.com/bootchk/resynthesizer")
+    (synopsis "GIMP plugins for texture synthesis")
+    (description
+     "This package provides resynthesizer plugins for GIMP, which encompasses
+tools for healing selections (content-aware fill), enlarging the canvas and
+healing the border, increasing the resolution while adding detail, and
+transfering the style of an image.")
+    (license license:gpl3+)))

From de68ad095db7cdd06c45c53c47e7cbcb3fdf8bf6 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 9 Oct 2018 05:32:35 +0200
Subject: [PATCH 638/909] gnu: zstd: Update to 1.3.6.

* gnu/packages/compression.scm (zstd): Update to 1.3.6.
[source]: Remove merged patches.
* gnu/packages/patches/zstd-fix-stdin-list-test.patch,
gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
---
 gnu/local.mk                                  |  4 +-
 gnu/packages/compression.scm                  |  8 +--
 .../patches/zstd-fix-stdin-list-test.patch    | 30 ---------
 .../zstd-fix-stdin-list-without-tty.patch     | 67 -------------------
 4 files changed, 3 insertions(+), 106 deletions(-)
 delete mode 100644 gnu/packages/patches/zstd-fix-stdin-list-test.patch
 delete mode 100644 gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index ea2d650e28..821e83a675 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1247,9 +1247,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/xinetd-CVE-2013-4342.patch		\
   %D%/packages/patches/xmodmap-asprintf.patch 			\
   %D%/packages/patches/zathura-pdf-mupdf-link-to-jpeg-libraries.patch \
-  %D%/packages/patches/zathura-plugindir-environment-variable.patch	\
-  %D%/packages/patches/zstd-fix-stdin-list-without-tty.patch	\
-  %D%/packages/patches/zstd-fix-stdin-list-test.patch
+  %D%/packages/patches/zathura-plugindir-environment-variable.patch
 
 MISC_DISTRO_FILES =				\
   %D%/packages/ld-wrapper.in
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 666c9bfc3e..38d72f1386 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1694,7 +1694,7 @@ or junctions, and always follows hard links.")
 (define-public zstd
   (package
     (name "zstd")
-    (version "1.3.5")
+    (version "1.3.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/facebook/zstd/archive/v"
@@ -1702,11 +1702,7 @@ or junctions, and always follows hard links.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1sifbq18p0hc978g0pq8fymrlpzz1fcxqkbxfqk44z6v9jg5bqfn"))
-              ;; Fix a regression that causes the tests to fail.  Both patches
-              ;; have been merged upstream and will be part of the next release.
-              (patches (search-patches "zstd-fix-stdin-list-without-tty.patch"
-                                       "zstd-fix-stdin-list-test.patch"))))
+                "1iwxcpxg51yskiwfw5nhsflvcm3pk4184kkfpm61hsxniwa1cmbz"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
diff --git a/gnu/packages/patches/zstd-fix-stdin-list-test.patch b/gnu/packages/patches/zstd-fix-stdin-list-test.patch
deleted file mode 100644
index a10355448c..0000000000
--- a/gnu/packages/patches/zstd-fix-stdin-list-test.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From 8e7bdc18d62632adcee029b2f8f5013d11549dd7 Mon Sep 17 00:00:00 2001
-From: "W. Felix Handte" <w@felixhandte.com>
-Date: Fri, 29 Jun 2018 16:31:22 -0400
-Subject: [PATCH] Fix Tests of `--list` Behavior with `stdin`
-
----
- tests/playTests.sh | 10 ++++++++--
- 1 file changed, 8 insertions(+), 2 deletions(-)
-
-diff --git a/tests/playTests.sh b/tests/playTests.sh
-index 09a7377f2..aa5535d59 100755
---- a/tests/playTests.sh
-+++ b/tests/playTests.sh
-@@ -731,8 +731,14 @@ $ECHO "\n===>  zstd --list/-l error detection tests "
- ! $ZSTD -lv tmp1*
- ! $ZSTD --list -v tmp2 tmp12.zst
- 
--$ECHO "\n===>  zstd --list/-l exits 1 when stdin is piped in"
--! echo "piped STDIN" | $ZSTD --list
-+$ECHO "\n===>  zstd --list/-l errors when presented with stdin / no files"
-+! $ZSTD -l
-+! $ZSTD -l -
-+! $ZSTD -l < tmp1.zst
-+! $ZSTD -l - < tmp1.zst
-+! $ZSTD -l - tmp1.zst
-+! $ZSTD -l - tmp1.zst < tmp1.zst
-+$ZSTD -l tmp1.zst < tmp1.zst # but doesn't error just because stdin is not a tty
- 
- $ECHO "\n===>  zstd --list/-l test with null files "
- ./datagen -g0 > tmp5
diff --git a/gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch b/gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch
deleted file mode 100644
index 47fa3e59a7..0000000000
--- a/gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch
+++ /dev/null
@@ -1,67 +0,0 @@
-From 712a9fd9721c314f4b0238577d803b012845f6d2 Mon Sep 17 00:00:00 2001
-From: "W. Felix Handte" <w@felixhandte.com>
-Date: Fri, 29 Jun 2018 15:33:44 -0400
-Subject: [PATCH] Allow Invoking `zstd --list` When `stdin` is not a `tty`
-
-Also now returns an error when no inputs are given.
-
-New proposed behavior:
-
-```
-felix@odin:~/prog/zstd (list-stdin-check)$ ./zstd -l; echo $?
-No files given
-1
-felix@odin:~/prog/zstd (list-stdin-check)$ ./zstd -l Makefile.zst; echo $?
-Frames  Skips  Compressed  Uncompressed  Ratio  Check  Filename
-     1      0     3.08 KB      10.92 KB  3.544  XXH64  Makefile.zst
-0
-felix@odin:~/prog/zstd (list-stdin-check)$ ./zstd -l <Makefile.zst; echo $?
-zstd: --list does not support reading from standard input
-No files given
-1
-felix@odin:~/prog/zstd (list-stdin-check)$ ./zstd -l Makefile.zst <Makefile.zst; echo $?
-Frames  Skips  Compressed  Uncompressed  Ratio  Check  Filename
-     1      0     3.08 KB      10.92 KB  3.544  XXH64  Makefile.zst
-0
-felix@odin:~/prog/zstd (list-stdin-check)$
-```
----
- programs/fileio.c | 16 ++++++++++------
- 1 file changed, 10 insertions(+), 6 deletions(-)
-
-diff --git a/programs/fileio.c b/programs/fileio.c
-index 0175b3163..b4eed28d1 100644
---- a/programs/fileio.c
-+++ b/programs/fileio.c
-@@ -2017,21 +2017,25 @@ static int FIO_listFile(fileInfo_t* total, const char* inFileName, int displayLe
- }
- 
- int FIO_listMultipleFiles(unsigned numFiles, const char** filenameTable, int displayLevel){
--
--    if (!IS_CONSOLE(stdin)) {
--        DISPLAYOUT("zstd: --list does not support reading from standard input\n");
--        return 1;
-+    unsigned u;
-+    for (u=0; u<numFiles;u++) {
-+        if (!strcmp (filenameTable[u], stdinmark)) {
-+            DISPLAYOUT("zstd: --list does not support reading from standard input\n");
-+            return 1;
-+        }
-     }
- 
-     if (numFiles == 0) {
-+        if (!IS_CONSOLE(stdin)) {
-+            DISPLAYOUT("zstd: --list does not support reading from standard input\n");
-+        }
-         DISPLAYOUT("No files given\n");
--        return 0;
-+        return 1;
-     }
-     if (displayLevel <= 2) {
-         DISPLAYOUT("Frames  Skips  Compressed  Uncompressed  Ratio  Check  Filename\n");
-     }
-     {   int error = 0;
--        unsigned u;
-         fileInfo_t total;
-         memset(&total, 0, sizeof(total));
-         total.usesCheck = 1;

From f6ccb95a86ef22ae678e80b0e9a353e5b2404334 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 8 Oct 2018 16:20:19 +0200
Subject: [PATCH 639/909] gnu: docx2txt: End phases with #t.

* gnu/packages/textutils.scm (docx2txt)[arguments]: End 'fix-install'
phase with #t.
---
 gnu/packages/textutils.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 7e26bdcf63..8780bb2829 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -735,7 +735,8 @@ measuring and checking the width of strings, with support east asian text.")
                                  unzip
                                  "/bin/unzip',")))
                ;; Makefile is wrong.
-               (chmod config #o644)))))))
+               (chmod config #o644)
+               #t))))))
     (synopsis "Recover text from @file{.docx} files, with good formatting")
     (description
      "@command{docx2txt} is a Perl based command line utility to convert

From 317e80cead5d8f78ed021069a3ef108d44824f76 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 8 Oct 2018 16:38:27 +0200
Subject: [PATCH 640/909] gnu: unison: End all phases with #t.

* gnu/packages/ocaml.scm (unison)[arguments]: End all phases with #t.
---
 gnu/packages/ocaml.scm | 31 +++++++++++++++----------------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 0756aecd6d..6b55e84fed 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -820,7 +820,8 @@ libpanel, librsvg and quartz.")
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin")))
                  ;; 'unison-fsmonitor' is used in "unison -repeat watch" mode.
-                 (install-file "src/unison-fsmonitor" bin))))
+                 (install-file "src/unison-fsmonitor" bin)
+                 #t)))
            (add-after 'install 'install-doc
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((doc (string-append (assoc-ref outputs "doc")
@@ -829,21 +830,19 @@ libpanel, librsvg and quartz.")
                  ;; This file needs write-permissions, because it's
                  ;; overwritten by 'docs' during documentation generation.
                  (chmod "src/strings.ml" #o600)
-                 (and (zero? (system* "make" "docs"
-                                      "TEXDIRECTIVES=\\\\draftfalse"))
-                      (begin
-                        (for-each (lambda (f)
-                                    (install-file f doc))
-                                  (map (lambda (ext)
-                                         (string-append
-                                          "doc/unison-manual." ext))
-                                       ;; Install only html documentation,
-                                       ;; since the build is currently
-                                       ;; non-reproducible with the ps, pdf,
-                                       ;; and dvi docs.
-                                       '(;;"ps" "pdf" "dvi"
-                                         "html")))
-                        #t))))))))
+                 (invoke "make" "docs"
+                         "TEXDIRECTIVES=\\\\draftfalse")
+                 (for-each (lambda (f)
+                             (install-file f doc))
+                           (map (lambda (ext)
+                                  (string-append "doc/unison-manual." ext))
+                                ;; Install only html documentation,
+                                ;; since the build is currently
+                                ;; non-reproducible with the ps, pdf,
+                                ;; and dvi docs.
+                                '(;; "ps" "pdf" "dvi"
+                                  "html")))
+                 #t))))))
     (home-page "https://www.cis.upenn.edu/~bcpierce/unison/")
     (synopsis "File synchronizer")
     (description

From 3880537c7403c3677ec46e991da9d25ca542c64b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Tue, 9 Oct 2018 05:46:00 +0200
Subject: [PATCH 641/909] gnu: zstd: Don't use unstable tarball.

* gnu/packages/compression.scm (zstd)[source]: Use release archive.
---
 gnu/packages/compression.scm | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 38d72f1386..8c940f3036 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1695,14 +1695,13 @@ or junctions, and always follows hard links.")
   (package
     (name "zstd")
     (version "1.3.6")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/facebook/zstd/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1iwxcpxg51yskiwfw5nhsflvcm3pk4184kkfpm61hsxniwa1cmbz"))))
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/facebook/zstd/releases/download/"
+                           "v" version "/zstd-" version ".tar.gz"))
+       (sha256
+        (base32 "1525b31jmbiczjj1n58nckdzky4cdnbwcsil3zgy4cx03v0a0cp8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

From 07b0662754014f7ac8ab81ce6a8878d0cc206b19 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 9 Oct 2018 09:56:02 +0300
Subject: [PATCH 642/909] gnu: abiword: Remove wmf support.

* gnu/packages/abiword.scm (abiword)[arguments]: Remove 'wmf' from the
list of enabled plugins.
---
 gnu/packages/abiword.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/abiword.scm b/gnu/packages/abiword.scm
index cf906c6ea4..02f132f6f0 100644
--- a/gnu/packages/abiword.scm
+++ b/gnu/packages/abiword.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Marek Benc <merkur32@gmail.com>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;;
@@ -62,7 +62,7 @@
     (build-system glib-or-gtk-build-system)
     (arguments                   ;; NOTE: rsvg is disabled, since Abiword
       `(#:configure-flags        ;; supports it directly, and its BS is broken.
-        (list
+        (list                    ;; wmf was removed from Guix for security.
           "--enable-clipart"     ;; TODO: The following plugins have unresolved
           "--enable-templates"   ;; dependencies: aiksaurus, grammar, wpg, gda,
           (string-append         ;; wordperfect, psion, mathview.
@@ -73,7 +73,7 @@
               "latex " "loadbindings " "mht " "mif " "mswrite " "opendocument "
               "openwriter " "openxml " "opml " "ots " "paint " "passepartout "
               "pdb " "pdf " "presentation " "s5 " "sdw " "t602 " "urldict "
-              "wikipedia " "wmf " "wml " "xslfo"))
+              "wikipedia " "wml " "xslfo"))
         ;; tests fail with: Gtk-CRITICAL **: gtk_settings_get_for_screen:
         ;;                  assertion 'GDK_IS_SCREEN (screen)' failed
         ;;                  GLib-GObject-CRITICAL **: g_object_get_qdata:

From 31f45cf7be18d1cfc46a0ae785a3057227c4b185 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 9 Oct 2018 10:31:02 +0300
Subject: [PATCH 643/909] gnu: agg: Don't build examples.

* gnu/packages/graphics.scm (agg)[arguments]: Disable building the
examples.
---
 gnu/packages/graphics.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index 58c742b825..79fd134bbe 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -705,7 +705,8 @@ and understanding different BRDFs (and other component functions).")
        (list (string-append "--x-includes=" (assoc-ref %build-inputs "libx11")
                             "/include")
              (string-append "--x-libraries=" (assoc-ref %build-inputs "libx11")
-                            "/lib"))
+                            "/lib")
+             "--disable-examples")
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'autoreconf

From 8d18edde755f4bf5b4723fc9ce89e1cd831d2b7b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 9 Oct 2018 10:32:16 +0300
Subject: [PATCH 644/909] * gnu: agg: Replace bootstrap phase.

* gnu/packages/graphics.scm (agg)[arguments]: Remove custom 'autoreconf
phase and replace default 'bootstrap phase. Use INVOKE.
[native-inputs]: Remove bash.
---
 gnu/packages/graphics.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index 79fd134bbe..c3c1a4a580 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -709,17 +709,16 @@ and understanding different BRDFs (and other component functions).")
              "--disable-examples")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'autoreconf
+         (replace 'bootstrap
            (lambda _
              ;; let's call configure from configure phase and not now
              (substitute* "autogen.sh" (("./configure") "# ./configure"))
-             (zero? (system* "sh" "autogen.sh")))))))
+             (invoke "sh" "autogen.sh"))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("libtool" ,libtool)
        ("autoconf" ,autoconf)
-       ("automake" ,automake)
-       ("bash" ,bash)))
+       ("automake" ,automake)))
     (inputs
      `(("libx11" ,libx11)
        ("freetype" ,freetype)

From 8658b81b1acb2d84171914236f63f5b9038f76ea Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 9 Oct 2018 11:01:39 +0300
Subject: [PATCH 645/909] gnu: augeas: Update to 1.11.0.

* gnu/packages/augeas.scm (augeas): Update to 1.11.0.
[source]: Remove snippet.
---
 gnu/packages/augeas.scm | 16 +++-------------
 1 file changed, 3 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/augeas.scm b/gnu/packages/augeas.scm
index 9495d4a0a4..fcba5bae7b 100644
--- a/gnu/packages/augeas.scm
+++ b/gnu/packages/augeas.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -32,24 +32,14 @@
 (define-public augeas
   (package
     (name "augeas")
-    (version "1.10.1")
+    (version "1.11.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://download.augeas.net/augeas-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0k9nssn7lk58cl5zv3c8kv2zx9cm2yks3sj7q4fd6qdjz9m2bnsj"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; The gnulib test-lock test is prone to writer starvation
-                  ;; with our glibc@2.25, which prefers readers, so disable it.
-                  ;; The gnulib commit b20e8afb0b2 should fix this once
-                  ;; incorporated here.
-                  (substitute* "gnulib/tests/Makefile.in"
-                    (("test-lock\\$\\(EXEEXT\\) ") ""))
-                  #t))))
+                "1c507qj6dfn2dnsl27w94zs9r45xrgm07y8bqba9ry2s0psfhg1r"))))
     (build-system gnu-build-system)
     ;; Marked as "required" in augeas.pc
     (propagated-inputs

From 1fe57b3746de17c523a01e6c3e5a29bde5843018 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 9 Oct 2018 12:04:13 +0300
Subject: [PATCH 646/909] gnu: bs1770gain: Update to 0.5.0.

* gnu/packages/audio.scm (bs1770gain): Update to 0.5.0.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 17b6363f7c..b858a35359 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3087,7 +3087,7 @@ with support for HD extensions.")
 (define-public bs1770gain
   (package
     (name "bs1770gain")
-    (version "0.4.12")
+    (version "0.5.0")
     (source
      (origin
        (method url-fetch)
@@ -3095,7 +3095,7 @@ with support for HD extensions.")
                            version "/bs1770gain-" version ".tar.gz"))
        (sha256
         (base32
-         "0n9skdap1vnl6w52fx0gsrjlk7w3xgdwi62ycyf96h29rx059z6a"))))
+         "0vd7320k7s2zcn2vganclxbr1vav18ghld27rcwskvcc3dm8prii"))))
     (build-system gnu-build-system)
     (inputs `(("ffmpeg" ,ffmpeg)
               ("sox" ,sox)))

From 276f368051ff52cf202ede9fce579e49d9d744ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 09:24:24 +0200
Subject: [PATCH 647/909] tests: "make check-system" produces colored output.

* build-aux/run-system-tests.scm (run-system-tests): Use 'with-status-report'.
---
 build-aux/run-system-tests.scm | 49 ++++++++++++++++++----------------
 1 file changed, 26 insertions(+), 23 deletions(-)

diff --git a/build-aux/run-system-tests.scm b/build-aux/run-system-tests.scm
index 8b44f579a2..953ba3e221 100644
--- a/build-aux/run-system-tests.scm
+++ b/build-aux/run-system-tests.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,6 +19,7 @@
 (define-module (run-system-tests)
   #:use-module (gnu tests)
   #:use-module (guix store)
+  #:use-module (guix status)
   #:use-module (guix monads)
   #:use-module (guix derivations)
   #:use-module (guix ui)
@@ -63,25 +64,27 @@
           (length tests))
 
   (with-store store
-    (run-with-store store
-      (mlet* %store-monad ((drv (mapm %store-monad system-test-value tests))
-                           (out -> (map derivation->output-path drv)))
-        (mbegin %store-monad
-          (show-what-to-build* drv)
-          (set-build-options* #:keep-going? #t #:keep-failed? #t
-                              #:print-build-trace #t
-                              #:fallback? #t)
-          (built-derivations* drv)
-          (mlet %store-monad ((valid  (filterm (store-lift valid-path?)
-                                               out))
-                              (failed (filterm (store-lift
-                                                (negate valid-path?))
-                                               out)))
-            (format #t "TOTAL: ~a\n" (length drv))
-            (for-each (lambda (item)
-                        (format #t "PASS: ~a~%" item))
-                      valid)
-            (for-each (lambda (item)
-                        (format #t "FAIL: ~a~%" item))
-                      failed)
-            (exit (null? failed))))))))
+    (with-status-report print-build-event
+      (run-with-store store
+        (mlet* %store-monad ((drv (mapm %store-monad system-test-value tests))
+                             (out -> (map derivation->output-path drv)))
+          (mbegin %store-monad
+            (show-what-to-build* drv)
+            (set-build-options* #:keep-going? #t #:keep-failed? #t
+                                #:print-build-trace #t
+                                #:print-extended-build-trace? #t
+                                #:fallback? #t)
+            (built-derivations* drv)
+            (mlet %store-monad ((valid  (filterm (store-lift valid-path?)
+                                                 out))
+                                (failed (filterm (store-lift
+                                                  (negate valid-path?))
+                                                 out)))
+              (format #t "TOTAL: ~a\n" (length drv))
+              (for-each (lambda (item)
+                          (format #t "PASS: ~a~%" item))
+                        valid)
+              (for-each (lambda (item)
+                          (format #t "FAIL: ~a~%" item))
+                        failed)
+              (exit (null? failed)))))))))

From fe17037b387c6eca0c45f0526d2761e982a192bb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 09:53:02 +0200
Subject: [PATCH 648/909] status: Gracefully handle invalid UTF-8 in build
 logs.

* guix/status.scm (maybe-utf8->string): New procedure.
(build-event-output-port): Use it in lieu of 'utf8->string'.
* tests/status.scm ("build-output-port, UTF-8")
("current-build-output-port, UTF-8 + garbage"): New tests.
---
 guix/status.scm  | 19 ++++++++++++++++++-
 tests/status.scm | 22 +++++++++++++++++++++-
 2 files changed, 39 insertions(+), 2 deletions(-)

diff --git a/guix/status.scm b/guix/status.scm
index c6956066fd..13537c70cd 100644
--- a/guix/status.scm
+++ b/guix/status.scm
@@ -34,6 +34,7 @@
   #:use-module (ice-9 match)
   #:use-module (ice-9 format)
   #:use-module (ice-9 binary-ports)
+  #:autoload   (ice-9 rdelim) (read-string)
   #:use-module (rnrs bytevectors)
   #:use-module ((system foreign)
                 #:select (bytevector->pointer pointer->bytevector))
@@ -429,6 +430,22 @@ ON-CHANGE can display the build status, build events, etc."
 (define %newline
   (char-set #\return #\newline))
 
+(define (maybe-utf8->string bv)
+  "Attempt to decode BV as UTF-8 string and return it.  Gracefully handle the
+case where BV does not contain only valid UTF-8."
+  (catch 'decoding-error
+    (lambda ()
+      (utf8->string bv))
+    (lambda _
+      ;; This is the sledgehammer but it's the only safe way we have to
+      ;; properly handle this.  It's expensive but it's rarely needed.
+      (let ((port (open-bytevector-input-port bv)))
+        (set-port-encoding! port "UTF-8")
+        (set-port-conversion-strategy! port 'substitute)
+        (let ((str (read-string port)))
+          (close-port port)
+          str)))))
+
 (define* (build-event-output-port proc #:optional (seed (build-status)))
   "Return an output port for use as 'current-build-output-port' that calls
 PROC with its current state value, initialized with SEED, on every build
@@ -464,7 +481,7 @@ The second return value is a thunk to retrieve the current state."
       (pointer->bytevector ptr count)))
 
   (define (write! bv offset count)
-    (let loop ((str (utf8->string (bytevector-range bv offset count))))
+    (let loop ((str (maybe-utf8->string (bytevector-range bv offset count))))
       (match (string-index str %newline)
         ((? integer? cr)
          (let ((tail (string-take str (+ 1 cr))))
diff --git a/tests/status.scm b/tests/status.scm
index 04dedb702c..486ad04dd2 100644
--- a/tests/status.scm
+++ b/tests/status.scm
@@ -20,7 +20,9 @@
   #:use-module (guix status)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-11)
-  #:use-module (srfi srfi-64))
+  #:use-module (srfi srfi-64)
+  #:use-module (rnrs bytevectors)
+  #:use-module (rnrs io ports))
 
 (test-begin "status")
 
@@ -112,4 +114,22 @@
       (display "@ substituter-succeeded baz\n" port)
       (list first (get-status)))))
 
+(test-equal "build-output-port, UTF-8"
+  '((build-log "lambda is λ!\n"))
+  (let-values (((port get-status) (build-event-output-port cons '()))
+               ((bv)              (string->utf8 "lambda is λ!\n")))
+    (put-bytevector port bv)
+    (force-output port)
+    (get-status)))
+
+(test-equal "current-build-output-port, UTF-8 + garbage"
+  ;; What about a mixture of UTF-8 + garbage?
+  '((build-log "garbage: �lambda: λ\n"))
+  (let-values (((port get-status) (build-event-output-port cons '())))
+    (display "garbage: " port)
+    (put-bytevector port #vu8(128))
+    (put-bytevector port (string->utf8 "lambda: λ\n"))
+    (force-output port)
+    (get-status)))
+
 (test-end "status")

From e54aec7b8e5ef1aa53df043e3c0b06f25d2936a4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 10:52:39 +0200
Subject: [PATCH 649/909] pull: '-l' now honors '-p'.

* guix/scripts/pull.scm (process-query): Add 'profile' parameter and
remove 'profile' local variable.
(guix-pull): Adjust caller.
---
 guix/scripts/pull.scm | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 803f7cf142..0d65857beb 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -341,11 +341,8 @@ and ALIST2 differ, display HEADING upfront."
   (display-new/upgraded-packages (package-alist gen1)
                                  (package-alist gen2)))
 
-(define (process-query opts)
-  "Process any query specified by OPTS."
-  (define profile
-    (string-append (config-directory) "/current"))
-
+(define (process-query opts profile)
+  "Process any query on PROFILE specified by OPTS."
   (match (assoc-ref opts 'query)
     (('list-generations pattern)
      (define (list-generations profile numbers)
@@ -445,7 +442,7 @@ Use '~/.config/guix/channels.scm' instead."))
                           (string-append (config-directory) "/current"))))
 
        (cond ((assoc-ref opts 'query)
-              (process-query opts))
+              (process-query opts profile))
              ((assoc-ref opts 'dry-run?)
               #t)                                 ;XXX: not very useful
              (else

From 88d9eccc116f29000df6062fdabe2b1377da158b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 11:49:26 +0200
Subject: [PATCH 650/909] profiles: Make Geiser happy.

* guix/profiles.scm (manual-database)[config.scm]: Use ungexp/quote
trick to placate Geiser, which otherwise thinks it's in (guix config).
---
 guix/profiles.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/profiles.scm b/guix/profiles.scm
index 669ebe04e5..de3a044646 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -1249,7 +1249,7 @@ the entries in MANIFEST."
   (define config.scm
     (scheme-file "config.scm"
                  #~(begin
-                     (define-module (guix config)
+                     (define-module #$'(guix config) ;placate Geiser
                        #:export (%libz))
 
                      (define %libz

From 64965a068d82d1730097e61f6443a8812051934b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 15:21:54 +0200
Subject: [PATCH 651/909] gnu: Add ttf2pt1.

* gnu/packages/fontutils.scm (ttf2pt1): New variable.
---
 gnu/packages/fontutils.scm | 53 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index 30143eba34..09ba9b7e4a 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -190,6 +191,58 @@ TTF (TrueType/OpenType Font) files.")
     (license license:bsd-2)
     (home-page "https://github.com/wget/ttf2eot")))
 
+(define-public ttf2pt1
+  (package
+    (name "ttf2pt1")
+    (version "3.4.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/ttf2pt1/ttf2pt1/"
+                                  version "/ttf2pt1-" version ".tgz"))
+              (sha256
+               (base32
+                "1l718n4k4widx49xz7qrj4mybzb8q67kp2jw7f47604ips4654mf"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove trailing backslashes in the sed expression of the
+                  ;; 'install' rule since sed would otherwise fail.
+                  (substitute* "Makefile"
+                    (("\\|;\\\\[[:space:]]*$") "|; "))
+                  #t))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f                                ;no tests
+       #:phases (modify-phases %standard-phases
+                  (replace 'configure
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((out (assoc-ref outputs "out")))
+                        (substitute* "Makefile"
+                          (("INSTDIR =.*")
+                           (string-append "INSTDIR = " out "\n"))
+                          (("OWNER = .*")
+                           "OWNER = `id -un`\n")
+                          (("GROUP = .*")
+                           "GROUP = `id -g`\n"))
+                        #t)))
+                  (replace 'build
+                    (lambda _
+                      (invoke "make" "-j"
+                              (number->string (parallel-job-count))
+                              "all" "CC=gcc"))))))
+    (inputs `(("perl" ,perl)))
+    (synopsis "Convert TrueType fonts to Postscript Type 1")
+    (description
+     "TTF2PT1 provides tools to convert most TrueType fonts (or other formats
+supported by the FreeType library) to an Adobe Type 1 @file{.pfa} or
+@file{.pfb} file.  Another use is as a hinting engine: feed it an unhinted or
+poorly hinted Adobe Type 1 font through the FreeType library and get it back
+with freshly generated hints.  The files produced by default are in
+human-readable form, which further needs to be encoded with t1utilities to
+work with most software requiring Type 1 fonts.")
+    (home-page "http://ttf2pt1.sourceforge.net/")
+    (license license:bsd-3)))
+
 (define-public woff2
   (let ((commit "4e698b8c6c5e070d53c340db9ddf160e21070ede")
         (revision "1"))

From b33e191c86b7638517ea838b63a54d031a033554 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 18:52:37 +0200
Subject: [PATCH 652/909] guix build: '-f' accepts file-like objects.

* guix/scripts/build.scm (options->things-to-build)[validate-type]:
Check for 'file-like?'.
(options->derivations): Accept 'file-like?'.
* tests/guix-build.sh: Add a test with 'computed-file'.
* doc/guix.texi (Additional Build Options): Mention file-like objects.
---
 doc/guix.texi          | 5 ++---
 guix/scripts/build.scm | 6 +++++-
 tests/guix-build.sh    | 4 ++++
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 3c116fc0be..9b37270a83 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -6365,9 +6365,8 @@ retrieved using the @option{--log-file} option.
 
 @item --file=@var{file}
 @itemx -f @var{file}
-
-Build the package or derivation that the code within @var{file}
-evaluates to.
+Build the package, derivation, or other file-like object that the code within
+@var{file} evaluates to (@pxref{G-Expressions, file-like objects}).
 
 As an example, @var{file} might contain a package definition like this
 (@pxref{Defining Packages}):
diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index 5a6ba62bc3..f3aa5512d5 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -623,7 +623,7 @@ must be one of 'package', 'all', or 'transitive'~%")
   "Read the arguments from OPTS and return a list of high-level objects to
 build---packages, gexps, derivations, and so on."
   (define (validate-type x)
-    (unless (or (package? x) (derivation? x) (gexp? x) (procedure? x))
+    (unless (or (derivation? x) (file-like? x) (gexp? x) (procedure? x))
       (leave (G_ "~s: not something we can build~%") x)))
 
   (define (ensure-list x)
@@ -700,6 +700,10 @@ package '~a' has no source~%")
                               (set-guile-for-build (default-guile))
                               (proc))
                             #:system system)))
+                   ((? file-like? obj)
+                    (list (run-with-store store
+                            (lower-object obj system
+                                          #:target (assoc-ref opts 'target)))))
                    ((? gexp? gexp)
                     (list (run-with-store store
                             (mbegin %store-monad
diff --git a/tests/guix-build.sh b/tests/guix-build.sh
index 92e7299321..7842ce87c6 100644
--- a/tests/guix-build.sh
+++ b/tests/guix-build.sh
@@ -221,6 +221,10 @@ guix build -e "(begin
 guix build -e '#~(mkdir #$output)' -d
 guix build -e '#~(mkdir #$output)' -d | grep 'gexp\.drv'
 
+# Same with a file-like object.
+guix build -e '(computed-file "foo" #~(mkdir #$output))' -d
+guix build -e '(computed-file "foo" #~(mkdir #$output))' -d | grep 'foo\.drv'
+
 # Building from a package file.
 cat > "$module_dir/package.scm"<<EOF
 (use-modules (gnu))

From b2eda4a55e4ccf61a493fc76aa6a96ac589ed8da Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Tue, 9 Oct 2018 17:38:17 +0200
Subject: [PATCH 653/909] gnu: java-w3c-svg: Fix build.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Reported-by: Björn Höfling <bjoern.hoefling@bjoernhoefling.de>

* gnu/packages/batik.scm (java-w3c-svg)[arguments]<#:phases>: Delete
"patch-interface" phase.
---
 gnu/packages/batik.scm | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index cdd1e44713..180d7e7676 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -23,6 +23,7 @@
   #:use-module (guix git-download)
   #:use-module (guix packages)
   #:use-module (guix build-system ant)
+  #:use-module (guix build utils)
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages java)
@@ -155,6 +156,11 @@ public interface EventListenerInitializer {
         (sha256
          (base32
           "0jicqcrxav8ggs37amgvvwgc2f0qp1c5wns4rb2i3si83s2m09ns"))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments java-w3c-svg-1.0)
+       ((#:phases phases)
+       `(modify-phases ,phases
+          (delete 'patch-interface)))))
     (propagated-inputs
      `())))
 

From 9096c00629f2582c218d0f081aa78ef43560570c Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Tue, 9 Oct 2018 17:39:10 +0200
Subject: [PATCH 654/909] gnu: java-w3c-svg: Update synopsis and description.

* gnu/packages/batik.scm (java-w3c-svg-1.0)[synopsis]: Modify.
[description]: Modify.
(java-w3c-svg)[synopsis]: Modify.
[description]: Modify.
---
 gnu/packages/batik.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/batik.scm b/gnu/packages/batik.scm
index 180d7e7676..8296c0fbd6 100644
--- a/gnu/packages/batik.scm
+++ b/gnu/packages/batik.scm
@@ -140,8 +140,8 @@ public interface EventListenerInitializer {
     (native-inputs
      `(("unzip" ,unzip)))
     (home-page "https://www.w3.org/Style/CSS/SAC/")
-    (synopsis "W3C SVG interface")
-    (description "This package provides a SVG interface.")
+    (synopsis "W3C SVG 1.0 interface")
+    (description "This package provides a SVG 1.0 interface.")
     (license license:w3c)))
 
 (define-public java-w3c-svg
@@ -162,7 +162,9 @@ public interface EventListenerInitializer {
        `(modify-phases ,phases
           (delete 'patch-interface)))))
     (propagated-inputs
-     `())))
+     `())
+    (synopsis "W3C SVG interface")
+    (description "This package provides a SVG interface.")))
 
 (define-public java-w3c-sac
   (package

From 006a1d59ba66ac260a3f3e027db403a7d46eb3a5 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Wed, 10 Oct 2018 09:32:48 +0200
Subject: [PATCH 655/909] gnu: vkd3d: Update to 1.1.

* gnu/packages/vulkan.scm (vkd3d): Update to 1.1.
---
 gnu/packages/vulkan.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm
index f256e21187..2474d640d7 100644
--- a/gnu/packages/vulkan.scm
+++ b/gnu/packages/vulkan.scm
@@ -346,11 +346,10 @@ shader compilation.")
       (license license:asl2.0))))
 
 (define-public vkd3d
-  (let ((commit "020c119e2da0786d8be0615cff961c190b00d62d") ; Release 1.0.
-        (revision "0"))
+  (let ((commit "ecda316ef54d70bf1b3e860755241bb75873e53f")) ; Release 1.1.
     (package
      (name "vkd3d")
-     (version "1.0")
+     (version "1.1")
      (source
       (origin
        (method git-fetch)
@@ -359,7 +358,7 @@ shader compilation.")
              (commit commit)))
        (sha256
         (base32
-         "084svxhigs8r0725jv6gs7wwrxb9x4igyg5bgvgpcfw4aq0k69gn"))
+         "05a28kspy8gzng181w28zjqdb3pj2ss83b0lwnppxbcdzsz7rvrf"))
        (file-name (string-append name "-" version "-checkout"))))
      (build-system gnu-build-system)
      (arguments

From e4c399fe155b2d268e41656edc0a55f718cb1100 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 9 Oct 2018 20:27:37 +0300
Subject: [PATCH 656/909] gnu: clisp: Update to 2.49.92.

* gnu/packages/lisp.scm (clisp): Update to 2.49.92.
[source]: Switch to git-fetch. Remove unneeded patch.
[arguments]: Remove '--enable-portability' flag, add CFLAGS for
armhf-linux. Update list of files needing substitutions in custom
'patch-sh-and-pwd phase.
[home-page]: Update to new home-page.
* gnu/packages/patches/clisp-glibc-2.26.patch: Remove file.
& gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                |  1 -
 gnu/packages/lisp.scm                       | 36 ++++++++++++---------
 gnu/packages/patches/clisp-glibc-2.26.patch | 20 ------------
 3 files changed, 21 insertions(+), 36 deletions(-)
 delete mode 100644 gnu/packages/patches/clisp-glibc-2.26.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 821e83a675..af3773c893 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -621,7 +621,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/clementine-fix-sqlite.patch		\
   %D%/packages/patches/clementine-remove-crypto++-dependency.patch	\
   %D%/packages/patches/clementine-use-openssl.patch		\
-  %D%/packages/patches/clisp-glibc-2.26.patch			\
   %D%/packages/patches/clisp-remove-failing-test.patch		\
   %D%/packages/patches/clucene-pkgconfig.patch			\
   %D%/packages/patches/clx-remove-demo.patch			\
diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 82ba6eedf0..ef98de057a 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -35,7 +35,6 @@
   #:use-module (gnu packages m4)
   #:use-module (guix download)
   #:use-module (guix git-download)
-  #:use-module (guix hg-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system asdf)
@@ -256,28 +255,31 @@ supporting ASDF, Sockets, Gray streams, MOP, and other useful components.")
 (define-public clisp
   (package
     (name "clisp")
-    (version "2.49-60")
+    (version "2.49-92")
     (source
      (origin
-       (method hg-fetch)
-       (uri (hg-reference
-             (url "http://hg.code.sf.net/p/clisp/clisp")
-             (changeset "clisp_2_49_60-2017-06-25")))
-       (file-name (string-append name "-" version "-checkout"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://gitlab.com/gnu-clisp/clisp")
+             (commit "clisp-2.49.92-2018-02-18")))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0qjv3z274rbdmb941hy03hl63f4z7bmci234f8dyz4skgfr82d3i"))
-       (patches (search-patches "clisp-glibc-2.26.patch"
-                                "clisp-remove-failing-test.patch"))))
+        (base32 "0k2dmgl0miz3767iks4p0mvp6xw0ysyxhjpklyh11j010rmh6hqb"))
+       (patches (search-patches "clisp-remove-failing-test.patch"))))
     (build-system gnu-build-system)
     (inputs `(("libffcall" ,libffcall)
               ("ncurses" ,ncurses)
               ("readline" ,readline)
               ("libsigsegv" ,libsigsegv)))
     (arguments
-     '(#:configure-flags '("--enable-portability"
-                           "--with-dynamic-ffi"
-                           "--with-dynamic-modules"
-                           "--with-module=rawsock")
+     `(#:configure-flags '(,@(if (string-prefix? "armhf-linux"
+                                                 (or (%current-system)
+                                                     (%current-target-system)))
+                                 '("CFLAGS=-falign-functions=4")
+                                 '())
+                            "--with-dynamic-ffi"
+                            "--with-dynamic-modules"
+                            "--with-module=rawsock")
        #:build #f
        #:phases
        (modify-phases %standard-phases
@@ -288,6 +290,10 @@ supporting ASDF, Sockets, Gray streams, MOP, and other useful components.")
              ;; many places where our automatic patching misses them.  Therefore
              ;; we do the following, in this early (post-unpack) phase, to solve
              ;; the problem from its root.
+             (substitute* '("src/clisp-link.in"
+                            "src/unix.d"
+                            "src/makemake.in")
+               (("/bin/sh") (which "sh")))
              (substitute* (find-files "." "configure|Makefile")
                (("/bin/sh") "sh"))
              (substitute* '("src/clisp-link.in")
@@ -295,7 +301,7 @@ supporting ASDF, Sockets, Gray streams, MOP, and other useful components.")
              #t)))
        ;; Makefiles seem to have race conditions.
        #:parallel-build? #f))
-    (home-page "http://www.clisp.org/")
+    (home-page "https://clisp.sourceforge.io/")
     (synopsis "A Common Lisp implementation")
     (description
      "GNU CLISP is an implementation of ANSI Common Lisp.  Common Lisp is a
diff --git a/gnu/packages/patches/clisp-glibc-2.26.patch b/gnu/packages/patches/clisp-glibc-2.26.patch
deleted file mode 100644
index c8920ceccc..0000000000
--- a/gnu/packages/patches/clisp-glibc-2.26.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-This patch comes from Debian.
-
-Description: cfree is not present in glibc-2.26, stop wrapping it
-Author: Adam Conrad <adconrad@ubuntu.com>
-Bug: https://sourceforge.net/p/clisp/bugs/717/
-Bug-Debian: https://bugs.debian.org/880686
-Applied-Upstream: https://sourceforge.net/p/clisp/clisp/ci/3bc928712d150ff1e5f6b2bfb7838655f3ff52fa/
-Reviewed-By: Sébastien Villemot <sebastien@debian.org>
-Last-Update: 2017-11-27
-
---- clisp-2.49.20170913.orig/modules/bindings/glibc/linux.lisp
-+++ clisp-2.49.20170913/modules/bindings/glibc/linux.lisp
-@@ -649,7 +649,6 @@
- (def-call-out calloc (:arguments (nmemb size_t) (size size_t))
-   (:return-type c-pointer))
- (def-call-out free (:arguments (ptr c-pointer)) (:return-type nil))
--(def-call-out cfree (:arguments (ptr c-pointer)) (:return-type nil))
- (def-call-out valloc (:arguments (size size_t)) (:return-type c-pointer))
- 
- (def-call-out abort (:arguments) (:return-type nil))

From 5ff15b86fcd2eae7d9f16f45597db0dce5ee5943 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 9 Oct 2018 20:30:35 +0300
Subject: [PATCH 657/909] gnu: lisp.scm: Arrange imported modules
 alphabetically.

* gnu/packages/lisp.scm: Arrange imported modules alphabetically.
---
 gnu/packages/lisp.scm | 30 ++++++++++++++----------------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index ef98de057a..8b8b9229b5 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -29,40 +29,38 @@
   #:use-module (gnu packages)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
-  #:use-module (gnu packages readline)
-  #:use-module (gnu packages texinfo)
-  #:use-module (gnu packages tex)
-  #:use-module (gnu packages m4)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system asdf)
   #:use-module (guix build-system trivial)
+  #:use-module (gnu packages admin)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages bdw-gc)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages ed)
   #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages gettext)
+  #:use-module (gnu packages gl)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages m4)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages bdw-gc)
-  #:use-module (gnu packages libffi)
   #:use-module (gnu packages libffcall)
-  #:use-module (gnu packages readline)
-  #:use-module (gnu packages sdl)
+  #:use-module (gnu packages libffi)
   #:use-module (gnu packages libsigsegv)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages admin)
-  #:use-module (gnu packages ed)
-  #:use-module (gnu packages gl)
-  #:use-module (gnu packages gcc)
-  #:use-module (gnu packages glib)
-  #:use-module (gnu packages gettext)
-  #:use-module (gnu packages m4)
+  #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages readline)
+  #:use-module (gnu packages sdl)
+  #:use-module (gnu packages tex)
+  #:use-module (gnu packages texinfo)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages xorg)
-  #:use-module (gnu packages perl)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
 

From e7cdd311ae2696713da59a4f27614a246ca0f58a Mon Sep 17 00:00:00 2001
From: Mark Meyer <mark@ofosos.org>
Date: Fri, 14 Sep 2018 22:58:29 +0200
Subject: [PATCH 658/909] gnu: mlt: Prepare for kdenlive.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/video.scm (mlt): Update to 6.10.0.
[inputs]: Add frei0r-plugins, gdk-pixbuf, gtk+-2, qtbase,qtsvg.
[make-flags]: Add "CXX=g++ -std=gnu++11".

Co-authored-by: Gábor Boskovits <boskovits@gmail.com>
Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
---
 gnu/packages/video.scm | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 2f6a89e14d..3e191ef6da 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -29,6 +29,8 @@
 ;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
+;;; Copyright © 2018 Gábor Boskovit <boskovits@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1942,7 +1944,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.")
 (define-public mlt
   (package
     (name "mlt")
-    (version "6.4.1")
+    (version "6.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/mltframework/mlt/"
@@ -1950,7 +1952,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "10m3ry0b2pvqx3bk34qh5dq337nn8pkc2gzfyhsj4nv9abskln47"))
+                "1zzdj1g3g24q6v8hd0v34lv0pkh37a13fhjpl44h1ffi00mz3577"))
               (modules '((guix build utils)))
               (snippet '(begin
                           ;; As of glibc 2.26, <xlocale.h> no longer is.
@@ -1960,7 +1962,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.")
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no tests
-       #:make-flags '("CC=gcc")
+       #:make-flags '("CC=gcc" "CXX=g++ -std=gnu++11")
        #:configure-flags
        (list "--enable-gpl3"
              "--enable-gpl")
@@ -1979,11 +1981,16 @@ from sites like Twitch.tv and pipes them into a video player of choice.")
      `(("alsa-lib" ,alsa-lib)
        ("ffmpeg" ,ffmpeg-3.4)
        ("fftw" ,fftw)
+       ("frei0r-plugins" ,frei0r-plugins)
+       ("gdk-pixbuf" ,gdk-pixbuf)
+       ("gtk+" ,gtk+-2)
        ("libxml2" ,libxml2)
        ("jack" ,jack-1)
        ("ladspa" ,ladspa)
        ("libsamplerate" ,libsamplerate)
        ("pulseaudio" ,pulseaudio)
+       ("qtbase" ,qtbase)
+       ("qtsvg" ,qtsvg)
        ("sdl" ,sdl)
        ("sox" ,sox)))
     (native-inputs

From a50f5258c785929a5f77a80e1805b502dd0c78c8 Mon Sep 17 00:00:00 2001
From: Mark Meyer <mark@ofosos.org>
Date: Sat, 22 Sep 2018 21:28:25 +0200
Subject: [PATCH 659/909] gnu: Add kdenlive.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/kde.scm (kdenlive): New variable.

Co-authored-by: Gábor Boskovits <boskovits@gmail.com>
Signed-off-by: Gábor Boskovits <boskovits@gmail.com>
---
 gnu/packages/kde.scm | 83 +++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 82 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm
index a835f42749..3dfba6d383 100644
--- a/gnu/packages/kde.scm
+++ b/gnu/packages/kde.scm
@@ -1,8 +1,9 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017 Mark Meyer <mark@ofosos.org>
+;;; Copyright © 2017, 2018 Mark Meyer <mark@ofosos.org>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,6 +23,7 @@
 (define-module (gnu packages kde)
   #:use-module (guix build-system cmake)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix utils)
@@ -47,8 +49,87 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages video)
   #:use-module (gnu packages xorg))
 
+(define-public kdenlive
+  (let ((version "18.08.1"))
+    (package
+      (name "kdenlive")
+      (version version)
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "git://anongit.kde.org/kdenlive.git")
+               (commit (string-append "v" version))))
+         (file-name (string-append name "-" version "-checkout"))
+         (sha256
+          (base32
+           "0ifnaclsz7w08mc485i3j1kkcpd1m8q5qamckrfwc375ac13xf4g"))))
+      (build-system cmake-build-system)
+      (native-inputs
+       `(("extra-cmake-modules" ,extra-cmake-modules)
+         ("qttools" ,qttools)))
+      (propagated-inputs
+       `(("mlt" ,mlt)))
+      (inputs
+       `(("shared-mime-info" ,shared-mime-info)
+         ("frei0r-plugins" ,frei0r-plugins)
+         ("qtbase" ,qtbase)
+         ("qtscript" ,qtscript)
+         ("qtsvg" ,qtsvg)
+         ("kparts" ,kparts)
+         ("knotifications" ,knotifications)
+         ("karchive" ,karchive)
+         ("kdbusaddons" ,kdbusaddons)
+         ("kcrash" ,kcrash)
+         ("kguiaddons" ,kguiaddons)
+         ("knewstuff" ,knewstuff)
+         ("knotifyconfig" ,knotifyconfig)
+         ("kfilemetadata" ,kfilemetadata)
+         ("kdoctools" ,kdoctools)
+         ("kdeclarative", kdeclarative)
+         ("qtdeclarative", qtdeclarative)
+         ("qtquickcontrols", qtquickcontrols)
+         ("kiconthemes", kiconthemes)
+         ("qtgraphicaleffects" ,qtgraphicaleffects)
+         ("kplotting", kplotting)))
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'install 'wrap-executable
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (qtquickcontrols (assoc-ref inputs "qtquickcontrols"))
+                      (qtbase (assoc-ref inputs "qtbase"))
+                      (qtdeclarative (assoc-ref inputs "qtdeclarative"))
+                      (frei0r (assoc-ref inputs "frei0r-plugins"))
+                      (qml "/lib/qt5/qml"))
+                 (wrap-program (string-append out "/bin/kdenlive")
+                   `("QT_PLUGIN_PATH" ":" prefix
+                     ,(map (lambda (label)
+                             (string-append (assoc-ref inputs label)
+                                            "/lib/qt5/plugins/"))
+                           '("qtbase", "qtsvg")))
+                   `("FREI0R_PATH" ":" =
+                     (,(string-append frei0r "/lib/frei0r-1/")))
+                   `("QT_QPA_PLATFORM_PLUGIN_PATH" ":" =
+                     (,(string-append qtbase "/lib/qt5/plugins/platforms")))
+                   `("QML2_IMPORT_PATH" ":" prefix
+                     (,(string-append qtquickcontrols qml)
+                      ,(string-append qtdeclarative qml)))))
+               #t)))))
+      (home-page "https://kdenlive.org")
+      (synopsis "Non-linear video editor")
+      (description "Kdenlive is an acronym for KDE Non-Linear Video Editor.
+
+Non-linear video editing is much more powerful than beginner's (linear)
+editors, hence it requires a bit more organization before starting.  However,
+it is not reserved to specialists and can be used for small personal
+projects.")
+      (license license:gpl2+))))
+
 (define-public kdevelop
   (package
     (name "kdevelop")

From 296ad592166841c3b6762bc4e9114d12451498cf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 10 Oct 2018 11:49:47 +0200
Subject: [PATCH 660/909] gnu: haunt: Make sure Guile-CommonMark and
 Guile-Reader are always visible.

* gnu/packages/guile.scm (haunt)[arguments]: In 'wrap-haunt' phase, add
Guile-Reader and Guile-CommonMark to the search paths.
---
 gnu/packages/guile.scm | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 1d330668a7..f7baff4718 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1192,13 +1192,15 @@ Guile's foreign function interface.")
        #:tests? #f ; test suite is non-deterministic :(
        #:phases (modify-phases %standard-phases
                   (add-after 'install 'wrap-haunt
-                    (lambda* (#:key outputs #:allow-other-keys)
+                    (lambda* (#:key inputs outputs #:allow-other-keys)
                       ;; Wrap the 'haunt' command to refer to the right
                       ;; modules.
                       (let* ((out  (assoc-ref outputs "out"))
                              (bin  (string-append out "/bin"))
                              (site (string-append
-                                    out "/share/guile/site")))
+                                    out "/share/guile/site"))
+                             (deps (list (assoc-ref inputs "guile-reader")
+                                         (assoc-ref inputs "guile-commonmark"))))
                         (match (scandir site)
                           (("." ".." version)
                            (let ((modules (string-append site "/" version))
@@ -1207,9 +1209,19 @@ Guile's foreign function interface.")
                                                     "/site-ccache")))
                              (wrap-program (string-append bin "/haunt")
                                `("GUILE_LOAD_PATH" ":" prefix
-                                 (,modules))
+                                 (,modules
+                                  ,@(map (lambda (dep)
+                                           (string-append dep
+                                                          "/share/guile/site/"
+                                                          version))
+                                         deps)))
                                `("GUILE_LOAD_COMPILED_PATH" ":" prefix
-                                 (,compiled-modules)))
+                                 (,compiled-modules
+                                  ,@(map (lambda (dep)
+                                           (string-append dep "/lib/guile/"
+                                                          version
+                                                          "/site-ccache"))
+                                         deps))))
                              #t)))))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)

From 6b009dbfea3e44a66533a5ea41879df669923cff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 10 Oct 2018 14:30:39 +0200
Subject: [PATCH 661/909] gnu: openal: Update source and home page URLs.

Fixes <https://bugs.gnu.org/33000>.
Reported by Nam Nguyen <namn@berkeley.edu>.

* gnu/packages/audio.scm (openal)[source, home-page]: Update URLs.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index b858a35359..d233940f23 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1913,7 +1913,7 @@ lv2-c++-tools.")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "http://kcat.strangesoft.net/openal-releases/openal-soft-"
+                    "http://openal-soft.org/openal-releases/openal-soft-"
                     version ".tar.bz2"))
               (sha256
                (base32
@@ -1950,7 +1950,7 @@ emitters are among the features handled by the API.  More advanced effects,
 including air absorption, occlusion, and environmental reverb, are available
 through the EFX extension.  It also facilitates streaming audio, multi-channel
 buffers, and audio capture.")
-    (home-page "http://kcat.strangesoft.net/openal.html")
+    (home-page "http://openal-soft.org/")
     (license license:lgpl2.0+)))
 
 (define-public freealut

From 121f32a104de6d88774c4a819eb40334a618199c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 10 Oct 2018 14:48:46 +0200
Subject: [PATCH 662/909] gnu: guile-next: Update to 2.9.1.

* gnu/packages/guile.scm (guile-next): Update to 2.9.1.
[native-inputs, arguments]: Remove.
[properties]: New field.
---
 gnu/packages/guile.scm | 39 ++++++++-------------------------------
 1 file changed, 8 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index f7baff4718..e223edb9fc 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -323,39 +323,14 @@ without requiring the source code to be rewritten.")
     (package
       (inherit guile-2.2)
       (name "guile-next")
-      (version (git-version "2.99" revision commit))
+      (version "2.9.1")
       (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://git.savannah.gnu.org/git/guile.git")
-                      (commit commit)))
+                (inherit (package-source guile-2.2))
+                (uri (string-append "https://alpha.gnu.org/gnu/guile/guile-"
+                                    version ".tar.xz"))
                 (sha256
                  (base32
-                  "1c2xy5cflg0hws48914rz3z8mdmf8w3lblfic0kxnymcmdv9cbhv"))
-                (file-name (git-file-name name version))))
-      (native-inputs
-       `(("autoconf", autoconf)
-         ("automake" ,automake)
-         ("libtool" ,libtool)
-         ("gettext" ,gnu-gettext)
-         ("texinfo" ,texinfo)
-         ("flex" ,flex)
-         ,@(package-native-inputs guile-2.2)))
-      (arguments
-       (substitute-keyword-arguments (package-arguments guile-2.2)
-         ((#:phases phases '%standard-phases)
-          ;; XXX: The default 'bootstrap' phase tries to execute the
-          ;; ./bootstrap directory.
-          `(modify-phases ,phases
-             (replace 'bootstrap
-               (lambda _
-                 (patch-shebang "build-aux/git-version-gen")
-                 (invoke "autoreconf" "-vfi")))
-             (add-before 'check 'skip-version-test
-               (lambda _
-                 ;; Remove this test that's bound to fail.
-                 (delete-file "test-suite/tests/version.test")
-                 #t))))))
+                  "0iba93yqn6mvgid0rfsrg4amym36pg9m8cqdplxsy222blrj9gh1"))))
       (native-search-paths
        (list (search-path-specification
               (variable "GUILE_LOAD_PATH")
@@ -363,7 +338,9 @@ without requiring the source code to be rewritten.")
              (search-path-specification
               (variable "GUILE_LOAD_COMPILED_PATH")
               (files '("lib/guile/3.0/site-ccache"
-                       "share/guile/site/3.0"))))))))
+                       "share/guile/site/3.0")))))
+      (properties '((ftp-server . "alpha.gnu.org")
+                    (upstream-name . "guile"))))))
 
 (define (make-guile-readline guile)
   (package

From 099bb0175f681e5f68dafb8ad973866f31fe515c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 10 Oct 2018 14:54:18 +0200
Subject: [PATCH 663/909] self: Use Guile 2.2 unconditionally for recent 'guix
 pull'.

Fixes <https://bugs.gnu.org/32929>.
Reported by Michael Bowcutt <mwb71@case.edu>.

* guix/self.scm (guix-derivation)[guile]: Use "2.2" when PULL-VERSION >= 1.
Likewise for the #:guile-version argument.
---
 guix/self.scm | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/guix/self.scm b/guix/self.scm
index 126116e08a..ecf846490f 100644
--- a/guix/self.scm
+++ b/guix/self.scm
@@ -911,7 +911,11 @@ is not supported."
         version))
 
   (define guile
-    (guile-for-build guile-version))
+    ;; When PULL-VERSION >= 1, produce a self-contained Guix and use Guile 2.2
+    ;; unconditionally.
+    (guile-for-build (if (>= pull-version 1)
+                         "2.2"
+                         guile-version)))
 
   (mbegin %store-monad
     (set-guile-for-build guile)
@@ -920,9 +924,11 @@ is not supported."
                                #:name (string-append "guix-"
                                                      (shorten version))
                                #:pull-version pull-version
-                               #:guile-version (match guile-version
-                                                 ("2.2.2" "2.2")
-                                                 (version version))
+                               #:guile-version (if (>= pull-version 1)
+                                                   "2.2"
+                                                   (match guile-version
+                                                     ("2.2.2" "2.2")
+                                                     (version version)))
                                #:guile-for-build guile)))
       (if guix
           (lower-object guix)

From 903378910e32a6981199a1669e67c46ca9be2187 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 17:32:53 +0200
Subject: [PATCH 664/909] gnu: Add numlockx.

* gnu/packages/xdisorg.scm (numlockx): New variable.
---
 gnu/packages/xdisorg.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index c31680b246..c92dbd1784 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -1497,3 +1497,27 @@ before the system goes to sleep.")
      "Pyperclip is a clipboard module for Python, handling copy/pasting from
 the X11 clipboard")
     (license license:bsd-3)))
+
+(define-public numlockx
+  (package
+    (name "numlockx")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    ;; It seems that upstream is gone.
+                    (url "https://github.com/rg3/numlockx")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1w49fayhwzn5rx0z1q2lrvm7z8jrd34lgb89p853a024bixc3cf2"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("xorg-server" ,xorg-server)))
+    (home-page "https://github.com/rg3/numlockx")
+    (synopsis "Turns on the numlock key in X11")
+    (description "@command{numlockx} is a tiny program that lets you turn on
+the numlock key in X11.  It can be called from the user's initialization files
+to automatically turn it on on login.")
+    (license license:expat)))

From d634db9401ac320383d45e24431442259cf6a2a4 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 17:33:42 +0200
Subject: [PATCH 665/909] etc: Use git-file-name if origin is git-fetch.

* etc/snippets/scheme-mode/guix-origin: Use git-file-name.
---
 etc/snippets/scheme-mode/guix-origin | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/etc/snippets/scheme-mode/guix-origin b/etc/snippets/scheme-mode/guix-origin
index 68d47135db..1a068f8859 100644
--- a/etc/snippets/scheme-mode/guix-origin
+++ b/etc/snippets/scheme-mode/guix-origin
@@ -15,7 +15,9 @@
                  ((equal yas-text "hg-fetch")  "hg-reference...")
                  ((equal yas-text "cvs-fetch") "cvs-reference...")
                  (t "(string-append \\"https://\\" version \\".tar.gz\\")"))}$0)
- ${1:$(cond ((member yas-text '("git-fetch" "svn-fetch" "hg-fetch" "cvs-fetch"))
+ ${1:$(cond ((equal yas-text "git-fetch")
+             "(file-name (git-file-name name version))")
+            ((member yas-text '("svn-fetch" "hg-fetch" "cvs-fetch"))
              "(file-name (string-append name \\"-\\" version \\"-checkout\\"))")
             (t ""))}
  (sha256

From 3e70c3a06ed7cc93e8d25c2c7e69c1bc7d7cb57b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 17:43:51 +0200
Subject: [PATCH 666/909] gnu: emacs-evil-collection: Update to 0.0.1.

* gnu/packages/emacs.scm (emacs-evil-collection): Update to 0.0.1.
---
 gnu/packages/emacs.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index c9493dabd4..8945fcd5df 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5200,11 +5200,11 @@ extensions.")
       (license license:gpl3+))))
 
 (define-public emacs-evil-collection
-  (let ((commit "b55ae90f367e103e6568ae00779a8a51c68a0104")
-        (revision "3"))
+  (let ((commit "abc9dd60f71ccc1f24803a12d853f84b4a8b258c")
+        (revision "4"))
     (package
       (name "emacs-evil-collection")
-      (version (git-version "20180911" revision commit))
+      (version (git-version "0.0.1" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -5213,7 +5213,7 @@ extensions.")
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "0n7bzi5s7rqi78l1424sxvsk2g46z7ksq02xx5jrmqymnij90jml"))))
+                  "0c9l93vrsl6kzx8gg305dq8qkb2dr3s10fww7lh382911pdmsh7v"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-evil" ,emacs-evil)))

From 8f3dc810b18280052fed56090a1f8034f7b5b008 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 17:45:07 +0200
Subject: [PATCH 667/909] gnu: emacs-slime: Update to 2.22.

* gnu/packages/emacs.scm (emacs-slime): Update to 2.22.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 8945fcd5df..4b013eb292 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3034,7 +3034,7 @@ in @code{html-mode}.")
 (define-public emacs-slime
   (package
     (name "emacs-slime")
-    (version "2.20")
+    (version "2.22")
     (source
      (origin
        (file-name (string-append name "-" version ".tar.gz"))
@@ -3044,7 +3044,7 @@ in @code{html-mode}.")
              version ".tar.gz"))
        (sha256
         (base32
-         "086lq5y4pvj9wihy0si02xxvyzpzz8mcg3hz1cvy9zxlyjwzr1gk"))))
+         "07vaib1n4zyh5yy30gdpq0bc5cv6w84piml5b3mfc9ibjhaykkms"))))
     (build-system emacs-build-system)
     (native-inputs
      `(("texinfo" ,texinfo)))

From 4feb589bf48cbbd2d524002456fa822acf856bc3 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 18:06:08 +0200
Subject: [PATCH 668/909] doc: Add recommendations for good origin URLs.

* doc/contributing.texi (Submitting Patches): URL recommendations.
---
 doc/contributing.texi | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/doc/contributing.texi b/doc/contributing.texi
index 68d8e7e2fb..91a87ef2dd 100644
--- a/doc/contributing.texi
+++ b/doc/contributing.texi
@@ -468,6 +468,14 @@ Please follow our code formatting rules, possibly running the
 @command{etc/indent-code.el} script to do that automatically for you
 (@pxref{Formatting Code}).
 
+@item
+When possible, use mirrors in the source URL (@pxref{Invoking guix download}).
+Use reliable URLs, not generated ones.  For instance, GitHub archives are not
+necessarily identical from one generation to the next, so in this case it's
+often better to clone the repository.  Don't use the @command{name} field in
+the URL: it is not very useful and if the name changes, the URL will probably
+be wrong.
+
 @end enumerate
 
 When posting a patch to the mailing list, use @samp{[PATCH] @dots{}} as

From 8984dbd0deb380f6706d36bc9f1aaa061c0e751a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 19:45:27 +0200
Subject: [PATCH 669/909] gnu: volume-key: Update to 0.3.12.

* gnu/packages/disk.scm (volume-key): Update to 0.3.12.
---
 gnu/packages/disk.scm | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index fa3a0431a5..a9c355e412 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -559,28 +559,28 @@ automatically finding out which program to use for what file type.")
 (define-public volume-key
   (package
     (name "volume-key")
-    (version "0.3.11")
+    (version "0.3.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://releases.pagure.org/volume_key/volume_key-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0vaz15rcgdkh5z4yxc22x76wi44gh50jxnrqz5avaxz4bb17kcp6"))))
+                "16rhfz6sjwxlmss1plb2wv2i3jq6wza02rmz1d2jrlnsq67p98vc"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("util-linux" ,util-linux)
        ("swig" ,swig)
-       ("python" ,python-3)))           ; Used to generate the Python bindings.
+       ("python" ,python-3)))           ; used to generate the Python bindings
     (inputs
      `(("cryptsetup" ,cryptsetup)
        ("nss" ,nss)
-       ("lvm2" ,lvm2)                   ; For "-ldevmapper".
+       ("lvm2" ,lvm2)                   ; for "-ldevmapper"
        ("glib" ,glib)
        ("gpgme" ,gpgme)))
     (arguments
-     `(#:tests? #f ; Not sure how tests are supposed to pass, even when run manually.
+     `(#:tests? #f ; not sure how tests are supposed to pass, even when run manually
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'patch-python.h-path

From 4273a7ef65ce3b89b592093e2a07ecb5a9081d7a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 20:05:18 +0200
Subject: [PATCH 670/909] gnu: libblockdev: Update to 2.20.

* gnu/packages/disk.scm (libblockdev): Update to 2.20.
[license]: Update to match fixed licence headers.
---
 gnu/packages/disk.scm | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index a9c355e412..338678b8d1 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -698,14 +698,15 @@ to create devices with respective mappings for the ATARAID sets discovered.")
 (define-public libblockdev
   (package
     (name "libblockdev")
-    (version "2.18")
+    (version "2.20")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/storaged-project/libblockdev/releases/download/"
+              (uri (string-append "https://github.com/storaged-project/"
+                                  "libblockdev/releases/download/"
                                   version "-1/libblockdev-" version ".tar.gz"))
               (sha256
                (base32
-                "1a3kpdr9s6g7nfibazi92i27wbv692b5gm2r24gimis6l6jq4pbh"))))
+                "092snk5jyv48na4d46v1ckiy859zwpb3r0ivnxv3km5vzsp76y7q"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -738,6 +739,4 @@ manipulation of block devices.  It has a plugin-based architecture where each
 technology (like LVM, Btrfs, MD RAID, Swap...) is implemented in a separate
 plugin, possibly with multiple implementations (e.g. using LVM CLI or the new
 LVM D-Bus API).")
-    ;; XXX: Copying says LGPL2.1, but the source files with license
-    ;; information are GPL2+.
-    (license license:gpl2+)))
+    (license license:lgpl2.1+)))

From 1f033795e25f177bb52efe8e98aee7001ba8ccd0 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 21:10:23 +0200
Subject: [PATCH 671/909] gnu: ndctl: Update to 63.

* gnu/packages/disk.scm (ndctl): Update to 63.
[source]: Use GIT-FILE-NAME.
[native-inputs]: Add bash-completion.
[arguments]: Add '--disable-asciidoctor' and '--without-systemd'
 #:configure-flags.  Don't bother patching unused ./autogen.sh in
'patch-FHS-file-names' phase.
---
 gnu/packages/disk.scm | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 338678b8d1..04fe3deb38 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -600,27 +600,28 @@ passphrases.")
 (define-public ndctl
   (package
     (name "ndctl")
-    (version "61.2")
+    (version "63")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/pmem/ndctl")
+                    (url "https://github.com/pmem/ndctl.git")
                     (commit (string-append "v" version))))
-              (file-name (string-append name "-" version "-checkout"))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0vid78jzhmzh505bpwn8mvlamfhcvl6rlfjc29y4yn7zslpydxl7"))))
+                "060nsza8xic769bxj3pvl70a9885bwrc0myw16l095i3z6w7yzwq"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("asciidoc" ,asciidoc)
        ("automake" ,automake)
        ("autoconf" ,autoconf)
+       ("bash-completion" ,bash-completion)
        ("docbook-xsl" ,docbook-xsl)
        ("libtool" ,libtool)
        ("libxml2" ,libxml2)
        ("pkg-config" ,pkg-config)
        ("xmlto" ,xmlto)
-       ;; Required for offline docbook generation:
+       ;; Required for offline docbook generation.
        ("which" ,which)))
     (inputs
      `(("eudev" ,eudev)
@@ -628,12 +629,13 @@ passphrases.")
        ("kmod" ,kmod)
        ("util-linux" ,util-linux)))
     (arguments
-     `(#:phases
+     `(#:configure-flags
+       (list "--disable-asciidoctor"    ; use docbook-xsl instead
+             "--without-systemd")
+       #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'patch-FHS-file-names
            (lambda _
-             (substitute* "autogen.sh"
-               (("/bin/sh") (which "sh")))
              (substitute* "git-version-gen"
                (("/bin/sh") (which "sh")))
              (substitute* "git-version"

From 3820d51bec3997bb336d6f7c5eff7c97958b13ae Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 22:10:52 +0200
Subject: [PATCH 672/909] Order (gnu packages disk) module imports
 alphabetically.

* gnu/packages/disk.scm (define-module): Order module imports
alphabetically.
---
 gnu/packages/disk.scm | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 04fe3deb38..8b843a7417 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -30,22 +30,24 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages disk)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix download)
-  #:use-module (guix git-download)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system trivial)
-  #:use-module (guix build-system python)
   #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages bash)
+  #:use-module (gnu packages c)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages cryptsetup)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages docbook)
+  #:use-module (gnu packages documentation)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
-  #:use-module (gnu packages gtk)
   #:use-module (gnu packages gnome)
+  #:use-module (gnu packages gnupg)
+  #:use-module (gnu packages gnuzilla)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages guile)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
@@ -53,20 +55,18 @@
   #:use-module (gnu packages popt)
   #:use-module (gnu packages python)
   #:use-module (gnu packages readline)
-  #:use-module (gnu packages guile)
-  #:use-module (gnu packages compression)
+  #:use-module (gnu packages swig)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages w3m)
-  #:use-module (gnu packages xml)
-  #:use-module (gnu packages cryptsetup)
-  #:use-module (gnu packages gnuzilla)
-  #:use-module (gnu packages gnupg)
-  #:use-module (gnu packages swig)
-  #:use-module (gnu packages autotools)
   #:use-module (gnu packages web)
-  #:use-module (gnu packages documentation)
-  #:use-module (gnu packages bash)
-  #:use-module (gnu packages c))
+  #:use-module (gnu packages xml)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system trivial)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages))
 
 (define-public parted
   (package

From 3d0fdb34a24dda76130aae3e60743e2191fe3e3d Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 22:05:37 +0200
Subject: [PATCH 673/909] gnu: ranger: Update to 1.9.2.

* gnu/packages/disk.scm (ranger): Update to 1.9.2.
[native-inputs]: Order alphabetically.
[arguments]: Actually run tests and remove useless #:test-target.
---
 gnu/packages/disk.scm | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 8b843a7417..d88dbc8921 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -517,25 +517,24 @@ Duperemove can also take input from the @command{fdupes} program.")
 (define-public ranger
   (package
     (name "ranger")
-    (version "1.9.1")
+    (version "1.9.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ranger.github.io/"
                                   "ranger-" version ".tar.gz"))
               (sha256
                (base32
-                "1lnzkrxcnlwnyi3z0v8ybyp8d5rm26qm35rr68kbs2lbs06inha0"))))
+                "12kbsqakbxs09y0x8hy66mmaf72rk0p850x7ryk2ghkq7wfin78f"))))
     (build-system python-build-system)
     (inputs
      `(("w3m" ,w3m)))
     (native-inputs                      ;for tests
-     `(("python-pytest" ,python-pytest)
+     `(("python-flake8" ,python-flake8)
        ("python-pylint" ,python-pylint)
-       ("python-flake8" ,python-flake8)
+       ("python-pytest" ,python-pytest)
        ("which" ,which)))
     (arguments
-     '(#:test-target "test"
-       #:phases
+     '(#:phases
        (modify-phases %standard-phases
          (add-after 'configure 'wrap-program
            ;; Tell 'ranger' where 'w3mimgdisplay' is.
@@ -547,7 +546,11 @@ Duperemove can also take input from the @command{fdupes} program.")
                                    "/libexec/w3m/w3mimgdisplay")))
                (wrap-program ranger
                  `("W3MIMGDISPLAY_PATH" ":" prefix (,w3mimgdisplay)))
-               #t))))))
+               #t)))
+         (replace 'check
+           ;; Running 'make test' simply prints 'Ran 0 tests in 0.000s'.
+           (lambda _
+             (invoke "py.test" "tests"))))))
     (home-page "https://ranger.github.io/")
     (synopsis "Console file manager")
     (description "ranger is a console file manager with Vi key bindings.  It

From 47f9fb18a3b40a702368cc2dd70e3db1c95679f7 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Wed, 10 Oct 2018 12:16:51 +0200
Subject: [PATCH 674/909] gnu: Add kicad-symbols.

* gnu/packages/engineering.scm (kicad-symbols): New variable.
---
 gnu/packages/engineering.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index ee524ec78e..0080356494 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -823,6 +823,30 @@ electrical diagrams), gerbview (viewing Gerber files) and others.")
 render model libraries.")
       (license license:lgpl2.0+))))
 
+(define-public kicad-symbols
+  (package
+    (name "kicad-symbols")
+    (version "5.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/KiCad/kicad-symbols.git")
+                    (commit version)))
+              (file-name (string-append "kicad-symbols-" version "-checkout"))
+              (sha256
+               (base32
+                "18z5vpdq7hy2mpvm5vz1dz3ra3a5iybavvlzi8q2bmmdb6gsvf64"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f)) ; No tests exist
+    (home-page "http://kicad-pcb.org/")
+    (synopsis "Official KiCad schematic symbol libraries for KiCad 5")
+    (description "This package contains the official KiCad schematic symbol
+libraries for KiCad 5.")
+    ;; TODO: Exception: "To the extent that the creation of electronic designs that use 'Licensed Material' can be considered to be 'Adapted Material', then the copyright holder waives article 3 of the license with respect to these designs and any generated files which use data provided as part of the 'Licensed Material'."
+    ;; See <https://github.com/KiCad/kicad-symbols/blob/master/LICENSE.md>.
+    (license license:cc-by-sa4.0)))
+
 (define-public linsmith
   (package
     (name "linsmith")

From 43c97cceae055fc59ca14ddc5b3475d66f98de37 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 22:28:40 +0200
Subject: [PATCH 675/909] gnu: ranger: More test tweaks.

There's no functional difference between 'make test_pytest' and running
'py.test' directly, but there may be in future.

This follows up on commit 14173b3c6765bd8fcb2b12ea28fc27226645c7e1.

* gnu/packages/disk.scm (ranger)[arguments]: Use #:test-target to run
the (same) tests through 'make'.
[native-inputs]: Remove left-over python-flake8 and python-pylint.
---
 gnu/packages/disk.scm | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index d88dbc8921..2158da6a81 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -528,13 +528,15 @@ Duperemove can also take input from the @command{fdupes} program.")
     (build-system python-build-system)
     (inputs
      `(("w3m" ,w3m)))
-    (native-inputs                      ;for tests
-     `(("python-flake8" ,python-flake8)
-       ("python-pylint" ,python-pylint)
-       ("python-pytest" ,python-pytest)
-       ("which" ,which)))
+    (native-inputs
+     `(("which" ,which)
+
+       ;; For tests.
+       ("python-pytest" ,python-pytest)))
     (arguments
-     '(#:phases
+     '( ;; The 'test' target runs developer tools like pylint, which fail.
+       #:test-target "test_pytest"
+       #:phases
        (modify-phases %standard-phases
          (add-after 'configure 'wrap-program
            ;; Tell 'ranger' where 'w3mimgdisplay' is.
@@ -548,9 +550,9 @@ Duperemove can also take input from the @command{fdupes} program.")
                  `("W3MIMGDISPLAY_PATH" ":" prefix (,w3mimgdisplay)))
                #t)))
          (replace 'check
-           ;; Running 'make test' simply prints 'Ran 0 tests in 0.000s'.
-           (lambda _
-             (invoke "py.test" "tests"))))))
+           ;; The default check phase simply prints 'Ran 0 tests in 0.000s'.
+           (lambda* (#:key test-target #:allow-other-keys)
+             (invoke "make" test-target))))))
     (home-page "https://ranger.github.io/")
     (synopsis "Console file manager")
     (description "ranger is a console file manager with Vi key bindings.  It

From f825faa502b0c149c430a08268bc972ff5e8c1cd Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 22:44:16 +0200
Subject: [PATCH 676/909] gnu: python-pickleshare: Update to 0.7.5.

* gnu/packages/databases.scm (python-pickleshare): Update to 0.7.5.
---
 gnu/packages/databases.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 9c966494ad..73026c5e66 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2420,13 +2420,13 @@ SQLAlchemy Database Toolkit for Python.")
 (define-public python-pickleshare
   (package
     (name "python-pickleshare")
-    (version "0.7.4")
+    (version "0.7.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pickleshare" version))
        (sha256
-        (base32 "0yvk14dzxk7g6qpr7iw23vzqbsr0dh4ij4xynkhnzpfz4xr2bac4"))))
+        (base32 "1jmghg3c53yp1i8cm6pcrm280ayi8621rwyav9fac7awjr3kss47"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases

From 893c340c3af3fb1426d11f7a9f613f9837054ac5 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 22:59:13 +0200
Subject: [PATCH 677/909] gnu: haveged: Update to 1.9.4.

* gnu/packages/linux.scm (haveged): Update to 1.9.4.
[source]: Use GIT-FETCH and GIT-FILE-NAME from new (development) home.
---
 gnu/packages/linux.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index d52e8d7d19..c6c5a585e1 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3737,15 +3737,16 @@ such as frequency and voltage scaling.")
 (define-public haveged
   (package
     (name "haveged")
-    (version "1.9.2")
+    (version "1.9.4")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "http://www.issihosts.com/haveged/haveged-"
-                           version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jirka-h/haveged.git")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "0w5ypz6451msckivjriwyw8djydlwffam7x23xh626s2vzdrlzgp"))))
+        (base32 "1hrwzjd4byq4fdrg8svww3d8x449k80jxxrjy9v6jvzhfv19rvxr"))))
     (build-system gnu-build-system)
     (home-page "http://www.issihosts.com/haveged")
     (synopsis "Entropy source for the Linux random number generator")

From b71a34887bc21d84e0f6d44d3bb765f3ad50eeb9 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 23:00:38 +0200
Subject: [PATCH 678/909] gnu: haveged: Mark up description.

* gnu/packages/linux.scm (haveged)[description]: Use @dfn{} and
split into two paragraphs.
---
 gnu/packages/linux.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index c6c5a585e1..b7457a4687 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3755,11 +3755,12 @@ such as frequency and voltage scaling.")
 Linux's @file{/dev/random} and @file{/dev/urandom} devices.  The kernel's
 standard mechanisms for filling the entropy pool may not be sufficient for
 systems with high needs or limited user interaction, such as headless servers.
+
 @command{haveged} runs as a privileged daemon, harvesting randomness from the
 indirect effects of hardware events on hidden processor state using the HArdware
-Volatile Entropy Gathering and Expansion (HAVEGE) algorithm.  It tunes itself to
-its environment and provides the same built-in test suite for the output stream
-as used on certified hardware security devices.")
+Volatile Entropy Gathering and Expansion (@dfn{HAVEGE}) algorithm.  It tunes
+itself to its environment and provides the same built-in test suite for the
+output stream as used on certified hardware security devices.")
     (license (list (license:non-copyleft "file://nist/mconf.h")
                    (license:non-copyleft "file://nist/packtest.c")
                    license:public-domain        ; nist/dfft.c

From 50298d4a8139f188d2bc4882e9808ccb8b16a387 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 23:43:23 +0200
Subject: [PATCH 679/909] gnu: perftest: Update to 4.4-0.4.

* gnu/packages/linux.scm (perftest): Update to 4.4-0.4.
---
 gnu/packages/linux.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b7457a4687..b65bf9ba09 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3626,14 +3626,14 @@ The following service daemons are also provided:
 (define-public perftest
   (package
     (name "perftest")
-    (version "4.2-0.8")
+    (version "4.4-0.4")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append "https://github.com/linux-rdma/perftest/releases/download/V"
-                           version "/perftest-" version ".g0e24e67.tar.gz"))
+       (uri (string-append "https://github.com/linux-rdma/perftest/releases/download/v"
+                           version "/perftest-" version ".g0927198.tar.gz"))
        (sha256
-        (base32 "1r3pxn7cx3grb8myb4q1b0pk447pc06cifd0v7ym13xw00372dlx"))))
+        (base32 "11ix4h0rrmqqyi84y55a9xnkvwsmwq0sywr46hvxzm4rqz4ma8vq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases

From 43abffa1a3f216aa7cffaa748d3453e30f3e8839 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 23:45:55 +0200
Subject: [PATCH 680/909] gnu: hdparm: Update to 9.56.

* gnu/packages/linux.scm (hdparm): Update to 9.56.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b65bf9ba09..9b16083eab 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2668,14 +2668,14 @@ isolation or root privileges.")
 (define-public hdparm
   (package
     (name "hdparm")
-    (version "9.55")
+    (version "9.56")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/" name "/" name "/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1ivdvrzimaayiq03by8mcq0mhmdljndj06h012zkdpw34irnpixm"))))
+                "1np42qyhb503khvacnjcl3hb1dqly68gj0a1xip3j5qhbxlyvybg"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags (let ((out (assoc-ref %outputs "out")))

From 272fc9dca35c06d431e59e68a2a05ed8c2c3ce96 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 23:54:17 +0200
Subject: [PATCH 681/909] gnu: tlp: Return #t from phases.

* gnu/packages/linux.scm (tlp)[argument]: Return #t all from phases.
---
 gnu/packages/linux.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 9b16083eab..344f3ea397 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -4250,12 +4250,14 @@ Light is the successor of lightscript.")
                (setenv "TLP_SHCPL"
                        (string-append out "/share/bash-completion/completions"))
                (setenv "TLP_MAN" (string-append out "/share/man"))
-               (setenv "TLP_META" (string-append out "/share/metainfo")))))
+               (setenv "TLP_META" (string-append out "/share/metainfo"))
+               #t)))
          (delete 'check)                ; no tests
          (add-before 'install 'fix-installation
            (lambda _
              ;; Stop the Makefile from trying to create system directories.
-             (substitute* "Makefile" (("\\[ -f \\$\\(_CONF\\) \\]") "#"))))
+             (substitute* "Makefile" (("\\[ -f \\$\\(_CONF\\) \\]") "#"))
+             #t))
          (replace 'install
            (lambda _
              (invoke "make" "install-tlp" "install-man")
@@ -4289,7 +4291,8 @@ Light is the successor of lightscript.")
                                                        "pciutils"
                                                        "rfkill"
                                                        "wireless-tools"))))))
-                         bin-files)))))))
+                         bin-files)
+               #t))))))
     (home-page "http://linrunner.de/en/tlp/tlp.html")
     (synopsis "Power management tool for Linux")
     (description "TLP is a power management tool for Linux.  It comes with

From dc5282f9ea1142230b8361c788b30c9355af575b Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 23:57:29 +0200
Subject: [PATCH 682/909] gnu: hexchat: Update to 2.14.2.

* gnu/packages/messaging.scm (hexchat): Update to 2.14.2.
---
 gnu/packages/messaging.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 8ac86a852f..d2b61b9ec5 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -249,14 +249,14 @@ access to servers running the Discord protocol.")
 (define-public hexchat
   (package
     (name "hexchat")
-    (version "2.14.1")
+    (version "2.14.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://dl.hexchat.net/hexchat/hexchat-"
                                   version ".tar.xz"))
               (sha256
                (base32
-                "18h3l34zmazjlfx3irg7k7swppa62ad9ffbl0j3ry8p2xfyf8cmh"))))
+                "064nq151nzsljv97dmkifyl162d2738vbgvm1phx7yv04pjvk4kp"))))
     (build-system meson-build-system)
     (native-inputs `(("gettext" ,gettext-minimal)
                      ("perl" ,perl)

From e05fe1f91701c28e1a05ae13057601cef7aacf3c Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 10 Oct 2018 23:17:14 -0400
Subject: [PATCH 683/909] gnu: linux-libre@4.4: Update to 4.4.160.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.160.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 344f3ea397..6020330cd3 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -452,8 +452,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.159"
-                    "12wrhni1ikmakwv55cgzsznx9llzp82irsisbjjs7bc8z2hzwr6l"
+  (make-linux-libre "4.4.160"
+                    "1337p94j1hyc2gaw51wvlv622wwj2af1y8rafyfgp1403cs7ghp4"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 0e8f0803b5b2abd1c99408c508e8b36db32df9c5 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 10 Oct 2018 23:17:53 -0400
Subject: [PATCH 684/909] gnu: linux-libre@4.9: Update to 4.9.132.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.132.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 6020330cd3..261a8e28fa 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.131"
-                    "11pxwl7dmisbf2szg9qzkvhlpk68clh5l478n7b62q7hd8j3hxlv"
+  (make-linux-libre "4.9.132"
+                    "1s4zsv04bdafqqn8i6ab3lxjbh45v20dbm31mb52hfyzlfp4sjp5"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From 4f1d7e386b8ff6f83f109e06ca3ccbaa0f9f617f Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 10 Oct 2018 23:18:28 -0400
Subject: [PATCH 685/909] gnu: linux-libre@4.14: Update to 4.14.75.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.75.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 261a8e28fa..367ee4da29 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.74")
-(define %linux-libre-4.14-hash "0cxyx2yinnc8q0hmhb0swjgdz3s0ry7wxzyqss9f2i74xjjz4rm0")
+(define %linux-libre-4.14-version "4.14.75")
+(define %linux-libre-4.14-hash "0ljcjsc6lxq4q5dxy9kgnngasyqmv6rhl9yyqxrfzm41qbqfn64l")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From 2faf2edf5880a47d70b716b1780465eb1671c855 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 10 Oct 2018 23:19:36 -0400
Subject: [PATCH 686/909] gnu: linux-libre: Update to 4.18.13.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.13.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 367ee4da29..8983ed35e4 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.12")
-(define %linux-libre-hash "1mcnb1mm7m6i9s591c3kx0f1vbzhbl3w92w137swcm9zifqpci5r")
+(define %linux-libre-version "4.18.13")
+(define %linux-libre-hash "0jqlmzml67dp5708d4giga48vv4npgs3mbnzdrigaxgca5c69qck")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch

From a8fa86c47781e3e5f6cb58468446ede59b3ba3f4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 11 Oct 2018 10:30:00 +0200
Subject: [PATCH 687/909] gnu: Add python-cvxopt.

* gnu/packages/maths.scm (python-cvxopt, python2-cvxopt): New variables.
---
 gnu/packages/maths.scm | 44 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 766c6e920f..d4128f55c4 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -239,6 +239,50 @@ triangulations.")
     (license (license:non-copyleft "file://COPYING.txt"
                                    "See COPYING in the distribution."))))
 
+(define-public python-cvxopt
+  (package
+    (name "python-cvxopt")
+    (version "1.2.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/cvxopt/cvxopt.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'find-libraries
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "CVXOPT_BLAS_LIB" "openblas")
+             (setenv "CVXOPT_BUILD_FFTW" "1")
+             (setenv "CVXOPT_BUILD_GLPK" "1")
+             (setenv "CVXOPT_BUILD_GSL" "1")
+             #t)))))
+    (inputs
+     `(("fftw" ,fftw)
+       ("glpk" ,glpk)
+       ("gsl" ,gsl)
+       ("lapack" ,lapack)
+       ("openblas" ,openblas)
+       ("suitesparse" ,suitesparse)))
+    (home-page "https://www.cvxopt.org")
+    (synopsis "Python library for convex optimization")
+    (description
+     "CVXOPT is a package for convex optimization based on the Python
+programming language.  Its main purpose is to make the development of software
+for convex optimization applications straightforward by building on Python’s
+extensive standard library and on the strengths of Python as a high-level
+programming language.")
+    (license license:gpl3+)))
+
+(define-public python2-cvxopt
+  (package-with-python2 python-cvxopt))
+
 (define-public units
   (package
    (name "units")

From e8a7eab169b84ef66c0fb39b3f20ec8af047d5c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 11 Oct 2018 16:12:11 +0200
Subject: [PATCH 688/909] gnu: kallisto: Update to 0.44.0.

* gnu/packages/bioinformatics.scm (kallisto): Update to 0.44.0.
[source]: Fetch from git.
[arguments]: Add build phase to use htslib from Guix.
[inputs]: Add htslib.
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++-------
 1 file changed, 27 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ed713cd144..91bb94c549 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11735,19 +11735,39 @@ using nucleotide or amino-acid sequence data.")
 (define-public kallisto
   (package
     (name "kallisto")
-    (version "0.43.1")
+    (version "0.44.0")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/pachterlab/"
-                                  "kallisto/archive/v" version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/pachterlab/kallisto.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11"))))
+                "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m"))))
     (build-system cmake-build-system)
-    (arguments `(#:tests? #f))          ; no "check" target
+    (arguments
+     `(#:tests? #f          ; no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-htslib
+           (lambda _
+             (substitute* "CMakeLists.txt"
+               (("^ExternalProject_Add" m)
+                (string-append "if (NEVER)\n" m))
+               (("^\\)")
+                (string-append ")\nendif(NEVER)"))
+               (("include_directories\\(\\$\\{htslib_PREFIX.*" m)
+                (string-append "# " m)))
+             (substitute* "src/CMakeLists.txt"
+               (("target_link_libraries\\(kallisto kallisto_core pthread \
+\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)")
+                "target_link_libraries(kallisto kallisto_core pthread hts)")
+               (("include_directories\\(\\.\\./ext/htslib\\)") ""))
+             #t)))))
     (inputs
      `(("hdf5" ,hdf5)
+       ("htslib" ,htslib)
        ("zlib" ,zlib)))
     (home-page "http://pachterlab.github.io/kallisto/")
     (synopsis "Near-optimal RNA-Seq quantification")

From 77dcfb4c028417bed53c523dbb8c314e9556f85b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 11 Oct 2018 18:04:51 +0200
Subject: [PATCH 689/909] profiles: Add 'ensure-profile-directory'.

* guix/scripts/package.scm (ensure-default-profile): Move
/var/guix/profiles/per-user handling to...
* guix/profiles.scm (ensure-profile-directory): ... here.  New
procedure.
* po/guix/POTFILES.in: Add 'guix/profiles.scm'.
---
 guix/profiles.scm        | 43 +++++++++++++++++++++++++++++++++++++++-
 guix/scripts/package.scm | 40 ++-----------------------------------
 po/guix/POTFILES.in      |  1 +
 3 files changed, 45 insertions(+), 39 deletions(-)

diff --git a/guix/profiles.scm b/guix/profiles.scm
index de3a044646..6c3b26423e 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -28,7 +28,8 @@
   #:use-module ((guix config) #:select (%state-directory))
   #:use-module ((guix utils) #:hide (package-name->name+version))
   #:use-module ((guix build utils)
-                #:select (package-name->name+version))
+                #:select (package-name->name+version mkdir-p))
+  #:use-module (guix i18n)
   #:use-module (guix records)
   #:use-module (guix packages)
   #:use-module (guix derivations)
@@ -127,6 +128,7 @@
             %user-profile-directory
             %profile-directory
             %current-profile
+            ensure-profile-directory
             canonicalize-profile
             user-friendly-profile))
 
@@ -1610,6 +1612,45 @@ because the NUMBER is zero.)"
   ;; coexist with Nix profiles.
   (string-append %profile-directory "/guix-profile"))
 
+(define (ensure-profile-directory)
+  "Attempt to create /…/profiles/per-user/$USER if needed."
+  (let ((s (stat %profile-directory #f)))
+    (unless (and s (eq? 'directory (stat:type s)))
+      (catch 'system-error
+        (lambda ()
+          (mkdir-p %profile-directory))
+        (lambda args
+          ;; Often, we cannot create %PROFILE-DIRECTORY because its
+          ;; parent directory is root-owned and we're running
+          ;; unprivileged.
+          (raise (condition
+                  (&message
+                   (message
+                    (format #f
+                            (G_ "while creating directory `~a': ~a")
+                            %profile-directory
+                            (strerror (system-error-errno args)))))
+                  (&fix-hint
+                   (hint
+                    (format #f (G_ "Please create the @file{~a} directory, \
+with you as the owner.")
+                            %profile-directory))))))))
+
+    ;; Bail out if it's not owned by the user.
+    (unless (or (not s) (= (stat:uid s) (getuid)))
+      (raise (condition
+              (&message
+               (message
+                (format #f (G_ "directory `~a' is not owned by you")
+                        %profile-directory)))
+              (&fix-hint
+               (hint
+                (format #f (G_ "Please change the owner of @file{~a} \
+to user ~s.")
+                        %profile-directory (or (getenv "USER")
+                                               (getenv "LOGNAME")
+                                               (getuid))))))))))
+
 (define (canonicalize-profile profile)
   "If PROFILE is %USER-PROFILE-DIRECTORY, return %CURRENT-PROFILE.  Otherwise
 return PROFILE unchanged.  The goal is to treat '-p ~/.guix-profile' as if
diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index 93a77915fe..e588ff81ed 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -68,50 +68,14 @@
 
 (define (ensure-default-profile)
   "Ensure the default profile symlink and directory exist and are writable."
-
-  (define (rtfm)
-    (format (current-error-port)
-            (G_ "Try \"info '(guix) Invoking guix package'\" for \
-more information.~%"))
-    (exit 1))
+  (ensure-profile-directory)
 
   ;; Create ~/.guix-profile if it doesn't exist yet.
   (when (and %user-profile-directory
              %current-profile
              (not (false-if-exception
                    (lstat %user-profile-directory))))
-    (symlink %current-profile %user-profile-directory))
-
-  (let ((s (stat %profile-directory #f)))
-    ;; Attempt to create /…/profiles/per-user/$USER if needed.
-    (unless (and s (eq? 'directory (stat:type s)))
-      (catch 'system-error
-        (lambda ()
-          (mkdir-p %profile-directory))
-        (lambda args
-          ;; Often, we cannot create %PROFILE-DIRECTORY because its
-          ;; parent directory is root-owned and we're running
-          ;; unprivileged.
-          (format (current-error-port)
-                  (G_ "error: while creating directory `~a': ~a~%")
-                  %profile-directory
-                  (strerror (system-error-errno args)))
-          (format (current-error-port)
-                  (G_ "Please create the `~a' directory, with you as the owner.~%")
-                  %profile-directory)
-          (rtfm))))
-
-    ;; Bail out if it's not owned by the user.
-    (unless (or (not s) (= (stat:uid s) (getuid)))
-      (format (current-error-port)
-              (G_ "error: directory `~a' is not owned by you~%")
-              %profile-directory)
-      (format (current-error-port)
-              (G_ "Please change the owner of `~a' to user ~s.~%")
-              %profile-directory (or (getenv "USER")
-                                     (getenv "LOGNAME")
-                                     (getuid)))
-      (rtfm))))
+    (symlink %current-profile %user-profile-directory)))
 
 (define (delete-generations store profile generations)
   "Delete GENERATIONS from PROFILE.
diff --git a/po/guix/POTFILES.in b/po/guix/POTFILES.in
index df2cf12de2..2e37a19407 100644
--- a/po/guix/POTFILES.in
+++ b/po/guix/POTFILES.in
@@ -41,4 +41,5 @@ guix/status.scm
 guix/http-client.scm
 guix/nar.scm
 guix/channels.scm
+guix/profiles.scm
 nix/nix-daemon/guix-daemon.cc

From 50c72ecd9e272d959dfc346b5baea9137f6820ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 11:51:12 +0200
Subject: [PATCH 690/909] profiles: Generalize 'canonicalize-profile'.

* guix/profiles.scm (canonicalize-profile): Rewrite to work with any
profile that lives under %PROFILE-DIRECTORY.
---
 guix/profiles.scm | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/guix/profiles.scm b/guix/profiles.scm
index 6c3b26423e..99e6fe7371 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -1652,19 +1652,18 @@ to user ~s.")
                                                (getuid))))))))))
 
 (define (canonicalize-profile profile)
-  "If PROFILE is %USER-PROFILE-DIRECTORY, return %CURRENT-PROFILE.  Otherwise
-return PROFILE unchanged.  The goal is to treat '-p ~/.guix-profile' as if
-'-p' was omitted."                           ; see <http://bugs.gnu.org/17939>
-
-  ;; Trim trailing slashes so that the basename comparison below works as
-  ;; intended.
+  "If PROFILE points to a profile in %PROFILE-DIRECTORY, return that.
+Otherwise return PROFILE unchanged.  The goal is to treat '-p ~/.guix-profile'
+as if '-p' was omitted."  ; see <http://bugs.gnu.org/17939>
+  ;; Trim trailing slashes so 'readlink' can do its job.
   (let ((profile (string-trim-right profile #\/)))
-    (if (and %user-profile-directory
-             (string=? (canonicalize-path (dirname profile))
-                       (dirname %user-profile-directory))
-             (string=? (basename profile) (basename %user-profile-directory)))
-        %current-profile
-        profile)))
+    (catch 'system-error
+      (lambda ()
+        (let ((target (readlink profile)))
+          (if (string=? (dirname target) %profile-directory)
+              target
+              profile)))
+      (const profile))))
 
 (define (user-friendly-profile profile)
   "Return either ~/.guix-profile if that's what PROFILE refers to, directly or

From 795d430d90e41eb172315bfccf79c9f13fc0ebfa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Tue, 9 Oct 2018 11:51:44 +0200
Subject: [PATCH 691/909] pull: Turn ~/.config/guix/current into a symlink to
 /var/guix/profiles.

This is more consistent with what 'guix package' does, more pleasant for
users (we no longer clobber ~/.config/guix), and more
cluster-friendly (since /var/guix/profiles is usually an NFS share
already.)

* guix/scripts/pull.scm (%current-profile, %user-profile-directory): New
variables.
(migrate-generations, ensure-default-profile): New procedures.
(guix-pull): Use %CURRENT-PROFILE by default.  Call
'ensure-default-profile'.
* doc/guix.texi (Invoking guix pull): Adjust 'guix package -p
~/.config/guix/current' example.
* guix/scripts.scm (warn-about-old-distro): Check %PROFILE-DIRECTORY
"/current-guix".
---
 doc/guix.texi         |  2 +-
 guix/scripts.scm      |  4 ++--
 guix/scripts/pull.scm | 52 ++++++++++++++++++++++++++++++++++++++++---
 3 files changed, 52 insertions(+), 6 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 9b37270a83..5ae80917a9 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -2831,7 +2831,7 @@ generation---i.e., the previous Guix---and so on:
 $ guix package -p ~/.config/guix/current --roll-back
 switched from generation 3 to 2
 $ guix package -p ~/.config/guix/current --delete-generations=1
-deleting /home/charlie/.config/guix/current-1-link
+deleting /var/guix/profiles/per-user/charlie/current-guix-1-link
 @end example
 
 The @command{guix pull} command is usually invoked with no arguments,
diff --git a/guix/scripts.scm b/guix/scripts.scm
index 4cbbbeb96f..98751bc812 100644
--- a/guix/scripts.scm
+++ b/guix/scripts.scm
@@ -26,6 +26,7 @@
   #:use-module (guix monads)
   #:use-module (guix packages)
   #:use-module (guix derivations)
+  #:use-module ((guix profiles) #:select (%profile-directory))
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-19)
   #:use-module (srfi srfi-37)
@@ -169,8 +170,7 @@ Show what and how will/would be built."
 
     (define age
       (match (false-if-not-found
-              (lstat (string-append (config-directory #:ensure? #f)
-                                    "/current")))
+              (lstat (string-append %profile-directory "/current-guix")))
         (#f    #f)
         (stat  (- (time-second (current-time time-utc))
                   (stat:mtime stat)))))
diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 0d65857beb..5fecc11de3 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -225,6 +225,53 @@ Download and deploy the latest version of Guix.\n"))
     (lambda (key err)
       (report-git-error err))))
 
+
+;;;
+;;; Profile.
+;;;
+
+(define %current-profile
+  ;; The "real" profile under /var/guix.
+  (string-append %profile-directory "/current-guix"))
+
+(define %user-profile-directory
+  ;; The user-friendly name of %CURRENT-PROFILE.
+  (string-append (config-directory #:ensure? #f) "/current"))
+
+(define (migrate-generations profile directory)
+  "Migration the generations of PROFILE to DIRECTORY."
+  (format (current-error-port)
+          (G_ "Migrating profile generations to '~a'...~%")
+          %profile-directory)
+  (for-each (lambda (generation)
+              (let ((source (generation-file-name profile generation))
+                    (target (string-append directory "/current-guix-"
+                                           (number->string generation)
+                                           "-link")))
+                (rename-file source target)))
+            (profile-generations profile)))
+
+(define (ensure-default-profile)
+  (ensure-profile-directory)
+
+  ;; In 0.15.0+ we'd create ~/.config/guix/current-[0-9]*-link symlinks.  Move
+  ;; them to %PROFILE-DIRECTORY.
+  (unless (string=? %profile-directory
+                    (dirname (canonicalize-profile %user-profile-directory)))
+    (migrate-generations %user-profile-directory %profile-directory))
+
+  ;; Make sure ~/.config/guix/current points to /var/guix/profiles/….
+  (let ((link %user-profile-directory))
+    (unless (equal? (false-if-exception (readlink link))
+                    %current-profile)
+      (catch 'system-error
+        (lambda ()
+          (false-if-exception (delete-file link))
+          (symlink %current-profile link))
+        (lambda args
+          (leave (G_ "while creating symlink '~a': ~a~%")
+                 link (strerror (system-error-errno args))))))))
+
 
 ;;;
 ;;; Queries.
@@ -438,9 +485,8 @@ Use '~/.config/guix/channels.scm' instead."))
                                           (list %default-options)))
             (cache    (string-append (cache-directory) "/pull"))
             (channels (channel-list opts))
-            (profile  (or (assoc-ref opts 'profile)
-                          (string-append (config-directory) "/current"))))
-
+            (profile  (or (assoc-ref opts 'profile) %current-profile)))
+       (ensure-default-profile)
        (cond ((assoc-ref opts 'query)
               (process-query opts profile))
              ((assoc-ref opts 'dry-run?)

From ed9d7cb4d95f8f4776e6fee2778ab52bc2852969 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 11 Oct 2018 18:27:21 +0200
Subject: [PATCH 692/909] gnu: guix-daemon: Run 'guix' from
 /var/guix/profiles/per-user/root.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes <https://bugs.gnu.org/32183>.
Reported by Pjotr Prins <pjotr.public12@thebird.nl>
and Konrad Hinsen <konrad.hinsen@fastmail.net>.

* gnu/packages/package-management.scm (guix-daemon)[arguments]: Execute
/var/guix/profiles/per-user/root/current-guix/bin/guix instead of ~root/….
---
 gnu/packages/package-management.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 500abd5125..9a0023233f 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -347,12 +347,14 @@ the Nix package manager.")
                        "install-nodist_pkglibexecSCRIPTS")
 
                ;; We need to tell 'guix-daemon' which 'guix' command to use.
-               ;; Here we use a questionable hack where we hard-code
-               ;; "~root/.config", which could be wrong (XXX).
+               ;; Here we use a questionable hack where we hard-code root's
+               ;; current guix, which could be wrong (XXX).  Note that scripts
+               ;; like 'guix perform-download' do not run as root so we assume
+               ;; that they have access to /var/guix/profiles/per-user/root.
                (let ((out (assoc-ref outputs "out")))
                  (substitute* (find-files (string-append out "/libexec"))
                    (("exec \".*/bin/guix\"")
-                    "exec ~root/.config/guix/current/bin/guix"))
+                    "exec /var/guix/profiles/per-user/root/current-guix/bin/guix"))
                  #t)))
            (delete 'wrap-program)))))))
 

From 3bee949b032186cca4dbb5173f4f4fecd34da368 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Thu, 11 Oct 2018 13:03:58 -0400
Subject: [PATCH 693/909] gnu: Krita: Update to 4.1.5.

* gnu/packages/kde.scm (krita): Update to 4.1.5.
---
 gnu/packages/kde.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/kde.scm b/gnu/packages/kde.scm
index 3dfba6d383..c2164250e9 100644
--- a/gnu/packages/kde.scm
+++ b/gnu/packages/kde.scm
@@ -317,7 +317,7 @@ plugins, as well as code to create plugins, or complete applications.")
 (define-public krita
   (package
     (name "krita")
-    (version "4.1.3")
+    (version "4.1.5")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -326,7 +326,7 @@ plugins, as well as code to create plugins, or complete applications.")
                     "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0d546dxs552z0pxnaka1jm7ksravw17f777wf593z0pl4ds8dgdx"))))
+                "1by8p8ifdp03f05bhg8ygdd1j036anfpjjnzbx63l2fbmy9k6q10"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f

From fd15eb286e9b2effaf19a65e17e9e0e6d19b2111 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 11 Oct 2018 20:44:56 +0300
Subject: [PATCH 694/909] gnu: python-more-itertools: Fix building on 32-bit
 architectures.

* gnu/packages/python.scm (python-more-itertools)[arguments]: Add a
custom phase to prevent overflowing on 32-bit architectures.
---
 gnu/packages/python.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index d63e263e3c..1667f4801b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -142,7 +142,8 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
-  #:use-module (srfi srfi-1))
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-26))
 
 (define-public python-2.7
   (package
@@ -13550,6 +13551,20 @@ file system events on Linux.")
         (base32
          "17h3na0rdh8xq30w4b9pizgkdxmm51896bxw600x84jflg9vaxn4"))))
     (build-system python-build-system)
+    (arguments
+     `(,@(if (any (cute string-prefix? <> (or (%current-system)
+                                              (%current-target-system)))
+                  '("armhf" "i686"))
+        '(#:phases
+          (modify-phases %standard-phases
+          ;; This is required for 32-bit hardware.
+          ;; TODO: Try to remove this when upgrading.
+          (add-after 'unpack 'patch-test
+            (lambda _
+              (substitute* "more_itertools/tests/test_more.py"
+                (("10 \\*\\* 10") "9 ** 9"))
+              #t))))
+        '())))
     (propagated-inputs
      `(("python-six" ,python-six-bootstrap)))
     (home-page "https://github.com/erikrose/more-itertools")

From 0ea6af996b06ba453b803f2d4b014ffa709db4b7 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 11 Oct 2018 22:33:59 +0300
Subject: [PATCH 695/909] gnu: python-testtools: Fix regression in test suite.

* gnu/packages/check.scm (python-testtools)[source]: Add patch.
* gnu/packages/patches/python-testtools.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                |  1 +
 gnu/packages/check.scm                      |  3 +-
 gnu/packages/patches/python-testtools.patch | 57 +++++++++++++++++++++
 3 files changed, 60 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/python-testtools.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 15c8159460..e5745ba9e6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1087,6 +1087,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-configobj-setuptools.patch	\
   %D%/packages/patches/python-faker-fix-build-32bit.patch	\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
+  %D%/packages/patches/python-testtools.patch			\
   %D%/packages/patches/python-paste-remove-website-test.patch	\
   %D%/packages/patches/python-paste-remove-timing-test.patch	\
   %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch	\
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 2868f72cf9..1ae6355a93 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -879,7 +879,8 @@ subprocess and see the output as well as any file modifications.")
        (uri (pypi-uri "testtools" version))
        (sha256
         (base32
-         "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq"))))
+         "0n8519lk8aaa91vymz842831181wf7fss98hyllhygi3z1nfq9sq"))
+       (patches (search-patches "python-testtools.patch"))))
     (build-system python-build-system)
     (arguments '(#:tests? #f))
     (propagated-inputs
diff --git a/gnu/packages/patches/python-testtools.patch b/gnu/packages/patches/python-testtools.patch
new file mode 100644
index 0000000000..42536e50f9
--- /dev/null
+++ b/gnu/packages/patches/python-testtools.patch
@@ -0,0 +1,57 @@
+https://github.com/testing-cabal/testtools/commit/29004731f9c480b7c44a9c2605513d50d372898f.patch
+Should be fixed in the next release
+
+From 29004731f9c480b7c44a9c2605513d50d372898f Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Miro=20Hron=C4=8Dok?= <miro@hroncok.cz>
+Date: Thu, 17 May 2018 17:52:26 +0200
+Subject: [PATCH] Fix the tests on Python 3.7
+
+Exception's repr got changed not to include trailing comma
+
+Fixes https://github.com/testing-cabal/testtools/issues/270
+---
+ .travis.yml                                |  1 +
+ testtools/tests/matchers/test_exception.py | 11 +++++++++--
+ 2 files changed, 10 insertions(+), 2 deletions(-)
+
+diff --git a/.travis.yml b/.travis.yml
+index 7f1f4db7..784608e0 100644
+--- a/.travis.yml
++++ b/.travis.yml
+@@ -5,6 +5,7 @@ python:
+   - "3.4"
+   - "3.5"
+   - "3.6"
++  - "3.7-dev"
+   - "pypy"
+ 
+ install:
+diff --git a/testtools/tests/matchers/test_exception.py b/testtools/tests/matchers/test_exception.py
+index 6cd80af1..acd39252 100644
+--- a/testtools/tests/matchers/test_exception.py
++++ b/testtools/tests/matchers/test_exception.py
+@@ -32,15 +32,22 @@ class TestMatchesExceptionInstanceInterface(TestCase, TestMatchersInterface):
+     matches_matches = [error_foo]
+     matches_mismatches = [error_bar, error_base_foo]
+ 
++    if sys.version_info >= (3, 7):
++        # exception's repr has changed
++        _e = ''
++    else:
++        _e = ','
++
+     str_examples = [
+-        ("MatchesException(Exception('foo',))",
++        ("MatchesException(Exception('foo'%s))" % _e,
+          MatchesException(Exception('foo')))
+         ]
+     describe_examples = [
+         ("%r is not a %r" % (Exception, ValueError),
+          error_base_foo,
+          MatchesException(ValueError("foo"))),
+-        ("ValueError('bar',) has different arguments to ValueError('foo',).",
++        ("ValueError('bar'%s) has different arguments to ValueError('foo'%s)."
++         % (_e, _e),
+          error_bar,
+          MatchesException(ValueError("foo"))),
+         ]

From fc346e30a0e266ee7e2edcc057a22fdac3c98124 Mon Sep 17 00:00:00 2001
From: Brett Gilio <brettg@posteo.net>
Date: Thu, 11 Oct 2018 16:31:08 -0400
Subject: [PATCH 696/909] gnu: godot: Update to 3.0.6.

* gnu/packages/game-development.scm (godot): Update to 3.0.6.
---
 gnu/packages/game-development.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index bfebcc433e..6b7e71f6c0 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1080,7 +1080,7 @@ games.")
 (define-public godot
   (package
     (name "godot")
-    (version "3.0.4")
+    (version "3.0.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1089,7 +1089,7 @@ games.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0i4ssfb6igga9zwvsmahrnasx9cyqrsd6mlmssjgc482fy9q2kz4"))
+                "0g64h0x8dlv6aa9ggfcidk2mknkfl5li7z1phcav8aqp9srj8avf"))
               (modules '((guix build utils)))
               (snippet
                '(begin

From e1d1ec143569d35eb3e222e6f49d1db0e5423be9 Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@debian.org>
Date: Sun, 7 Oct 2018 20:16:47 -0700
Subject: [PATCH 697/909] gnu: u-boot: Update to 2018.09.

* gnu/packages/bootloaders.scm (u-boot): Update to 2018.09.
(u-boot-tools)[arguments]: Substitute "coverage" for "python-coverage". Update
workaround for only 99% test coverage.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/bootloaders.scm | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 4ba9d2e043..bce12d324d 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -360,7 +360,7 @@ tree binary files.  These are board description files used by Linux and BSD.")
 (define u-boot
   (package
     (name "u-boot")
-    (version "2018.07")
+    (version "2018.09")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -368,7 +368,7 @@ tree binary files.  These are board description files used by Linux and BSD.")
                     "u-boot-" version ".tar.bz2"))
               (sha256
                (base32
-                "1m7nw64mxflpc6sqvnz2kb5fxfkb4mrpy8b1wi15dcwipj4dy44z"))))
+                "0s122kyz1svvs2yjzj4j9qravl3ra4vn0fjqgski7rlczqyg56w3"))))
     (native-inputs
      `(("bc" ,bc)
        ("bison" ,bison)
@@ -403,6 +403,12 @@ also initializes the boards (RAM etc).")
               (("/bin/false") (which "false")))
              (substitute* "tools/dtoc/fdt_util.py"
               (("'cc'") "'gcc'"))
+             (substitute* "tools/patman/test_util.py"
+              ;; python-coverage is simply called coverage in guix.
+              (("python-coverage") "coverage")
+              ;; XXX Allow for only 99% test coverage.
+              ;; TODO: Find out why that is needed.
+              (("if coverage != '100%':") "if not int(coverage.rstrip('%')) >= 99:"))
              (substitute* "test/run"
               ;; Make it easier to find test failures.
               (("#!/bin/bash") "#!/bin/bash -x")
@@ -417,8 +423,6 @@ also initializes the boards (RAM etc).")
               (("def test_ctrl_c")
                "@pytest.mark.skip(reason='Guix has problems with SIGINT')
 def test_ctrl_c"))
-             (substitute* "tools/binman/binman.py"
-              (("100%") "99%")) ; TODO: Find out why that is needed.
              #t))
          (replace 'configure
            (lambda* (#:key make-flags #:allow-other-keys)

From 8155a209071f981fbf359975f463be4bcf8fa23e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 11 Oct 2018 23:53:18 +0200
Subject: [PATCH 698/909] pull: Create
 /var/guix/profiles/per-user/USER/current-guix.

Previously the migration code would fail to create that file, so
~/.config/guix/current would be dangling.

* guix/scripts/pull.scm (migrate-generations): Create
/var/guix/profiles/per-user/USER/current-guix.
---
 guix/scripts/pull.scm | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 5fecc11de3..8e0595076a 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -243,13 +243,17 @@ Download and deploy the latest version of Guix.\n"))
   (format (current-error-port)
           (G_ "Migrating profile generations to '~a'...~%")
           %profile-directory)
-  (for-each (lambda (generation)
-              (let ((source (generation-file-name profile generation))
-                    (target (string-append directory "/current-guix-"
-                                           (number->string generation)
-                                           "-link")))
-                (rename-file source target)))
-            (profile-generations profile)))
+  (let ((current (basename
+                  (generation-file-name profile
+                                        (generation-number profile)))))
+    (for-each (lambda (generation)
+                (let ((source (generation-file-name profile generation))
+                      (target (string-append directory "/current-guix-"
+                                             (number->string generation)
+                                             "-link")))
+                  (rename-file source target)))
+              (profile-generations profile))
+    (symlink current (string-append directory "/current-guix"))))
 
 (define (ensure-default-profile)
   (ensure-profile-directory)

From 1c795c4fd2c0f82892c5d1683de197868ecc5214 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 12 Oct 2018 00:12:00 +0200
Subject: [PATCH 699/909] profiles: 'user-friendly-profile' now recognizes
 ~/.config/guix/current.

* guix/profiles.scm (%known-shorthand-profiles): New variable.
(user-friendly-profile): Use it.
---
 guix/profiles.scm | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/guix/profiles.scm b/guix/profiles.scm
index 99e6fe7371..89e92ea2ba 100644
--- a/guix/profiles.scm
+++ b/guix/profiles.scm
@@ -1665,13 +1665,20 @@ as if '-p' was omitted."  ; see <http://bugs.gnu.org/17939>
               profile)))
       (const profile))))
 
+(define %known-shorthand-profiles
+  ;; Known shorthand forms for profiles that the user manipulates.
+  (list (string-append (config-directory #:ensure? #f) "/current")
+        %user-profile-directory))
+
 (define (user-friendly-profile profile)
-  "Return either ~/.guix-profile if that's what PROFILE refers to, directly or
-indirectly, or PROFILE."
-  (if (and %user-profile-directory
-           (false-if-exception
-            (string=? (readlink %user-profile-directory) profile)))
-      %user-profile-directory
+  "Return either ~/.guix-profile or ~/.config/guix/current if that's what
+PROFILE refers to, directly or indirectly, or PROFILE."
+  (or (find (lambda (shorthand)
+              (and shorthand
+                   (let ((target (false-if-exception
+                                  (readlink shorthand))))
+                     (and target (string=? target profile)))))
+            %known-shorthand-profiles)
       profile))
 
 ;;; profiles.scm ends here

From e9ab649e1e6400cdbf5147144903c1212cba798a Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 7 Oct 2018 10:37:40 +0100
Subject: [PATCH 700/909] gnu: Remove duplicate ruby-concurrent package
 definition.

* gnu/packages/ruby.scm (ruby-concurrent): Remove one of the two definitions
for this variable.
---
 gnu/packages/ruby.scm | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 2080944cae..2c5777fdf8 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -194,25 +194,6 @@ a focus on simplicity and productivity.")
                (("/bin/sh") (which "sh")))
              #t)))))))
 
-(define-public ruby-concurrent
-  (package
-    (name "ruby-concurrent")
-    (version "1.0.5")
-    (source (origin
-              (method url-fetch)
-              (uri (rubygems-uri "concurrent-ruby" version))
-              (sha256
-               (base32
-                "183lszf5gx84kcpb779v6a2y0mx9sssy8dgppng1z9a505nj1qcf"))))
-    (build-system ruby-build-system)
-    (arguments `(#:tests? #f)); No rakefile
-    (home-page "https://github.com/ruby-concurrency/concurrent-ruby")
-    (synopsis "Concurrency tools for Ruby")
-    (description "This gem provides concurrency tools for Ruby.  It provides
-a library of common thread-safe types and data-structures as well as abstractions
-for concurrency and communication between threads.")
-    (license license:expat)))
-
 (define-public ruby-highline
   (package
     (name "ruby-highline")

From 50135ff896441f6b9e10fbfc9bfd35bf06ff1c13 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 7 Oct 2018 10:38:26 +0100
Subject: [PATCH 701/909] gnu: Remove duplicate ruby-yard package definition.

* gnu/packages/ruby.scm (ruby-yard): Remove one of the two package
definitions, and update the other to the latest release.
---
 gnu/packages/ruby.scm | 25 ++-----------------------
 1 file changed, 2 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 2c5777fdf8..7e8c8be290 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3766,7 +3766,7 @@ A modified copy of yajl is used, and included in the package.")
 (define-public ruby-yard
   (package
     (name "ruby-yard")
-    (version "0.9.6")
+    (version "0.9.16")
     (source
      (origin
        (method url-fetch)
@@ -3776,7 +3776,7 @@ A modified copy of yajl is used, and included in the package.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0rsz4bghgx7fryzyhlz8wlnd2m9xgyvf1xhrq58mnzfrrfm41bdg"))))
+         "0sqpbayy9sb406jh0zqg6qha1xds863qz9531dh6vp58hc00clfq"))))
     (build-system ruby-build-system)
     (arguments
      `(#:phases
@@ -5673,27 +5673,6 @@ support the tests found in Prawn, a pure Ruby PDF generation library.")
 functionality from Prawn.")
     (license license:gpl3+)))
 
-(define-public ruby-yard
-  (package
-    (name "ruby-yard")
-    (version "0.9.16")
-    (source (origin
-              (method url-fetch)
-              (uri (rubygems-uri "yard" version))
-              (sha256
-               (base32
-                "0lmmr1839qgbb3zxfa7jf5mzy17yjl1yirwlgzdhws4452gqhn67"))))
-    (build-system ruby-build-system)
-    (arguments `(#:test-target "spec"))
-    (home-page "https://yardoc.org/")
-    (synopsis "Ruby documentation tool")
-    (description "YARD is a documentation generation tool for the Ruby
-programming language.  It enables the user to generate consistent, usable
-documentation that can be exported to a number of formats very easily, and
-also supports extending for custom Ruby constructs such as custom class level
-definitions.")
-    (license license:expat)))
-
 (define-public ruby-prawn
   (package
     (name "ruby-prawn")

From 28f436a904cbfc2d7bb6e5e8d91de23c03b134b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 12 Oct 2018 15:04:44 +0200
Subject: [PATCH 702/909] build: Remove obsolete reference to
 'GUIX_ASSERT_LIBGCRYPT_USABLE'.

Reported by Mark H Weaver <mhw@netris.org>.
Fixes <https://bugs.gnu.org/33023>.

* configure.ac: Remove use of 'GUIX_ASSERT_LIBGCRYPT_USABLE'.
Add "^GUIX_" to the forbidden M4 patterns.
---
 configure.ac | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/configure.ac b/configure.ac
index c83d4d8a28..104a0e4b09 100644
--- a/configure.ac
+++ b/configure.ac
@@ -88,6 +88,7 @@ dnl Make sure they are available.
 m4_pattern_forbid([PKG_CHECK_MODULES])
 m4_pattern_forbid([GUILE_MODULE_AVAILABLE])
 m4_pattern_forbid([^GUILE_P$])
+m4_pattern_forbid([^GUIX_])
 
 dnl Search for 'guile' and 'guild'.  This macro defines
 dnl 'GUILE_EFFECTIVE_VERSION'.
@@ -232,8 +233,6 @@ AC_SUBST([LIBGCRYPT])
 AC_SUBST([LIBGCRYPT_PREFIX])
 AC_SUBST([LIBGCRYPT_LIBDIR])
 
-GUIX_ASSERT_LIBGCRYPT_USABLE
-
 dnl Library name of zlib suitable for 'dynamic-link'.
 GUIX_LIBZ_LIBDIR([libz_libdir])
 if test "x$libz_libdir" = "x"; then

From dde49cfe5312b95f44060155256036532f3cb22a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 12 Oct 2018 15:09:56 +0200
Subject: [PATCH 703/909] build: Fine-tune the forbidden M4 patterns.

* configure.ac: Forbid "^GUILE_P", allow "^GUILE_PKG_ERRORS".
---
 configure.ac | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/configure.ac b/configure.ac
index 104a0e4b09..2a1edbc321 100644
--- a/configure.ac
+++ b/configure.ac
@@ -87,7 +87,8 @@ dnl We require pkg.m4 (from pkg-config) and guile.m4 (from Guile.)
 dnl Make sure they are available.
 m4_pattern_forbid([PKG_CHECK_MODULES])
 m4_pattern_forbid([GUILE_MODULE_AVAILABLE])
-m4_pattern_forbid([^GUILE_P$])
+m4_pattern_forbid([^GUILE_P])
+m4_pattern_allow([^GUILE_PKG_ERRORS])
 m4_pattern_forbid([^GUIX_])
 
 dnl Search for 'guile' and 'guild'.  This macro defines

From 8036b0942b89022147aaf9cd9940988fdbcc19ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 12 Oct 2018 15:11:50 +0200
Subject: [PATCH 704/909] pull: Don't use rename(2) across potentially
 different devices.

Reported by Formbi on #guix.

* guix/scripts/pull.scm (migrate-generations): Use 'symlink' and
'delete-file' instead of 'rename-file'.  The latter could lead to EXDEV
when $HOME and /var were different partitions.
---
 guix/scripts/pull.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 8e0595076a..660a2b9110 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -239,7 +239,7 @@ Download and deploy the latest version of Guix.\n"))
   (string-append (config-directory #:ensure? #f) "/current"))
 
 (define (migrate-generations profile directory)
-  "Migration the generations of PROFILE to DIRECTORY."
+  "Migrate the generations of PROFILE to DIRECTORY."
   (format (current-error-port)
           (G_ "Migrating profile generations to '~a'...~%")
           %profile-directory)
@@ -251,7 +251,10 @@ Download and deploy the latest version of Guix.\n"))
                       (target (string-append directory "/current-guix-"
                                              (number->string generation)
                                              "-link")))
-                  (rename-file source target)))
+                  ;; Note: Don't use 'rename-file' as SOURCE and TARGET might
+                  ;; live on different file systems.
+                  (symlink (readlink source) target)
+                  (delete-file source)))
               (profile-generations profile))
     (symlink current (string-append directory "/current-guix"))))
 

From 6826f1e1ede0526dd1247546aa5ec195bacd5cc5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong@member.fsf.org>
Date: Mon, 8 Oct 2018 21:42:28 +0800
Subject: [PATCH 705/909] gnu: Add libpd.

* gnu/packages/music.scm (libpd): New variable.
---
 gnu/packages/music.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index e1bac6f51e..13a6ecc36f 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1777,6 +1777,42 @@ programming methods as well as for realizing complex systems for large-scale
 projects.")
     (license license:bsd-3)))
 
+(define-public libpd
+  (package
+    (name "libpd")
+    (version "0.11.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/libpd/libpd.git")
+                    (commit version)
+                    (recursive? #t)))   ; for the 'pure-data' submodule
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1bcg1d9iyf9n37hwwphmih0c8rd1xcqykil5z1cax6xfs76552nk"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f                      ; no tests
+       #:make-flags '("CC=gcc")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ; no configure script
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (invoke "make" "install"
+                       (string-append "prefix=" out)
+                       ;; XXX: Fix the last 2 lines of 'install' target.
+                       "LIBPD_IMPLIB=NO"
+                       "LIBPD_DEF=NO")))))))
+    (home-page "http://libpd.cc/")
+    (synopsis "Pure Data as an embeddable audio synthesis library")
+    (description
+     "Libpd provides Pure Data as an embeddable audio synthesis library.  Its
+main purpose is to liberate raw audio rendering from audio and MIDI drivers.")
+    (license license:bsd-3)))
+
 (define-public portmidi
   (package
     (name "portmidi")

From aa227b3be3d7728331a08dbd139c47c9b271dc23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 12 Oct 2018 16:43:18 +0200
Subject: [PATCH 706/909] pull: Fix target of
 /var/guix/profiles/per-user/USER/current-guix.

This is a followup to 8155a209071f981fbf359975f463be4bcf8fa23e.

* guix/scripts/pull.scm (migrate-generations): Compute the right target
for /var/guix/profiles/per-user/USER/current-guix.  Previously we'd
return "current-N-link" instead of "current-guix-N-link'.
---
 guix/scripts/pull.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index 660a2b9110..d3fd624228 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -243,9 +243,7 @@ Download and deploy the latest version of Guix.\n"))
   (format (current-error-port)
           (G_ "Migrating profile generations to '~a'...~%")
           %profile-directory)
-  (let ((current (basename
-                  (generation-file-name profile
-                                        (generation-number profile)))))
+  (let ((current (generation-number profile)))
     (for-each (lambda (generation)
                 (let ((source (generation-file-name profile generation))
                       (target (string-append directory "/current-guix-"
@@ -256,7 +254,9 @@ Download and deploy the latest version of Guix.\n"))
                   (symlink (readlink source) target)
                   (delete-file source)))
               (profile-generations profile))
-    (symlink current (string-append directory "/current-guix"))))
+    (symlink (string-append "current-guix-"
+                            (number->string current) "-link")
+             (string-append directory "/current-guix"))))
 
 (define (ensure-default-profile)
   (ensure-profile-directory)

From a60e868629cbc471a2d511aa8f1bcbbd18caea8f Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 12 Oct 2018 22:16:54 -0400
Subject: [PATCH 707/909] gnu: Wireshark: Update to 2.6.4 [fixes
 CVE-2018-{12086,18225,18226,18227}].

* gnu/packages/networking.scm (wireshark): Update to 2.6.4.
---
 gnu/packages/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index e3486ffadc..5a0c464252 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -581,7 +581,7 @@ of the same name.")
 (define-public wireshark
   (package
     (name "wireshark")
-    (version "2.6.3")
+    (version "2.6.4")
     (source
      (origin
        (method url-fetch)
@@ -589,7 +589,7 @@ of the same name.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "1v538h02y8avwy3cr11xz6wkyf9xd8qva4ng4sl9f2fw4skahn6i"))))
+         "0qf81dk726sdsmjqa9nd251j1cwvzkyb4hrlp6w4iwa3cdz00sx0"))))
     (build-system gnu-build-system)
     (inputs `(("c-ares" ,c-ares)
               ("glib" ,glib)

From 3584eeb9a17e873778c9b36ca7a691d45e364856 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 12 Oct 2018 22:42:21 -0400
Subject: [PATCH 708/909] gnu: ImageMagick: Update to 6.9.10-12.

* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.10-12.
---
 gnu/packages/imagemagick.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index ec2ac08909..e29ec6255b 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -47,14 +47,14 @@
     ;; The 7 release series has an incompatible API, while the 6 series is still
     ;; maintained. Don't update to 7 until we've made sure that the ImageMagick
     ;; users are ready for the 7-series API.
-    (version "6.9.10-10")
+    (version "6.9.10-12")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "0b0wwxm6mgaxq0i0hazxcpbk7xd5j1329r1vk9h07iz4v3k8i57h"))))
+               "0ri96yqihdk921k5qx23y2sbhraxbp2avdccxiy6m3srjkirym2l"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")

From 3c4d307e8697c36ebb9df939a5d2f0d905cc5474 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 12 Oct 2018 23:19:20 -0400
Subject: [PATCH 709/909] gnu: python-icalendar: Update to 4.0.2.

* gnu/packages/python.scm (python-icalendar: Update to 4.0.2.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 6a2bd6e8f5..35262a2c77 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7576,13 +7576,13 @@ minimal and fast API targeting the following uses:
 (define-public python-icalendar
   (package
     (name "python-icalendar")
-    (version "4.0.1")
+    (version "4.0.2")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "icalendar" version))
              (sha256
               (base32
-               "139y79y6ijl39m5bj771r43vpah9s4ly7d1k76la6hrx7l144ak8"))))
+               "13003kw2vbas1ha146vv3x2rdg9k7w38rdzxj63vi1i67jgjldl0"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)

From f1be3735db479157f3c83922a4e60608ebd7165a Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 12 Oct 2018 23:19:42 -0400
Subject: [PATCH 710/909] gnu: khal: Update to 0.9.10.

* gnu/packages/calendar.scm (khal): Update to 0.9.10.
---
 gnu/packages/calendar.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm
index 79cef99826..c2bbf139c1 100644
--- a/gnu/packages/calendar.scm
+++ b/gnu/packages/calendar.scm
@@ -96,13 +96,13 @@ data units.")
 (define-public khal
   (package
     (name "khal")
-    (version "0.9.9")
+    (version "0.9.10")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "khal" version))
              (sha256
               (base32
-               "0dq9aqb9pqjfqrnfg43mhpb7m0szmychxy1ydb3lwzf3500c9rsh"))))
+               "03h0j0d3xyqh98x5v2gv63wv3g91hip3vsaxvybsn5iz331d23h4"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases

From d7814696b884a7c5e4a58f539ece53f4998689a3 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 12 Oct 2018 23:38:01 -0400
Subject: [PATCH 711/909] gnu: python-configargparse: Use pypi-uri.

* gnu/packages/python.scm (python-configargparse,
python2-configargparse)[source]: Use pypi-uri.
---
 gnu/packages/python.scm | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 35262a2c77..29371d0494 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7353,9 +7353,7 @@ config files.")
     (version "0.12.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://pypi.io/packages/source/C/ConfigArgParse/"
-                    "ConfigArgParse-" version ".tar.gz"))
+              (uri (pypi-uri "ConfigArgParse" version))
               (sha256
                (base32
                 "0fgkiqh6r3rbkdq3k8c48m85g52k96686rw3a6jg4lcncrkpvk98"))))

From 40f856fae80ee8a274067fba0837cccb74d9642d Mon Sep 17 00:00:00 2001
From: Brett Gilio <brettg@posteo.net>
Date: Sun, 14 Oct 2018 09:37:34 +0800
Subject: [PATCH 712/909] gnu: csound: Update to 6.11.0.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/audio.scm (csound): Update to 6.11.0.
[home-page]: Change to "https://csound.com/".

Signed-off-by: 宋文武 <iyzsong@member.fsf.org>
---
 gnu/packages/audio.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index d233940f23..6197f549dd 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2018 okapi <okapi@firemail.cc>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Brett Gilio <brettg@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -650,7 +651,7 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
 (define-public csound
   (package
     (name "csound")
-    (version "6.09.1")
+    (version "6.11.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -659,7 +660,7 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0xqpqws4jsv7fyawcjzwaw544qbfh29xq164kdf30a9v1n3yklp4"))))
+                "072pk5h9w0vhw0ncc9dn90haw1yv18v04iwwjn8nsp6930w7dvxd"))))
     (build-system cmake-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
@@ -674,7 +675,7 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
      `(("bison" ,bison)
        ("flex" ,flex)
        ("zlib" ,zlib)))
-    (home-page "http://csound.github.io/")
+    (home-page "https://csound.com/")
     (synopsis "Sound and music computing system")
     (description
      "Csound is a user-programmable and user-extensible sound processing

From 89f9df6cfd75d5180bd135c2b14fbfdc0eb6171b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Tue, 25 Sep 2018 07:45:18 +0300
Subject: [PATCH 713/909] gnu: icecat: Build with rust-1.24.

* gnu/packages/gnuzilla.scm (icecat)[native-inputs]: Use the oldest
compatable rust over newer releases when building icecat.
---
 gnu/packages/gnuzilla.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index d2110f3290..39281b59e5 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
@@ -620,8 +620,9 @@ security standards.")
        ("zip" ,zip)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("rust" ,rust)
-       ("cargo" ,rust "cargo")
+      ;; Icecat 60 checkes for rust>=1.24
+     `(("rust" ,rust-1.24)
+       ("cargo" ,rust-1.24 "cargo")
        ("perl" ,perl)
        ("python" ,python-2) ; Python 3 not supported
        ("python2-pysqlite" ,python2-pysqlite)

From c2397a869549b6786b801ab816acdba68555494a Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 14 Oct 2018 11:04:13 +0300
Subject: [PATCH 714/909] gnu: gdk-pixbuf: Increase test timeout.

* gnu/packages/gtk.scm (gdk-pixbuf)[arguments]: Increase test timeout.
---
 gnu/packages/gtk.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index ccedec6398..cec10504c5 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -469,7 +469,11 @@ highlighting and other features typical of a source code editor.")
              ;; ERROR:pixbuf-jpeg.c:74:test_type9_rotation_exif_tag:
              ;; assertion failed (error == NULL): Data differ
              ;; (gdk-pixbuf-error-quark, 0)
-             ((".*'pixbuf-jpeg'.*") ""))
+             ((".*'pixbuf-jpeg'.*") "")
+             ;; Extend the timeout of the test suite.
+             ;; TODO: Check upstreaming effort:
+             ;; https://gitlab.gnome.org/GNOME/gdk-pixbuf/merge_requests/21
+             (("300") "1800"))
            #t))
         (add-before 'configure 'aid-install-script
           (lambda* (#:key outputs #:allow-other-keys)

From e0caff9ed0c2238eafba63a65f01d96eeaf02fab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 14 Oct 2018 21:25:46 +0200
Subject: [PATCH 715/909] describe: Canonicalize the profile.

Fixes a regression introduced in
795d430d90e41eb172315bfccf79c9f13fc0ebfa whereby 'guix describe' would
no longer display the generation number of ~/.config/guix/current.

* guix/scripts/describe.scm (guix-describe): Call 'canonicalize-profile'.
---
 guix/scripts/describe.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/scripts/describe.scm b/guix/scripts/describe.scm
index c1a20fe26c..e59502076c 100644
--- a/guix/scripts/describe.scm
+++ b/guix/scripts/describe.scm
@@ -158,4 +158,4 @@ in the format specified by FMT."
         (#f
          (display-checkout-info format))
         (profile
-         (display-profile-info profile format))))))
+         (display-profile-info (canonicalize-profile profile) format))))))

From 2510bd87562bfee9d82348f1c08dd78ccea12dd1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 14 Oct 2018 23:19:59 +0200
Subject: [PATCH 716/909] guix-install.sh: Recognize armhf-linux.

* etc/guix-install.sh (chk_sys_arch): Add "armv7l" case.
---
 etc/guix-install.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/etc/guix-install.sh b/etc/guix-install.sh
index d9f1955098..ca6874ba0f 100755
--- a/etc/guix-install.sh
+++ b/etc/guix-install.sh
@@ -160,6 +160,9 @@ chk_sys_arch()
         aarch64)
             local arch=aarch64
             ;;
+	armv7l)
+	    local arch=armhf
+	    ;;
         *)
             _err "${ERR}Unsupported CPU type: ${arch}"
             exit 1

From 38a2f5eafb43b6407f8d9755da31dcb50ce64167 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Sun, 14 Oct 2018 23:46:42 +0200
Subject: [PATCH 717/909] status: Avoid "sucessfully built" messages when in
 quiet mode.

* guix/status.scm (print-build-event): Print "successfully built"
messages only when PRINT-LOG? is true, like we do for
'substituter-started' events.
---
 guix/status.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/guix/status.scm b/guix/status.scm
index 13537c70cd..d8d761dc23 100644
--- a/guix/status.scm
+++ b/guix/status.scm
@@ -319,8 +319,9 @@ addition to build events."
      (format port (info (G_ "building ~a...")) drv)
      (newline port))
     (('build-succeeded drv . _)
-     (format port (success (G_ "successfully built ~a")) drv)
-     (newline port)
+     (when (or print-log? (not (extended-build-trace-supported?)))
+       (format port (success (G_ "successfully built ~a")) drv)
+       (newline port))
      (match (build-status-building status)
        (() #t)
        (ongoing                                   ;when max-jobs > 1

From 2dd1bfcb5800aad8f360c113cbd769019b5c9d84 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 14 Oct 2018 19:07:35 -0400
Subject: [PATCH 718/909] gnu: linux-libre@4.4: Update to 4.4.161.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.161.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 8983ed35e4..08d1a813ca 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -452,8 +452,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.160"
-                    "1337p94j1hyc2gaw51wvlv622wwj2af1y8rafyfgp1403cs7ghp4"
+  (make-linux-libre "4.4.161"
+                    "1q6bsndpjgw72mybhl5l8vrxs4mimg6821bjgi1pjkxbc7nd921b"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From f266e82ad21eb7be963e7d70beaa2f503cfa4e78 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 14 Oct 2018 19:09:24 -0400
Subject: [PATCH 719/909] gnu: linux-libre@4.9: Update to 4.9.133.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.133.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 08d1a813ca..c1bd01055e 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.132"
-                    "1s4zsv04bdafqqn8i6ab3lxjbh45v20dbm31mb52hfyzlfp4sjp5"
+  (make-linux-libre "4.9.133"
+                    "1vr94czdv5alzsgm2k1r6wqm01r2zafrayjn10l6kdr4g7aga488"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From b0fe6b5785472895259c6d60f06024042450679b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 14 Oct 2018 19:13:56 -0400
Subject: [PATCH 720/909] gnu: linux-libre@4.14: Update to 4.14.76.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.76.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index c1bd01055e..812da7ca3c 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.75")
-(define %linux-libre-4.14-hash "0ljcjsc6lxq4q5dxy9kgnngasyqmv6rhl9yyqxrfzm41qbqfn64l")
+(define %linux-libre-4.14-version "4.14.76")
+(define %linux-libre-4.14-hash "1y5zqf84ngb6f5f85xpd4bdy6mlxr52x19bx3mdrp82awc9fvr7q")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From 614f49c49aa751718978a3b9da8719609ec36922 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 14 Oct 2018 19:27:46 -0400
Subject: [PATCH 721/909] gnu: linux-libre: Update to 4.18.14.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.14.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 812da7ca3c..7aaa7fb644 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.13")
-(define %linux-libre-hash "0jqlmzml67dp5708d4giga48vv4npgs3mbnzdrigaxgca5c69qck")
+(define %linux-libre-version "4.18.14")
+(define %linux-libre-hash "1gwwx8l283w8v1zylw2haqahvjns5dzqxx9li2586nnl8cfmfnwc")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch

From 0731fc1ce7f397724708f4956e6bdeb9c01c6762 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Wed, 29 Aug 2018 00:05:07 -0400
Subject: [PATCH 722/909] gnu: python-mimeparse: Update to 1.6.0.

* gnu/packages/python.scm (python-mimeparse): Update to 1.6.0.
[phases]: Enable tests with a custom check phase.
---
 gnu/packages/python.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 29371d0494..8261fefd93 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1699,7 +1699,7 @@ software.")
 (define-public python-mimeparse
   (package
     (name "python-mimeparse")
-    (version "0.1.4")
+    (version "1.6.0")
     (source
      (origin
        (method url-fetch)
@@ -1708,10 +1708,14 @@ software.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1hyxg09kaj02ri0rmwjqi86wk4nd1akvv7n0dx77azz76wga4s9w"))))
+         "0y2g6cl660bpz11srgqyvvm8gmywpgyx8g0xfvbiyr0af0yv1r3n"))))
     (build-system python-build-system)
     (arguments
-     '(#:tests? #f)) ; no setup.py test command
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke "./mimeparse_test.py"))))))
     (home-page
      "https://github.com/dbtsai/python-mimeparse")
     (synopsis "Python library for parsing MIME types")

From bb840999c8592b0077c78170e135b59bc79638ed Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Wed, 29 Aug 2018 00:06:28 -0400
Subject: [PATCH 723/909] gnu: Add python-falcon.

* gnu/packages/python-web.scm (python-falcon): New variable.
---
 gnu/packages/python-web.scm | 54 +++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2a7487202a..77fb99dc56 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -26,6 +26,7 @@
 ;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
 ;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -127,6 +128,59 @@ asynchronous DNS resolutions with a synchronous looking interface by
 using @url{https://github.com/saghul/pycares,pycares}.")
     (license license:expat)))
 
+(define-public python-falcon
+  (package
+    (name "python-falcon")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "falcon" version))
+       (sha256
+        (base32
+         "1i0vmqsk24z4biirqhpvas9h28wy7nmpy3jvnb6rz2imq04zd09r"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (invoke "pytest"))))))
+    (propagated-inputs
+     `(("python-mimeparse" ,python-mimeparse)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("python-cython" ,python-cython) ;for faster binaries
+       ("python-pytest" ,python-pytest)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-requests" ,python-requests)
+       ("python-testtools" ,python-testtools)
+       ("python-jsonschema" ,python-jsonschema)
+       ("python-msgpack" ,python-msgpack)))
+    (home-page "https://falconframework.org")
+    (synopsis
+     "Web framework for building APIs and application backends")
+    (description
+     "Falcon is a web API framework for building microservices, application
+backends and higher-level frameworks.  Among its features are:
+@itemize
+@item Optimized and extensible code base
+@item Routing via URI templates and REST-inspired resource
+classes
+@item Access to headers and bodies through request and response
+classes
+@item Request processing via middleware components and hooks
+@item Idiomatic HTTP error responses
+@item Straightforward exception handling
+@item Unit testing support through WSGI helpers and mocks
+@item Compatible with both CPython and PyPy
+@item Cython support for better performance when used with CPython
+@end itemize")
+    (license license:asl2.0)))
+
+(define-public python2-falcon
+  (package-with-python2 python-falcon))
+
 (define-public python-furl
   (package
     (name "python-furl")

From 66a9f08bb9c9ba2d7cd4ee3c2d48ea9a8e41c2c4 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Wed, 29 Aug 2018 00:33:17 -0400
Subject: [PATCH 724/909] gnu: Add python-falcon-cors.

* gnu/packages/python-web.scm (python-falcon-cors): New variable.
---
 gnu/packages/python-web.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 77fb99dc56..f8052458a1 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -181,6 +181,32 @@ classes
 (define-public python2-falcon
   (package-with-python2 python-falcon))
 
+(define-public python-falcon-cors
+  (package
+    (name "python-falcon-cors")
+    (version "1.1.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "falcon-cors" version))
+       (sha256
+        (base32
+         "12pym7hwsbd8b0c1azn95nas8gm3f1qpr6lpyx0958xm65ffr20p"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-falcon" ,python-falcon)))
+    (home-page
+     "https://github.com/lwcolton/falcon-cors")
+    (synopsis "Falcon @dfn{cross-origin resource sharing} (CORS) library")
+    (description "This middleware provides @dfn{cross-origin resource
+sharing} (CORS) support for Falcon.  It allows applying a specially crafted
+CORS object to the incoming requests, enabling the ability to serve resources
+over a different origin than that of the web application.")
+    (license license:asl2.0)))
+
+(define-public python2-falcon-cors
+  (package-with-python2 python-falcon-cors))
+
 (define-public python-furl
   (package
     (name "python-furl")

From 3a6e1fe8c8dc7bb556f81568fc878310a15e03e3 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 14 Oct 2018 23:53:19 +0200
Subject: [PATCH 725/909] gnu: perl-xml-feed: Update to 0.55.

* gnu/packages/xml.scm (perl-xml-feed): Update to 0.55.
---
 gnu/packages/xml.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index e14524a684..489541b4f5 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -770,14 +770,14 @@ server, collect the answer, and finally decoding the XML to Perl.")
 (define-public perl-xml-feed
   (package
     (name "perl-xml-feed")
-    (version "0.54")
+    (version "0.55")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://cpan/authors/id/D/DA/DAVECROSS/"
                                   "XML-Feed-" version ".tar.gz"))
               (sha256
                (base32
-                "0ydyi7wdhv8325h7j27vrlwiqxll56sn8zy5nbzhpma3nrf61bci"))))
+                "0am345qzy5rxxnzh13l6p18a7drgkzmmlkgrgl4cv3b2j1pwls3i"))))
     (build-system perl-build-system)
     (arguments
      `(#:tests? #f))                    ; tests require internet connection

From 9cac043cc02670fbec6964cc8f858c4b1e43dbfa Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 15 Oct 2018 03:42:42 +0200
Subject: [PATCH 726/909] gnu: restic: Update to 0.9.3.

* gnu/packages/backup.scm (restic): Update to 0.9.3.
[arguments]: Disable 'restic self-update'.
---
 gnu/packages/backup.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 408b64b48d..52afcbc676 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -862,7 +862,7 @@ is like a time machine for your data. ")
 (define-public restic
   (package
     (name "restic")
-    (version "0.9.2")
+    (version "0.9.3")
     ;; TODO Try packaging the bundled / vendored dependencies in the 'vendor/'
     ;; directory.
     (source (origin
@@ -873,7 +873,7 @@ is like a time machine for your data. ")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "15bwkydxcg4xhrnqxvxji8wacrsndb1a6frj98wggfaijqzfx3lg"))))
+                "1l1ddnf61pfsrry97qwhhdzywin2mgnbrkhcc9pabsdfk602anmr"))))
     (build-system go-build-system)
     (arguments
      `(#:import-path "github.com/restic/restic"
@@ -887,6 +887,8 @@ is like a time machine for your data. ")
              (with-directory-excursion (string-append
                                         "src/github.com/restic/restic-"
                                         ,version)
+               ;; Disable 'restic self-update'.  It makes little sense in Guix.
+               (substitute* "build.go" (("selfupdate") ""))
                (invoke "go" "run" "build.go"))))
 
          (replace 'check

From 4702d45280425f69f70cfb891ccacaf94cbd2790 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Sun, 14 Oct 2018 22:02:50 +0200
Subject: [PATCH 727/909] gnu: opensm: Update to 3.3.21.

* gnu/packages/fabric-management.scm (opensm): Update to 3.3.21.
[source]: Update tarball URI.
[native-inputs]: Add autoconf, automake, and libtool.
[arguments]: Rename 'doc' phase to 'install-doc'.
Omit AUTHORS and ChangeLog files. They are more than a decade old.
---
 gnu/packages/fabric-management.scm | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/fabric-management.scm b/gnu/packages/fabric-management.scm
index 76ef9eef2e..ff6ad898b1 100644
--- a/gnu/packages/fabric-management.scm
+++ b/gnu/packages/fabric-management.scm
@@ -1,5 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2017 Dave Love <fx@gnu.org>
+;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,33 +42,38 @@
 (define-public opensm
   (package
     (name "opensm")
-    (version "3.3.20")
+    (version "3.3.21")
     (source
      (origin
        (method url-fetch)
        (uri
-        (string-append "https://www.openfabrics.org/downloads/management/opensm-"
-                       version ".tar.gz"))
-       (sha256 (base32 "162sg1w7kgy8ayl8a4dcbrfacmnfy2lr9a2yjyq0k65rmd378zg1"))))
+        (string-append "https://github.com/linux-rdma/opensm/releases/download/"
+                       version "/opensm-" version ".tar.gz"))
+       (sha256
+        (base32 "0j4vp118w1l47vs4had46ynybklyacxjlya0r15jg0y01l4j9l2h"))))
     (build-system gnu-build-system)
     (native-inputs
-     `(("flex" ,flex)
-       ("bison" ,bison)))
+     `(("bison" ,bison)
+       ("flex" ,flex)
+
+       ;; The 3.3.21 'release' tarball isn't properly bootstrapped.
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
     (inputs
      `(("rdma-core" ,rdma-core)))
     (arguments
      `(#:configure-flags '("--disable-static")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'install 'doc
+         (add-after 'install 'install-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((base (assoc-ref outputs "out"))
                     (doc  (string-append base "/share/doc/"
                                          ,name "-" ,version)))
                (for-each (lambda (file)
                            (install-file file doc))
-                         (append (list "AUTHORS" "COPYING" "ChangeLog")
-                                 (find-files "doc")))
+                         (find-files "doc"))
                #t))))))
     (home-page "https://www.openfabrics.org/")
     (synopsis "OpenIB InfiniBand Subnet Manager and management utilities")

From dfe05297f3922a0403a9d788bc4d87502e148d87 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 15 Oct 2018 06:04:49 +0200
Subject: [PATCH 728/909] gnu: x265: Update to 2.9.

* gnu/packages/video.scm (x265): Update to 2.9.
[source]: Remove x265-fix-ppc64le-build.patch.
* gnu/packages/patches/x265-fix-ppc64le-build.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                  |  1 -
 .../patches/x265-fix-ppc64le-build.patch      | 25 -------------------
 gnu/packages/video.scm                        |  7 +++---
 3 files changed, 3 insertions(+), 30 deletions(-)
 delete mode 100644 gnu/packages/patches/x265-fix-ppc64le-build.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index af3773c893..4c0485c04f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1228,7 +1228,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/wpa-supplicant-krack-followups.patch	\
   %D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch	\
   %D%/packages/patches/x265-arm-asm-primitives.patch		\
-  %D%/packages/patches/x265-fix-ppc64le-build.patch		\
   %D%/packages/patches/xapian-revert-5489fb2f8.patch		\
   %D%/packages/patches/xboing-CVE-2004-0149.patch		\
   %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
diff --git a/gnu/packages/patches/x265-fix-ppc64le-build.patch b/gnu/packages/patches/x265-fix-ppc64le-build.patch
deleted file mode 100644
index f71d2436ab..0000000000
--- a/gnu/packages/patches/x265-fix-ppc64le-build.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-https://sources.debian.org/data/main/x/x265/2.8-3/debian/patches/0003-Fix-build-error-on-on-ppc64le.patch
-
-This patch also fixes building on armhf-linux and aarch64-linux
-
-From: Jayashree <jayashree.c@multicorewareinc.com>
-Date: Fri, 25 May 2018 10:26:05 +0530
-Subject: Fix build error on on ppc64le
-
----
- source/common/param.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/source/common/param.cpp b/source/common/param.cpp
-index 31bcbc7..4a6d0c8 100644
---- a/source/common/param.cpp
-+++ b/source/common/param.cpp
-@@ -633,7 +633,7 @@ int x265_param_parse(x265_param* p, const char* name, const char* value)
-         if (bValueWasNull)
-             p->cpuid = atobool(value);
-         else
--            p->cpuid = parseCpuName(value, bError);
-+            p->cpuid = parseCpuName(value, bError, false);
- #endif
-     }
-     OPT("fps")
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 3e191ef6da..e281bf8fff 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -392,7 +392,7 @@ and creating Matroska files from other media files (@code{mkvmerge}).")
 (define-public x265
   (package
     (name "x265")
-    (version "2.8")
+    (version "2.9")
     (source
       (origin
         (method url-fetch)
@@ -400,9 +400,8 @@ and creating Matroska files from other media files (@code{mkvmerge}).")
                             "x265_" version ".tar.gz"))
         (sha256
          (base32
-          "0qx8mavwdzdpkkby7n29i9av7zsnklavacwfz537mf62q2pzjnbf"))
-        (patches (search-patches "x265-fix-ppc64le-build.patch"
-                                 "x265-arm-asm-primitives.patch"))
+          "090hp4216isis8q5gb7bwzia8rfyzni54z21jnwm97x3hiy6ibpb"))
+        (patches (search-patches "x265-arm-asm-primitives.patch"))
         (modules '((guix build utils)))
         (snippet '(begin
                     (delete-file-recursively "source/compat/getopt")

From 4a147986a0839103a9c5bf1b5b74047c7d398349 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 11 Oct 2018 00:19:13 +0200
Subject: [PATCH 729/909] gnu: haveged: Teach the controversy.

* gnu/packages/linux.scm (haveged)[description]: Suggest adding
additional entropy sources.
---
 gnu/packages/linux.scm | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 7aaa7fb644..79a1b0b46a 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3760,7 +3760,11 @@ systems with high needs or limited user interaction, such as headless servers.
 indirect effects of hardware events on hidden processor state using the HArdware
 Volatile Entropy Gathering and Expansion (@dfn{HAVEGE}) algorithm.  It tunes
 itself to its environment and provides the same built-in test suite for the
-output stream as used on certified hardware security devices.")
+output stream as used on certified hardware security devices.
+
+The quality of the randomness produced by this algorithm has not been proven.
+It is recommended to run it together with another entropy source like rngd, and
+not as a replacement for it.")
     (license (list (license:non-copyleft "file://nist/mconf.h")
                    (license:non-copyleft "file://nist/packtest.c")
                    license:public-domain        ; nist/dfft.c

From e02013b7de5c9f30d6b451dcc1c00769992dc3a8 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 10 Oct 2018 23:58:03 +0200
Subject: [PATCH 730/909] gnu: hexchat: Use HTTPS home page.

* gnu/packages/messaging.scm (hexchat)[home-page]: Use HTTPS.
---
 gnu/packages/messaging.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index d2b61b9ec5..d50732dfc4 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -295,7 +295,7 @@ window shows the list of currently connected networks and their channels, the
 current conversation and the list of users.  It uses colors to differentiate
 between users and to highlight messages.  It checks spelling using available
 dictionaries.  HexChat can be extended with multiple addons.")
-    (home-page "http://hexchat.net/")
+    (home-page "https://hexchat.net/")
     (license license:gpl2+)))
 
 (define-public ngircd

From 2d5fa80e83190b6bdbeb8a45e68a885b283e2490 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Thu, 4 Oct 2018 22:32:14 +0200
Subject: [PATCH 731/909] gnu: audacity: Update home page.

* gnu/packages/audio.scm (audacity)[home-page]: Update.
---
 gnu/packages/audio.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 6197f549dd..69b5d01d6f 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -418,7 +418,7 @@ engineers, musicians, soundtrack editors and composers.")
        ;; and fails with various errors.  See
        ;; <http://sourceforge.net/p/audacity/mailman/message/33524292/>.
        #:tests? #f))
-    (home-page "http://audacity.sourceforge.net/")
+    (home-page "https://www.audacityteam.org/")
     (synopsis "Software for recording and editing sounds")
     (description
      "Audacity is a multi-track audio editor designed for recording, playing

From f1a9c6e581e3b90713d11801dbab9a611f6fe63a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 15 Oct 2018 10:31:24 +0200
Subject: [PATCH 732/909] gnu: lsof: Fix builds on glibc 2.28.

* gnu/packages/lsof.scm (lsof)[arguments]: In 'disable-failing-tests',
add 'substitute*' use for "tests/LTlib.c".
---
 gnu/packages/lsof.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/lsof.scm b/gnu/packages/lsof.scm
index 8b3ebe2945..311e244608 100644
--- a/gnu/packages/lsof.scm
+++ b/gnu/packages/lsof.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -77,6 +78,12 @@
             #t))
         (add-before 'check 'disable-failing-tests
           (lambda _
+            ;; In libc 2.28, the 'major' and 'minor' macros are provided by
+            ;; <sys/sysmacros.h> only so include it.
+            (substitute* "tests/LTlib.c"
+              (("#ifndef lint")
+               "#include <sys/sysmacros.h>\n\n#ifndef lint"))
+
             (substitute* "tests/Makefile"
               ;; Fails with ‘ERROR!!! client gethostbyaddr() failure’.
               (("(STDTST=.*) LTsock" _ prefix) prefix)

From 68b0226b2abc7aa9bf029800699338762e2a2e12 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 15 Oct 2018 10:39:45 +0200
Subject: [PATCH 733/909] gnu: gcal: Apply Gnulib fixes.

* gnu/packages/gcal.scm (gcal)[modules, snippet]: New fields.
---
 gnu/packages/gcal.scm | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/gcal.scm b/gnu/packages/gcal.scm
index 425fa1f9a8..32d3849faa 100644
--- a/gnu/packages/gcal.scm
+++ b/gnu/packages/gcal.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -32,7 +32,23 @@
                                  version ".tar.xz"))
              (sha256
               (base32
-               "1av11zkfirbixn05hyq4xvilin0ncddfjqzc4zd9pviyp506rdci"))))
+               "1av11zkfirbixn05hyq4xvilin0ncddfjqzc4zd9pviyp506rdci"))
+             (modules '((guix build utils)))
+             (snippet
+              '(begin
+                 ;; Adjust the bundled gnulib to work with glibc 2.28.  See e.g.
+                 ;; "m4-gnulib-libio.patch".  This is a phase rather than patch
+                 ;; or snippet to work around <https://bugs.gnu.org/32347>.
+                 (substitute* (find-files "lib" "\\.c$")
+                   (("#if defined _IO_ftrylockfile")
+                    "#if defined _IO_EOF_SEEN"))
+                 (substitute* "lib/stdio-impl.h"
+                   (("^/\\* BSD stdio derived implementations")
+                    (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
+                                   "# define _IO_IN_BACKUP 0x100\n"
+                                   "#endif\n\n"
+                                   "/* BSD stdio derived implementations")))
+                 #t))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/gcal/")
     (synopsis "Calculating and printing a wide variety of calendars")

From b7028a16e6fe4f9634cd7d550b3a79450fc4e0db Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 15 Oct 2018 11:33:51 +0300
Subject: [PATCH 734/909] gnu: x265: Fix building on armhf-linux and
 aarch64-linux.

* gnu/packages/video.scm (x265)[source]: Update list of patches.
[arguments]: Change configure flag to ensure PIC for all architectures.
* gnu/packages/patches/x265-arm-asm-primitives.patch: Remove file.
* gnu/packages/patches/x265-detect512-all-arches.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update patch registry.
---
 gnu/local.mk                                  |   2 +-
 .../patches/x265-arm-asm-primitives.patch     | 360 ------------------
 .../patches/x265-detect512-all-arches.patch   |  37 ++
 gnu/packages/video.scm                        |  10 +-
 4 files changed, 41 insertions(+), 368 deletions(-)
 delete mode 100644 gnu/packages/patches/x265-arm-asm-primitives.patch
 create mode 100644 gnu/packages/patches/x265-detect512-all-arches.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 4c0485c04f..1fa2eaba31 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1227,7 +1227,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch	\
   %D%/packages/patches/wpa-supplicant-krack-followups.patch	\
   %D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch	\
-  %D%/packages/patches/x265-arm-asm-primitives.patch		\
+  %D%/packages/patches/x265-detect512-all-arches.patch		\
   %D%/packages/patches/xapian-revert-5489fb2f8.patch		\
   %D%/packages/patches/xboing-CVE-2004-0149.patch		\
   %D%/packages/patches/xf86-video-ark-remove-mibstore.patch	\
diff --git a/gnu/packages/patches/x265-arm-asm-primitives.patch b/gnu/packages/patches/x265-arm-asm-primitives.patch
deleted file mode 100644
index f49aafe577..0000000000
--- a/gnu/packages/patches/x265-arm-asm-primitives.patch
+++ /dev/null
@@ -1,360 +0,0 @@
-From <https://git.busybox.net/buildroot/tree/package/x265/0003-arm-asm-primitives.patch?id=57d4a27eaf1a9e59d767c321e7b7500c5060a2ac>.
-This fixes build errors like:
-
-  cd /tmp/guix-build-x265-2.8.drv-0/x265_2.8/build/encoder && /gnu/store/cd5q2pni1d95fs3cdabbclyh9hqhw2nq-gcc-5.5.0/bin/c++  -DEXPORT_C_API=1 -DHAVE_ARMV6=1 -DHAVE_INT_TYPES_H=1 -DHAVE_NEON -DHIGH_BIT_DEPTH=0 -DX265_ARCH_ARM=1 -DX265_DEPTH=8 -DX265_NS=x265 -D__STDC_LIMIT_MACROS=1 -I/tmp/guix-build-x265-2.8.drv-0/x265_2.8/source/. -I/tmp/guix-build-x265-2.8.drv-0/x265_2.8/source/common -I/tmp/guix-build-x265-2.8.drv-0/x265_2.8/source/encoder -I/tmp/guix-build-x265-2.8.drv-0/x265_2.8/build  -O2 -g -DNDEBUG   -Wall -Wextra -Wshadow -std=gnu++98 -fPIC -mcpu=native -mfloat-abi=hard -mfpu=neon -marm -fPIC -Wno-array-bounds -ffast-math -fno-exceptions -Wno-uninitialized -o CMakeFiles/encoder.dir/search.cpp.o -c /tmp/guix-build-x265-2.8.drv-0/x265_2.8/source/encoder/search.cpp
-  /tmp/guix-build-x265-2.8.drv-0/x265_2.8/source/common/arm/asm-primitives.cpp:437:38: error: incompatible types in assignment of ?void(const pixel*, intptr_t, int16_t*, intptr_t) {aka void(const unsigned char*, int, short int*, int)}? to ?void (* [2])(const pixel*, intptr_t, int16_t*, intptr_t) {aka void (* [2])(const unsigned char*, int, short int*, int)}?
-	   p.pu[LUMA_64x48].convert_p2s = PFX(filterPixelToShort_64x48_neon);
-					^
-
-Downloaded from upstream bug report:
-https://bitbucket.org/multicoreware/x265/issues/406
-
-Signed-off-by: Bernd Kuhls <bernd.kuhls@t-online.de>
-
---- ./source/common/arm/asm-primitives.cpp.orig	2018-05-21 02:33:10.000000000 -0600
-+++ ./source/common/arm/asm-primitives.cpp	2018-05-28 20:38:37.302378303 -0600
-@@ -48,77 +48,77 @@ void setupAssemblyPrimitives(EncoderPrim
-         p.ssim_4x4x2_core = PFX(ssim_4x4x2_core_neon);
- 
-         // addAvg
--         p.pu[LUMA_4x4].addAvg   = PFX(addAvg_4x4_neon);
--         p.pu[LUMA_4x8].addAvg   = PFX(addAvg_4x8_neon);
--         p.pu[LUMA_4x16].addAvg  = PFX(addAvg_4x16_neon);
--         p.pu[LUMA_8x4].addAvg   = PFX(addAvg_8x4_neon);
--         p.pu[LUMA_8x8].addAvg   = PFX(addAvg_8x8_neon);
--         p.pu[LUMA_8x16].addAvg  = PFX(addAvg_8x16_neon);
--         p.pu[LUMA_8x32].addAvg  = PFX(addAvg_8x32_neon);
--         p.pu[LUMA_12x16].addAvg = PFX(addAvg_12x16_neon);
--         p.pu[LUMA_16x4].addAvg  = PFX(addAvg_16x4_neon);
--         p.pu[LUMA_16x8].addAvg  = PFX(addAvg_16x8_neon);
--         p.pu[LUMA_16x12].addAvg = PFX(addAvg_16x12_neon);
--         p.pu[LUMA_16x16].addAvg = PFX(addAvg_16x16_neon);
--         p.pu[LUMA_16x32].addAvg = PFX(addAvg_16x32_neon);
--         p.pu[LUMA_16x64].addAvg = PFX(addAvg_16x64_neon);
--         p.pu[LUMA_24x32].addAvg = PFX(addAvg_24x32_neon);
--         p.pu[LUMA_32x8].addAvg  = PFX(addAvg_32x8_neon);
--         p.pu[LUMA_32x16].addAvg = PFX(addAvg_32x16_neon);
--         p.pu[LUMA_32x24].addAvg = PFX(addAvg_32x24_neon);
--         p.pu[LUMA_32x32].addAvg = PFX(addAvg_32x32_neon);
--         p.pu[LUMA_32x64].addAvg = PFX(addAvg_32x64_neon);
--         p.pu[LUMA_48x64].addAvg = PFX(addAvg_48x64_neon);
--         p.pu[LUMA_64x16].addAvg = PFX(addAvg_64x16_neon);
--         p.pu[LUMA_64x32].addAvg = PFX(addAvg_64x32_neon);
--         p.pu[LUMA_64x48].addAvg = PFX(addAvg_64x48_neon);
--         p.pu[LUMA_64x64].addAvg = PFX(addAvg_64x64_neon);
-+         p.pu[LUMA_4x4].addAvg[ALIGNED]   = PFX(addAvg_4x4_neon);
-+         p.pu[LUMA_4x8].addAvg[ALIGNED]   = PFX(addAvg_4x8_neon);
-+         p.pu[LUMA_4x16].addAvg[ALIGNED]  = PFX(addAvg_4x16_neon);
-+         p.pu[LUMA_8x4].addAvg[ALIGNED]   = PFX(addAvg_8x4_neon);
-+         p.pu[LUMA_8x8].addAvg[ALIGNED]   = PFX(addAvg_8x8_neon);
-+         p.pu[LUMA_8x16].addAvg[ALIGNED]  = PFX(addAvg_8x16_neon);
-+         p.pu[LUMA_8x32].addAvg[ALIGNED]  = PFX(addAvg_8x32_neon);
-+         p.pu[LUMA_12x16].addAvg[ALIGNED] = PFX(addAvg_12x16_neon);
-+         p.pu[LUMA_16x4].addAvg[ALIGNED]  = PFX(addAvg_16x4_neon);
-+         p.pu[LUMA_16x8].addAvg[ALIGNED]  = PFX(addAvg_16x8_neon);
-+         p.pu[LUMA_16x12].addAvg[ALIGNED] = PFX(addAvg_16x12_neon);
-+         p.pu[LUMA_16x16].addAvg[ALIGNED] = PFX(addAvg_16x16_neon);
-+         p.pu[LUMA_16x32].addAvg[ALIGNED] = PFX(addAvg_16x32_neon);
-+         p.pu[LUMA_16x64].addAvg[ALIGNED] = PFX(addAvg_16x64_neon);
-+         p.pu[LUMA_24x32].addAvg[ALIGNED] = PFX(addAvg_24x32_neon);
-+         p.pu[LUMA_32x8].addAvg[ALIGNED]  = PFX(addAvg_32x8_neon);
-+         p.pu[LUMA_32x16].addAvg[ALIGNED] = PFX(addAvg_32x16_neon);
-+         p.pu[LUMA_32x24].addAvg[ALIGNED] = PFX(addAvg_32x24_neon);
-+         p.pu[LUMA_32x32].addAvg[ALIGNED] = PFX(addAvg_32x32_neon);
-+         p.pu[LUMA_32x64].addAvg[ALIGNED] = PFX(addAvg_32x64_neon);
-+         p.pu[LUMA_48x64].addAvg[ALIGNED] = PFX(addAvg_48x64_neon);
-+         p.pu[LUMA_64x16].addAvg[ALIGNED] = PFX(addAvg_64x16_neon);
-+         p.pu[LUMA_64x32].addAvg[ALIGNED] = PFX(addAvg_64x32_neon);
-+         p.pu[LUMA_64x48].addAvg[ALIGNED] = PFX(addAvg_64x48_neon);
-+         p.pu[LUMA_64x64].addAvg[ALIGNED] = PFX(addAvg_64x64_neon);
- 
-         // chroma addAvg
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x2].addAvg   = PFX(addAvg_4x2_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x4].addAvg   = PFX(addAvg_4x4_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x8].addAvg   = PFX(addAvg_4x8_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x16].addAvg  = PFX(addAvg_4x16_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_6x8].addAvg   = PFX(addAvg_6x8_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x2].addAvg   = PFX(addAvg_8x2_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x4].addAvg   = PFX(addAvg_8x4_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x6].addAvg   = PFX(addAvg_8x6_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x8].addAvg   = PFX(addAvg_8x8_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x16].addAvg  = PFX(addAvg_8x16_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x32].addAvg  = PFX(addAvg_8x32_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_12x16].addAvg = PFX(addAvg_12x16_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x4].addAvg  = PFX(addAvg_16x4_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x8].addAvg  = PFX(addAvg_16x8_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x12].addAvg = PFX(addAvg_16x12_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x16].addAvg = PFX(addAvg_16x16_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x32].addAvg = PFX(addAvg_16x32_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_24x32].addAvg = PFX(addAvg_24x32_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x8].addAvg  = PFX(addAvg_32x8_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x16].addAvg = PFX(addAvg_32x16_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x24].addAvg = PFX(addAvg_32x24_neon);
--        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x32].addAvg = PFX(addAvg_32x32_neon);
--
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_4x8].addAvg   = PFX(addAvg_4x8_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_4x16].addAvg  = PFX(addAvg_4x16_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_4x32].addAvg  = PFX(addAvg_4x32_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_6x16].addAvg  = PFX(addAvg_6x16_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x4].addAvg   = PFX(addAvg_8x4_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x8].addAvg   = PFX(addAvg_8x8_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x12].addAvg  = PFX(addAvg_8x12_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x16].addAvg  = PFX(addAvg_8x16_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x32].addAvg  = PFX(addAvg_8x32_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x64].addAvg  = PFX(addAvg_8x64_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_12x32].addAvg = PFX(addAvg_12x32_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x8].addAvg  = PFX(addAvg_16x8_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x16].addAvg = PFX(addAvg_16x16_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x24].addAvg = PFX(addAvg_16x24_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x32].addAvg = PFX(addAvg_16x32_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x64].addAvg = PFX(addAvg_16x64_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_24x64].addAvg = PFX(addAvg_24x64_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x16].addAvg = PFX(addAvg_32x16_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x32].addAvg = PFX(addAvg_32x32_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x48].addAvg = PFX(addAvg_32x48_neon);
--        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x64].addAvg = PFX(addAvg_32x64_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x2].addAvg[ALIGNED]   = PFX(addAvg_4x2_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x4].addAvg[ALIGNED]   = PFX(addAvg_4x4_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x8].addAvg[ALIGNED]   = PFX(addAvg_4x8_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_4x16].addAvg[ALIGNED]  = PFX(addAvg_4x16_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_6x8].addAvg[ALIGNED]   = PFX(addAvg_6x8_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x2].addAvg[ALIGNED]   = PFX(addAvg_8x2_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x4].addAvg[ALIGNED]   = PFX(addAvg_8x4_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x6].addAvg[ALIGNED]   = PFX(addAvg_8x6_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x8].addAvg[ALIGNED]   = PFX(addAvg_8x8_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x16].addAvg[ALIGNED]  = PFX(addAvg_8x16_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_8x32].addAvg[ALIGNED]  = PFX(addAvg_8x32_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_12x16].addAvg[ALIGNED] = PFX(addAvg_12x16_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x4].addAvg[ALIGNED]  = PFX(addAvg_16x4_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x8].addAvg[ALIGNED]  = PFX(addAvg_16x8_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x12].addAvg[ALIGNED] = PFX(addAvg_16x12_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x16].addAvg[ALIGNED] = PFX(addAvg_16x16_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_16x32].addAvg[ALIGNED] = PFX(addAvg_16x32_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_24x32].addAvg[ALIGNED] = PFX(addAvg_24x32_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x8].addAvg[ALIGNED]  = PFX(addAvg_32x8_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x16].addAvg[ALIGNED] = PFX(addAvg_32x16_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x24].addAvg[ALIGNED] = PFX(addAvg_32x24_neon);
-+        p.chroma[X265_CSP_I420].pu[CHROMA_420_32x32].addAvg[ALIGNED] = PFX(addAvg_32x32_neon);
-+
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_4x8].addAvg[ALIGNED]   = PFX(addAvg_4x8_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_4x16].addAvg[ALIGNED]  = PFX(addAvg_4x16_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_4x32].addAvg[ALIGNED]  = PFX(addAvg_4x32_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_6x16].addAvg[ALIGNED]  = PFX(addAvg_6x16_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x4].addAvg[ALIGNED]   = PFX(addAvg_8x4_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x8].addAvg[ALIGNED]   = PFX(addAvg_8x8_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x12].addAvg[ALIGNED]  = PFX(addAvg_8x12_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x16].addAvg[ALIGNED]  = PFX(addAvg_8x16_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x32].addAvg[ALIGNED]  = PFX(addAvg_8x32_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_8x64].addAvg[ALIGNED]  = PFX(addAvg_8x64_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_12x32].addAvg[ALIGNED] = PFX(addAvg_12x32_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x8].addAvg[ALIGNED]  = PFX(addAvg_16x8_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x16].addAvg[ALIGNED] = PFX(addAvg_16x16_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x24].addAvg[ALIGNED] = PFX(addAvg_16x24_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x32].addAvg[ALIGNED] = PFX(addAvg_16x32_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_16x64].addAvg[ALIGNED] = PFX(addAvg_16x64_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_24x64].addAvg[ALIGNED] = PFX(addAvg_24x64_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x16].addAvg[ALIGNED] = PFX(addAvg_32x16_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x32].addAvg[ALIGNED] = PFX(addAvg_32x32_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x48].addAvg[ALIGNED] = PFX(addAvg_32x48_neon);
-+        p.chroma[X265_CSP_I422].pu[CHROMA_422_32x64].addAvg[ALIGNED] = PFX(addAvg_32x64_neon);
- 
-         // quant
-          p.quant = PFX(quant_neon);
-@@ -402,7 +402,7 @@ void setupAssemblyPrimitives(EncoderPrim
-         p.scale2D_64to32  = PFX(scale2D_64to32_neon);
- 
-         // scale1D_128to64
--        p.scale1D_128to64 = PFX(scale1D_128to64_neon);
-+        p.scale1D_128to64[ALIGNED] = PFX(scale1D_128to64_neon);
- 
-         // copy_count
-         p.cu[BLOCK_4x4].copy_cnt     = PFX(copy_cnt_4_neon);
-@@ -411,37 +411,37 @@ void setupAssemblyPrimitives(EncoderPrim
-         p.cu[BLOCK_32x32].copy_cnt   = PFX(copy_cnt_32_neon);
- 
-         // filterPixelToShort
--        p.pu[LUMA_4x4].convert_p2s   = PFX(filterPixelToShort_4x4_neon);
--        p.pu[LUMA_4x8].convert_p2s   = PFX(filterPixelToShort_4x8_neon);
--        p.pu[LUMA_4x16].convert_p2s  = PFX(filterPixelToShort_4x16_neon);
--        p.pu[LUMA_8x4].convert_p2s   = PFX(filterPixelToShort_8x4_neon);
--        p.pu[LUMA_8x8].convert_p2s   = PFX(filterPixelToShort_8x8_neon);
--        p.pu[LUMA_8x16].convert_p2s  = PFX(filterPixelToShort_8x16_neon);
--        p.pu[LUMA_8x32].convert_p2s  = PFX(filterPixelToShort_8x32_neon);
--        p.pu[LUMA_12x16].convert_p2s = PFX(filterPixelToShort_12x16_neon);
--        p.pu[LUMA_16x4].convert_p2s  = PFX(filterPixelToShort_16x4_neon);
--        p.pu[LUMA_16x8].convert_p2s  = PFX(filterPixelToShort_16x8_neon);
--        p.pu[LUMA_16x12].convert_p2s = PFX(filterPixelToShort_16x12_neon);
--        p.pu[LUMA_16x16].convert_p2s = PFX(filterPixelToShort_16x16_neon);
--        p.pu[LUMA_16x32].convert_p2s = PFX(filterPixelToShort_16x32_neon);
--        p.pu[LUMA_16x64].convert_p2s = PFX(filterPixelToShort_16x64_neon);
--        p.pu[LUMA_24x32].convert_p2s = PFX(filterPixelToShort_24x32_neon);
--        p.pu[LUMA_32x8].convert_p2s  = PFX(filterPixelToShort_32x8_neon);
--        p.pu[LUMA_32x16].convert_p2s = PFX(filterPixelToShort_32x16_neon);
--        p.pu[LUMA_32x24].convert_p2s = PFX(filterPixelToShort_32x24_neon);
--        p.pu[LUMA_32x32].convert_p2s = PFX(filterPixelToShort_32x32_neon);
--        p.pu[LUMA_32x64].convert_p2s = PFX(filterPixelToShort_32x64_neon);
--        p.pu[LUMA_48x64].convert_p2s = PFX(filterPixelToShort_48x64_neon);
--        p.pu[LUMA_64x16].convert_p2s = PFX(filterPixelToShort_64x16_neon);
--        p.pu[LUMA_64x32].convert_p2s = PFX(filterPixelToShort_64x32_neon);
--        p.pu[LUMA_64x48].convert_p2s = PFX(filterPixelToShort_64x48_neon);
--        p.pu[LUMA_64x64].convert_p2s = PFX(filterPixelToShort_64x64_neon);
-+        p.pu[LUMA_4x4].convert_p2s[ALIGNED]   = PFX(filterPixelToShort_4x4_neon);
-+        p.pu[LUMA_4x8].convert_p2s[ALIGNED]   = PFX(filterPixelToShort_4x8_neon);
-+        p.pu[LUMA_4x16].convert_p2s[ALIGNED]  = PFX(filterPixelToShort_4x16_neon);
-+        p.pu[LUMA_8x4].convert_p2s[ALIGNED]   = PFX(filterPixelToShort_8x4_neon);
-+        p.pu[LUMA_8x8].convert_p2s[ALIGNED]   = PFX(filterPixelToShort_8x8_neon);
-+        p.pu[LUMA_8x16].convert_p2s[ALIGNED]  = PFX(filterPixelToShort_8x16_neon);
-+        p.pu[LUMA_8x32].convert_p2s[ALIGNED]  = PFX(filterPixelToShort_8x32_neon);
-+        p.pu[LUMA_12x16].convert_p2s[ALIGNED] = PFX(filterPixelToShort_12x16_neon);
-+        p.pu[LUMA_16x4].convert_p2s[ALIGNED]  = PFX(filterPixelToShort_16x4_neon);
-+        p.pu[LUMA_16x8].convert_p2s[ALIGNED]  = PFX(filterPixelToShort_16x8_neon);
-+        p.pu[LUMA_16x12].convert_p2s[ALIGNED] = PFX(filterPixelToShort_16x12_neon);
-+        p.pu[LUMA_16x16].convert_p2s[ALIGNED] = PFX(filterPixelToShort_16x16_neon);
-+        p.pu[LUMA_16x32].convert_p2s[ALIGNED] = PFX(filterPixelToShort_16x32_neon);
-+        p.pu[LUMA_16x64].convert_p2s[ALIGNED] = PFX(filterPixelToShort_16x64_neon);
-+        p.pu[LUMA_24x32].convert_p2s[ALIGNED] = PFX(filterPixelToShort_24x32_neon);
-+        p.pu[LUMA_32x8].convert_p2s[ALIGNED]  = PFX(filterPixelToShort_32x8_neon);
-+        p.pu[LUMA_32x16].convert_p2s[ALIGNED] = PFX(filterPixelToShort_32x16_neon);
-+        p.pu[LUMA_32x24].convert_p2s[ALIGNED] = PFX(filterPixelToShort_32x24_neon);
-+        p.pu[LUMA_32x32].convert_p2s[ALIGNED] = PFX(filterPixelToShort_32x32_neon);
-+        p.pu[LUMA_32x64].convert_p2s[ALIGNED] = PFX(filterPixelToShort_32x64_neon);
-+        p.pu[LUMA_48x64].convert_p2s[ALIGNED] = PFX(filterPixelToShort_48x64_neon);
-+        p.pu[LUMA_64x16].convert_p2s[ALIGNED] = PFX(filterPixelToShort_64x16_neon);
-+        p.pu[LUMA_64x32].convert_p2s[ALIGNED] = PFX(filterPixelToShort_64x32_neon);
-+        p.pu[LUMA_64x48].convert_p2s[ALIGNED] = PFX(filterPixelToShort_64x48_neon);
-+        p.pu[LUMA_64x64].convert_p2s[ALIGNED] = PFX(filterPixelToShort_64x64_neon);
- 
-         // Block_fill
--        p.cu[BLOCK_4x4].blockfill_s   = PFX(blockfill_s_4x4_neon);
--        p.cu[BLOCK_8x8].blockfill_s   = PFX(blockfill_s_8x8_neon);
--        p.cu[BLOCK_16x16].blockfill_s = PFX(blockfill_s_16x16_neon);
--        p.cu[BLOCK_32x32].blockfill_s = PFX(blockfill_s_32x32_neon);
-+        p.cu[BLOCK_4x4].blockfill_s[ALIGNED]   = PFX(blockfill_s_4x4_neon);
-+        p.cu[BLOCK_8x8].blockfill_s[ALIGNED]   = PFX(blockfill_s_8x8_neon);
-+        p.cu[BLOCK_16x16].blockfill_s[ALIGNED] = PFX(blockfill_s_16x16_neon);
-+        p.cu[BLOCK_32x32].blockfill_s[ALIGNED] = PFX(blockfill_s_32x32_neon);
- 
-         // Blockcopy_ss
-         p.cu[BLOCK_4x4].copy_ss   = PFX(blockcopy_ss_4x4_neon);
-@@ -495,21 +495,21 @@ void setupAssemblyPrimitives(EncoderPrim
-         p.chroma[X265_CSP_I422].cu[BLOCK_422_32x64].copy_sp = PFX(blockcopy_sp_32x64_neon);
- 
-         // pixel_add_ps
--        p.cu[BLOCK_4x4].add_ps   = PFX(pixel_add_ps_4x4_neon);
--        p.cu[BLOCK_8x8].add_ps   = PFX(pixel_add_ps_8x8_neon);
--        p.cu[BLOCK_16x16].add_ps = PFX(pixel_add_ps_16x16_neon);
--        p.cu[BLOCK_32x32].add_ps = PFX(pixel_add_ps_32x32_neon);
--        p.cu[BLOCK_64x64].add_ps = PFX(pixel_add_ps_64x64_neon);
-+        p.cu[BLOCK_4x4].add_ps[ALIGNED]   = PFX(pixel_add_ps_4x4_neon);
-+        p.cu[BLOCK_8x8].add_ps[ALIGNED]   = PFX(pixel_add_ps_8x8_neon);
-+        p.cu[BLOCK_16x16].add_ps[ALIGNED] = PFX(pixel_add_ps_16x16_neon);
-+        p.cu[BLOCK_32x32].add_ps[ALIGNED] = PFX(pixel_add_ps_32x32_neon);
-+        p.cu[BLOCK_64x64].add_ps[ALIGNED] = PFX(pixel_add_ps_64x64_neon);
- 
-         // chroma add_ps
--        p.chroma[X265_CSP_I420].cu[BLOCK_420_4x4].add_ps   = PFX(pixel_add_ps_4x4_neon);
--        p.chroma[X265_CSP_I420].cu[BLOCK_420_8x8].add_ps   = PFX(pixel_add_ps_8x8_neon);
--        p.chroma[X265_CSP_I420].cu[BLOCK_420_16x16].add_ps = PFX(pixel_add_ps_16x16_neon);
--        p.chroma[X265_CSP_I420].cu[BLOCK_420_32x32].add_ps = PFX(pixel_add_ps_32x32_neon);
--        p.chroma[X265_CSP_I422].cu[BLOCK_422_4x8].add_ps   = PFX(pixel_add_ps_4x8_neon);
--        p.chroma[X265_CSP_I422].cu[BLOCK_422_8x16].add_ps  = PFX(pixel_add_ps_8x16_neon);
--        p.chroma[X265_CSP_I422].cu[BLOCK_422_16x32].add_ps = PFX(pixel_add_ps_16x32_neon);
--        p.chroma[X265_CSP_I422].cu[BLOCK_422_32x64].add_ps = PFX(pixel_add_ps_32x64_neon);
-+        p.chroma[X265_CSP_I420].cu[BLOCK_420_4x4].add_ps[ALIGNED]   = PFX(pixel_add_ps_4x4_neon);
-+        p.chroma[X265_CSP_I420].cu[BLOCK_420_8x8].add_ps[ALIGNED]   = PFX(pixel_add_ps_8x8_neon);
-+        p.chroma[X265_CSP_I420].cu[BLOCK_420_16x16].add_ps[ALIGNED] = PFX(pixel_add_ps_16x16_neon);
-+        p.chroma[X265_CSP_I420].cu[BLOCK_420_32x32].add_ps[ALIGNED] = PFX(pixel_add_ps_32x32_neon);
-+        p.chroma[X265_CSP_I422].cu[BLOCK_422_4x8].add_ps[ALIGNED]   = PFX(pixel_add_ps_4x8_neon);
-+        p.chroma[X265_CSP_I422].cu[BLOCK_422_8x16].add_ps[ALIGNED]  = PFX(pixel_add_ps_8x16_neon);
-+        p.chroma[X265_CSP_I422].cu[BLOCK_422_16x32].add_ps[ALIGNED] = PFX(pixel_add_ps_16x32_neon);
-+        p.chroma[X265_CSP_I422].cu[BLOCK_422_32x64].add_ps[ALIGNED] = PFX(pixel_add_ps_32x64_neon);
- 
-         // cpy2Dto1D_shr
-         p.cu[BLOCK_4x4].cpy2Dto1D_shr   = PFX(cpy2Dto1D_shr_4x4_neon);
-@@ -518,10 +518,10 @@ void setupAssemblyPrimitives(EncoderPrim
-         p.cu[BLOCK_32x32].cpy2Dto1D_shr = PFX(cpy2Dto1D_shr_32x32_neon);
- 
-         // ssd_s
--        p.cu[BLOCK_4x4].ssd_s   = PFX(pixel_ssd_s_4x4_neon);
--        p.cu[BLOCK_8x8].ssd_s   = PFX(pixel_ssd_s_8x8_neon);
--        p.cu[BLOCK_16x16].ssd_s = PFX(pixel_ssd_s_16x16_neon);
--        p.cu[BLOCK_32x32].ssd_s = PFX(pixel_ssd_s_32x32_neon);
-+        p.cu[BLOCK_4x4].ssd_s[ALIGNED]   = PFX(pixel_ssd_s_4x4_neon);
-+        p.cu[BLOCK_8x8].ssd_s[ALIGNED]   = PFX(pixel_ssd_s_8x8_neon);
-+        p.cu[BLOCK_16x16].ssd_s[ALIGNED] = PFX(pixel_ssd_s_16x16_neon);
-+        p.cu[BLOCK_32x32].ssd_s[ALIGNED] = PFX(pixel_ssd_s_32x32_neon);
- 
-         // sse_ss
-         p.cu[BLOCK_4x4].sse_ss   = PFX(pixel_sse_ss_4x4_neon);
-@@ -548,10 +548,10 @@ void setupAssemblyPrimitives(EncoderPrim
-         p.chroma[X265_CSP_I422].cu[BLOCK_422_32x64].sub_ps = PFX(pixel_sub_ps_32x64_neon);
- 
-         // calc_Residual
--        p.cu[BLOCK_4x4].calcresidual   = PFX(getResidual4_neon);
--        p.cu[BLOCK_8x8].calcresidual   = PFX(getResidual8_neon);
--        p.cu[BLOCK_16x16].calcresidual = PFX(getResidual16_neon);
--        p.cu[BLOCK_32x32].calcresidual = PFX(getResidual32_neon);
-+        p.cu[BLOCK_4x4].calcresidual[ALIGNED]   = PFX(getResidual4_neon);
-+        p.cu[BLOCK_8x8].calcresidual[ALIGNED]   = PFX(getResidual8_neon);
-+        p.cu[BLOCK_16x16].calcresidual[ALIGNED] = PFX(getResidual16_neon);
-+        p.cu[BLOCK_32x32].calcresidual[ALIGNED] = PFX(getResidual32_neon);
- 
-         // sse_pp
-         p.cu[BLOCK_4x4].sse_pp   = PFX(pixel_sse_pp_4x4_neon);
-@@ -722,31 +722,31 @@ void setupAssemblyPrimitives(EncoderPrim
-         p.pu[LUMA_64x64].sad_x4 = PFX(sad_x4_64x64_neon);
- 
-         // pixel_avg_pp
--        p.pu[LUMA_4x4].pixelavg_pp   = PFX(pixel_avg_pp_4x4_neon);
--        p.pu[LUMA_4x8].pixelavg_pp   = PFX(pixel_avg_pp_4x8_neon);
--        p.pu[LUMA_4x16].pixelavg_pp  = PFX(pixel_avg_pp_4x16_neon);
--        p.pu[LUMA_8x4].pixelavg_pp   = PFX(pixel_avg_pp_8x4_neon);
--        p.pu[LUMA_8x8].pixelavg_pp   = PFX(pixel_avg_pp_8x8_neon);
--        p.pu[LUMA_8x16].pixelavg_pp  = PFX(pixel_avg_pp_8x16_neon);
--        p.pu[LUMA_8x32].pixelavg_pp  = PFX(pixel_avg_pp_8x32_neon);
--        p.pu[LUMA_12x16].pixelavg_pp = PFX(pixel_avg_pp_12x16_neon);
--        p.pu[LUMA_16x4].pixelavg_pp  = PFX(pixel_avg_pp_16x4_neon);
--        p.pu[LUMA_16x8].pixelavg_pp  = PFX(pixel_avg_pp_16x8_neon);
--        p.pu[LUMA_16x12].pixelavg_pp = PFX(pixel_avg_pp_16x12_neon);
--        p.pu[LUMA_16x16].pixelavg_pp = PFX(pixel_avg_pp_16x16_neon);
--        p.pu[LUMA_16x32].pixelavg_pp = PFX(pixel_avg_pp_16x32_neon);
--        p.pu[LUMA_16x64].pixelavg_pp = PFX(pixel_avg_pp_16x64_neon);
--        p.pu[LUMA_24x32].pixelavg_pp = PFX(pixel_avg_pp_24x32_neon);
--        p.pu[LUMA_32x8].pixelavg_pp  = PFX(pixel_avg_pp_32x8_neon);
--        p.pu[LUMA_32x16].pixelavg_pp = PFX(pixel_avg_pp_32x16_neon);
--        p.pu[LUMA_32x24].pixelavg_pp = PFX(pixel_avg_pp_32x24_neon);
--        p.pu[LUMA_32x32].pixelavg_pp = PFX(pixel_avg_pp_32x32_neon);
--        p.pu[LUMA_32x64].pixelavg_pp = PFX(pixel_avg_pp_32x64_neon);
--        p.pu[LUMA_48x64].pixelavg_pp = PFX(pixel_avg_pp_48x64_neon);
--        p.pu[LUMA_64x16].pixelavg_pp = PFX(pixel_avg_pp_64x16_neon);
--        p.pu[LUMA_64x32].pixelavg_pp = PFX(pixel_avg_pp_64x32_neon);
--        p.pu[LUMA_64x48].pixelavg_pp = PFX(pixel_avg_pp_64x48_neon);
--        p.pu[LUMA_64x64].pixelavg_pp = PFX(pixel_avg_pp_64x64_neon);
-+        p.pu[LUMA_4x4].pixelavg_pp[ALIGNED]   = PFX(pixel_avg_pp_4x4_neon);
-+        p.pu[LUMA_4x8].pixelavg_pp[ALIGNED]   = PFX(pixel_avg_pp_4x8_neon);
-+        p.pu[LUMA_4x16].pixelavg_pp[ALIGNED]  = PFX(pixel_avg_pp_4x16_neon);
-+        p.pu[LUMA_8x4].pixelavg_pp[ALIGNED]   = PFX(pixel_avg_pp_8x4_neon);
-+        p.pu[LUMA_8x8].pixelavg_pp[ALIGNED]   = PFX(pixel_avg_pp_8x8_neon);
-+        p.pu[LUMA_8x16].pixelavg_pp[ALIGNED]  = PFX(pixel_avg_pp_8x16_neon);
-+        p.pu[LUMA_8x32].pixelavg_pp[ALIGNED]  = PFX(pixel_avg_pp_8x32_neon);
-+        p.pu[LUMA_12x16].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_12x16_neon);
-+        p.pu[LUMA_16x4].pixelavg_pp[ALIGNED]  = PFX(pixel_avg_pp_16x4_neon);
-+        p.pu[LUMA_16x8].pixelavg_pp[ALIGNED]  = PFX(pixel_avg_pp_16x8_neon);
-+        p.pu[LUMA_16x12].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_16x12_neon);
-+        p.pu[LUMA_16x16].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_16x16_neon);
-+        p.pu[LUMA_16x32].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_16x32_neon);
-+        p.pu[LUMA_16x64].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_16x64_neon);
-+        p.pu[LUMA_24x32].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_24x32_neon);
-+        p.pu[LUMA_32x8].pixelavg_pp[ALIGNED]  = PFX(pixel_avg_pp_32x8_neon);
-+        p.pu[LUMA_32x16].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_32x16_neon);
-+        p.pu[LUMA_32x24].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_32x24_neon);
-+        p.pu[LUMA_32x32].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_32x32_neon);
-+        p.pu[LUMA_32x64].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_32x64_neon);
-+        p.pu[LUMA_48x64].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_48x64_neon);
-+        p.pu[LUMA_64x16].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_64x16_neon);
-+        p.pu[LUMA_64x32].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_64x32_neon);
-+        p.pu[LUMA_64x48].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_64x48_neon);
-+        p.pu[LUMA_64x64].pixelavg_pp[ALIGNED] = PFX(pixel_avg_pp_64x64_neon);
- 
-         // planecopy
-         p.planecopy_cp = PFX(pixel_planecopy_cp_neon);
diff --git a/gnu/packages/patches/x265-detect512-all-arches.patch b/gnu/packages/patches/x265-detect512-all-arches.patch
new file mode 100644
index 0000000000..4d39d868fd
--- /dev/null
+++ b/gnu/packages/patches/x265-detect512-all-arches.patch
@@ -0,0 +1,37 @@
+https://sources.debian.org/data/main/x/x265/2.9-3/debian/patches/0003-detect512-is-needed-on-all-architectures.patch
+
+From: Adam Sampson <unknown@bitbucket>
+Date: Sun, 14 Oct 2018 14:04:18 +0200
+Subject: detect512 is needed on all architectures
+
+---
+ source/common/cpu.cpp | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/source/common/cpu.cpp b/source/common/cpu.cpp
+index 0681ff5..fa687da 100644
+--- a/source/common/cpu.cpp
++++ b/source/common/cpu.cpp
+@@ -110,6 +110,11 @@ const cpu_name_t cpu_names[] =
+     { "", 0 },
+ };
+ 
++bool detect512()
++{
++    return(enable512);
++}
++
+ #if X265_ARCH_X86
+ 
+ extern "C" {
+@@ -123,10 +128,6 @@ uint64_t PFX(cpu_xgetbv)(int xcr);
+ #pragma warning(disable: 4309) // truncation of constant value
+ #endif
+ 
+-bool detect512()
+-{
+-    return(enable512);
+-}
+ uint32_t cpu_detect(bool benableavx512 )
+ {
+ 
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index e281bf8fff..88357dfb45 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -401,7 +401,7 @@ and creating Matroska files from other media files (@code{mkvmerge}).")
         (sha256
          (base32
           "090hp4216isis8q5gb7bwzia8rfyzni54z21jnwm97x3hiy6ibpb"))
-        (patches (search-patches "x265-arm-asm-primitives.patch"))
+        (patches (search-patches "x265-detect512-all-arches.patch"))
         (modules '((guix build utils)))
         (snippet '(begin
                     (delete-file-recursively "source/compat/getopt")
@@ -409,12 +409,8 @@ and creating Matroska files from other media files (@code{mkvmerge}).")
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; tests are skipped if cpu-optimized code isn't built
-       ;; Currently the source code doesn't check for aarch64.
-       ,@(if (any (cute string-prefix? <> (or (%current-system)
-                                              (%current-target-system)))
-                  '("armhf" "aarch64"))
-           '(#:configure-flags '("-DENABLE_PIC=TRUE"))
-           '())
+       ;; Ensure position independent code for everyone.
+       #:configure-flags '("-DENABLE_PIC=TRUE")
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'prepare-build

From 2c89b4b5500ab940411d43c97291c931c3f5b8d0 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Mon, 15 Oct 2018 10:03:34 +0200
Subject: [PATCH 735/909] gnu: wine-staging: Update to 3.18.

* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 3.18.
* gnu/packages/wine.scm (wine-staging): Update to 3.18.
---
 gnu/packages/wine.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index 68839038b7..169cc6e3c5 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -225,7 +225,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
    (name "wine-staging-patchset-data")
-   (version "3.17")
+   (version "3.18")
    (source
     (origin
       (method git-fetch)
@@ -235,7 +235,7 @@ integrate Windows applications into your desktop.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-        "1ds9q90xjg59ikic98kqkhmijnqx4yplvwsm6rav4mx72yci7d4w"))))
+        "18g1lmqzkc7ngppynimfvza1gkdhqlnjbvnckmaws847ns4i0kzp"))))
    (build-system trivial-build-system)
    (native-inputs
     `(("bash" ,bash)
@@ -281,7 +281,7 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "08fcziadw40153a9rv630m7iz6ipfzylms5y191z4sj2vvhy5vac"))))
+                "0xqs76hxcym8nb95r7l72xx0msbscp7fhkr1wrv4r0923d5x9s4v"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
               ("gtk+" ,gtk+)
               ("libva" ,libva)

From 2ab321ca37d1c00c1540d78d587226d3d487b2d4 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 15 Oct 2018 13:51:41 +0300
Subject: [PATCH 736/909] gnu: go@1.4: Add support for aarch64-linux.

* gnu/packages/golang.scm (go@1.4)[arguments]: Build for armhf-linux
when building for aarch64-linux.
[supported-systems]: Add aarch64-linux.
---
 gnu/packages/golang.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 7f26fbdab6..f14057417d 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Matthew Jordan <matthewjordandevops@yandex.com>
 ;;; Copyright © 2016 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
@@ -77,6 +77,10 @@
                   (guix build utils)
                   (srfi srfi-1))
        #:tests? #f ; Tests are run by the all.bash script.
+       ,@(if (string-prefix? "aarch64-linux" (or (%current-system)
+                                                 (%current-target-system)))
+             '(#:system "armhf-linux")
+             '())
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -213,7 +217,7 @@ programming language designed primarily for systems programming.  Go is a
 compiled, statically typed language in the tradition of C and C++, but adds
 garbage collection, various safety features, and concurrent programming features
 in the style of communicating sequential processes (@dfn{CSP}).")
-    (supported-systems '("x86_64-linux" "i686-linux" "armhf-linux"))
+    (supported-systems '("x86_64-linux" "i686-linux" "armhf-linux" "aarch64-linux"))
     (license license:bsd-3)))
 
 (define-public go-1.9

From 0627f93db6a57e7411cb332b7509f35753b149e4 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 15 Oct 2018 21:45:08 +0300
Subject: [PATCH 737/909] gnu: clang-runtime: Adapt for glibc@2.28.

* gnu/packages/llvm.scm (clang-runtime@3.7, clang-runtime@3.8,
clang-runtime@3.9)[patches]: Add patch to work around removed ustat.h.
* gnu/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
---
 gnu/local.mk                                  |  1 +
 gnu/packages/llvm.scm                         | 10 ++--
 .../clang-3.5-libsantitizer-ustat-fix.patch   | 46 +++++++++++++++++++
 3 files changed, 54 insertions(+), 3 deletions(-)
 create mode 100644 gnu/packages/patches/clang-3.5-libsantitizer-ustat-fix.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index e5745ba9e6..0c40d6c0b8 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -613,6 +613,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ceph-skip-unittest_blockdev.patch	\
   %D%/packages/patches/chmlib-inttypes.patch			\
   %D%/packages/patches/clang-3.5-libc-search-path.patch		\
+  %D%/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch	\
   %D%/packages/patches/clang-3.8-libc-search-path.patch		\
   %D%/packages/patches/clang-6.0-libc-search-path.patch		\
   %D%/packages/patches/clang-runtime-asan-build-fixes.patch	\
diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm
index d0791d00cc..aef24b3bac 100644
--- a/gnu/packages/llvm.scm
+++ b/gnu/packages/llvm.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -270,7 +271,8 @@ code analysis tools.")
    llvm-3.9.1
    "16gc2gdmp5c800qvydrdhsp0bzb97s8wrakl6i8a4lgslnqnf2fk"
    '("clang-runtime-asan-build-fixes.patch"
-     "clang-runtime-esan-build-fixes.patch")))
+     "clang-runtime-esan-build-fixes.patch"
+     "clang-3.5-libsantitizer-ustat-fix.patch")))
 
 (define-public clang-3.9.1
   (clang-from-llvm llvm-3.9.1 clang-runtime-3.9.1
@@ -294,7 +296,8 @@ code analysis tools.")
   (clang-runtime-from-llvm
    llvm-3.8
    "0p0y85c7izndbpg2l816z7z7558axq11d5pwkm4h11sdw7d13w0d"
-   '("clang-runtime-asan-build-fixes.patch")))
+   '("clang-runtime-asan-build-fixes.patch"
+     "clang-3.5-libsantitizer-ustat-fix.patch")))
 
 (define-public clang-3.8
   (clang-from-llvm llvm-3.8 clang-runtime-3.8
@@ -317,7 +320,8 @@ code analysis tools.")
   (clang-runtime-from-llvm
    llvm-3.7
    "10c1mz2q4bdq9bqfgr3dirc6hz1h3sq8573srd5q5lr7m7j6jiwx"
-   '("clang-runtime-asan-build-fixes.patch")))
+   '("clang-runtime-asan-build-fixes.patch"
+     "clang-3.5-libsantitizer-ustat-fix.patch")))
 
 (define-public clang-3.7
   (clang-from-llvm llvm-3.7 clang-runtime-3.7
diff --git a/gnu/packages/patches/clang-3.5-libsantitizer-ustat-fix.patch b/gnu/packages/patches/clang-3.5-libsantitizer-ustat-fix.patch
new file mode 100644
index 0000000000..cfb09a8ce3
--- /dev/null
+++ b/gnu/packages/patches/clang-3.5-libsantitizer-ustat-fix.patch
@@ -0,0 +1,46 @@
+From d9d97cac3702b99a00cd113de98c41eb535d47ed Mon Sep 17 00:00:00 2001
+From: Efraim Flashner <efraim@flashner.co.il>
+Date: Sun, 14 Oct 2018 12:11:30 +0300
+Subject: [PATCH] patch modified from the gcc patch series, also dealing with
+ ustat.
+
+---
+ .../sanitizer_platform_limits_posix.cc            | 15 +++++++++++++--
+ 1 file changed, 13 insertions(+), 2 deletions(-)
+
+diff --git a/lib/sanitizer_common/sanitizer_platform_limits_posix.cc b/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
+index 29fea6e..570b9a5 100644
+--- a/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
++++ b/lib/sanitizer_common/sanitizer_platform_limits_posix.cc
+@@ -129,7 +129,6 @@
+ #include <sys/statvfs.h>
+ #include <sys/timex.h>
+ #include <sys/user.h>
+-#include <sys/ustat.h>
+ #include <linux/cyclades.h>
+ #include <linux/if_eql.h>
+ #include <linux/if_plip.h>
+@@ -222,7 +221,19 @@ namespace __sanitizer {
+ #endif  // SANITIZER_LINUX || SANITIZER_FREEBSD
+ 
+ #if SANITIZER_LINUX && !SANITIZER_ANDROID
+-  unsigned struct_ustat_sz = sizeof(struct ustat);
++  // Use pre-computed size of struct ustat to avoid <sys/ustat.h> which
++  // has been removed from glibc 2.28.
++#if defined(__aarch64__) || defined(__s390x__) || defined (__mips64) \
++  || defined(__powerpc64__) || defined(__arch64__) || defined(__sparcv9) \
++  || defined(__x86_64__)
++#define SIZEOF_STRUCT_USTAT 32
++#elif defined(__arm__) || defined(__i386__) || defined(__mips__) \
++  || defined(__powerpc__) || defined(__s390__)
++#define SIZEOF_STRUCT_USTAT 20
++#else
++#error Unknown size of struct ustat
++#endif
++  unsigned struct_ustat_sz = SIZEOF_STRUCT_USTAT;
+   unsigned struct_rlimit64_sz = sizeof(struct rlimit64);
+   unsigned struct_statvfs64_sz = sizeof(struct statvfs64);
+ #endif  // SANITIZER_LINUX && !SANITIZER_ANDROID
+-- 
+2.19.1
+

From 1a2d8d06b53c3c8cf8f94920c6e8734c71b8369b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Mon, 15 Oct 2018 21:51:23 +0300
Subject: [PATCH 738/909] * gnu: clang-runtime: Fix typo in patch name.

This is a follow-up to 0627f93db6a57e7411cb332b7509f35753b149e4.

* gnu/packages/patches/libsantitizer-ustat-fix.patch: Rename to
gnu/packages/patches/libsanitizer-ustat-fix.patch.
* gnu/packages/llvm.scm (clang-runtime@3.7, clang-runtime@3.8,
clang-runtime@3.9)[patches]: Fix patch name.
---
 gnu/packages/llvm.scm                                       | 6 +++---
 ...tat-fix.patch => clang-3.5-libsanitizer-ustat-fix.patch} | 0
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename gnu/packages/patches/{clang-3.5-libsantitizer-ustat-fix.patch => clang-3.5-libsanitizer-ustat-fix.patch} (100%)

diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm
index aef24b3bac..54a17be8f4 100644
--- a/gnu/packages/llvm.scm
+++ b/gnu/packages/llvm.scm
@@ -272,7 +272,7 @@ code analysis tools.")
    "16gc2gdmp5c800qvydrdhsp0bzb97s8wrakl6i8a4lgslnqnf2fk"
    '("clang-runtime-asan-build-fixes.patch"
      "clang-runtime-esan-build-fixes.patch"
-     "clang-3.5-libsantitizer-ustat-fix.patch")))
+     "clang-3.5-libsanitizer-ustat-fix.patch")))
 
 (define-public clang-3.9.1
   (clang-from-llvm llvm-3.9.1 clang-runtime-3.9.1
@@ -297,7 +297,7 @@ code analysis tools.")
    llvm-3.8
    "0p0y85c7izndbpg2l816z7z7558axq11d5pwkm4h11sdw7d13w0d"
    '("clang-runtime-asan-build-fixes.patch"
-     "clang-3.5-libsantitizer-ustat-fix.patch")))
+     "clang-3.5-libsanitizer-ustat-fix.patch")))
 
 (define-public clang-3.8
   (clang-from-llvm llvm-3.8 clang-runtime-3.8
@@ -321,7 +321,7 @@ code analysis tools.")
    llvm-3.7
    "10c1mz2q4bdq9bqfgr3dirc6hz1h3sq8573srd5q5lr7m7j6jiwx"
    '("clang-runtime-asan-build-fixes.patch"
-     "clang-3.5-libsantitizer-ustat-fix.patch")))
+     "clang-3.5-libsanitizer-ustat-fix.patch")))
 
 (define-public clang-3.7
   (clang-from-llvm llvm-3.7 clang-runtime-3.7
diff --git a/gnu/packages/patches/clang-3.5-libsantitizer-ustat-fix.patch b/gnu/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch
similarity index 100%
rename from gnu/packages/patches/clang-3.5-libsantitizer-ustat-fix.patch
rename to gnu/packages/patches/clang-3.5-libsanitizer-ustat-fix.patch

From 6ef61cc4c30e94acbd7437f19c893f63a7112267 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 15 Oct 2018 22:40:35 +0200
Subject: [PATCH 739/909] daemon: Support multiplexed build output.

This allows clients to tell whether output comes from the daemon or, if
it comes from a builder, from which builder it comes.  The latter is
particularly useful when MAX-BUILD-JOBS > 1.

* nix/libstore/build.cc (DerivationGoal::tryBuildHook)
(DerivationGoal::startBuilder): Print the child's PID in "@ build-started"
traces.
(DerivationGoal::handleChildOutput): Define 'prefix', pass it to
'writeToStderr'.
* nix/libstore/globals.cc (Settings:Settings): Initialize
'multiplexedBuildOutput'.
(Settings::update): Likewise.
* nix/libstore/globals.hh (Settings)[multiplexedBuildOutput]: New field.
Update 'printBuildTrace' documentation.
* nix/libstore/worker-protocol.hh (PROTOCOL_VERSION): Bump to 0.163.
* nix/nix-daemon/nix-daemon.cc (performOp) <wopSetOptions>: Special-case
"multiplexed-build-output" and remove "use-ssh-substituter".
* guix/store.scm (set-build-options): Add #:multiplexed-build-output?
and honor it.
(%protocol-version): Bump to #x163.
* tests/store.scm ("multiplexed-build-output"): New test.

fixlet
---
 guix/store.scm                  | 15 +++++++-
 nix/libstore/build.cc           | 25 +++++++++----
 nix/libstore/globals.cc         |  2 ++
 nix/libstore/globals.hh         |  9 ++++-
 nix/libstore/worker-protocol.hh |  2 +-
 nix/nix-daemon/nix-daemon.cc    |  2 +-
 tests/store.scm                 | 63 +++++++++++++++++++++++++++++++++
 7 files changed, 108 insertions(+), 10 deletions(-)

diff --git a/guix/store.scm b/guix/store.scm
index 8b35fc8d7a..b1bdbf3813 100644
--- a/guix/store.scm
+++ b/guix/store.scm
@@ -155,7 +155,7 @@
             derivation-log-file
             log-file))
 
-(define %protocol-version #x162)
+(define %protocol-version #x163)
 
 (define %worker-magic-1 #x6e697863)               ; "nixc"
 (define %worker-magic-2 #x6478696f)               ; "dxio"
@@ -709,6 +709,15 @@ encoding conversion errors."
                             ;; disabled by default.
                             print-extended-build-trace?
 
+                            ;; When true, the daemon prefixes builder output
+                            ;; with "@ build-log" traces so we can
+                            ;; distinguish it from daemon output, and we can
+                            ;; distinguish each builder's output
+                            ;; (PRINT-BUILD-TRACE must be true as well.)  The
+                            ;; latter is particularly useful when
+                            ;; MAX-BUILD-JOBS > 1.
+                            multiplexed-build-output?
+
                             build-cores
                             (use-substitutes? #t)
 
@@ -757,6 +766,10 @@ encoding conversion errors."
                            `(("print-extended-build-trace"
                               . ,(if print-extended-build-trace? "1" "0")))
                            '())
+                     ,@(if multiplexed-build-output?
+                           `(("multiplexed-build-output"
+                              . ,(if multiplexed-build-output? "true" "false")))
+                           '())
                      ,@(if timeout
                            `(("build-timeout" . ,(number->string timeout)))
                            '())
diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc
index b2c319f00b..d7b8b0f0ca 100644
--- a/nix/libstore/build.cc
+++ b/nix/libstore/build.cc
@@ -1652,8 +1652,8 @@ HookReply DerivationGoal::tryBuildHook()
     worker.childStarted(shared_from_this(), hook->pid, fds, false, false);
 
     if (settings.printBuildTrace)
-        printMsg(lvlError, format("@ build-started %1% - %2% %3%")
-            % drvPath % drv.platform % logFile);
+        printMsg(lvlError, format("@ build-started %1% - %2% %3% %4%")
+            % drvPath % drv.platform % logFile % hook->pid);
 
     return rpAccept;
 }
@@ -2038,8 +2038,8 @@ void DerivationGoal::startBuilder()
     if (!msg.empty()) throw Error(msg);
 
     if (settings.printBuildTrace) {
-        printMsg(lvlError, format("@ build-started %1% - %2% %3%")
-            % drvPath % drv.platform % logFile);
+        printMsg(lvlError, format("@ build-started %1% - %2% %3% %4%")
+            % drvPath % drv.platform % logFile % pid);
     }
 
 }
@@ -2736,6 +2736,19 @@ void DerivationGoal::deleteTmpDir(bool force)
 
 void DerivationGoal::handleChildOutput(int fd, const string & data)
 {
+    string prefix;
+
+    if (settings.multiplexedBuildOutput) {
+	/* Print a prefix that allows clients to determine whether a message
+	   comes from the daemon or from a build process, and in the latter
+	   case, which build process it comes from.  The PID here matches the
+	   one given in "@ build-started" traces; it's shorter that the
+	   derivation file name, hence this choice.  */
+	prefix = "@ build-log "
+	    + std::to_string(pid < 0 ? hook->pid : pid)
+	    + " " + std::to_string(data.size()) + "\n";
+    }
+
     if ((hook && fd == hook->builderOut.readSide) ||
         (!hook && fd == builderOut.readSide))
     {
@@ -2748,7 +2761,7 @@ void DerivationGoal::handleChildOutput(int fd, const string & data)
             return;
         }
         if (verbosity >= settings.buildVerbosity)
-            writeToStderr(data);
+            writeToStderr(prefix + data);
 
 	if (gzLogFile) {
 	    if (data.size() > 0) {
@@ -2767,7 +2780,7 @@ void DerivationGoal::handleChildOutput(int fd, const string & data)
     }
 
     if (hook && fd == hook->fromHook.readSide)
-        writeToStderr(data);
+        writeToStderr(prefix + data);
 }
 
 
diff --git a/nix/libstore/globals.cc b/nix/libstore/globals.cc
index 94c2e516f8..4b5b485e65 100644
--- a/nix/libstore/globals.cc
+++ b/nix/libstore/globals.cc
@@ -36,6 +36,7 @@ Settings::Settings()
     buildTimeout = 0;
     useBuildHook = true;
     printBuildTrace = false;
+    multiplexedBuildOutput = false;
     reservedSize = 8 * 1024 * 1024;
     fsyncMetadata = true;
     useSQLiteWAL = true;
@@ -120,6 +121,7 @@ void Settings::update()
     _get(maxBuildJobs, "build-max-jobs");
     _get(buildCores, "build-cores");
     _get(thisSystem, "system");
+    _get(multiplexedBuildOutput, "multiplexed-build-output");
     _get(maxSilentTime, "build-max-silent-time");
     _get(buildTimeout, "build-timeout");
     _get(reservedSize, "gc-reserved-space");
diff --git a/nix/libstore/globals.hh b/nix/libstore/globals.hh
index 4c142e6933..a6935c3337 100644
--- a/nix/libstore/globals.hh
+++ b/nix/libstore/globals.hh
@@ -127,7 +127,7 @@ struct Settings {
        a fixed format to allow its progress to be monitored.  Each
        line starts with a "@".  The following are defined:
 
-       @ build-started <drvpath> <outpath> <system> <logfile>
+       @ build-started <drvpath> <outpath> <system> <logfile> <pid>
        @ build-failed <drvpath> <outpath> <exitcode> <error text>
        @ build-succeeded <drvpath> <outpath>
        @ substituter-started <outpath> <substituter>
@@ -139,6 +139,13 @@ struct Settings {
        builders. */
     bool printBuildTrace;
 
+    /* When true, 'buildDerivations' prefixes lines coming from builders so
+       that clients know exactly which line comes from which builder, and
+       which line comes from the daemon itself.  The prefix for data coming
+       from builders is "log:PID:LEN:DATA" where PID uniquely identifies the
+       builder (PID is given in "build-started" traces.)  */
+    bool multiplexedBuildOutput;
+
     /* Amount of reserved space for the garbage collector
        (/nix/var/nix/db/reserved). */
     off_t reservedSize;
diff --git a/nix/libstore/worker-protocol.hh b/nix/libstore/worker-protocol.hh
index 103d60a8c2..ea67b10a5b 100644
--- a/nix/libstore/worker-protocol.hh
+++ b/nix/libstore/worker-protocol.hh
@@ -6,7 +6,7 @@ namespace nix {
 #define WORKER_MAGIC_1 0x6e697863
 #define WORKER_MAGIC_2 0x6478696f
 
-#define PROTOCOL_VERSION 0x162
+#define PROTOCOL_VERSION 0x163
 #define GET_PROTOCOL_MAJOR(x) ((x) & 0xff00)
 #define GET_PROTOCOL_MINOR(x) ((x) & 0x00ff)
 
diff --git a/nix/nix-daemon/nix-daemon.cc b/nix/nix-daemon/nix-daemon.cc
index 782e4acfc5..2939422172 100644
--- a/nix/nix-daemon/nix-daemon.cc
+++ b/nix/nix-daemon/nix-daemon.cc
@@ -594,7 +594,7 @@ static void performOp(bool trusted, unsigned int clientVersion,
                 if (name == "build-timeout" || name == "build-max-silent-time"
                     || name == "build-max-jobs" || name == "build-cores"
                     || name == "build-repeat"
-                    || name == "use-ssh-substituter")
+                    || name == "multiplexed-build-output")
                     settings.set(name, value);
                 else
                     settings.set(trusted ? name : "untrusted-" + name, value);
diff --git a/tests/store.scm b/tests/store.scm
index 2858369706..3ff526cdcf 100644
--- a/tests/store.scm
+++ b/tests/store.scm
@@ -31,6 +31,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages bootstrap)
   #:use-module (ice-9 match)
+  #:use-module (ice-9 regex)
   #:use-module (rnrs bytevectors)
   #:use-module (rnrs io ports)
   #:use-module (web uri)
@@ -1021,4 +1022,66 @@
                  (call-with-input-file (derivation->output-path drv2)
                    read))))))
 
+(test-equal "multiplexed-build-output"
+  '("Hello from first." "Hello from second.")
+  (with-store store
+    (let* ((build  (add-text-to-store store "build.sh"
+                                      "echo Hello from $NAME.; echo > $out"))
+           (bash   (add-to-store store "bash" #t "sha256"
+                                 (search-bootstrap-binary "bash"
+                                                          (%current-system))))
+           (drv1   (derivation store "one" bash
+                               `("-e" ,build)
+                               #:inputs `((,bash) (,build))
+                               #:env-vars `(("NAME" . "first")
+                                            ("x" . ,(random-text)))))
+           (drv2   (derivation store "two" bash
+                               `("-e" ,build)
+                               #:inputs `((,bash) (,build))
+                               #:env-vars `(("NAME" . "second")
+                                            ("x" . ,(random-text))))))
+      (set-build-options store
+                         #:print-build-trace #t
+                         #:multiplexed-build-output? #t
+                         #:max-build-jobs 10)
+      (let ((port (open-output-string)))
+        ;; Send the build log to PORT.
+        (parameterize ((current-build-output-port port))
+          (build-derivations store (list drv1 drv2)))
+
+        ;; Retrieve the build log; make sure it contains valid "@ build-log"
+        ;; traces that allow us to retrieve each builder's output (we assume
+        ;; there's exactly one "build-output" trace for each builder, which is
+        ;; reasonable.)
+        (let* ((log     (get-output-string port))
+               (started (fold-matches
+                         (make-regexp "@ build-started ([^ ]+) - ([^ ]+) ([^ ]+) ([0-9]+)")
+                         log '() cons))
+               (done    (fold-matches
+                         (make-regexp "@ build-succeeded (.*) - (.*) (.*) (.*)")
+                         log '() cons))
+               (output  (fold-matches
+                         (make-regexp "@ build-log ([[:digit:]]+) ([[:digit:]]+)\n([A-Za-z .*]+)\n")
+                         log '() cons))
+               (drv-pid (lambda (name)
+                          (lambda (m)
+                            (let ((drv (match:substring m 1))
+                                  (pid (string->number
+                                        (match:substring m 4))))
+                              (and (string-suffix? name drv) pid)))))
+               (pid-log (lambda (pid)
+                          (lambda (m)
+                            (let ((n   (string->number
+                                        (match:substring m 1)))
+                                  (len (string->number
+                                        (match:substring m 2)))
+                                  (str (match:substring m 3)))
+                              (and (= pid n)
+                                   (= (string-length str) (- len 1))
+                                   str)))))
+               (pid1    (any (drv-pid "one.drv") started))
+               (pid2    (any (drv-pid "two.drv") started)))
+          (list (any (pid-log pid1) output)
+                (any (pid-log pid2) output)))))))
+
 (test-end "store")

From f9a8fce10f2d99efec7cb1dd0f6c5f0df9d1b2df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 15 Oct 2018 23:06:55 +0200
Subject: [PATCH 740/909] status: Build upon multiplexed build output.

This allows for more accurate status tracking and parsing of extended
build traces.

* guix/status.scm (multiplexed-output-supported?): New procedure.
(print-build-event): Don't print \r when PRINT-LOG? is true.
Adjust 'build-log' handling for when 'multiplexed-output-supported?'
returns true.
(bytevector-index, split-lines): New procedures.
(build-event-output-port)[%build-output-pid, %build-output]
[%build-output-left]: New variables.
[process-line]: Handle "@ build-output" traces.
[process-build-output]: New procedure.
[write!]: Add case for when %BUILD-OUTPUT-PID is true.  Use
'bytevector-index' rather than 'string-index'.
(compute-status): Add #:derivation-path->output-path.  Use it.
* tests/status.scm ("compute-status, multiplexed build output"):
New test.
("build-output-port, UTF-8")
("current-build-output-port, UTF-8 + garbage"): Adjust to new
'build-log' output.
* guix/scripts/build.scm (set-build-options-from-command-line):
Pass #:multiplexed-build-output?.
(%default-options): Add 'multiplexed-build-output?'.
* guix/scripts/environment.scm (%default-options): Likewise.
* guix/scripts/pack.scm (%default-options): Likewise.
* guix/scripts/package.scm (%default-options): Likewise.
* guix/scripts/pull.scm (%default-options): Likewise.
* guix/scripts/system.scm (%default-options): Likewise.
---
 guix/scripts/build.scm       |   3 +
 guix/scripts/environment.scm |   1 +
 guix/scripts/pack.scm        |   1 +
 guix/scripts/package.scm     |   3 +-
 guix/scripts/pull.scm        |   1 +
 guix/scripts/system.scm      |   1 +
 guix/status.scm              | 169 ++++++++++++++++++++++++++---------
 tests/status.scm             |  51 ++++++++++-
 8 files changed, 184 insertions(+), 46 deletions(-)

diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index f3aa5512d5..13978abb77 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -395,6 +395,8 @@ options handled by 'set-build-options-from-command-line', and listed in
                      #:print-build-trace (assoc-ref opts 'print-build-trace?)
                      #:print-extended-build-trace?
                      (assoc-ref opts 'print-extended-build-trace?)
+                     #:multiplexed-build-output?
+                     (assoc-ref opts 'multiplexed-build-output?)
                      #:verbosity (assoc-ref opts 'verbosity)))
 
 (define set-build-options-from-command-line*
@@ -505,6 +507,7 @@ options handled by 'set-build-options-from-command-line', and listed in
     (build-hook? . #t)
     (print-build-trace? . #t)
     (print-extended-build-trace? . #t)
+    (multiplexed-build-output? . #t)
     (verbosity . 0)))
 
 (define (show-help)
diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm
index 9fc7edcd36..5965e3426e 100644
--- a/guix/scripts/environment.scm
+++ b/guix/scripts/environment.scm
@@ -176,6 +176,7 @@ COMMAND or an interactive shell in that environment.\n"))
     (graft? . #t)
     (print-build-trace? . #t)
     (print-extended-build-trace? . #t)
+    (multiplexed-build-output? . #t)
     (verbosity . 0)))
 
 (define (tag-package-arg opts arg)
diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm
index 163f5b1dc1..fb3c50521d 100644
--- a/guix/scripts/pack.scm
+++ b/guix/scripts/pack.scm
@@ -541,6 +541,7 @@ please email '~a'~%")
     (graft? . #t)
     (print-build-trace? . #t)
     (print-extended-build-trace? . #t)
+    (multiplexed-build-output? . #t)
     (verbosity . 0)
     (symlinks . ())
     (compressor . ,(first %compressors))))
diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index e588ff81ed..5d146b8427 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -296,7 +296,8 @@ ENTRIES, a list of manifest entries, in the context of PROFILE."
     (substitutes? . #t)
     (build-hook? . #t)
     (print-build-trace? . #t)
-    (print-extended-build-trace? . #t)))
+    (print-extended-build-trace? . #t)
+    (multiplexed-build-output? . #t)))
 
 (define (show-help)
   (display (G_ "Usage: guix package [OPTION]...
diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index d3fd624228..188237aa90 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -64,6 +64,7 @@
     (build-hook? . #t)
     (print-build-trace? . #t)
     (print-extended-build-trace? . #t)
+    (multiplexed-build-output? . #t)
     (graft? . #t)
     (verbosity . 0)))
 
diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm
index f9d6b9e5b6..f9af38b7c5 100644
--- a/guix/scripts/system.scm
+++ b/guix/scripts/system.scm
@@ -1082,6 +1082,7 @@ Some ACTIONS support additional ARGS.\n"))
     (build-hook? . #t)
     (print-build-trace? . #t)
     (print-extended-build-trace? . #t)
+    (multiplexed-build-output? . #t)
     (graft? . #t)
     (verbosity . 0)
     (file-system-type . "ext4")
diff --git a/guix/status.scm b/guix/status.scm
index d8d761dc23..8e05d4eb76 100644
--- a/guix/status.scm
+++ b/guix/status.scm
@@ -116,7 +116,10 @@
     (string=? item (download-item download))))
 
 (define* (compute-status event status
-                         #:key (current-time current-time))
+                         #:key
+                         (current-time current-time)
+                         (derivation-path->output-path
+                          derivation-path->output-path))
   "Given EVENT, a tuple like (build-started \"/gnu/store/...-foo.drv\" ...),
 compute a new status based on STATUS."
   (match event
@@ -142,8 +145,7 @@ compute a new status based on STATUS."
       (inherit status)
       (building (remove (lambda (drv)
                           (equal? (false-if-exception
-                                   (derivation->output-path
-                                    (read-derivation-from-file drv)))
+                                   (derivation-path->output-path drv))
                                   item))
                         (build-status-building status)))
       (downloading (cons (download item uri #:size size
@@ -219,6 +221,12 @@ build traces\" such as \"@ download-progress\" traces."
   (and (current-store-protocol-version)
        (>= (current-store-protocol-version) #x162)))
 
+(define (multiplexed-output-supported?)
+  "Return true if the daemon supports \"multiplexed output\"--i.e., \"@
+build-log\" traces."
+  (and (current-store-protocol-version)
+       (>= (current-store-protocol-version) #x163)))
+
 (define spin!
   (let ((steps (circular-list "\\" "|" "/" "-")))
     (lambda (port)
@@ -313,7 +321,8 @@ addition to build events."
         (lambda (line)
           (spin! port))))
 
-  (display "\r" port)                             ;erase the spinner
+  (unless print-log?
+    (display "\r" port))                          ;erase the spinner
   (match event
     (('build-started drv . _)
      (format port (info (G_ "building ~a...")) drv)
@@ -384,21 +393,28 @@ addition to build events."
   expected hash: ~a
   actual hash:   ~a~%"))
              expected actual))
-    (('build-log line)
-     ;; TODO: Better distinguish daemon messages and build log lines.
-     (cond ((string-prefix? "substitute: " line)
-            ;; The daemon prefixes early messages coming with 'guix
-            ;; substitute' with "substitute:".  These are useful ("updating
-            ;; substitutes from URL"), so let them through.
-            (format port line)
-            (force-output port))
-           ((string-prefix? "waiting for locks" line)
-            ;; This is when a derivation is already being built and we're just
-            ;; waiting for the build to complete.
-            (display (info (string-trim-right line)) port)
-            (newline))
-           (else
-            (print-log-line line))))
+    (('build-log pid line)
+     (if (multiplexed-output-supported?)
+         (if (not pid)
+             (begin
+               ;; LINE comes from the daemon, not from builders.  Let it
+               ;; through.
+               (display line port)
+               (force-output port))
+             (print-log-line line))
+         (cond ((string-prefix? "substitute: " line)
+                ;; The daemon prefixes early messages coming with 'guix
+                ;; substitute' with "substitute:".  These are useful ("updating
+                ;; substitutes from URL"), so let them through.
+                (display line port)
+                (force-output port))
+               ((string-prefix? "waiting for locks" line)
+                ;; This is when a derivation is already being built and we're just
+                ;; waiting for the build to complete.
+                (display (info (string-trim-right line)) port)
+                (newline))
+               (else
+                (print-log-line line)))))
     (_
      event)))
 
@@ -428,9 +444,6 @@ ON-CHANGE can display the build status, build events, etc."
 ;;; Build port.
 ;;;
 
-(define %newline
-  (char-set #\return #\newline))
-
 (define (maybe-utf8->string bv)
   "Attempt to decode BV as UTF-8 string and return it.  Gracefully handle the
 case where BV does not contain only valid UTF-8."
@@ -447,6 +460,28 @@ case where BV does not contain only valid UTF-8."
           (close-port port)
           str)))))
 
+(define (bytevector-index bv number offset count)
+  "Search for NUMBER in BV starting from OFFSET and reading up to COUNT bytes;
+return the offset where NUMBER first occurs or #f if it could not be found."
+  (let loop ((offset offset)
+             (count count))
+    (cond ((zero? count) #f)
+          ((= (bytevector-u8-ref bv offset) number) offset)
+          (else (loop (+ 1 offset) (- count 1))))))
+
+(define (split-lines str)
+  "Split STR into lines in a way that preserves newline characters."
+  (let loop ((str str)
+             (result '()))
+    (if (string-null? str)
+        (reverse result)
+        (match (string-index str #\newline)
+          (#f
+           (loop "" (cons str result)))
+          (index
+           (loop (string-drop str (+ index 1))
+                 (cons (string-take str (+ index 1)) result)))))))
+
 (define* (build-event-output-port proc #:optional (seed (build-status)))
   "Return an output port for use as 'current-build-output-port' that calls
 PROC with its current state value, initialized with SEED, on every build
@@ -467,33 +502,83 @@ The second return value is a thunk to retrieve the current state."
     ;; Current state for PROC.
     seed)
 
+  ;; When true, this represents the current state while reading a
+  ;; "@ build-log" trace: the current builder PID, the previously-read
+  ;; bytevectors, and the number of bytes that remain to be read.
+  (define %build-output-pid #f)
+  (define %build-output '())
+  (define %build-output-left #f)
+
   (define (process-line line)
-    (if (string-prefix? "@ " line)
-        (match (string-tokenize (string-drop line 2))
-          (((= string->symbol event-name) args ...)
-           (set! %state
-             (proc (cons event-name args)
-                   %state))))
-        (set! %state (proc (list 'build-log line)
-                           %state))))
+    (cond ((string-prefix? "@ " line)
+           (match (string-tokenize (string-drop line 2))
+             (("build-log" (= string->number pid) (= string->number len))
+              (set! %build-output-pid pid)
+              (set! %build-output '())
+              (set! %build-output-left len))
+             (((= string->symbol event-name) args ...)
+              (set! %state
+                (proc (cons event-name args)
+                      %state)))))
+          (else
+           (set! %state (proc (list 'build-log #f line)
+                              %state)))))
+
+  (define (process-build-output pid output)
+    ;; Transform OUTPUT in 'build-log' events or download events as generated
+    ;; by extended build traces.
+    (define (line->event line)
+      (match (and (string-prefix? "@ " line)
+                  (string-tokenize (string-drop line 2)))
+        ((type . args)
+         (if (or (string-prefix? "download-" type)
+                 (string=? "build-remote" type))
+             (cons (string->symbol type) args)
+             `(build-log ,pid ,line)))
+        (_
+         `(build-log ,pid ,line))))
+
+    (let* ((lines  (split-lines output))
+           (events (map line->event lines)))
+      (set! %state (fold proc %state events))))
 
   (define (bytevector-range bv offset count)
     (let ((ptr (bytevector->pointer bv offset)))
       (pointer->bytevector ptr count)))
 
   (define (write! bv offset count)
-    (let loop ((str (maybe-utf8->string (bytevector-range bv offset count))))
-      (match (string-index str %newline)
-        ((? integer? cr)
-         (let ((tail (string-take str (+ 1 cr))))
-           (process-line (string-concatenate-reverse
-                          (cons tail %fragments)))
-           (set! %fragments '())
-           (loop (string-drop str (+ 1 cr)))))
-        (#f
-         (unless (string-null? str)
-           (set! %fragments (cons str %fragments)))
-         count))))
+    (if %build-output-pid
+        (let ((keep (min count %build-output-left)))
+          (set! %build-output
+            (let ((bv* (make-bytevector keep)))
+              (bytevector-copy! bv offset bv* 0 keep)
+              (cons bv* %build-output)))
+          (set! %build-output-left
+            (- %build-output-left keep))
+
+          (when (zero? %build-output-left)
+            (process-build-output %build-output-pid
+                                  (string-concatenate-reverse
+                                   (map maybe-utf8->string %build-output))) ;XXX
+            (set! %build-output '())
+            (set! %build-output-pid #f))
+          keep)
+        (match (bytevector-index bv (char->integer #\newline)
+                                 offset count)
+          ((? integer? cr)
+           (let* ((tail (maybe-utf8->string
+                         (bytevector-range bv offset (- cr -1 offset))))
+                  (line (string-concatenate-reverse
+                         (cons tail %fragments))))
+             (process-line line)
+             (set! %fragments '())
+             (- cr -1 offset)))
+          (#f
+           (unless (zero? count)
+             (let ((str (maybe-utf8->string
+                         (bytevector-range bv offset count))))
+               (set! %fragments (cons str %fragments))))
+           count))))
 
   (define port
     (make-custom-binary-output-port "filtering-input-port"
diff --git a/tests/status.scm b/tests/status.scm
index 486ad04dd2..3b74946673 100644
--- a/tests/status.scm
+++ b/tests/status.scm
@@ -22,7 +22,8 @@
   #:use-module (srfi srfi-11)
   #:use-module (srfi srfi-64)
   #:use-module (rnrs bytevectors)
-  #:use-module (rnrs io ports))
+  #:use-module (rnrs io ports)
+  #:use-module (ice-9 match))
 
 (test-begin "status")
 
@@ -115,7 +116,7 @@
       (list first (get-status)))))
 
 (test-equal "build-output-port, UTF-8"
-  '((build-log "lambda is λ!\n"))
+  '((build-log #f "lambda is λ!\n"))
   (let-values (((port get-status) (build-event-output-port cons '()))
                ((bv)              (string->utf8 "lambda is λ!\n")))
     (put-bytevector port bv)
@@ -124,7 +125,7 @@
 
 (test-equal "current-build-output-port, UTF-8 + garbage"
   ;; What about a mixture of UTF-8 + garbage?
-  '((build-log "garbage: �lambda: λ\n"))
+  '((build-log #f "garbage: �lambda: λ\n"))
   (let-values (((port get-status) (build-event-output-port cons '())))
     (display "garbage: " port)
     (put-bytevector port #vu8(128))
@@ -132,4 +133,48 @@
     (force-output port)
     (get-status)))
 
+(test-equal "compute-status, multiplexed build output"
+  (list (build-status
+         (building '("foo.drv"))
+         (downloading (list (download "bar" "http://example.org/bar"
+                                      #:size 999
+                                      #:start 'now))))
+        (build-status
+         (building '("foo.drv"))
+         (downloading (list (download "bar" "http://example.org/bar"
+                                      #:size 999
+                                      #:transferred 42
+                                      #:start 'now))))
+        (build-status
+         ;; XXX: Should "bar.drv" be present twice?
+         (builds-completed '("bar.drv" "foo.drv"))
+         (downloads-completed (list (download "bar" "http://example.org/bar"
+                                              #:size 999
+                                              #:transferred 999
+                                              #:start 'now
+                                              #:end 'now)))))
+  (let-values (((port get-status)
+                (build-event-output-port (lambda (event status)
+                                           (compute-status event status
+                                                           #:current-time
+                                                           (const 'now)
+                                                           #:derivation-path->output-path
+                                                           (match-lambda
+                                                             ("bar.drv" "bar")))))))
+    (display "@ build-started foo.drv 121\n" port)
+    (display "@ build-started bar.drv 144\n" port)
+    (display "@ build-log 121 6\nHello!" port)
+    (display "@ build-log 144 50
+@ download-started bar http://example.org/bar 999\n" port)
+    (let ((first (get-status)))
+      (display "@ build-log 121 30\n@ build-started FAKE!.drv 555\n")
+      (display "@ build-log 144 54
+@ download-progress bar http://example.org/bar 999 42\n"
+               port)
+      (let ((second (get-status)))
+        (display "@ download-succeeded bar http://example.org/bar 999\n" port)
+        (display "@ build-succeeded foo.drv\n" port)
+        (display "@ build-succeeded bar.drv\n" port)
+        (list first second (get-status))))))
+
 (test-end "status")

From 532f92c8f39ef8fa9441bf0840ae642016fac7a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Mon, 15 Oct 2018 23:54:20 +0200
Subject: [PATCH 741/909] gnu: guix: Update to f9a8fce.

* gnu/packages/package-management.scm (guix): Update to f9a8fce.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 9a0023233f..fbbb4c3811 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -101,8 +101,8 @@
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
   (let ((version "0.15.0")
-        (commit "1d0be47ab680db938ac8da1ee65e1de91e198f67")
-        (revision 5))
+        (commit "f9a8fce10f2d99efec7cb1dd0f6c5f0df9d1b2df")
+        (revision 6))
     (package
       (name "guix")
 
@@ -118,7 +118,7 @@
                       (commit commit)))
                 (sha256
                  (base32
-                  "19cn4ndmr9cqd7qh6w3nchbmdpaawdl9kc6g0v6g680vzcja417k"))
+                  "1733d5id0h44rrkyj9xw4fcqr1wawcfi8igpgk5wsn1iq4qqwv5f"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments

From 503fe87098a23c0b7d848df5a926ebc22aba7fa6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Tue, 16 Oct 2018 10:57:50 +0200
Subject: [PATCH 742/909] gnu: emacs-xelb: Update to 0.16.

* gnu/packages/emacs.scm (emacs-xelb): Update to 0.16.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 4b013eb292..fe9047691e 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -6576,14 +6576,14 @@ which code derived from Kelvin H's org-page.")
 (define-public emacs-xelb
   (package
     (name "emacs-xelb")
-    (version "0.15")
+    (version "0.16")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://elpa.gnu.org/packages/xelb-"
                                   version ".tar"))
               (sha256
                (base32
-                "031rvgprsqhf344p9wsczr50vj2qcpwdmhxi80jdbrsm7wyxf3qz"))))
+                "03wsr1jr7f7zfd80h864rd4makwh4widdnj1kjv2xyjwdgap9rl8"))))
     (build-system emacs-build-system)
     ;; The following functions and variables needed by emacs-xelb are
     ;; not included in emacs-minimal:

From f1376bfabe81608db85d439351f00505b97e944f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Lassieur?= <clement@lassieur.org>
Date: Tue, 16 Oct 2018 10:58:06 +0200
Subject: [PATCH 743/909] gnu: emacs-exwm: Update to 0.20.

* gnu/packages/emacs.scm (emacs-exwm): Update to 0.20.
[source]: Remove emacs-exwm-fix-fullscreen-issue.patch.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/emacs-exwm-fix-fullscreen-issue.patch: Remove patch.
---
 gnu/local.mk                                  |  1 -
 gnu/packages/emacs.scm                        |  5 ++--
 .../emacs-exwm-fix-fullscreen-issue.patch     | 27 -------------------
 3 files changed, 2 insertions(+), 31 deletions(-)
 delete mode 100644 gnu/packages/patches/emacs-exwm-fix-fullscreen-issue.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 1fa2eaba31..b8248e8da0 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -659,7 +659,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/elogind-glibc-2.27.patch			\
   %D%/packages/patches/einstein-build.patch			\
   %D%/packages/patches/emacs-exec-path.patch			\
-  %D%/packages/patches/emacs-exwm-fix-fullscreen-issue.patch	\
   %D%/packages/patches/emacs-fix-scheme-indent-function.patch	\
   %D%/packages/patches/emacs-json-reformat-fix-tests.patch	\
   %D%/packages/patches/emacs-highlight-stages-add-gexp.patch	\
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index fe9047691e..d30a4cc568 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -6615,7 +6615,7 @@ It should enable you to implement low-level X11 applications.")
 (define-public emacs-exwm
   (package
     (name "emacs-exwm")
-    (version "0.19")
+    (version "0.20")
     (synopsis "Emacs X window manager")
     (source (origin
               (method url-fetch)
@@ -6623,8 +6623,7 @@ It should enable you to implement low-level X11 applications.")
                                   version ".tar"))
               (sha256
                (base32
-                "11xd2w4h3zdwkdxypvmcz8s7q72cn76lfr9js77jbizyj6b04lr0"))
-              (patches (search-patches "emacs-exwm-fix-fullscreen-issue.patch"))))
+                "0nhhzbkm0mkj7sd1dy2c19cmn56gyaj9nl8kgy86h4fp63hjaz04"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-xelb" ,emacs-xelb)))
diff --git a/gnu/packages/patches/emacs-exwm-fix-fullscreen-issue.patch b/gnu/packages/patches/emacs-exwm-fix-fullscreen-issue.patch
deleted file mode 100644
index 5c9bd36598..0000000000
--- a/gnu/packages/patches/emacs-exwm-fix-fullscreen-issue.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-From 13a14579cc1bb772735f895dd5b4b90c6812f3ee Mon Sep 17 00:00:00 2001
-From: Chris Feng <chris.w.feng@gmail.com>
-Date: Sun, 29 Jul 2018 00:00:00 +0000
-Subject: [PATCH] Fix issues with destroying full screen X windows
-
-* exwm-manage.el (exwm-manage--unmanage-window): Set the Emacs window
-of an full screen X window as non-dedicated before killing its buffer
-so as not to cause other side effects.
----
- exwm-manage.el | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/exwm-manage.el b/exwm-manage.el
-index a0a9e05..349157f 100644
---- a/exwm-manage.el
-+++ b/exwm-manage.el
-@@ -392,6 +392,10 @@ manager is shutting down."
-                                :window window :parent exwm--root :x 0 :y 0))
-             (xcb:+request exwm--connection
-                 (make-instance 'xcb:DestroyWindow :window container))))
-+        (when (exwm-layout--fullscreen-p)
-+          (let ((window (get-buffer-window)))
-+            (when window
-+              (set-window-dedicated-p window nil))))
-         (exwm-manage--set-client-list)
-         (xcb:flush exwm--connection))
-       (let ((kill-buffer-func

From 2d4a753a7cd38a3e7b95066bc92f1c0196737b70 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Tue, 16 Oct 2018 14:23:04 +0200
Subject: [PATCH 744/909] gnu: xpra: Update to 2.4.

* gnu/packages/xorg.scm (xpra): Update to 2.4.
---
 gnu/packages/xorg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 7c80e70dac..4cf8eb2de4 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -5936,7 +5936,7 @@ basic eye-candy effects.")
 (define-public xpra
   (package
     (name "xpra")
-    (version "2.3.4")
+    (version "2.4")
     (source
      (origin
        (method url-fetch)
@@ -5944,7 +5944,7 @@ basic eye-candy effects.")
                            version ".tar.xz"))
        (sha256
         (base32
-         "0wa3kx54himy3i1b2801hlzfilh3cf4kjk40k1cjl0ds28m5hija"))))
+         "0blzx231sr1ri1zwzpwzf611sq9104bv3ccvnap9pbvfrc05sfwx"))))
     (build-system python-build-system)
     (inputs `(("ffmpeg" ,ffmpeg)
               ("flac" ,flac)

From 08f535eb2d438e52c1e84cefc1c270b9ad50620d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 16 Oct 2018 16:20:11 +0200
Subject: [PATCH 745/909] gnu: chez: Adjust to zlib static output.

* gnu/packages/chez.scm (chez-scheme)[inputs]: Add ZLIB:STATIC.
[arguments]: Reference libz.a from that instead of ZLIB.
---
 gnu/packages/chez.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/chez.scm b/gnu/packages/chez.scm
index c8e76b8ab4..929e50ee9b 100644
--- a/gnu/packages/chez.scm
+++ b/gnu/packages/chez.scm
@@ -85,6 +85,7 @@
        ("xorg-rgb" ,xorg-rgb)
        ("nanopass" ,nanopass)
        ("zlib" ,zlib)
+       ("zlib:static" ,zlib "static")
        ("stex" ,stex)))
     (native-inputs
      `(("texlive" ,texlive)
@@ -128,6 +129,7 @@
                    (nanopass (assoc-ref inputs "nanopass"))
                    (stex (assoc-ref inputs "stex"))
                    (zlib (assoc-ref inputs "zlib"))
+                   (zlib-static (assoc-ref inputs "zlib:static"))
                    (unpack (assoc-ref %standard-phases 'unpack))
                    (patch-source-shebangs
                     (assoc-ref %standard-phases 'patch-source-shebangs)))
@@ -148,7 +150,7 @@
                  (("\\$\\{Kernel\\}: \\$\\{kernelobj\\} \\.\\./zlib/libz\\.a")
                   "${Kernel}: ${kernelobj}")
                  (("ld ([-a-zA-Z0-9_${} ]+) \\.\\./zlib/libz\\.a" all args)
-                  (string-append "ld " args " " zlib "/lib/libz.a"))
+                  (string-append "ld " args " " zlib-static "/lib/libz.a"))
                  (("\\(cd \\.\\./zlib; ([-a-zA-Z0-9=./ ]+))")
                   (which "true")))
                (substitute* (find-files "mats" "Mf-.*")

From 29e53b446ccb8959db8a96161c04d98e873e2371 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 16 Oct 2018 16:30:45 +0200
Subject: [PATCH 746/909] gnu: libinput: Update to 1.12.1.

* gnu/packages/freedesktop.scm (libinput): Update to 1.12.1.
---
 gnu/packages/freedesktop.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index cf8047e5fe..8853ce1ceb 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -148,14 +148,14 @@ freedesktop.org project.")
 (define-public libinput
   (package
     (name "libinput")
-    (version "1.12.0")
+    (version "1.12.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://freedesktop.org/software/libinput/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1901wxh9k8kz3krfmvacf8xa8r4idfyisw8d80a2ql0bxiw2pb0m"))))
+                "14l6bvgq76ls63qc9c448r435q9xiig0rv8ilx6rnjvlgg64h32p"))))
     (build-system meson-build-system)
     (arguments
      `(#:configure-flags '("-Ddocumentation=false")))

From 56112a577ce445646aaddb9701f4af6b5626fb70 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 16 Oct 2018 16:44:31 +0200
Subject: [PATCH 747/909] gnu: perl-unicode-utf8: Disable tests on 32-bit
 systems.

* gnu/packages/perl.scm (perl-unicode-utf8)[arguments]: New field.
---
 gnu/packages/perl.scm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index ac71eaf07b..cadef602e4 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -43,6 +43,7 @@
   #:use-module (gnu packages)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
   #:use-module (gnu packages base)
@@ -8998,6 +8999,9 @@ defined by Annex #11 is used to determine breaking positions.")
                (base32
                 "1xnhazbdvpyfpnxd90krzhxkvabf8fa2ji6xzlrf75j6nz8251zs"))))
     (build-system perl-build-system)
+    ;; FIXME: Tests fail on 32-bit architectures:
+    ;; <https://rt.cpan.org/Public/Bug/Display.html?id=127007>.
+    (arguments `(#:tests? ,(target-64bit?)))
     (native-inputs
      `(("perl-test-fatal" ,perl-test-fatal)
        ("perl-test-leaktrace" ,perl-test-leaktrace)

From 02d5ed4a2700e8613aaf0642333734b60caff0f7 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 16 Oct 2018 12:54:17 -0400
Subject: [PATCH 748/909] gnu: GStreamer plugins: Update MP3 features for
 GStreamer 1.14.

GStreamer moved all MPEG-1 audio (mp1, mp2, and mp3) decoders and encoders to
the group of "good" plugins in GStreamer 1.14.0. See the 'NEWS' file for more
information.

* gnu/packages/gstreamer.scm (gst-plugins-ugly)[inputs]: Remove lame, mpg123,
and twolame.
(gst-plugins-bad): Remove mpg123.
(gst-plugins-good): Add lame, mpg123, and twolame.
---
 gnu/packages/gstreamer.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index f556861857..435c3e5b3a 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -227,6 +227,7 @@ for the GStreamer multimedia library.")
        ("gdk-pixbuf" ,gdk-pixbuf)
        ("gst-plugins-base" ,gst-plugins-base)
        ("jack" ,jack-1)
+       ("lame" ,lame)
        ("libavc1394" ,libavc1394)
        ("libcaca" ,libcaca)
        ("libdv" ,libdv)
@@ -236,10 +237,12 @@ for the GStreamer multimedia library.")
        ("libshout" ,libshout)
        ("libsoup" ,libsoup)
        ("libvpx" ,libvpx)
+       ("mpg123" ,mpg123)
        ("orc" ,orc)
        ("pulseaudio" ,pulseaudio)
        ("speex" ,speex)
        ("taglib" ,taglib)
+       ("twolame" ,twolame)
        ("wavpack" ,wavpack)))
     (native-inputs
      `(("glib:bin" ,glib "bin")
@@ -320,7 +323,6 @@ developers consider to have good quality code and correct functionality.")
        ("libxml2" ,libxml2)
        ("lrdf" ,lrdf)
        ("mesa" ,mesa)
-       ("mpg123" ,mpg123)
        ("neon" ,neon)
        ("openal" ,openal)
        ("openexr" ,openexr)
@@ -357,13 +359,10 @@ par compared to the rest.")
     (inputs
      `(("gst-plugins-base" ,gst-plugins-base)
        ("liba52" ,liba52)
-       ("lame" ,lame)
        ("libcdio" ,libcdio)
-       ("twolame" ,twolame)
        ("libmpeg2" ,libmpeg2)
        ("libdvdread" ,libdvdread)
        ("libx264" ,libx264)
-       ("mpg123" ,mpg123)
        ;; TODO:
        ;; * opencore-amr (for the AMR-NB decoder and encoder and the
        ;;   AMR-WB decoder) <http://sourceforge.net/projects/opencore-amr/>

From ad0082afe041af1a6e8e8f04415fdcae23e8fc0f Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Tue, 16 Oct 2018 14:35:41 +0200
Subject: [PATCH 749/909] import: json: Handle the error case.

* guix/import/json.scm (json-fetch-alist): Handle the error case.
---
 guix/import/json.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/guix/import/json.scm b/guix/import/json.scm
index 4f96a513df..81ea5e7b31 100644
--- a/guix/import/json.scm
+++ b/guix/import/json.scm
@@ -47,4 +47,5 @@ the query."
 (define (json-fetch-alist url)
   "Return an alist representation of the JSON resource URL, or #f if URL
 returns 403 or 404."
-  (hash-table->alist (json-fetch url)))
+  (and=> (json-fetch url)
+         hash-table->alist))

From c8e3651a824bbc28915802265d9a5e7cc6405eea Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@cray.com>
Date: Wed, 10 Oct 2018 13:26:54 -0500
Subject: [PATCH 750/909] gnu: guile2.0-guix: Fix build.

* gnu/packages/gnupg.scm (guile2.0-gcrypt): New variable.
* gnu/packages/guile.scm (guile2.0-sqlite3): New variable.
* gnu/packages/package-management.scm (guile2.0-guix)[propagated-inputs]: Use
them.
---
 gnu/packages/gnupg.scm              | 12 ++++++++++--
 gnu/packages/guile.scm              |  4 ++++
 gnu/packages/package-management.scm |  2 ++
 3 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 067a2338d4..c38fe64200 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015, 2018 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2018 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
@@ -67,7 +67,8 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
-  #:use-module (guix build-system python))
+  #:use-module (guix build-system python)
+  #:use-module (srfi srfi-1))
 
 (define-public libgpg-error
   (package
@@ -485,6 +486,13 @@ strong randomness, and more.  It is implemented using the foreign function
 interface (FFI) of Guile.")
     (license license:gpl3+)))
 
+(define-public guile2.0-gcrypt
+  (package (inherit guile-gcrypt)
+    (name "guile2.0-gcrypt")
+    (inputs
+     `(("guile" ,guile-2.0)
+       ,@(alist-delete "guile" (package-inputs guile-gcrypt))))))
+
 (define-public python-gpg
   (package
     (name "python-gpg")
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index e223edb9fc..912b0218ef 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
+;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1151,6 +1152,9 @@ Guile's foreign function interface.")
      "This package provides Guile bindings to the SQLite database system.")
     (license license:gpl3+)))
 
+(define-public guile2.0-sqlite3
+  (package-for-guile-2.0 guile-sqlite3))
+
 (define-public haunt
   (package
     (name "haunt")
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index fbbb4c3811..f06a39ddd6 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -367,7 +367,9 @@ the Nix package manager.")
        ,@(alist-delete "guile" (package-inputs guix))))
     (propagated-inputs
      `(("gnutls" ,gnutls/guile-2.0)
+       ("guile-gcrypt" ,guile2.0-gcrypt)
        ("guile-json" ,guile2.0-json)
+       ("guile-sqlite3" ,guile2.0-sqlite3)
        ("guile-ssh" ,guile2.0-ssh)
        ("guile-git" ,guile2.0-git)))))
 

From 6f1ce09d79fa6148459c90120881e825551651b2 Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@cray.com>
Date: Wed, 10 Oct 2018 13:33:15 -0500
Subject: [PATCH 751/909] gnu: Add guix-minimal.

* gnu/packages/guile.scm (guile-2.0.13): New variable.
* gnu/packages/package-management.scm (guix)[arguments]: Adjust 'wrap-program'
phase to handle "missing" inputs.
(guix-minimal): New variable.
---
 gnu/packages/guile.scm              | 14 ++++++++++++++
 gnu/packages/package-management.scm | 22 ++++++++++++++++++++--
 2 files changed, 34 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 912b0218ef..9e33003375 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -226,6 +226,20 @@ without requiring the source code to be rewritten.")
    (home-page "https://www.gnu.org/software/guile/")
    (license license:lgpl3+)))
 
+(define-public guile-2.0.13
+  ;; For testing a "minimal" Guix
+  (hidden-package
+   (package (inherit guile-2.0)
+     (name "guile")
+     (version "2.0.13")
+     (source (origin
+               (method url-fetch)
+               (uri (string-append "mirror://gnu/guile/guile-" version
+                                   ".tar.xz"))
+               (sha256
+                (base32
+                 "12yqkr974y91ylgw6jnmci2v90i90s7h9vxa4zk0sai8vjnz4i1p")))))))
+
 (define-public guile-2.2
   (package (inherit guile-2.0)
     (name "guile")
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index f06a39ddd6..fd01545082 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
+;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -232,13 +233,13 @@
                                         (map (cut string-append <>
                                                   "/share/guile/site/"
                                                   effective)
-                                             deps)
+                                             (delete #f deps))
                                         ":"))
                                (gopath (string-join
                                         (map (cut string-append <>
                                                   "/lib/guile/" effective
                                                   "/site-ccache")
-                                             deps)
+                                             (delete #f deps))
                                         ":")))
 
                           (wrap-program (string-append out "/bin/guix")
@@ -373,6 +374,23 @@ the Nix package manager.")
        ("guile-ssh" ,guile2.0-ssh)
        ("guile-git" ,guile2.0-git)))))
 
+(define-public guix-minimal
+  ;; A version of Guix which is built with the minimal set of dependencies, as
+  ;; outlined in the README "Requirements" section.  Intended as a CI job, so
+  ;; marked as hidden.
+  (let ((guix guile2.0-guix))
+    (hidden-package
+     (package
+       (inherit guix)
+       (name "guix-minimal")
+       (inputs
+        `(("guile" ,guile-2.0.13)
+          ,@(alist-delete "guile" (package-inputs guix))))
+       (propagated-inputs
+        (fold alist-delete
+              (package-propagated-inputs guix)
+              '("guile-json" "guile-ssh")))))))
+
 (define (source-file? file stat)
   "Return true if FILE is likely a source file, false if it is a typical
 generated file."

From 278f86a43f1561b1c064ce88da012db414ec7efc Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@cray.com>
Date: Wed, 10 Oct 2018 16:42:02 -0500
Subject: [PATCH 752/909] ui: Fix port-buffering with guile@2.0.

* guix/status.scm (build-event-output-port)[guile@2.0]: Do not call 'setvbuf'
on custom binary port.
* tests/status.scm (current-build-output-port, UTF-8 + garbage)[guile@2.0]:
Use "?" in place of REPLACEMENT CHARACTER.
---
 guix/status.scm  | 5 +++--
 tests/status.scm | 5 ++++-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/guix/status.scm b/guix/status.scm
index 8e05d4eb76..ffa9d9e93c 100644
--- a/guix/status.scm
+++ b/guix/status.scm
@@ -588,8 +588,9 @@ The second return value is a thunk to retrieve the current state."
 
   ;; The build port actually receives Unicode strings.
   (set-port-encoding! port "UTF-8")
-  (setvbuf port (cond-expand (guile-2.2 'line) (else _IOLBF)))
-
+  (cond-expand
+    ((and guile-2 (not guile-2.2)) #t)
+    (else (setvbuf port 'line)))
   (values port (lambda () %state)))
 
 (define (call-with-status-report on-event thunk)
diff --git a/tests/status.scm b/tests/status.scm
index 3b74946673..99abb41c8b 100644
--- a/tests/status.scm
+++ b/tests/status.scm
@@ -125,7 +125,10 @@
 
 (test-equal "current-build-output-port, UTF-8 + garbage"
   ;; What about a mixture of UTF-8 + garbage?
-  '((build-log #f "garbage: �lambda: λ\n"))
+  (let ((replacement (cond-expand
+                      ((and guile-2 (not guile-2.2)) "?")
+                      (else "�"))))
+    `((build-log #f ,(string-append "garbage: " replacement "lambda: λ\n"))))
   (let-values (((port get-status) (build-event-output-port cons '())))
     (display "garbage: " port)
     (put-bytevector port #vu8(128))

From 24220e0f09592ae6a3991929a62f79eff2d1df44 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Date: Tue, 16 Oct 2018 22:40:44 -0400
Subject: [PATCH 753/909] gnu: emacs-nodejs-repl: Update to 0.2.0.

* gnu/packages/emacs.scm (emacs-nodejs-repl): Update to 0.2.0.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index d30a4cc568..f7ee26179a 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -4307,14 +4307,14 @@ strings, and code folding.")
 (define-public emacs-nodejs-repl
   (package
     (name "emacs-nodejs-repl")
-    (version "0.1.6")
+    (version "0.2.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/abicky/nodejs-repl.el"
                                   "/archive/" version ".tar.gz"))
               (sha256
                (base32
-                "0sphg1jxi3a5l0gqdp27d0qgyjaiq2p293av9zm8ksm0vwqp3fr9"))
+                "0hq2cqdq2668yf48g7qnkci90nhih1gnhacsgz355jnib56lhmkz"))
               (file-name (string-append name "-" version ".tar.gz"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/abicky/nodejs-repl.el")

From da39ff58987d7ed082233ab9ac3ae8d6d0f50b5d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 17 Oct 2018 10:54:58 +0300
Subject: [PATCH 754/909] gnu: boost-for-mysql: Remove unnecessary phase.

* gnu/packages/boost.scm (boost-for-mysql)[arguments]: Remove custom
'provide-libboost_python phase. Add removed '/bin/sh' substitution.
---
 gnu/packages/boost.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm
index d1b359b2cb..897987f71c 100644
--- a/gnu/packages/boost.scm
+++ b/gnu/packages/boost.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,6 +28,7 @@
 
 (define-module (gnu packages boost)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
@@ -134,6 +136,15 @@ across a broad spectrum of applications.")
               (sha256
                (base32
                 "1jj1aai5rdmd72g90a3pd8sw9vi32zad46xv5av8fhnr48ir6ykj"))))
+    (arguments (substitute-keyword-arguments (package-arguments boost)
+      ((#:phases phases)
+       `(modify-phases ,phases
+          ;; This was removed after boost-1.67.
+          (add-before 'configure 'more-bin-sh-patching
+            (lambda _
+              (substitute* "tools/build/doc/bjam.qbk"
+                (("/bin/sh") (which "sh")))))
+          (delete 'provide-libboost_python)))))
     (properties '((hidden? . #t)))))
 
 (define-public boost-sync

From 15b283e712a23cbffc9a50bebc8bca94283a3fe6 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 17 Oct 2018 11:24:07 +0300
Subject: [PATCH 755/909] gnu: streamlink: Update to 0.14.2.

* gnu/packages/video.scm (streamlink): Update to 0.14.2.
[source]: Download from pypi.
---
 gnu/packages/video.scm | 63 +++++++++++++++++++-----------------------
 1 file changed, 29 insertions(+), 34 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 88357dfb45..ab57ee4b45 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1860,41 +1860,36 @@ and custom quantization matrices.")
     (license license:gpl2+)))
 
 (define-public streamlink
-  ;; Release tarball doesn't contain ‘tests/resources/dash/’ directory.
-  (let ((commit "2dca7930a938f60b48d8e23260963ea7c49d979f"))
-    (package
-      (name "streamlink")
-      (version (git-version "0.13.0" "1" commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/streamlink/streamlink.git")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "0vq19aspshim63aj8yl2p64ykrbk2mwwlawdx427b3j2djlc5qhw"))))
-      (build-system python-build-system)
-      (home-page "https://github.com/streamlink/streamlink")
-      (native-inputs
-       `(("python-freezegun" ,python-freezegun)
-         ("python-pytest" ,python-pytest)
-         ("python-mock" ,python-mock)
-         ("python-requests-mock" ,python-requests-mock)))
-      (propagated-inputs
-       `(("python-pysocks" ,python-pysocks)
-         ("python-websocket-client" ,python-websocket-client)
-         ("python-iso3166" ,python-iso3166)
-         ("python-iso639" ,python-iso639)
-         ("python-isodate", python-isodate)
-         ("python-pycryptodome" ,python-pycryptodome)
-         ("python-requests" ,python-requests)
-         ("python-urllib3" ,python-urllib3)))
-      (synopsis "Extract streams from various services")
-      (description "Streamlink is command-line utility that extracts streams
+  (package
+    (name "streamlink")
+    (version "0.14.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "streamlink" version))
+        (sha256
+         (base32
+          "0l2145fd60i76afjisfxd48cwhwyir07i7s3bnimdq5db2kzkix8"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/streamlink/streamlink")
+    (native-inputs
+     `(("python-freezegun" ,python-freezegun)
+       ("python-pytest" ,python-pytest)
+       ("python-mock" ,python-mock)
+       ("python-requests-mock" ,python-requests-mock)))
+    (propagated-inputs
+     `(("python-pysocks" ,python-pysocks)
+       ("python-websocket-client" ,python-websocket-client)
+       ("python-iso3166" ,python-iso3166)
+       ("python-iso639" ,python-iso639)
+       ("python-isodate", python-isodate)
+       ("python-pycryptodome" ,python-pycryptodome)
+       ("python-requests" ,python-requests)
+       ("python-urllib3" ,python-urllib3)))
+    (synopsis "Extract streams from various services")
+    (description "Streamlink is command-line utility that extracts streams
 from sites like Twitch.tv and pipes them into a video player of choice.")
-      (license license:bsd-2))))
+    (license license:bsd-2)))
 
 (define-public livestreamer
   (deprecated-package "livestreamer" streamlink))

From 05f8943f048c30920b0a6dd546400d7c19740d10 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 17 Oct 2018 10:35:40 +0200
Subject: [PATCH 756/909] gnu: emacs-helm-system-packages: Add recutils to
 inputs.

* gnu/packages/emacs.scm (emacs-helm-system-packages)[inputs]: Use recutils.
---
 gnu/packages/emacs.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index f7ee26179a..57841e86fa 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5929,8 +5929,20 @@ Yasnippet.")
                (base32
                 "01by0c4lqi2cw8xmbxkjw7m9x78zssm31sx4hdpw5j35s2951j0f"))))
     (build-system emacs-build-system)
+    (inputs
+     `(("recutils" ,recutils)))
     (propagated-inputs
      `(("emacs-helm" ,emacs-helm)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((recutils (assoc-ref inputs "recutils")))
+               ;; Specify the absolute file names of the various
+               ;; programs so that everything works out-of-the-box.
+               (substitute* "helm-system-packages-guix.el"
+                 (("recsel") (string-append recutils "/bin/recsel")))))))))
     (home-page "https://github.com/emacs-helm/helm-system-packages")
     (synopsis "Helm System Packages is an interface to your package manager")
     (description "List all available packages in Helm (with installed

From fb3ff265cd8c6b4c6160f94240dc8932097e637b Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 17 Oct 2018 11:17:26 +0300
Subject: [PATCH 757/909] gnu: python-icalendar: Update to 4.0.3.

* gnu/packages/python.scm (python-icalendar): Update to 4.0.3.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 1667f4801b..2e88b0bc51 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7475,13 +7475,13 @@ minimal and fast API targeting the following uses:
 (define-public python-icalendar
   (package
     (name "python-icalendar")
-    (version "4.0.1")
+    (version "4.0.3")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "icalendar" version))
              (sha256
               (base32
-               "139y79y6ijl39m5bj771r43vpah9s4ly7d1k76la6hrx7l144ak8"))))
+               "0mk3dk1dxkcm46jy48v27j2w2349iv4sbimqj1yb5js43mx49hh7"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil" ,python-dateutil)

From c4d62443eb50a615d47b590a7fedcc7f7f0ec100 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 17 Oct 2018 13:06:25 +0200
Subject: [PATCH 758/909] import cran: Document "recursive" option.

* guix/scripts/import/cran.scm: (show-help): Document "recursive" option.
---
 guix/scripts/import/cran.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/guix/scripts/import/cran.scm b/guix/scripts/import/cran.scm
index 30ae6d4342..794fb710cd 100644
--- a/guix/scripts/import/cran.scm
+++ b/guix/scripts/import/cran.scm
@@ -47,6 +47,8 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
   (display (G_ "
   -h, --help             display this help and exit"))
   (display (G_ "
+  -r, --recursive        import packages recursively"))
+  (display (G_ "
   -V, --version          display version information and exit"))
   (newline)
   (show-bug-report-information))

From 82402f76bebfa3bb563a58227eb4081f9bdb6142 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Mon, 15 Oct 2018 20:00:03 -0400
Subject: [PATCH 759/909] gnu: hyperrogue: Update to 10.4t.

* gnu/packages/games.scm (hyperrogue): Update to 10.4t.
[arguments]: Modify 'make-flags'. Modify 'configure' and 'install' phases.
---
 gnu/packages/games.scm | 27 ++++++++++++++++-----------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 2547c72c23..972dec3419 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -3658,7 +3658,7 @@ throwing people around in pseudo-randomly generated buildings.")
 (define-public hyperrogue
   (package
     (name "hyperrogue")
-    (version "10.4j")
+    (version "10.4t")
     ;; When updating this package, be sure to update the "hyperrogue-data"
     ;; origin in native-inputs.
     (source (origin
@@ -3669,11 +3669,12 @@ throwing people around in pseudo-randomly generated buildings.")
                     "-src.tgz"))
               (sha256
                (base32
-                "0909p4xvbi1c2jc5rdgrf8b1c60fmsaapabsi6yyglh5znkf0k27"))))
+                "0phqhmnzmc16a23qb4fkil0flzb86kibdckf1r35nc3l0k4193nn"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no check target
-       #:make-flags '("CXXFLAGS=-std=c++11")
+       #:make-flags '("HYPERROGUE_USE_GLEW=1"
+                      "HYPERROGUE_USE_PNG=1")
        #:phases
        (modify-phases %standard-phases
          (add-after 'set-paths 'set-sdl-paths
@@ -3696,12 +3697,16 @@ throwing people around in pseudo-randomly generated buildings.")
                   (string-append dejavu-dir "/" dejavu-font)))
                (substitute* music-file
                  (("\\*/")
-                  (string-append share-dir "/sounds/"))))
-             ;; Fix Makefile.
-             (substitute* "Makefile"
-               (("g\\+\\+ langen.cpp")
-                "g++ langen.cpp ${CXXFLAGS}")
-               (("savepng.c") "savepng.cpp"))
+                  (string-append share-dir "/sounds/")))
+               (substitute* "sound.cpp"
+                 (("musicfile = \"\"")
+                  (string-append "musicfile = \""
+                                 share-dir "/" music-file "\"")))
+               ;; Disable build machine CPU optimizations and warnings treated
+               ;; as errors.
+               (substitute* "Makefile"
+                 (("-march=native") "")
+                 (("-Werror") "")))
              #t))
          (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -3709,7 +3714,7 @@ throwing people around in pseudo-randomly generated buildings.")
                     (bin (string-append out "/bin"))
                     (share-dir (string-append out "/share/hyperrogue")))
                (mkdir-p bin)
-               (copy-file "hyper" (string-append bin "/hyperrogue"))
+               (install-file "hyperrogue" bin)
                (install-file "hyperrogue-music.txt" share-dir))
              #t))
          (add-after 'install 'install-data
@@ -3741,7 +3746,7 @@ throwing people around in pseudo-randomly generated buildings.")
              "-win.zip"))
            (sha256
             (base32
-             "0w61iv2rn93hi0q3hxyyyf9xcr8vi9zd7fjvpz5adpgf94jm3zsc"))))
+             "1xd9v8zzgi8m5ar8g4gy1xx5zqwidz3gn1knz0lwib3kbxx4drpg"))))
        ("unzip" ,unzip)))
     (inputs
      `(("font-dejavu" ,font-dejavu)

From 1d43756107077797e0168190ac12ee2564c8e76d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 17 Oct 2018 21:10:19 +0300
Subject: [PATCH 760/909] gnu: strace: Check before enabling personalities.

* gnu/packages/linux.scm (strace)[arguments]: Add configure flag to
check for personality support.
---
 gnu/packages/linux.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 79a1b0b46a..cd4adf9b6f 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -961,6 +961,8 @@ Zerofree requires the file system to be unmounted or mounted read-only.")
              (substitute* "strace.c"
                (("/bin/sh") (which "sh")))
              #t)))
+       ;; Don't fail if the architecture doesn't support different personalities.
+       #:configure-flags '("--enable-mpers=check")
        ;; See <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=32459>.
        #:parallel-tests? #f))           ; undeterministic failures
     (native-inputs `(("perl" ,perl)))

From 90aeaee861845142843a0f988fa4ff016c723cdb Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 6 Oct 2018 16:47:05 +0200
Subject: [PATCH 761/909] gnu: python: Fix CVE-2018-14647.

* gnu/packages/patches/python-CVE-2018-14647.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/python.scm (python-3/fixed): New variable.
(python-3.6)[replacement]: New field.
(python-minimal, python-debug, wrap-python3): Use PACKAGE/INHERIT instead of
standard inheritance.
---
 gnu/local.mk                                  |  1 +
 .../patches/python-CVE-2018-14647.patch       | 61 +++++++++++++++++++
 gnu/packages/python.scm                       | 26 ++++++--
 3 files changed, 84 insertions(+), 4 deletions(-)
 create mode 100644 gnu/packages/patches/python-CVE-2018-14647.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index b8248e8da0..d30bbedee6 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1076,6 +1076,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-3-deterministic-build-info.patch	\
   %D%/packages/patches/python-3-search-paths.patch		\
   %D%/packages/patches/python-3-fix-tests.patch			\
+  %D%/packages/patches/python-CVE-2018-14647.patch		\
   %D%/packages/patches/python-axolotl-AES-fix.patch		\
   %D%/packages/patches/python-cairocffi-dlopen-path.patch	\
   %D%/packages/patches/python-fix-tests.patch			\
diff --git a/gnu/packages/patches/python-CVE-2018-14647.patch b/gnu/packages/patches/python-CVE-2018-14647.patch
new file mode 100644
index 0000000000..24f8d21820
--- /dev/null
+++ b/gnu/packages/patches/python-CVE-2018-14647.patch
@@ -0,0 +1,61 @@
+Fix CVE-2018-14647:
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-14647
+https://bugs.python.org/issue34623
+
+Taken from upstream:
+https://github.com/python/cpython/commit/f7666e828cc3d5873136473ea36ba2013d624fa1
+
+diff --git Include/pyexpat.h Include/pyexpat.h
+index 44259bf6d7..07020b5dc9 100644
+--- Include/pyexpat.h
++++ Include/pyexpat.h
+@@ -3,7 +3,7 @@
+ 
+ /* note: you must import expat.h before importing this module! */
+ 
+-#define PyExpat_CAPI_MAGIC  "pyexpat.expat_CAPI 1.0"
++#define PyExpat_CAPI_MAGIC  "pyexpat.expat_CAPI 1.1"
+ #define PyExpat_CAPSULE_NAME "pyexpat.expat_CAPI"
+ 
+ struct PyExpat_CAPI
+@@ -48,6 +48,8 @@ struct PyExpat_CAPI
+     enum XML_Status (*SetEncoding)(XML_Parser parser, const XML_Char *encoding);
+     int (*DefaultUnknownEncodingHandler)(
+         void *encodingHandlerData, const XML_Char *name, XML_Encoding *info);
++    /* might be none for expat < 2.1.0 */
++    int (*SetHashSalt)(XML_Parser parser, unsigned long hash_salt);
+     /* always add new stuff to the end! */
+ };
+ 
+diff --git Modules/_elementtree.c Modules/_elementtree.c
+index 707ab2912b..53f05f937f 100644
+--- Modules/_elementtree.c
++++ Modules/_elementtree.c
+@@ -3261,6 +3261,11 @@ _elementtree_XMLParser___init___impl(XMLParserObject *self, PyObject *html,
+         PyErr_NoMemory();
+         return -1;
+     }
++    /* expat < 2.1.0 has no XML_SetHashSalt() */
++    if (EXPAT(SetHashSalt) != NULL) {
++        EXPAT(SetHashSalt)(self->parser,
++                           (unsigned long)_Py_HashSecret.expat.hashsalt);
++    }
+ 
+     if (target) {
+         Py_INCREF(target);
+diff --git Modules/pyexpat.c Modules/pyexpat.c
+index 47c3e86c20..aa21d93c11 100644
+--- Modules/pyexpat.c
++++ Modules/pyexpat.c
+@@ -1887,6 +1887,11 @@ MODULE_INITFUNC(void)
+     capi.SetStartDoctypeDeclHandler = XML_SetStartDoctypeDeclHandler;
+     capi.SetEncoding = XML_SetEncoding;
+     capi.DefaultUnknownEncodingHandler = PyUnknownEncodingHandler;
++#if XML_COMBINED_VERSION >= 20100
++    capi.SetHashSalt = XML_SetHashSalt;
++#else
++    capi.SetHashSalt = NULL;
++#endif
+ 
+     /* export using capsule */
+     capi_object = PyCapsule_New(&capi, PyExpat_CAPSULE_NAME, NULL);
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8261fefd93..3e39866087 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -357,6 +357,7 @@ data types.")
   (package (inherit python-2)
     (name "python")
     (version "3.6.5")
+    (replacement python-3/fixed)
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.python.org/ftp/python/"
@@ -456,6 +457,24 @@ data types.")
 ;; Current 3.x version.
 (define-public python-3 python-3.6)
 
+(define python-3/fixed
+  (package
+    (inherit python-3)
+    (source (origin
+              (inherit (package-source python-3))
+              (patches (append (origin-patches (package-source python-3))
+                               (search-patches "python-CVE-2018-14647.patch")))))
+    (arguments
+     (substitute-keyword-arguments (package-arguments python-3)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'delete-broken-test
+             (lambda _
+               ;; Delete test which fails on recent kernels:
+               ;; <https://bugs.python.org/issue34587>.
+               (delete-file "Lib/test/test_socket.py")
+               #t))))))))
+
 ;; Current major version.
 (define-public python python-3)
 
@@ -474,7 +493,7 @@ data types.")
               ("zlib" ,zlib)))))
 
 (define-public python-minimal
-  (package (inherit python)
+  (package/inherit python
     (name "python-minimal")
     (outputs '("out"))
 
@@ -486,8 +505,7 @@ data types.")
               ("zlib" ,zlib)))))
 
 (define-public python-debug
-  (package
-    (inherit python)
+  (package/inherit python
     (name "python-debug")
     (outputs '("out" "debug"))
     (build-system gnu-build-system)
@@ -506,7 +524,7 @@ for more information.")))
 (define* (wrap-python3 python
                        #:optional
                        (name (string-append (package-name python) "-wrapper")))
-  (package (inherit python)
+  (package/inherit python
     (name name)
     (source #f)
     (build-system trivial-build-system)

From a55ebe2e3a7b438b4eec06c594440d3a0fb06a25 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 6 Oct 2018 18:50:47 +0200
Subject: [PATCH 762/909] gnu: python2: Add upstream security fixes.

This addresses CVE-2018-{1060,1061,14647,1000802}.

* gnu/packages/patches/python2-CVE-2018-1000802.patch,
gnu/packages/patches/python2-CVE-2018-1060.patch,
gnu/packages/patches/python2-CVE-2018-1061.patch,
gnu/packages/patches/python2-CVE-2018-14647.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/python.scm (python-2/fixed): New variable.
(python-2.7)[replacement]: New field.
(python2-minimal): Use PACKAGE/INHERIT.
---
 gnu/local.mk                                  |  4 ++
 .../patches/python2-CVE-2018-1000802.patch    | 47 ++++++++++++++
 .../patches/python2-CVE-2018-1060.patch       | 20 ++++++
 .../patches/python2-CVE-2018-1061.patch       | 20 ++++++
 .../patches/python2-CVE-2018-14647.patch      | 61 +++++++++++++++++++
 gnu/packages/python.scm                       | 15 ++++-
 6 files changed, 166 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/python2-CVE-2018-1000802.patch
 create mode 100644 gnu/packages/patches/python2-CVE-2018-1060.patch
 create mode 100644 gnu/packages/patches/python2-CVE-2018-1061.patch
 create mode 100644 gnu/packages/patches/python2-CVE-2018-14647.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index d30bbedee6..402505e229 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1068,6 +1068,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/pygpgme-disable-problematic-tests.patch  \
   %D%/packages/patches/pyqt-configure.patch			\
   %D%/packages/patches/pyqt-public-sip.patch			\
+  %D%/packages/patches/python2-CVE-2018-1060.patch		\
+  %D%/packages/patches/python2-CVE-2018-1061.patch		\
+  %D%/packages/patches/python2-CVE-2018-14647.patch		\
+  %D%/packages/patches/python2-CVE-2018-1000802.patch		\
   %D%/packages/patches/python-2-deterministic-build-info.patch	\
   %D%/packages/patches/python-2.7-adjust-tests.patch		\
   %D%/packages/patches/python-2.7-search-paths.patch		\
diff --git a/gnu/packages/patches/python2-CVE-2018-1000802.patch b/gnu/packages/patches/python2-CVE-2018-1000802.patch
new file mode 100644
index 0000000000..0d5bc77c84
--- /dev/null
+++ b/gnu/packages/patches/python2-CVE-2018-1000802.patch
@@ -0,0 +1,47 @@
+Fix CVE-2018-1000802:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1000802
+
+Taken from upstream commit (sans NEWS):
+https://github.com/python/cpython/commit/d8b103b8b3ef9644805341216963a64098642435
+
+diff --git a/Lib/shutil.py b/Lib/shutil.py
+index 3462f7c5e9..0ab1a06f52 100644
+--- a/Lib/shutil.py
++++ b/Lib/shutil.py
+@@ -413,17 +413,21 @@ def _make_tarball(base_name, base_dir, compress="gzip", verbose=0, dry_run=0,
+ 
+     return archive_name
+ 
+-def _call_external_zip(base_dir, zip_filename, verbose=False, dry_run=False):
++def _call_external_zip(base_dir, zip_filename, verbose, dry_run, logger):
+     # XXX see if we want to keep an external call here
+     if verbose:
+         zipoptions = "-r"
+     else:
+         zipoptions = "-rq"
+-    from distutils.errors import DistutilsExecError
+-    from distutils.spawn import spawn
++    cmd = ["zip", zipoptions, zip_filename, base_dir]
++    if logger is not None:
++        logger.info(' '.join(cmd))
++    if dry_run:
++        return
++    import subprocess
+     try:
+-        spawn(["zip", zipoptions, zip_filename, base_dir], dry_run=dry_run)
+-    except DistutilsExecError:
++        subprocess.check_call(cmd)
++    except subprocess.CalledProcessError:
+         # XXX really should distinguish between "couldn't find
+         # external 'zip' command" and "zip failed".
+         raise ExecError, \
+@@ -458,7 +462,7 @@ def _make_zipfile(base_name, base_dir, verbose=0, dry_run=0, logger=None):
+         zipfile = None
+ 
+     if zipfile is None:
+-        _call_external_zip(base_dir, zip_filename, verbose, dry_run)
++        _call_external_zip(base_dir, zip_filename, verbose, dry_run, logger)
+     else:
+         if logger is not None:
+             logger.info("creating '%s' and adding '%s' to it",
diff --git a/gnu/packages/patches/python2-CVE-2018-1060.patch b/gnu/packages/patches/python2-CVE-2018-1060.patch
new file mode 100644
index 0000000000..5eb7ccfbc9
--- /dev/null
+++ b/gnu/packages/patches/python2-CVE-2018-1060.patch
@@ -0,0 +1,20 @@
+Fix CVE-2018-1060:
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1060
+
+Taken from upstream commit (sans test and NEWS):
+https://github.com/python/cpython/commit/e052d40cea15f582b50947f7d906b39744dc62a2
+
+diff --git a/Lib/poplib.py b/Lib/poplib.py
+index b91e5f72d2ca..a238510b38fc 100644
+--- a/Lib/poplib.py
++++ b/Lib/poplib.py
+@@ -274,7 +274,7 @@ def rpop(self, user):
+         return self._shortcmd('RPOP %s' % user)
+ 
+ 
+-    timestamp = re.compile(r'\+OK.*(<[^>]+>)')
++    timestamp = re.compile(br'\+OK.[^<]*(<.*>)')
+ 
+     def apop(self, user, secret):
+         """Authorisation
+
diff --git a/gnu/packages/patches/python2-CVE-2018-1061.patch b/gnu/packages/patches/python2-CVE-2018-1061.patch
new file mode 100644
index 0000000000..6caab24b4d
--- /dev/null
+++ b/gnu/packages/patches/python2-CVE-2018-1061.patch
@@ -0,0 +1,20 @@
+Fix CVE-2018-1061:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1061
+
+Taken from upstream commit (sans test and NEWS):
+https://github.com/python/cpython/commit/e052d40cea15f582b50947f7d906b39744dc62a2
+
+diff --git a/Lib/difflib.py b/Lib/difflib.py
+index 1c6fbdbedcb7..788a92df3f89 100644
+--- a/Lib/difflib.py
++++ b/Lib/difflib.py
+@@ -1103,7 +1103,7 @@ def _qformat(self, aline, bline, atags, btags):
+ 
+ import re
+ 
+-def IS_LINE_JUNK(line, pat=re.compile(r"\s*#?\s*$").match):
++def IS_LINE_JUNK(line, pat=re.compile(r"\s*(?:#\s*)?$").match):
+     r"""
+     Return 1 for ignorable line: iff `line` is blank or contains a single '#'.
+
diff --git a/gnu/packages/patches/python2-CVE-2018-14647.patch b/gnu/packages/patches/python2-CVE-2018-14647.patch
new file mode 100644
index 0000000000..6226b06aca
--- /dev/null
+++ b/gnu/packages/patches/python2-CVE-2018-14647.patch
@@ -0,0 +1,61 @@
+Fix CVE-2018-14647:
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-14647
+https://bugs.python.org/issue34623
+
+Taken from upstream:
+https://github.com/python/cpython/commit/18b20bad75b4ff0486940fba4ec680e96e70f3a2
+
+diff --git a/Include/pyexpat.h b/Include/pyexpat.h
+index 5340ef5fa3..3fc5fa54da 100644
+--- a/Include/pyexpat.h
++++ b/Include/pyexpat.h
+@@ -3,7 +3,7 @@
+ 
+ /* note: you must import expat.h before importing this module! */
+ 
+-#define PyExpat_CAPI_MAGIC  "pyexpat.expat_CAPI 1.0"
++#define PyExpat_CAPI_MAGIC  "pyexpat.expat_CAPI 1.1"
+ #define PyExpat_CAPSULE_NAME "pyexpat.expat_CAPI"
+ 
+ struct PyExpat_CAPI 
+@@ -43,6 +43,8 @@ struct PyExpat_CAPI
+         XML_Parser parser, XML_UnknownEncodingHandler handler,
+         void *encodingHandlerData);
+     void (*SetUserData)(XML_Parser parser, void *userData);
++    /* might be none for expat < 2.1.0 */
++    int (*SetHashSalt)(XML_Parser parser, unsigned long hash_salt);
+     /* always add new stuff to the end! */
+ };
+ 
+diff --git a/Modules/_elementtree.c b/Modules/_elementtree.c
+index f7f992dd3a..b38e0ab329 100644
+--- a/Modules/_elementtree.c
++++ b/Modules/_elementtree.c
+@@ -2574,6 +2574,11 @@ xmlparser(PyObject* self_, PyObject* args, PyObject* kw)
+         PyErr_NoMemory();
+         return NULL;
+     }
++    /* expat < 2.1.0 has no XML_SetHashSalt() */
++    if (EXPAT(SetHashSalt) != NULL) {
++        EXPAT(SetHashSalt)(self->parser,
++                           (unsigned long)_Py_HashSecret.prefix);
++    }
+ 
+     ALLOC(sizeof(XMLParserObject), "create expatparser");
+ 
+diff --git a/Modules/pyexpat.c b/Modules/pyexpat.c
+index 2b4d31293c..1f8c0d70a5 100644
+--- a/Modules/pyexpat.c
++++ b/Modules/pyexpat.c
+@@ -2042,6 +2042,11 @@ MODULE_INITFUNC(void)
+     capi.SetProcessingInstructionHandler = XML_SetProcessingInstructionHandler;
+     capi.SetUnknownEncodingHandler = XML_SetUnknownEncodingHandler;
+     capi.SetUserData = XML_SetUserData;
++#if XML_COMBINED_VERSION >= 20100
++    capi.SetHashSalt = XML_SetHashSalt;
++#else
++    capi.SetHashSalt = NULL;
++#endif
+ 
+     /* export using capsule */
+     capi_object = PyCapsule_New(&capi, PyExpat_CAPSULE_NAME, NULL);
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3e39866087..e3a04b0344 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -148,6 +148,7 @@
   (package
     (name "python2")
     (version "2.7.14")
+    (replacement python-2/fixed)
     (source
      (origin
       (method url-fetch)
@@ -344,6 +345,18 @@ data types.")
 ;; Current 2.x version.
 (define-public python-2 python-2.7)
 
+(define python-2/fixed
+  (package
+    (inherit python-2)
+    (source (origin
+              (inherit (package-source python-2))
+              (patches (append
+                        (origin-patches (package-source python-2))
+                        (search-patches "python2-CVE-2018-1060.patch"
+                                        "python2-CVE-2018-1061.patch"
+                                        "python2-CVE-2018-14647.patch"
+                                        "python2-CVE-2018-1000802.patch")))))))
+
 (define-public python2-called-python
   ;; Both 2.x and 3.x used to be called "python".  In commit
   ;; a7714d42de2c3082f3609d1e63c83d703fb39cf9 (March 2018), we renamed the
@@ -482,7 +495,7 @@ data types.")
 ;; Python (Tk -> libxcb -> Python.)
 
 (define-public python2-minimal
-  (package (inherit python-2)
+  (package/inherit python-2
     (name "python2-minimal")
     (outputs '("out"))
 

From acce0a474c1493ab18912bc46285248e4ccb0314 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Mon, 9 Apr 2018 01:04:10 +0200
Subject: [PATCH 763/909] services: wpa-supplicant: Extend to support
 configuration parameters.

This allows using WPA Supplicant "standalone" without an additional
network manager.  The default configuration is unchanged.

* gnu/services/networking.scm (<wpa-supplicant-configuration>): New record type.
(wpa-supplicant-shepherd-service): Pass configuration records to the daemon.
(wpa-supplicant-service-type): Adjust accordingly.
* doc/guix.texi (Networking Services): Document the new service type.
---
 doc/guix.texi               | 39 ++++++++++++-----
 gnu/services/networking.scm | 84 ++++++++++++++++++++++++++++---------
 2 files changed, 92 insertions(+), 31 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 5ae80917a9..2cea52f02b 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -11737,19 +11737,36 @@ When true, enable connman's vpn plugin.
 @defvr {Scheme Variable} wpa-supplicant-service-type
 This is the service type to run @url{https://w1.fi/wpa_supplicant/,WPA
 supplicant}, an authentication daemon required to authenticate against
-encrypted WiFi or ethernet networks.  It is configured to listen for
-requests on D-Bus.
-
-The value of this service is the @code{wpa-supplicant} package to use.
-Thus, it can be instantiated like this:
-
-@lisp
-(use-modules (gnu services networking))
-
-(service wpa-supplicant-service-type)
-@end lisp
+encrypted WiFi or ethernet networks.
 @end defvr
 
+@deftp {Data Type} wpa-supplicant-configuration
+Data type representing the configuration of WPA Supplicant.
+
+It takes the following parameters:
+
+@table @asis
+@item @code{wpa-supplicant} (default: @code{wpa-supplicant})
+The WPA Supplicant package to use.
+
+@item @code{dbus?} (default: @code{#t})
+Whether to listen for requests on D-Bus.
+
+@item @code{pid-file} (default: @code{"/var/run/wpa_supplicant.pid"})
+Where to store the PID file.
+
+@item @code{interface} (default: @code{#f})
+If this is set, it must specify the name of a network interface that
+WPA supplicant will control.
+
+@item @code{config-file} (default: @code{#f})
+Optional configuration file to use.
+
+@item @code{extra-options} (default: @code{'()})
+List of additional command-line arguments to pass to the daemon.
+@end table
+@end deftp
+
 @cindex iptables
 @defvr {Scheme Variable} iptables-service-type
 This is the service type to set up an iptables configuration. iptables is a
diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index 3fdb2bb9f7..c809b4a4a4 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
@@ -101,6 +101,16 @@
             modem-manager-configuration
             modem-manager-configuration?
             modem-manager-service-type
+
+            <wpa-supplicant-configuration>
+            wpa-supplicant-configuration
+            wpa-supplicant-configuration?
+            wpa-supplicant-configuration-wpa-supplicant
+            wpa-supplicant-configuration-pid-file
+            wpa-supplicant-configuration-dbus?
+            wpa-supplicant-configuration-interface
+            wpa-supplicant-configuration-config-file
+            wpa-supplicant-configuration-extra-options
             wpa-supplicant-service-type
 
             openvswitch-service-type
@@ -1019,28 +1029,62 @@ networking."))))
 ;;; WPA supplicant
 ;;;
 
+(define-record-type* <wpa-supplicant-configuration>
+  wpa-supplicant-configuration make-wpa-supplicant-configuration
+  wpa-supplicant-configuration?
+  (wpa-supplicant     wpa-supplicant-configuration-wpa-supplicant ;<package>
+                      (default wpa-supplicant))
+  (pid-file           wpa-supplicant-configuration-pid-file       ;string
+                      (default "/var/run/wpa_supplicant.pid"))
+  (dbus?              wpa-supplicant-configuration-dbus?          ;Boolean
+                      (default #t))
+  (interface          wpa-supplicant-configuration-interface      ;#f | string
+                      (default #f))
+  (config-file        wpa-supplicant-configuration-config-file    ;#f | <file-like>
+                      (default #f))
+  (extra-options      wpa-supplicant-configuration-extra-options  ;list of strings
+                      (default '())))
 
-(define (wpa-supplicant-shepherd-service wpa-supplicant)
-  "Return a shepherd service for wpa_supplicant"
-  (list (shepherd-service
-         (documentation "Run WPA supplicant with dbus interface")
-         (provision '(wpa-supplicant))
-         (requirement '(user-processes dbus-system loopback))
-         (start #~(make-forkexec-constructor
-                   (list (string-append #$wpa-supplicant
-                                        "/sbin/wpa_supplicant")
-                         "-u" "-B" "-P/var/run/wpa_supplicant.pid")
-                   #:pid-file "/var/run/wpa_supplicant.pid"))
-         (stop #~(make-kill-destructor)))))
+(define wpa-supplicant-shepherd-service
+  (match-lambda
+    (($ <wpa-supplicant-configuration> wpa-supplicant pid-file dbus? interface
+                                       config-file extra-options)
+     (list (shepherd-service
+            (documentation "Run the WPA supplicant daemon")
+            (provision '(wpa-supplicant))
+            (requirement '(user-processes dbus-system loopback))
+            (start #~(make-forkexec-constructor
+                      (list (string-append #$wpa-supplicant
+                                           "/sbin/wpa_supplicant")
+                            (string-append "-P" #$pid-file)
+                            "-B"        ;run in background
+                            #$@(if dbus?
+                                   #~("-u")
+                                   #~())
+                            #$@(if interface
+                                   #~(string-append "-i" #$interface)
+                                   #~())
+                            #$@(if config-file
+                                   #~(string-append "-c" #$config-file)
+                                   #~())
+                            #$@extra-options)
+                      #:pid-file #$pid-file))
+            (stop #~(make-kill-destructor)))))))
 
 (define wpa-supplicant-service-type
-  (service-type (name 'wpa-supplicant)
-                (extensions
-                 (list (service-extension shepherd-root-service-type
-                                          wpa-supplicant-shepherd-service)
-                       (service-extension dbus-root-service-type list)
-                       (service-extension profile-service-type list)))
-                (default-value wpa-supplicant)))
+  (let ((config->package
+         (match-lambda
+           (($ <wpa-supplicant-configuration> wpa-supplicant)
+            (list wpa-supplicant)))))
+    (service-type (name 'wpa-supplicant)
+                  (extensions
+                   (list (service-extension shepherd-root-service-type
+                                            wpa-supplicant-shepherd-service)
+                         (service-extension dbus-root-service-type config->package)
+                         (service-extension profile-service-type config->package)))
+                  (description "Run the WPA Supplicant daemon, a service that
+implements authentication, key negotiation and more for wireless networks.")
+                  (default-value (wpa-supplicant-configuration)))))
 
 
 ;;;

From 16f14f63db7a370d3917cf9c7d7e3735b0f59855 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 17 Oct 2018 20:53:24 +0200
Subject: [PATCH 764/909] gnu: Python: Adjust grafts for core-updates merge.

This adjust the grafts from a55ebe2e3a7b438b4eec06c594440d3a0fb06a25 and
90aeaee861845142843a0f988fa4ff016c723cdb to apply to Python 2.7.15 and 3.7.0.

* gnu/packages/patches/python2-CVE-2018-1060.patch,
gnu/packages/patches/python2-CVE-2018-1061.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/python.scm (python-2/fixed): Remove patches that are already
present in 2.7.15.
(python-3/fixed): Remove obsolete phase.
---
 gnu/local.mk                                  |  2 --
 .../patches/python2-CVE-2018-1060.patch       | 20 -------------------
 .../patches/python2-CVE-2018-1061.patch       | 20 -------------------
 gnu/packages/python.scm                       | 16 ++-------------
 4 files changed, 2 insertions(+), 56 deletions(-)
 delete mode 100644 gnu/packages/patches/python2-CVE-2018-1060.patch
 delete mode 100644 gnu/packages/patches/python2-CVE-2018-1061.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 1181210da5..8d4d0d26ea 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1068,8 +1068,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/pygpgme-disable-problematic-tests.patch  \
   %D%/packages/patches/pyqt-configure.patch			\
   %D%/packages/patches/pyqt-public-sip.patch			\
-  %D%/packages/patches/python2-CVE-2018-1060.patch		\
-  %D%/packages/patches/python2-CVE-2018-1061.patch		\
   %D%/packages/patches/python2-CVE-2018-14647.patch		\
   %D%/packages/patches/python2-CVE-2018-1000802.patch		\
   %D%/packages/patches/python-2-deterministic-build-info.patch	\
diff --git a/gnu/packages/patches/python2-CVE-2018-1060.patch b/gnu/packages/patches/python2-CVE-2018-1060.patch
deleted file mode 100644
index 5eb7ccfbc9..0000000000
--- a/gnu/packages/patches/python2-CVE-2018-1060.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Fix CVE-2018-1060:
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1060
-
-Taken from upstream commit (sans test and NEWS):
-https://github.com/python/cpython/commit/e052d40cea15f582b50947f7d906b39744dc62a2
-
-diff --git a/Lib/poplib.py b/Lib/poplib.py
-index b91e5f72d2ca..a238510b38fc 100644
---- a/Lib/poplib.py
-+++ b/Lib/poplib.py
-@@ -274,7 +274,7 @@ def rpop(self, user):
-         return self._shortcmd('RPOP %s' % user)
- 
- 
--    timestamp = re.compile(r'\+OK.*(<[^>]+>)')
-+    timestamp = re.compile(br'\+OK.[^<]*(<.*>)')
- 
-     def apop(self, user, secret):
-         """Authorisation
-
diff --git a/gnu/packages/patches/python2-CVE-2018-1061.patch b/gnu/packages/patches/python2-CVE-2018-1061.patch
deleted file mode 100644
index 6caab24b4d..0000000000
--- a/gnu/packages/patches/python2-CVE-2018-1061.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Fix CVE-2018-1061:
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2018-1061
-
-Taken from upstream commit (sans test and NEWS):
-https://github.com/python/cpython/commit/e052d40cea15f582b50947f7d906b39744dc62a2
-
-diff --git a/Lib/difflib.py b/Lib/difflib.py
-index 1c6fbdbedcb7..788a92df3f89 100644
---- a/Lib/difflib.py
-+++ b/Lib/difflib.py
-@@ -1103,7 +1103,7 @@ def _qformat(self, aline, bline, atags, btags):
- 
- import re
- 
--def IS_LINE_JUNK(line, pat=re.compile(r"\s*#?\s*$").match):
-+def IS_LINE_JUNK(line, pat=re.compile(r"\s*(?:#\s*)?$").match):
-     r"""
-     Return 1 for ignorable line: iff `line` is blank or contains a single '#'.
-
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 39ec96fd66..63cf440014 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -323,9 +323,7 @@ data types.")
               (inherit (package-source python-2))
               (patches (append
                         (origin-patches (package-source python-2))
-                        (search-patches "python2-CVE-2018-1060.patch"
-                                        "python2-CVE-2018-1061.patch"
-                                        "python2-CVE-2018-14647.patch"
+                        (search-patches "python2-CVE-2018-14647.patch"
                                         "python2-CVE-2018-1000802.patch")))))))
 
 (define-public python2-called-python
@@ -419,17 +417,7 @@ data types.")
     (source (origin
               (inherit (package-source python-3))
               (patches (append (origin-patches (package-source python-3))
-                               (search-patches "python-CVE-2018-14647.patch")))))
-    (arguments
-     (substitute-keyword-arguments (package-arguments python-3)
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (add-after 'unpack 'delete-broken-test
-             (lambda _
-               ;; Delete test which fails on recent kernels:
-               ;; <https://bugs.python.org/issue34587>.
-               (delete-file "Lib/test/test_socket.py")
-               #t))))))))
+                               (search-patches "python-CVE-2018-14647.patch")))))))
 
 ;; Current major version.
 (define-public python python-3)

From 0592db2873c557048026570e75105cf41f86751c Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Wed, 17 Oct 2018 14:05:18 -0400
Subject: [PATCH 765/909] gnu: wesnoth: Update to 1.14.5.

* gnu/packages/games.scm (wesnoth): Update to 1.14.5.
---
 gnu/packages/games.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 972dec3419..83a30cb22c 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -2137,7 +2137,7 @@ falling, themeable graphics and sounds, and replays.")
 (define-public wesnoth
   (package
     (name "wesnoth")
-    (version "1.14.4")
+    (version "1.14.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/wesnoth/wesnoth-"
@@ -2146,7 +2146,7 @@ falling, themeable graphics and sounds, and replays.")
                                   name "-" version ".tar.bz2"))
               (sha256
                (base32
-                "1hw1ap8xxpdwyx1sf8fm1g75p6724y3hwb4kpvyqbsq7bwfwsb9i"))))
+                "1kgpj2f22nnx4mwd1zis3s5ny2983aasgqsmz7wnqaq7n6a7ac85"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f)) ; no check target

From b286e3b3686db15195da222b7a75351651f6b1db Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Wed, 17 Oct 2018 17:04:27 -0400
Subject: [PATCH 766/909] gnu: retux: Update to 1.3.6.

* gnu/packages/games.scm (retux): Update to 1.3.6.
---
 gnu/packages/games.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 83a30cb22c..e2d1a5d6a8 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -1000,7 +1000,7 @@ Every puzzle has a complete solution, although there may be more than one.")
 (define-public retux
   (package
     (name "retux")
-    (version "1.3.5")
+    (version "1.3.6")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://savannah/retux/"
@@ -1008,7 +1008,7 @@ Every puzzle has a complete solution, although there may be more than one.")
                                   version "-src.tar.gz"))
               (sha256
                (base32
-                "1pcrh3z16fl412r3k7xccrgika19ahb1xh90jihgl8yy7zza2i6p"))))
+                "01bidh4zisjp3nc436x0g85v60dvwb3ig37i7y01sa71j8fm4fmb"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; no check target

From 03fd37b4eb9ec7600c9292361177ca5a47814cf7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Wed, 17 Oct 2018 18:29:23 +0200
Subject: [PATCH 767/909] doc: Document 'guix-service-type'.

* doc/guix.texi (Base Services): Document 'guix-service-type'.  Remove
'guix-service'.
---
 doc/guix.texi | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 2cea52f02b..fde7892cfd 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -11000,6 +11000,12 @@ Return a service that runs a syslog daemon according to @var{config}.
 information on the configuration file syntax.
 @end deffn
 
+@defvr {Scheme Variable} guix-service-type
+This is the type of the service that runs the build daemon,
+@command{guix-daemon} (@pxref{Invoking guix-daemon}).  Its value must be a
+@code{guix-configuration} record as described below.
+@end defvr
+
 @anchor{guix-configuration-type}
 @deftp {Data Type} guix-configuration
 This data type represents the configuration of the Guix build daemon.
@@ -11060,11 +11066,6 @@ A directory path where the @command{guix-daemon} will perform builds.
 @end table
 @end deftp
 
-@deffn {Scheme Procedure} guix-service @var{config}
-Return a service that runs the Guix build daemon according to
-@var{config}.
-@end deffn
-
 @deffn {Scheme Procedure} udev-service [#:udev @var{eudev} #:rules @code{'()}]
 Run @var{udev}, which populates the @file{/dev} directory dynamically.
 udev rules can be provided as a list of files through the @var{rules}

From 39d7fdce453b0ca23ecbed72048647debbaa58a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 18 Oct 2018 00:45:05 +0200
Subject: [PATCH 768/909] services: dhcp-client: Deprecate
 'dhcp-client-service' procedure.

* gnu/services/networking.scm (dhcp-client-service-type): Add default
value.
* gnu/system/examples/bare-bones.tmpl: Use (service
dhcp-client-service-type) instead of (dhcp-client-service).
* gnu/system/examples/beaglebone-black.tmpl: Likewise.
* gnu/tests/base.scm (%avahi-os): Likewise.
* gnu/tests/databases.scm (%memcached-os): Likewise.
(%mongodb-os): Likewise.
* gnu/tests/dict.scm (%dicod-os): Likewise.
* gnu/tests/mail.scm (%opensmtpd-os): Likewise.
(%exim-os): Likewise.
(%dovecot-os): Likewise.
* gnu/tests/messaging.scm (run-xmpp-test): Likewise.
(run-bitlbee-test): Likewise.
* gnu/tests/monitoring.scm (%prometheus-node-exporter-os): Likewise.
* gnu/tests/networking.scm (%inetd-os): Likewise.
(run-iptables-test): Likewise.
* gnu/tests/nfs.scm (%base-os): Likewise.
* gnu/tests/rsync.scm (%rsync-os): Likewise.
* gnu/tests/ssh.scm (run-ssh-test): Likewise.
* gnu/tests/version-control.scm (%cgit-os): Likewise.
(%git-http-os): Likewise.
(%gitolite-os): Likewise.
* gnu/tests/virtualization.scm (%libvirt-os): Likewise.
* gnu/tests/web.scm (%httpd-os): Likewise.
(%nginx-os): Likewise.
(%varnish-os): Likewise.
(%php-fpm-os): Likewise.
(%hpcguix-web-os): Likewise.
(%tailon-os): Likewise.
* tests/guix-system.sh: Likewise.
* doc/guix.texi (Networking Services): Document
'dhcp-client-service-type' and remove 'dhcp-client-service'.
---
 doc/guix.texi                             | 11 ++++++-----
 gnu/services/networking.scm               |  6 ++++--
 gnu/system/examples/bare-bones.tmpl       |  2 +-
 gnu/system/examples/beaglebone-black.tmpl |  2 +-
 gnu/tests/base.scm                        |  2 +-
 gnu/tests/databases.scm                   |  4 ++--
 gnu/tests/dict.scm                        |  2 +-
 gnu/tests/mail.scm                        |  6 +++---
 gnu/tests/messaging.scm                   |  4 ++--
 gnu/tests/monitoring.scm                  |  2 +-
 gnu/tests/networking.scm                  |  4 ++--
 gnu/tests/nfs.scm                         |  2 +-
 gnu/tests/rsync.scm                       |  2 +-
 gnu/tests/ssh.scm                         |  2 +-
 gnu/tests/version-control.scm             |  6 +++---
 gnu/tests/virtualization.scm              |  2 +-
 gnu/tests/web.scm                         | 12 ++++++------
 guix/gexp.scm                             |  8 ++++++++
 tests/guix-system.sh                      |  4 ++--
 19 files changed, 47 insertions(+), 36 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index fde7892cfd..f4f19949f1 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -11546,10 +11546,11 @@ The @code{(gnu services networking)} module provides services to configure
 the network interface.
 
 @cindex DHCP, networking service
-@deffn {Scheme Procedure} dhcp-client-service [#:dhcp @var{isc-dhcp}]
-Return a service that runs @var{dhcp}, a Dynamic Host Configuration
-Protocol (DHCP) client, on all the non-loopback network interfaces.
-@end deffn
+@defvr {Scheme Variable} dhcp-client-service-type
+This is the type of services that run @var{dhcp}, a Dynamic Host Configuration
+Protocol (DHCP) client, on all the non-loopback network interfaces.  Its value
+is the DHCP client package to use, @code{isc-dhcp} by default.
+@end defvr
 
 @deffn {Scheme Procedure} dhcpd-service-type
 This type defines a service that runs a DHCP daemon.  To create a
@@ -17168,7 +17169,7 @@ A helper function to quickly add php to an @code{nginx-server-configuration}.
 
 A simple services setup for nginx with php can look like this:
 @example
-(services (cons* (dhcp-client-service)
+(services (cons* (service dhcp-client-service-type)
                  (service php-fpm-service-type)
                  (service nginx-service-type
                           (nginx-server-configuration
diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index c809b4a4a4..61a0e975c7 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -53,6 +53,7 @@
                static-networking-service-type)
   #:export (%facebook-host-aliases
             dhcp-client-service
+            dhcp-client-service-type
 
             dhcpd-service-type
             dhcpd-configuration
@@ -202,9 +203,10 @@ fe80::1%lo0 apps.facebook.com\n")
                                     "-pf" #$pid-file ifaces))))
                    (and (zero? (cdr (waitpid pid)))
                         (read-pid-file #$pid-file)))))
-      (stop #~(make-kill-destructor))))))
+      (stop #~(make-kill-destructor))))
+   isc-dhcp))
 
-(define* (dhcp-client-service #:key (dhcp isc-dhcp))
+(define* (dhcp-client-service #:key (dhcp isc-dhcp)) ;deprecated
   "Return a service that runs @var{dhcp}, a Dynamic Host Configuration
 Protocol (DHCP) client, on all the non-loopback network interfaces."
   (service dhcp-client-service-type dhcp))
diff --git a/gnu/system/examples/bare-bones.tmpl b/gnu/system/examples/bare-bones.tmpl
index b763258e52..889dcabe64 100644
--- a/gnu/system/examples/bare-bones.tmpl
+++ b/gnu/system/examples/bare-bones.tmpl
@@ -44,7 +44,7 @@
 
   ;; Add services to the baseline: a DHCP client and
   ;; an SSH server.
-  (services (cons* (dhcp-client-service)
+  (services (cons* (service dhcp-client-service-type)
                    (service openssh-service-type
                             (openssh-configuration
                               (port-number 2222)))
diff --git a/gnu/system/examples/beaglebone-black.tmpl b/gnu/system/examples/beaglebone-black.tmpl
index d1130c76b6..efef682e3a 100644
--- a/gnu/system/examples/beaglebone-black.tmpl
+++ b/gnu/system/examples/beaglebone-black.tmpl
@@ -45,7 +45,7 @@
   ;; Globally-installed packages.
   (packages (cons* screen openssh %base-packages))
 
-  (services (cons* (dhcp-client-service)
+  (services (cons* (service dhcp-client-service-type)
                    ;; mingetty does not work on serial lines.
                    ;; Use agetty with board-specific serial parameters.
                    (agetty-service
diff --git a/gnu/tests/base.scm b/gnu/tests/base.scm
index f97581de33..896d4a8f88 100644
--- a/gnu/tests/base.scm
+++ b/gnu/tests/base.scm
@@ -673,7 +673,7 @@ non-ASCII names from /tmp.")
     (name-service-switch %mdns-host-lookup-nss)
     (services (cons* (avahi-service #:debug? #t)
                      (dbus-service)
-                     (dhcp-client-service)        ;needed for multicast
+                     (service dhcp-client-service-type) ;needed for multicast
 
                      ;; Enable heavyweight debugging output.
                      (modify-services (operating-system-user-services
diff --git a/gnu/tests/databases.scm b/gnu/tests/databases.scm
index 5c8ca85c13..e0544bbcd2 100644
--- a/gnu/tests/databases.scm
+++ b/gnu/tests/databases.scm
@@ -35,7 +35,7 @@
 
 (define %memcached-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service memcached-service-type)))
 
 (define* (run-memcached-test #:optional (port 11211))
@@ -130,7 +130,7 @@
   (operating-system
     (inherit
      (simple-operating-system
-      (dhcp-client-service)
+      (service dhcp-client-service-type)
       (service mongodb-service-type)))
     (packages (cons* mongodb
                      %base-packages))))
diff --git a/gnu/tests/dict.scm b/gnu/tests/dict.scm
index dd60ffd464..c50e3cd6da 100644
--- a/gnu/tests/dict.scm
+++ b/gnu/tests/dict.scm
@@ -34,7 +34,7 @@
 
 (define %dicod-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service dicod-service-type
             (dicod-configuration
              (interfaces '("0.0.0.0"))
diff --git a/gnu/tests/mail.scm b/gnu/tests/mail.scm
index 5677969fac..33aa4d3437 100644
--- a/gnu/tests/mail.scm
+++ b/gnu/tests/mail.scm
@@ -36,7 +36,7 @@
 
 (define %opensmtpd-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service opensmtpd-service-type
             (opensmtpd-configuration
              (config-file
@@ -155,7 +155,7 @@ accept from any for local deliver to mbox
 
 (define %exim-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service mail-aliases-service-type '())
    (service exim-service-type
             (exim-configuration
@@ -283,7 +283,7 @@ acl_check_data:
 
 (define %dovecot-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (dovecot-service #:config
                     (dovecot-configuration
                      (disable-plaintext-auth? #f)
diff --git a/gnu/tests/messaging.scm b/gnu/tests/messaging.scm
index f5f99b9f56..36afb987af 100644
--- a/gnu/tests/messaging.scm
+++ b/gnu/tests/messaging.scm
@@ -35,7 +35,7 @@
   "Run a test of an OS running XMPP-SERVICE, which writes its PID to PID-FILE."
   (define os
     (marionette-operating-system
-     (simple-operating-system (dhcp-client-service)
+     (simple-operating-system (service dhcp-client-service-type)
                               xmpp-service)
      #:imported-modules '((gnu services herd))))
 
@@ -167,7 +167,7 @@
 (define (run-bitlbee-test)
   (define os
     (marionette-operating-system
-     (simple-operating-system (dhcp-client-service)
+     (simple-operating-system (service dhcp-client-service-type)
                               (service bitlbee-service-type
                                        (bitlbee-configuration
                                         (interface "0.0.0.0"))))
diff --git a/gnu/tests/monitoring.scm b/gnu/tests/monitoring.scm
index 67899987ce..3320a19a77 100644
--- a/gnu/tests/monitoring.scm
+++ b/gnu/tests/monitoring.scm
@@ -85,7 +85,7 @@
 
 (define %prometheus-node-exporter-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service prometheus-node-exporter-service-type
             (prometheus-node-exporter-configuration))))
 
diff --git a/gnu/tests/networking.scm b/gnu/tests/networking.scm
index ceba7f7d5d..9f12a4ae8d 100644
--- a/gnu/tests/networking.scm
+++ b/gnu/tests/networking.scm
@@ -39,7 +39,7 @@
 (define %inetd-os
   ;; Operating system with 2 inetd services.
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service inetd-service-type
             (inetd-configuration
              (entries (list
@@ -463,7 +463,7 @@ COMMIT
   (define os
     (marionette-operating-system
      (simple-operating-system
-      (dhcp-client-service)
+      (service dhcp-client-service-type)
       (service inetd-service-type
                (inetd-configuration
                 (entries (list
diff --git a/gnu/tests/nfs.scm b/gnu/tests/nfs.scm
index 140f03779b..7ef9f1f7bf 100644
--- a/gnu/tests/nfs.scm
+++ b/gnu/tests/nfs.scm
@@ -55,7 +55,7 @@
     (services (cons*
                (service rpcbind-service-type
                         (rpcbind-configuration))
-               (dhcp-client-service)
+               (service dhcp-client-service-type)
                %base-services))))
 
 (define (run-nfs-test name socket)
diff --git a/gnu/tests/rsync.scm b/gnu/tests/rsync.scm
index a6f8fa2bd1..096580022f 100644
--- a/gnu/tests/rsync.scm
+++ b/gnu/tests/rsync.scm
@@ -111,7 +111,7 @@ PORT."
   ;; Return operating system under test.
   (let ((base-os
          (simple-operating-system
-          (dhcp-client-service)
+          (service dhcp-client-service-type)
           (service rsync-service-type))))
     (operating-system
       (inherit base-os)
diff --git a/gnu/tests/ssh.scm b/gnu/tests/ssh.scm
index 2e40122add..e5cd439cdf 100644
--- a/gnu/tests/ssh.scm
+++ b/gnu/tests/ssh.scm
@@ -39,7 +39,7 @@ empty-password logins.
 When SFTP? is true, run an SFTP server test."
   (define os
     (marionette-operating-system
-     (simple-operating-system (dhcp-client-service) ssh-service)
+     (simple-operating-system (service dhcp-client-service-type) ssh-service)
      #:imported-modules '((gnu services herd)
                           (guix combinators))))
   (define vm
diff --git a/gnu/tests/version-control.scm b/gnu/tests/version-control.scm
index 4409b8a12b..230aa9edf9 100644
--- a/gnu/tests/version-control.scm
+++ b/gnu/tests/version-control.scm
@@ -92,7 +92,7 @@
   ;; Operating system under test.
   (let ((base-os
          (simple-operating-system
-          (dhcp-client-service)
+          (service dhcp-client-service-type)
           (service cgit-service-type
                    (cgit-configuration
                     (nginx %cgit-configuration-nginx)))
@@ -237,7 +237,7 @@ HTTP-PORT."
 
 (define %git-http-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service fcgiwrap-service-type)
    (service nginx-service-type %git-nginx-configuration)
    %test-repository-service))
@@ -328,7 +328,7 @@ HTTP-PORT."
 
 (define %gitolite-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service openssh-service-type)
    (service gitolite-service-type
             (gitolite-configuration
diff --git a/gnu/tests/virtualization.scm b/gnu/tests/virtualization.scm
index c2939355b2..fbdec20805 100644
--- a/gnu/tests/virtualization.scm
+++ b/gnu/tests/virtualization.scm
@@ -32,7 +32,7 @@
 
 (define %libvirt-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (dbus-service)
    (polkit-service)
    (service libvirt-service-type)))
diff --git a/gnu/tests/web.scm b/gnu/tests/web.scm
index 2e209fee97..319655396a 100644
--- a/gnu/tests/web.scm
+++ b/gnu/tests/web.scm
@@ -125,7 +125,7 @@ HTTP-PORT."
 
 (define %httpd-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service httpd-service-type
             (httpd-configuration
              (config
@@ -154,7 +154,7 @@ HTTP-PORT."
 (define %nginx-os
   ;; Operating system under test.
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service nginx-service-type
             (nginx-configuration
              (log-directory "/var/log/nginx")
@@ -188,7 +188,7 @@ sub vcl_synth {
 
 (define %varnish-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    ;; Pretend to be a web server that serves %index.html-contents.
    (service varnish-service-type
             (varnish-configuration
@@ -237,7 +237,7 @@ echo(\"Computed by php:\".((string)(2+3)));
 (define %php-fpm-os
   ;; Operating system under test.
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service php-fpm-service-type)
    (service nginx-service-type
             (nginx-configuration
@@ -392,7 +392,7 @@ HTTP-PORT, along with php-fpm."
 
 (define %hpcguix-web-os
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service hpcguix-web-service-type
             (hpcguix-web-configuration
              (specs %hpcguix-web-specs)))))
@@ -407,7 +407,7 @@ HTTP-PORT, along with php-fpm."
 (define %tailon-os
   ;; Operating system under test.
   (simple-operating-system
-   (dhcp-client-service)
+   (service dhcp-client-service-type)
    (service tailon-service-type
             (tailon-configuration
              (config-file
diff --git a/guix/gexp.scm b/guix/gexp.scm
index f7a23db872..ba0d642b17 100644
--- a/guix/gexp.scm
+++ b/guix/gexp.scm
@@ -438,6 +438,14 @@ This is the declarative counterpart of 'gexp->file'."
   (base   file-append-base)                    ;<package> | <derivation> | ...
   (suffix file-append-suffix))                 ;list of strings
 
+(define (write-file-append file port)
+  (match file
+    (($ <file-append> base suffix)
+     (format port "#<file-append ~s ~s>" base
+             (string-join suffix)))))
+
+(set-record-type-printer! <file-append> write-file-append)
+
 (define (file-append base . suffix)
   "Return a <file-append> object that expands to the concatenation of BASE and
 SUFFIX."
diff --git a/tests/guix-system.sh b/tests/guix-system.sh
index a129efdfcb..23d2da4903 100644
--- a/tests/guix-system.sh
+++ b/tests/guix-system.sh
@@ -153,8 +153,8 @@ cat > "$tmpfile" <<EOF
 
 (operating-system
   $OS_BASE
-  (services (cons* (dhcp-client-service)
-                   (dhcp-client-service) ;twice!
+  (services (cons* (service dhcp-client-service-type)
+                   (service dhcp-client-service-type) ;twice!
                    %base-services)))
 EOF
 

From 53fb0476ec4e5df9511490aaf8c3c70ba68aa83b Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Thu, 24 May 2018 00:21:49 +0800
Subject: [PATCH 769/909] gnu: javacc: 'javacc' now inherits from 'javacc-4'.

* gnu/packages/java.scm (javacc, javacc-4): 'javacc' now inherits from
'javacc-4' instead of the opposite around.
---
 gnu/packages/java.scm | 47 ++++++++++++++++++++++---------------------
 1 file changed, 24 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 93f5bb6aff..5447be41a5 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -1948,27 +1948,31 @@ designs.")
                      license:asl2.0
                      license:cpl1.0)))))
 
-(define-public javacc
+(define-public javacc-4
   (package
     (name "javacc")
-    (version "7.0.3")
+    (version "4.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/javacc/javacc/"
-                                  "archive/" version ".tar.gz"))
-              (file-name (string-append "javacc-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/javacc/javacc.git")
+                    (commit "release_41")))
+              (file-name (string-append "javacc-" version "-checkout"))
               (sha256
                (base32
-                "111xc9mnmc5a6qz6x3xbhqc07y1lg2b996ggzw0hrblg42zya9xf"))))
+                "07ysav7j8r1c6h8qxrgqk6lwdp74ly0ad1935lragxml0qqc3ka0"))))
     (build-system ant-build-system)
+    ;; Tests fail with
+    ;; /tmp/guix-build-javacc-4.1.drv-0/source/test/javacodeLA/build.xml:60:
+    ;; JAVACODE failed
     (arguments
-     `(#:test-target "test"
+     `(#:tests? #f
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'delete-bundled-libs
            (lambda _
              (delete-file-recursively "lib") #t))
-         (replace 'install (install-jars "target")))))
+         (replace 'install (install-jars "bin/lib")))))
     (home-page "https://javacc.org/")
     (synopsis "Java parser generator")
     (description "Java Compiler Compiler (JavaCC) is the most popular parser
@@ -1980,29 +1984,26 @@ as tree building (via a tool called JJTree included with JavaCC), actions,
 debugging, etc.")
     (license license:bsd-3)))
 
-(define-public javacc-4
-  (package (inherit javacc)
-    (version "4.1")
+(define-public javacc
+  (package
+    (inherit javacc-4)
+    (version "7.0.3")
     (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/javacc/javacc.git")
-                    (commit "release_41")))
-              (file-name (string-append "javacc-" version "-checkout"))
+              (method url-fetch)
+              (uri (string-append "https://github.com/javacc/javacc/"
+                                  "archive/" version ".tar.gz"))
+              (file-name (string-append "javacc-" version ".tar.gz"))
               (sha256
                (base32
-                "07ysav7j8r1c6h8qxrgqk6lwdp74ly0ad1935lragxml0qqc3ka0"))))
-    ;; Tests fail with
-    ;; /tmp/guix-build-javacc-4.1.drv-0/source/test/javacodeLA/build.xml:60:
-    ;; JAVACODE failed
+                "111xc9mnmc5a6qz6x3xbhqc07y1lg2b996ggzw0hrblg42zya9xf"))))
     (arguments
-     `(#:tests? #f
+     `(#:test-target "test"
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'delete-bundled-libs
            (lambda _
              (delete-file-recursively "lib") #t))
-         (replace 'install (install-jars "bin/lib")))))))
+         (replace 'install (install-jars "target")))))))
 
 ;; This is the last 3.x release of ECJ
 (define-public java-ecj-3

From 6662d65f96b948271eeaa0ba5c93d0e61663e7d3 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Fri, 25 May 2018 07:43:42 +0800
Subject: [PATCH 770/909] gnu: javacc: Use snippet to delete bundled jars.

* gnu/packages/java.scm (javacc-4)[source](snippet, modules): New fields.
[arguments]: Remove 'delete-bundled-libs' phase and add 'delete-tests'
phase.
* gnu/packages/java.scm (javacc)[source](snippet, modules): New fields.
[arguments]: Remove 'delete-bundled-libs' phase.
---
 gnu/packages/java.scm | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index 5447be41a5..d89ba6a005 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -1960,7 +1960,10 @@ designs.")
               (file-name (string-append "javacc-" version "-checkout"))
               (sha256
                (base32
-                "07ysav7j8r1c6h8qxrgqk6lwdp74ly0ad1935lragxml0qqc3ka0"))))
+                "07ysav7j8r1c6h8qxrgqk6lwdp74ly0ad1935lragxml0qqc3ka0"))
+              (modules '((guix build utils)))
+              ;; delete bundled jars
+              (snippet '(begin (delete-file-recursively "lib") #t))))
     (build-system ant-build-system)
     ;; Tests fail with
     ;; /tmp/guix-build-javacc-4.1.drv-0/source/test/javacodeLA/build.xml:60:
@@ -1969,9 +1972,18 @@ designs.")
      `(#:tests? #f
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'delete-bundled-libs
+         ;; Delete tests to avoid build failure (we don't run them anyway).
+         (add-after 'unpack 'delete-tests
            (lambda _
-             (delete-file-recursively "lib") #t))
+             (for-each delete-file
+                       '("src/org/javacc/JavaCCTestCase.java"
+                         "src/org/javacc/parser/ExpansionTest.java"
+                         "src/org/javacc/parser/OptionsTest.java"
+                         "src/org/javacc/jjtree/JJTreeOptionsTest.java"))
+             (for-each delete-file-recursively
+                       '("src/org/javacc/parser/test"
+                         "src/org/javacc/jjdoc/test"))
+             #t))
          (replace 'install (install-jars "bin/lib")))))
     (home-page "https://javacc.org/")
     (synopsis "Java parser generator")
@@ -1995,14 +2007,14 @@ debugging, etc.")
               (file-name (string-append "javacc-" version ".tar.gz"))
               (sha256
                (base32
-                "111xc9mnmc5a6qz6x3xbhqc07y1lg2b996ggzw0hrblg42zya9xf"))))
+                "111xc9mnmc5a6qz6x3xbhqc07y1lg2b996ggzw0hrblg42zya9xf"))
+              (modules '((guix build utils)))
+              ;; delete bundled jars
+              (snippet '(begin (delete-file-recursively "lib") #t))))
     (arguments
      `(#:test-target "test"
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'delete-bundled-libs
-           (lambda _
-             (delete-file-recursively "lib") #t))
          (replace 'install (install-jars "target")))))))
 
 ;; This is the last 3.x release of ECJ

From 33428d12672fefde745b313ce1f0c02ae9870e39 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Thu, 24 May 2018 00:32:51 +0800
Subject: [PATCH 771/909] gnu: javacc: Bootstrap from javacc-4 instead of
 bootstrap binary.

* gnu/packages/java.scm (javacc)[source](snippet): Delete bootstrap binary.
[arguments]: Set 'bootstrap-jar' path.
[native-inputs]: Add 'javacc-4'.
---
 gnu/packages/java.scm | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index d89ba6a005..f6d72edeea 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -2010,12 +2010,20 @@ debugging, etc.")
                 "111xc9mnmc5a6qz6x3xbhqc07y1lg2b996ggzw0hrblg42zya9xf"))
               (modules '((guix build utils)))
               ;; delete bundled jars
-              (snippet '(begin (delete-file-recursively "lib") #t))))
+              (snippet '(begin (for-each delete-file-recursively
+                                         '("bootstrap" "lib"))
+                               #t))))
     (arguments
-     `(#:test-target "test"
+     `(#:make-flags ; bootstrap from javacc-4
+       (list (string-append "-Dbootstrap-jar="
+                            (assoc-ref %build-inputs "javacc")
+                            "/share/java/javacc.jar"))
+       #:test-target "test"
        #:phases
        (modify-phases %standard-phases
-         (replace 'install (install-jars "target")))))))
+         (replace 'install (install-jars "target")))))
+    (native-inputs
+     `(("javacc" ,javacc-4)))))
 
 ;; This is the last 3.x release of ECJ
 (define-public java-ecj-3

From e8ef3cc4d62d573db5e7338a0342ef20df5f8b4d Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Thu, 18 Oct 2018 19:13:13 +0200
Subject: [PATCH 772/909] gnu: swig: Fix build on i686.

* gnu/packages/patches/swig-guile-gc.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/swig.scm (swig)[source](patches): Use it.
---
 gnu/local.mk                             |  1 +
 gnu/packages/patches/swig-guile-gc.patch | 76 ++++++++++++++++++++++++
 gnu/packages/swig.scm                    |  2 +
 3 files changed, 79 insertions(+)
 create mode 100644 gnu/packages/patches/swig-guile-gc.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 8d4d0d26ea..4b8c4c3d69 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1154,6 +1154,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/soundtouch-CVE-2018-1000223.patch 	\
   %D%/packages/patches/steghide-fixes.patch			\
   %D%/packages/patches/superlu-dist-scotchmetis.patch		\
+  %D%/packages/patches/swig-guile-gc.patch			\
   %D%/packages/patches/swish-e-search.patch			\
   %D%/packages/patches/swish-e-format-security.patch		\
   %D%/packages/patches/synfigstudio-fix-ui-with-gtk3.patch 	\
diff --git a/gnu/packages/patches/swig-guile-gc.patch b/gnu/packages/patches/swig-guile-gc.patch
new file mode 100644
index 0000000000..0e745a6247
--- /dev/null
+++ b/gnu/packages/patches/swig-guile-gc.patch
@@ -0,0 +1,76 @@
+Fix garbage collection for Guile versions >= 2.0.12.  This issue showed
+up when running the tests on i686-linux.
+
+Taken from this upstream commit:
+https://github.com/swig/swig/commit/38f2ab0c30e369e63bbd0a6152108488d0de68e1
+
+diff --git a/Lib/guile/guile_scm_run.swg b/Lib/guile/guile_scm_run.swg
+index 274f197158..0d04cb7c62 100644
+--- a/Lib/guile/guile_scm_run.swg
++++ b/Lib/guile/guile_scm_run.swg
+@@ -99,6 +99,7 @@ SWIG_Guile_scm2newstr(SCM str, size_t *len) {
+ static int swig_initialized = 0;
+ static scm_t_bits swig_tag = 0;
+ static scm_t_bits swig_collectable_tag = 0;
++static scm_t_bits swig_finalized_tag = 0;
+ static scm_t_bits swig_destroyed_tag = 0;
+ static scm_t_bits swig_member_function_tag = 0;
+ static SCM swig_make_func = SCM_EOL;
+@@ -163,7 +164,19 @@ SWIG_Guile_PointerType(SCM object)
+   }
+   else scm_wrong_type_arg("SWIG-Guile-PointerType", 1, object);
+ }
+-  
++
++SWIGINTERN int
++SWIG_Guile_IsValidSmob(SCM smob)
++{
++  /* We do not accept smobs representing destroyed pointers, but we have to
++     allow finalized smobs because Guile >= 2.0.12 sets all smob instances
++     to the 'finalized' type before calling their 'free' function. This change
++     was introduced to Guile in commit 8dff3af087c6eaa83ae0d72aa8b22aef5c65d65d */
++  return SCM_SMOB_PREDICATE(swig_tag, smob)
++    || SCM_SMOB_PREDICATE(swig_collectable_tag, smob)
++    || SCM_SMOB_PREDICATE(swig_finalized_tag, smob);
++}
++
+ SWIGINTERN int
+ SWIG_Guile_ConvertPtr(SCM s, void **result, swig_type_info *type, int flags)
+ {
+@@ -179,8 +192,7 @@ SWIG_Guile_ConvertPtr(SCM s, void **result, swig_type_info *type, int flags)
+     *result = SCM_POINTER_VALUE(s);
+     return SWIG_OK;
+ #endif /* if SCM_MAJOR_VERSION >= 2 */
+-  } else if (SCM_SMOB_PREDICATE(swig_tag, smob) || SCM_SMOB_PREDICATE(swig_collectable_tag, smob)) {
+-    /* we do not accept smobs representing destroyed pointers */
++  } else if (SWIG_Guile_IsValidSmob(smob)) {
+     from = (swig_type_info *) SCM_CELL_WORD_2(smob);
+     if (!from) return SWIG_ERROR;
+     if (type) {
+@@ -239,7 +251,7 @@ SWIG_Guile_MarkPointerNoncollectable(SCM s)
+ {
+   SCM smob = SWIG_Guile_GetSmob(s);
+   if (!SCM_NULLP(smob)) {
+-    if (SCM_SMOB_PREDICATE(swig_tag, smob) || SCM_SMOB_PREDICATE(swig_collectable_tag, smob)) {
++    if (SWIG_Guile_IsValidSmob(smob)) {
+       SCM_SET_CELL_TYPE(smob, swig_tag);
+     }
+     else scm_wrong_type_arg(NULL, 0, s);
+@@ -252,7 +264,7 @@ SWIG_Guile_MarkPointerDestroyed(SCM s)
+ {
+   SCM smob = SWIG_Guile_GetSmob(s);
+   if (!SCM_NULLP(smob)) {
+-    if (SCM_SMOB_PREDICATE(swig_tag, smob) || SCM_SMOB_PREDICATE(swig_collectable_tag, smob)) {
++    if (SWIG_Guile_IsValidSmob(smob)) {
+       SCM_SET_CELL_TYPE(smob, swig_destroyed_tag);
+     }
+     else scm_wrong_type_arg(NULL, 0, s);
+@@ -419,6 +431,8 @@ SWIG_Guile_Init ()
+     scm_set_smob_print(swig_collectable_tag, print_collectable_swig);
+     scm_set_smob_equalp(swig_collectable_tag, equalp_swig);
+     scm_set_smob_free(swig_collectable_tag, free_swig);
++    /* For Guile >= 2.0.12. See libguile/smob.c:clear_smobnum */
++    swig_finalized_tag = swig_collectable_tag & ~0xff00;
+   }
+   if (ensure_smob_tag(swig_module, &swig_destroyed_tag,
+ 		      "destroyed-swig-pointer", "destroyed-swig-pointer-tag")) {
diff --git a/gnu/packages/swig.scm b/gnu/packages/swig.scm
index b931db412b..61f6a8ccfe 100644
--- a/gnu/packages/swig.scm
+++ b/gnu/packages/swig.scm
@@ -22,6 +22,7 @@
   #:use-module (guix download)
   #:use-module (guix licenses)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages boost)
@@ -37,6 +38,7 @@
              (uri (string-append "mirror://sourceforge/" name "/" name "/"
                                  name "-" version "/"
                                  name "-" version ".tar.gz"))
+             (patches (search-patches "swig-guile-gc.patch"))
              (sha256
               (base32
                "0kf99ygrjs5616gsqhz1l7bib3a12izmxi7g48bwblbymr3z9ybw"))))

From 5fb543b3f7bf79208178429d38f2da047fc744c0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 18 Oct 2018 21:12:05 +0300
Subject: [PATCH 773/909] gnu: python-fonttools: Update to 3.30.0.

* gnu/packages/python.scm (python-fonttools): Update to 3.30.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 63cf440014..56923c31c2 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6072,13 +6072,13 @@ add functionality and customization to your projects with their own plugins.")
 (define-public python-fonttools
   (package
     (name "python-fonttools")
-    (version "3.28.0")
+    (version "3.30.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "fonttools" version ".zip"))
               (sha256
                (base32
-                "0vsvjhidpb5kywpjgz1j3fywzkddxkb0afqai18qa3h6lqjyxwpb"))))
+                "1i6229ylm12klljqfg643rikzpcslqrj56qf4cydr0w1n4cnbs4m"))))
     (build-system python-build-system)
     (native-inputs
      `(("unzip" ,unzip)

From 1febc93f9b13155be7a212fcaf93d5dd181c8aea Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 18 Oct 2018 21:21:14 +0300
Subject: [PATCH 774/909] Revert "gnu: python-fonttools: Update to 3.30.0."

This reverts commit 5fb543b3f7bf79208178429d38f2da047fc744c0.

python2-fonttools has 2700 dependants, only the python3 version is
failing.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 56923c31c2..63cf440014 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6072,13 +6072,13 @@ add functionality and customization to your projects with their own plugins.")
 (define-public python-fonttools
   (package
     (name "python-fonttools")
-    (version "3.30.0")
+    (version "3.28.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "fonttools" version ".zip"))
               (sha256
                (base32
-                "1i6229ylm12klljqfg643rikzpcslqrj56qf4cydr0w1n4cnbs4m"))))
+                "0vsvjhidpb5kywpjgz1j3fywzkddxkb0afqai18qa3h6lqjyxwpb"))))
     (build-system python-build-system)
     (native-inputs
      `(("unzip" ,unzip)

From f793b4ef96d53c548494b4b15b99a31d05c449a3 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 18 Oct 2018 21:30:44 +0300
Subject: [PATCH 775/909] gnu: squashfs-tools: Fix building with glibc@2.28.

* gnu/packages/compression.scm (squashfs-tools)[arguments]: Add
substitution to include missing import. Return #t from all phases.
---
 gnu/packages/compression.scm | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 6ec08136d5..4137dca8bb 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -7,7 +7,7 @@
 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015, 2017, 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2015 Jeff Mickey <j@codemac.net>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2016 Danny Milosavljevic <dannym@scratchpost.org>
 ;;; Copyright © 2016, 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -875,8 +875,16 @@ the LZ4 frame format.")
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
-                  (lambda _
-                    (chdir "squashfs-tools"))))))
+           (lambda _
+             (chdir "squashfs-tools")
+             #t))
+         (add-after 'unpack 'fix-glibc-compatability
+           (lambda _
+             (substitute* '("squashfs-tools/mksquashfs.c"
+                            "squashfs-tools/unsquashfs.c")
+               (("<sys/sysinfo.h>")
+                "<sys/sysinfo.h>\n#include <sys/sysmacros.h>"))
+             #t)))))
     (inputs
      `(("lz4" ,lz4)
        ("lzo" ,lzo)

From b50d58b3445a85bf4395e2b767da10c2e3438902 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 18 Oct 2018 21:46:09 +0300
Subject: [PATCH 776/909] gnu: sharutils: Fix bundled gnulib.

* gnu/packages/compression.scm (sharutils)[source]: Add snippet to fix
bundled gnulib.
---
 gnu/packages/compression.scm | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 4137dca8bb..44d1fd4bb5 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -584,7 +584,23 @@ decompressors when faced with corrupted input.")
       (patches (search-patches "sharutils-CVE-2018-1000097.patch"))
       (sha256
        (base32
-        "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b"))))
+        "16isapn8f39lnffc3dp4dan05b7x6mnc76v6q5nn8ysxvvvwy19b"))
+             (modules '((guix build utils)))
+             (snippet
+              '(begin
+                 ;; Adjust the bundled gnulib to work with glibc 2.28.  See e.g.
+                 ;; "m4-gnulib-libio.patch".  This is a phase rather than patch
+                 ;; or snippet to work around <https://bugs.gnu.org/32347>.
+                 (substitute* (find-files "lib" "\\.c$")
+                   (("#if defined _IO_ftrylockfile")
+                    "#if defined _IO_EOF_SEEN"))
+                 (substitute* "lib/stdio-impl.h"
+                   (("^/\\* BSD stdio derived implementations")
+                    (string-append "#if !defined _IO_IN_BACKUP && defined _IO_EOF_SEEN\n"
+                                   "# define _IO_IN_BACKUP 0x100\n"
+                                   "#endif\n\n"
+                                   "/* BSD stdio derived implementations")))
+                 #t))))
     (build-system gnu-build-system)
     (inputs
      `(("which" ,which)))

From d36cd888734da3c9d7ce27dafedb00f0e42a636e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Thu, 18 Oct 2018 23:56:47 +0200
Subject: [PATCH 777/909] gnu: grub-efi: Fix an uninitialized variable issue.

* gnu/packages/patches/grub-check-error-efibootmgr.patch: Add hunk to
correct uninitialized variable.
---
 .../patches/grub-check-error-efibootmgr.patch | 23 ++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/patches/grub-check-error-efibootmgr.patch b/gnu/packages/patches/grub-check-error-efibootmgr.patch
index b2fd160c9a..efeb20f213 100644
--- a/gnu/packages/patches/grub-check-error-efibootmgr.patch
+++ b/gnu/packages/patches/grub-check-error-efibootmgr.patch
@@ -160,7 +160,7 @@ index 5e4cdfd..690f180 100644
  
  	  /* Try to make this image bootable using the EFI Boot Manager, if available.  */
  	  if (!efi_distributor || efi_distributor[0] == '\0')
-@@ -1887,8 +1892,11 @@ main (int argc, char *argv[])
+@@ -1887,7 +1892,10 @@ main (int argc, char *argv[])
  			  efidir_grub_dev->disk->name,
  			  (part ? ",": ""), (part ? : ""));
  	  grub_free (part);
@@ -173,4 +173,25 @@ index 5e4cdfd..690f180 100644
 +			     strerror (ret));
  	}
        break;
+
+
+Below is a followup to the patch above: the uninitialized variable could lead
+‘grub-install’ to error out when it shouldn’t (seen on an AArch64 box where
+‘grub_install_remove_efi_entries_by_distributor’ didn't have any entry to
+remove):
+
+  grub-install: error: efibootmgr failed to register the boot entry: Unknown error 65535.
+
+See <http://lists.gnu.org/archive/html/bug-grub/2018-10/msg00006.html>.
+
+--- grub-2.02/grub-core/osdep/unix/platform.c	2018-10-17 22:21:53.015284846 +0200
++++ grub-2.02/grub-core/osdep/unix/platform.c	2018-10-17 22:21:55.595271222 +0200
+@@ -85,7 +85,7 @@ grub_install_remove_efi_entries_by_distr
+   pid_t pid = grub_util_exec_pipe ((const char * []){ "efibootmgr", NULL }, &fd);
+   char *line = NULL;
+   size_t len = 0;
+-  int rc;
++  int rc = 0;
  
+   if (!pid)
+     {

From 402e60859da609e95d16a04a253977da88f4077e Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Wed, 17 Oct 2018 20:09:19 -0400
Subject: [PATCH 778/909] gnu: linux-libre: Enable SHPC PCI Hotplug driver on
 ARM64.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes <https://bugs.gnu.org/32840> on ARM64.

* gnu/packages/aux-files/linux-libre/4.18-arm64.conf: Add
CONFIG_HOTPLUG_PCI_SHPC=y.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/aux-files/linux-libre/4.18-arm64.conf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/aux-files/linux-libre/4.18-arm64.conf b/gnu/packages/aux-files/linux-libre/4.18-arm64.conf
index ab30f51d2e..64b14b52c0 100644
--- a/gnu/packages/aux-files/linux-libre/4.18-arm64.conf
+++ b/gnu/packages/aux-files/linux-libre/4.18-arm64.conf
@@ -1,6 +1,6 @@
 #
 # Automatically generated file; DO NOT EDIT.
-# Linux/arm64 4.18.0-gnu Kernel Configuration
+# Linux/arm64 4.18.14-gnu Kernel Configuration
 #
 CONFIG_ARM64=y
 CONFIG_64BIT=y
@@ -481,7 +481,7 @@ CONFIG_HOTPLUG_PCI=y
 CONFIG_HOTPLUG_PCI_ACPI=y
 CONFIG_HOTPLUG_PCI_ACPI_IBM=m
 CONFIG_HOTPLUG_PCI_CPCI=y
-# CONFIG_HOTPLUG_PCI_SHPC is not set
+CONFIG_HOTPLUG_PCI_SHPC=y
 
 #
 # PCI controller drivers

From 3d472b5ee1a301a110087ebc08e8dcea8c3c0710 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 19 Oct 2018 03:03:05 +0200
Subject: [PATCH 779/909] services: WPA Supplicant: Fix syntax error.

This is a followup to commit acce0a474c1493ab18912bc46285248e4ccb0314.  No
idea how these disappeared.. :-/

* gnu/services/networking.scm (wpa-supplicant-shepherd-service): Add missing
parens.
---
 gnu/services/networking.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index 61a0e975c7..b764cde5ac 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -1064,10 +1064,10 @@ networking."))))
                                    #~("-u")
                                    #~())
                             #$@(if interface
-                                   #~(string-append "-i" #$interface)
+                                   #~((string-append "-i" #$interface))
                                    #~())
                             #$@(if config-file
-                                   #~(string-append "-c" #$config-file)
+                                   #~((string-append "-c" #$config-file))
                                    #~())
                             #$@extra-options)
                       #:pid-file #$pid-file))

From a908ffd1abff95e526a9224d35ca5f8d31fac95c Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 17 Oct 2018 21:41:20 +0200
Subject: [PATCH 780/909] gnu: notmuch: Update to 0.28.

* gnu/packages/mail.scm (notmuch): Update to 0.28.
---
 gnu/packages/mail.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 7348719ede..73a17fb21b 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -763,14 +763,14 @@ invoking @command{notifymuch} from the post-new hook.")
 (define-public notmuch
   (package
     (name "notmuch")
-    (version "0.27")
+    (version "0.28")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://notmuchmail.org/releases/notmuch-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0xh8vq2sa7r07xb3n13drc6gdiqhcgl0pj0za5xj43qkiwpikls0"))))
+                "0dqarmjc8544m2w7bqrqmvsfy55fw82707z3lz9cql8nr777bjmc"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)

From 2c0a3ed1f98e81c6c2f828c488ec7318181de539 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 17 Oct 2018 22:25:31 +0200
Subject: [PATCH 781/909] gnu: tmux: Update to 2.8.

* gnu/packages/tmux.scm (tmux): Update to 2.8.
---
 gnu/packages/tmux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/tmux.scm b/gnu/packages/tmux.scm
index 1bc947844a..d8af54ce57 100644
--- a/gnu/packages/tmux.scm
+++ b/gnu/packages/tmux.scm
@@ -34,7 +34,7 @@
 (define-public tmux
   (package
     (name "tmux")
-    (version "2.7")
+    (version "2.8")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -42,7 +42,7 @@
                     version "/tmux-" version ".tar.gz"))
              (sha256
               (base32
-               "0lnlhnafvi5700afr69g6gr62pblnd440jj0hxdbrxhk0c87vvcx"))))
+               "1fm22wva2znkcs5jczrnlxrpzsk2jlwdwy4dhzzyrbsgccsz6svz"))))
     (build-system gnu-build-system)
     (inputs
      `(("libevent" ,libevent)

From 29f40ee54729bf3e13d5dffaaae01c77a9cf254e Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Wed, 17 Oct 2018 22:29:38 +0200
Subject: [PATCH 782/909] gnu: libgit2: Update to 0.26.7.

* gnu/packages/version-control.scm (libgit2): Update to 0.26.7.
---
 gnu/packages/version-control.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 528d117e29..14a18c8c35 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -427,7 +427,7 @@ everything from small to very large projects with speed and efficiency.")
 (define-public libgit2
   (package
     (name "libgit2")
-    (version "0.26.6")
+    (version "0.26.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/libgit2/libgit2/"
@@ -435,7 +435,7 @@ everything from small to very large projects with speed and efficiency.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0qjn1v5q282v8jih8rqjdqxr5v4n4manr0c8i3nnrf6sxd3xssbn"))
+                "1vy4dnbvhcq3pw8n8zz6clnsv2xnkrichl8k96w3lb6yyk0lln35"))
               (patches (search-patches "libgit2-mtime-0.patch"))
 
               ;; Remove bundled software.

From 1e672a01bef602e33248467ada9fb523e8717517 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 18 Oct 2018 22:43:26 -0400
Subject: [PATCH 783/909] gnu: linux-libre@4.9: Update to 4.9.134.

* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.134.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index cd4adf9b6f..b639a57e27 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:configuration-file kernel-config))
 
 (define-public linux-libre-4.9
-  (make-linux-libre "4.9.133"
-                    "1vr94czdv5alzsgm2k1r6wqm01r2zafrayjn10l6kdr4g7aga488"
+  (make-linux-libre "4.9.134"
+                    "0f5qif27k0mhc57d98arbfkq7zlvg0ra2gz6g5fasblyjz3j7w7h"
                     %intel-compatible-systems
                     #:configuration-file kernel-config))
 

From ef8e7e3298e6f4f84717f304191ad64b5dc148d4 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 18 Oct 2018 22:44:09 -0400
Subject: [PATCH 784/909] gnu: linux-libre@4.14: Update to 4.14.77.

* gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.77.
(%linux-libre-4.14-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index b639a57e27..1c73532bae 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.")
                     #:patches %linux-libre-4.18-patches
                     #:configuration-file kernel-config))
 
-(define %linux-libre-4.14-version "4.14.76")
-(define %linux-libre-4.14-hash "1y5zqf84ngb6f5f85xpd4bdy6mlxr52x19bx3mdrp82awc9fvr7q")
+(define %linux-libre-4.14-version "4.14.77")
+(define %linux-libre-4.14-hash "18y81rga2lhsk7bjckglxz52pvnzf103ar0z2zj611g37wyf83r5")
 
 (define-public linux-libre-4.14
   (make-linux-libre %linux-libre-4.14-version

From 75b2afd95373612d386dba7f75c4de22857f9448 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 18 Oct 2018 22:52:09 -0400
Subject: [PATCH 785/909] gnu: linux-libre: Update to 4.18.15.

* gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.15.
(%linux-libre-hash): Update hash.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 1c73532bae..6a89caf277 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.")
 ;; supports qemu "virt" machine and possibly a large number of ARM boards.
 ;; See : https://wiki.debian.org/DebianKernel/ARMMP.
 
-(define %linux-libre-version "4.18.14")
-(define %linux-libre-hash "1gwwx8l283w8v1zylw2haqahvjns5dzqxx9li2586nnl8cfmfnwc")
+(define %linux-libre-version "4.18.15")
+(define %linux-libre-hash "0v6xs85qn1iy2dj3m6s3cfnhbwb1mjy21d9lagjni8dg3jic26hf")
 
 (define %linux-libre-4.18-patches
   (list %boot-logo-patch

From eed00f93e8999712191e39c59c15e23461520f43 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Tue, 16 Oct 2018 14:15:19 -0400
Subject: [PATCH 786/909] gnu: libssh: Update to 0.7.6 [fixes CVE-2018-10933].

* gnu/packages/ssh.scm (libssh): Update to 0.7.6.
* gnu/packages/patches/libssh-hostname-parser-bug.patch: Adjust patch.
---
 .../patches/libssh-hostname-parser-bug.patch  | 22 ++-----
 gnu/packages/ssh.scm                          | 62 +++++++++----------
 2 files changed, 33 insertions(+), 51 deletions(-)

diff --git a/gnu/packages/patches/libssh-hostname-parser-bug.patch b/gnu/packages/patches/libssh-hostname-parser-bug.patch
index 69f46cbdd6..de2336e86d 100644
--- a/gnu/packages/patches/libssh-hostname-parser-bug.patch
+++ b/gnu/packages/patches/libssh-hostname-parser-bug.patch
@@ -1,31 +1,17 @@
-Fix "Hostname" parsing in OpenSSH config files, as reported
-at <https://red.libssh.org/issues/260>.
-
-From: Niels Ole Salscheider <niels_ole@salscheider-online.de>
-Date: Mon, 8 May 2017 17:36:13 +0200
-Subject: [PATCH] Fix reading of the first parameter
-
-This is a fixup for 7b8b5eb4eac314a3a29be812bef0264c6611f6e7.
-Previously, it would return as long as the parameter was _not_ seen
-before. It also did not handle the case for the unsupported opcode (-1)
+It does not handle the case for the unsupported opcode (-1)
 which would cause a segfault when accessing the "seen" array.
----
- src/config.c | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
 
 diff --git a/src/config.c b/src/config.c
-index 7c03b27..238a655 100644
+index c5313ec8..72e07639 100644
 --- a/src/config.c
 +++ b/src/config.c
-@@ -218,8 +218,9 @@ static int ssh_config_parse_line(ssh_session session, const char *line,
+@@ -218,7 +218,8 @@ static int ssh_config_parse_line(ssh_session session, const char *line,
    }
  
    opcode = ssh_config_get_opcode(keyword);
 -  if (*parsing == 1 && opcode != SOC_HOST) {
--      if (seen[opcode] == 0) {
 +  if (*parsing == 1 && opcode != SOC_HOST &&
 +      opcode > SOC_UNSUPPORTED && opcode < SOC_END) {
-+      if (seen[opcode] == 1) {
+       if (seen[opcode] != 0) {
            return 0;
        }
-       seen[opcode] = 1;
diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm
index 362d427a2e..829977f5c5 100644
--- a/gnu/packages/ssh.scm
+++ b/gnu/packages/ssh.scm
@@ -65,40 +65,36 @@
   #:use-module (srfi srfi-1))
 
 (define-public libssh
-  ;; This commit from the 'v0-7' branch contains 7 memory-management-related
-  ;; bug fixes that we'd rather have.
-  (let ((commit "239d0f75b5f909174c2ef7fb08d23bcfa6b20ba0")
-        (revision "0"))
-    (package
-      (name "libssh")
-      (version (git-version "0.7.5" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://git.libssh.org/projects/libssh.git")
-                      (commit commit)))
-                (sha256
-                 (base32
-                  "01w72w1jsgs9ilj3n1gp6qkmdxr9n74i5h2nipi3x1vzm7bv8na1"))
-                (patches (search-patches "libssh-hostname-parser-bug.patch"))
-                (file-name (git-file-name name version))))
-      (build-system cmake-build-system)
-      (outputs '("out" "debug"))
-      (arguments
-       '(#:configure-flags '("-DWITH_GCRYPT=ON")
+  (package
+    (name "libssh")
+    (version "0.7.6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://git.libssh.org/projects/libssh.git")
+                    (commit (string-append "libssh-" version))))
+              (patches (search-patches "libssh-hostname-parser-bug.patch"))
+              (sha256
+               (base32
+                "0slwqa36mhyb6brdv2jvb9fxp7rvsv3ziv67kaxx615jxn52l5pa"))
+              (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (outputs '("out" "debug"))
+    (arguments
+     '(#:configure-flags '("-DWITH_GCRYPT=ON")
 
-         ;; TODO: Add 'CMockery' and '-DWITH_TESTING=ON' for the test suite.
-         #:tests? #f))
-      (inputs `(("zlib" ,zlib)
-                ("libgcrypt" ,libgcrypt)))
-      (synopsis "SSH client library")
-      (description
-       "libssh is a C library implementing the SSHv2 and SSHv1 protocol for
-client and server implementations.  With libssh, you can remotely execute
-programs, transfer files, and use a secure and transparent tunnel for your
-remote applications.")
-      (home-page "https://www.libssh.org")
-      (license license:lgpl2.1+))))
+       ;; TODO: Add 'CMockery' and '-DWITH_TESTING=ON' for the test suite.
+       #:tests? #f))
+    (inputs `(("zlib" ,zlib)
+              ("libgcrypt" ,libgcrypt)))
+    (synopsis "SSH client library")
+    (description
+     "libssh is a C library implementing the SSHv2 and SSHv1 protocol for client
+and server implementations.  With libssh, you can remotely execute programs,
+transfer files, and use a secure and transparent tunnel for your remote
+applications.")
+    (home-page "https://www.libssh.org")
+    (license license:lgpl2.1+)))
 
 (define-public libssh2
   (package

From 7277d06d8b956263ef1773c5f61e53dc65583ddd Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 12 Oct 2018 23:47:15 -0400
Subject: [PATCH 787/909] gnu: Use pypi.org.

<pypi.io> redirects to <pypi.org>.

* guix/build-system/python.scm (pypi-uri): Replace pypi.io with pypi.org.
* guix/import/pypi.scm (pypi-url?): Likewise.
* tests/pypi.scm: Likewise.
---
 guix/build-system/python.scm | 2 +-
 guix/import/pypi.scm         | 2 +-
 tests/pypi.scm               | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/guix/build-system/python.scm b/guix/build-system/python.scm
index ffed837313..b753940bad 100644
--- a/guix/build-system/python.scm
+++ b/guix/build-system/python.scm
@@ -50,7 +50,7 @@
   "Return a URI string for the Python package hosted on the Python Package
 Index (PyPI) corresponding to NAME and VERSION.  EXTENSION is the file name
 extension, such as '.tar.gz'."
-  (string-append "https://pypi.io/packages/source/"
+  (string-append "https://pypi.org/packages/source/"
                  (string-take name 1) "/" name "/"
                  name "-" version extension))
 
diff --git a/guix/import/pypi.scm b/guix/import/pypi.scm
index 87b047bdac..3a20fc4b9b 100644
--- a/guix/import/pypi.scm
+++ b/guix/import/pypi.scm
@@ -330,7 +330,7 @@ VERSION, SOURCE-URL, HOME-PAGE, SYNOPSIS, DESCRIPTION, and LICENSE."
   (define (pypi-url? url)
     (or (string-prefix? "https://pypi.org/" url)
         (string-prefix? "https://pypi.python.org/" url)
-        (string-prefix? "https://pypi.io/packages" url)))
+        (string-prefix? "https://pypi.org/packages" url)))
 
   (let ((source-url (and=> (package-source package) origin-uri))
         (fetch-method (and=> (package-source package) origin-method)))
diff --git a/tests/pypi.scm b/tests/pypi.scm
index 616ec191f5..6daa44a6e7 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -81,7 +81,7 @@ baz > 13.37")
    (dummy-package "foo"
                   (source (dummy-origin
                            (uri
-                            "https://pypi.io/packages/source/p/psutil/psutil-4.3.0.tar.gz"))))))
+                            "https://pypi.org/packages/source/p/psutil/psutil-4.3.0.tar.gz"))))))
 
 (test-equal "guix-package->pypi-name, new URL style"
   "certbot"

From 7d1f21c69aa89e4c7c57ace26af80d168157b243 Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Fri, 19 Oct 2018 08:41:25 +0200
Subject: [PATCH 788/909] gnu: vulkan-headers: Update to 1.1.85.0.

* gnu/packages/vulkan.scm (vulkan-headers): Update to 1.1.85.0.
* gnu/packages/vulkan.scm (vulkan-loader): Update hash.
* gnu/packages/vulkan.scm (vulkan-tools): Update hash.
---
 gnu/packages/vulkan.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/vulkan.scm b/gnu/packages/vulkan.scm
index 2474d640d7..ff1088d2e1 100644
--- a/gnu/packages/vulkan.scm
+++ b/gnu/packages/vulkan.scm
@@ -163,7 +163,7 @@ interpretation of the specifications for these languages.")
 (define-public vulkan-headers
   (package
     (name "vulkan-headers")
-    (version "1.1.82.0")
+    (version "1.1.85.0")
     (source
      (origin
        (method url-fetch)
@@ -172,7 +172,7 @@ interpretation of the specifications for these languages.")
              "archive/sdk-" version ".tar.gz"))
        (sha256
         (base32
-         "1rbra47f1dkw5bjzvm0k9s2f89c2x80j904ply4bxks7sl3xlwyz"))))
+         "166hqqb97kjg6h9vp8yxb1cq02i1kqaxvl693482gf8v21fl7ink"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f)) ; No tests.
@@ -195,7 +195,7 @@ interpretation of the specifications for these languages.")
              "archive/sdk-" version ".tar.gz"))
        (sha256
         (base32
-         "032vfysb8mi19c2lx08vc6k9mbzxmiy17wp7a22vpgwwv69kxkc6"))))
+         "04d53ynlc0ww8r67hv4sxwg5sirjhpr1laaa9hc6j4niliw0166n"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;FIXME: 23/39 tests fail.  Try "tests/run_all_tests.sh".
@@ -251,7 +251,7 @@ and the ICD.")
              "archive/sdk-" version ".tar.gz"))
        (sha256
         (base32
-         "175qhfg9lxxfm5zks6jxaybcxamwd9q5kvjq8ikf2dbmskgybr92"))))
+         "0r26px9rh09giddajlmafv21rx1la1y3bbnjgnpai8aw98wvq9mm"))))
     (build-system cmake-build-system)
     (inputs
      `(("glslang" ,glslang)

From 2f4d43584cb26315c028dfbd2197da0d175933a2 Mon Sep 17 00:00:00 2001
From: Chris Marusich <cmmarusich@gmail.com>
Date: Sat, 13 Oct 2018 22:50:36 -0700
Subject: [PATCH 789/909] system: Rename .zlogin to .zprofile.

Reported by Meiyo Peng <meiyo.peng@gmail.com>.

* gnu/system/shadow.scm (default-skeletons): Rename zlogin to zprofile.
---
 gnu/system/shadow.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/gnu/system/shadow.scm b/gnu/system/shadow.scm
index f800c3b546..63f544cec9 100644
--- a/gnu/system/shadow.scm
+++ b/gnu/system/shadow.scm
@@ -181,7 +181,7 @@ fi
 alias ls='ls -p --color=auto'
 alias ll='ls -l'
 alias grep='grep --color=auto'\n"))
-        (zlogin    (plain-file "zlogin" "\
+        (zprofile    (plain-file "zprofile" "\
 # Honor system-wide environment variables
 source /etc/profile\n"))
         (guile-wm  (computed-file "guile-wm" copy-guile-wm))
@@ -197,7 +197,10 @@ set debug-file-directory ~/.guix-profile/lib/debug
 set auto-load safe-path /gnu/store/*/lib\n")))
     `((".bash_profile" ,profile)
       (".bashrc" ,bashrc)
-      (".zlogin" ,zlogin)
+      ;; Zsh sources ~/.zprofile before ~/.zshrc, and it sources ~/.zlogin
+      ;; after ~/.zshrc.  To avoid interfering with any customizations a user
+      ;; may have made in their ~/.zshrc, put this in .zprofile, not .zlogin.
+      (".zprofile" ,zprofile)
       (".nanorc" ,(plain-file "nanorc" "\
 # Include all the syntax highlighting modules.
 include /run/current-system/profile/share/nano/*.nanorc\n"))

From 1d7fb035fcff87bea1caf229df576b0e29e0ea04 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 19 Oct 2018 10:25:04 +0200
Subject: [PATCH 790/909] gnu: guile-commonmark: Update to 0.1.1.

* gnu/packages/guile.scm (guile-commonmark): Update to 0.1.1.
[source](modules, snippet): Remove.
[native-inputs]: New field.
---
 gnu/packages/guile.scm | 20 ++++----------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 2d4d8c3218..bf2f2a14a4 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1618,7 +1618,7 @@ you send to a FIFO file.")
 (define-public guile-commonmark
   (package
     (name "guile-commonmark")
-    (version "0.1")
+    (version "0.1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/OrangeShark/" name
@@ -1626,24 +1626,12 @@ you send to a FIFO file.")
                                   "/" name "-" version ".tar.gz"))
               (sha256
                (base32
-                "12cb5fqvvgc87f5xp0ih5az305wnjia89l5jba83d0r2p8bfy0b0"))
-              (modules '((guix build utils)))
-              (snippet
-               ;; Use the real effective version of Guile in directory names
-               ;; instead of a hard-coded "/2.0".
-               '(begin
-                  (substitute* "configure"
-                    (("ac_subst_vars='")
-                     "ac_subst_vars='GUILE_EFFECTIVE_VERSION\n"))
-                  (substitute* "Makefile.in"
-                    (("moddir =.*")
-                     "moddir = $(datadir)/guile/site/@GUILE_EFFECTIVE_VERSION@\n")
-                    (("godir =.*")
-                     "godir = $(libdir)/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n"))
-                  #t))))
+                "0kzclwkfijj8xka3g9kfj53y67c34ndfy84swdbw3j7y962ndxq6"))))
     (build-system gnu-build-system)
     (inputs
      `(("guile" ,guile-2.2)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
     (synopsis "CommonMark parser for Guile")
     (description
      "guile-commonmark is a library for parsing CommonMark, a fully specified

From 0fd874ebd11324139ddf976a39d99e6bb6f6996f Mon Sep 17 00:00:00 2001
From: Rutger Helling <rhelling@mykolab.com>
Date: Fri, 19 Oct 2018 11:42:25 +0200
Subject: [PATCH 791/909] gnu: youtube-dl: Update to 2018.10.05.

* gnu/packages/video.scm (youtube-dl): Update to 2018.10.05.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index ab57ee4b45..a6930abfda 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1268,7 +1268,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2018.09.18")
+    (version "2018.10.05")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -1276,7 +1276,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0mlsdmddmyy3xaqy366k48xds14g17l81al3kglndjkbrrji63sb"))))
+                "1iq02kwxdgh07bf0w0fvbsjbdshs4kja35gy8m70ji9cj10l1mbw"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion

From b718793e2a3e09f458d93f1a000846308a7eb878 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 15:08:45 +0200
Subject: [PATCH 792/909] gnu: Add texlive-latex-ms.

* gnu/packages/tex.scm (texlive-latex-ms): New variable.
---
 gnu/packages/tex.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index be75bda7dd..9026c25596 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4492,3 +4492,33 @@ including:
 
 It also ensures compatibility with the @code{media9} and @code{animate} packages.")
     (license license:lppl)))
+
+(define-public texlive-latex-ms
+  (package
+    (name "texlive-latex-ms")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (texlive-ref "latex" "ms"))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0m4wx3yjb5al1qsv995z8fii8xxy96mcfihbnlx43lpgayiwz35s"))))
+    (build-system texlive-build-system)
+    (arguments
+     '(#:tex-directory "latex/ms"
+       #:tex-format "latex"))
+    (home-page "https://ctan.org/pkg/ms")
+    (synopsis "Various LATEX packages by Martin Schröder")
+    (description
+     "A bundle of LATEX packages by Martin Schröder; the collection comprises:
+
+@itemize
+@item @command{count1to}, make use of fixed TEX counters;
+@item @command{everysel}, set commands to execute every time a font is selected;
+@item @command{everyshi}, set commands to execute whenever a page is shipped out;
+@item @command{multitoc}, typeset the table of contents in multiple columns;
+@item @command{prelim2e}, mark typeset pages as preliminary; and
+@item @command{ragged2e}, typeset ragged text and allow hyphenation.
+@end itemize\n")
+    (license license:lppl1.3c+)))

From 707babdde428bfd67d4ea9438d2f834946b1959e Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 15:10:02 +0200
Subject: [PATCH 793/909] gnu: Add texlive-latex-needspace.

* gnu/packages/tex.scm (texlive-latex-needspace): New variable.
---
 gnu/packages/tex.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 9026c25596..064ec94243 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4522,3 +4522,28 @@ It also ensures compatibility with the @code{media9} and @code{animate} packages
 @item @command{ragged2e}, typeset ragged text and allow hyphenation.
 @end itemize\n")
     (license license:lppl1.3c+)))
+
+(define-public texlive-latex-needspace
+  (package
+    (name "texlive-latex-needspace")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (texlive-ref "latex" "needspace"))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "0kw80f5jh4gdpa2ka815abza3gr5z8b929w0745vrlc59pl0017y"))))
+    (build-system texlive-build-system)
+    (arguments
+     '(#:tex-directory "latex/needspace"
+       #:tex-format "latex"))
+    (inputs
+     `(("texlive-latex-filecontents" ,texlive-latex-filecontents)))
+    (home-page "https://www.ctan.org/pkg/needspace")
+    (synopsis "Insert pagebreak if not enough space")
+    (description
+     "Provides commands to disable pagebreaking within a given vertical
+space.  If there is not enough space between the command and the bottom of the
+page, a new page will be started.")
+    (license license:lppl)))

From 0e73c11bb23b47ca73707d7c528e0bdcf222635e Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 15:10:18 +0200
Subject: [PATCH 794/909] gnu: Add texlive-latex-eukdate.

* gnu/packages/tex.scm (texlive-latex-eukdate): New variable.
---
 gnu/packages/tex.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 064ec94243..2d5e0865c9 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4547,3 +4547,39 @@ It also ensures compatibility with the @code{media9} and @code{animate} packages
 space.  If there is not enough space between the command and the bottom of the
 page, a new page will be started.")
     (license license:lppl)))
+
+(define-public texlive-latex-eukdate
+  (package
+    (name "texlive-latex-eukdate")
+    (version (number->string %texlive-revision))
+    (source
+     (origin
+       (method svn-fetch)
+       (uri (svn-reference
+             (url (string-append "svn://www.tug.org/texlive/tags/"
+                                 %texlive-tag "/Master/texmf-dist/"
+                                 "/tex/latex/eukdate"))
+             (revision %texlive-revision)))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32
+         "18xan116l8w47v560bkw6nbhkrml7g04xrlzk3jrpc7qsyf3n5fz"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/tex/latex/eukdate")))
+           (mkdir-p target)
+           (copy-recursively (assoc-ref %build-inputs "source") target)
+           #t))))
+    (home-page "https://www.ctan.org/pkg/eukdate")
+    (synopsis "UK format dates, with weekday")
+    (description
+     "The package is used to change the format of @code{\\today}’s date,
+including the weekday, e.g., \"Saturday, 26 June 2008\", the 'UK format', which
+is preferred in many parts of the world, as distinct from that which is used in
+@code{\\maketitle} of the article class, \"June 26, 2008\", the 'US format'.")
+    (license license:lppl)))

From 910d67fb95aa70c562b74869294d931129b5ddb4 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 15:11:52 +0200
Subject: [PATCH 795/909] gnu: Add texlive-generic-ulem.

* gnu/packages/tex.scm (texlive-generic-ulem): New variable.
---
 gnu/packages/tex.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 2d5e0865c9..81c0feb079 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4583,3 +4583,40 @@ including the weekday, e.g., \"Saturday, 26 June 2008\", the 'UK format', which
 is preferred in many parts of the world, as distinct from that which is used in
 @code{\\maketitle} of the article class, \"June 26, 2008\", the 'US format'.")
     (license license:lppl)))
+
+(define-public texlive-generic-ulem
+  (package
+    (name "texlive-generic-ulem")
+    (version (number->string %texlive-revision))
+    (source
+     (origin
+       (method svn-fetch)
+       (uri (svn-reference
+             (url (string-append "svn://www.tug.org/texlive/tags/"
+                                 %texlive-tag "/Master/texmf-dist/"
+                                 "/tex/generic/ulem"))
+             (revision %texlive-revision)))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32
+         "1rzdniqq9zk39w8ch8ylx3ywh2mj87s4ivchrsk2b8nx06jyn797"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target (string-append (assoc-ref %outputs "out")
+                                      "/share/texmf-dist/tex/generic/ulem")))
+           (mkdir-p target)
+           (copy-recursively (assoc-ref %build-inputs "source") target)
+           #t))))
+    (home-page "https://www.ctan.org/pkg/ulem")
+    (synopsis "Underline text in TeX")
+    (description
+     "The package provides an @code{\\ul} (underline) command which will break
+over line ends; this technique may be used to replace @code{\\em} (both in that
+form and as the @code{\\emph} command), so as to make output look as if it comes
+from a typewriter.  The package also offers double and wavy underlining, and
+striking out (line through words) and crossing out (/// over words).")
+    (license license:lppl1.3c+)))

From 17ef5f1ff9b9bdf1bd19cf21528713cb362a18b6 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 15:16:40 +0200
Subject: [PATCH 796/909] gnu: Add texlive-latex-pgf.

* gnu/packages/tex.scm (texlive-latex-pgf): New variable.
---
 gnu/packages/tex.scm | 57 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 81c0feb079..4f0201425d 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4620,3 +4620,60 @@ form and as the @code{\\emph} command), so as to make output look as if it comes
 from a typewriter.  The package also offers double and wavy underlining, and
 striking out (line through words) and crossing out (/// over words).")
     (license license:lppl1.3c+)))
+
+(define-public texlive-latex-pgf
+  (package
+    (name "texlive-latex-pgf")
+    (version (number->string %texlive-revision))
+    (source
+     (origin
+       (method svn-fetch)
+       (uri (svn-reference
+             (url (string-append "svn://www.tug.org/texlive/tags/"
+                                 %texlive-tag "/Master/texmf-dist/"
+                                 "/tex/latex/pgf"))
+             (revision %texlive-revision)))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32
+         "1dq8p10pz8wn0vx412m7d7d5gj1syxly3yqdqvf7lv2xl8zndn5h"))))
+    (build-system trivial-build-system)
+    (native-inputs
+     `(("texlive-latex-pgf-generic"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+             (url (string-append "svn://www.tug.org/texlive/tags/"
+                                 %texlive-tag "/Master/texmf-dist/"
+                                 "/tex/generic/pgf"))
+             (revision %texlive-revision)))
+           (file-name (string-append "texlive-latex-pgf-generic" version "-checkout"))
+           (sha256
+            (base32
+             "0xkxw26sjzr5npjpzpr28yygwdbhzpdd0hsk80gjpidhcxmz393i"))))))
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((target-generic (string-append (assoc-ref %outputs "out")
+                                              "/share/texmf-dist/tex/generic/pgf"))
+               (target-latex (string-append (assoc-ref %outputs "out")
+                                            "/share/texmf-dist/tex/latex/pgf")))
+           (mkdir-p target-generic)
+           (mkdir-p target-latex)
+           (copy-recursively (assoc-ref %build-inputs "texlive-latex-pgf-generic") target-generic)
+           (copy-recursively (assoc-ref %build-inputs "source") target-latex)
+           #t))))
+    (home-page "https://www.ctan.org/pkg/tikz")
+    (synopsis "Create PostScript and PDF graphics in TeX")
+    (description
+     "PGF is a macro package for creating graphics.  It is platform- and
+format-independent and works together with the most important TeX backend
+drivers, including pdfTeX and dvips.  It comes with a user-friendly syntax layer
+called TikZ.
+
+Its usage is similar to pstricks and the standard picture environment.  PGF
+works with plain (pdf-)TeX, (pdf-)LaTeX, and ConTeXt.  Unlike pstricks, it can
+produce either PostScript or PDF output.")
+    (license license:lppl1.3c+)))

From e7b2937d1907ad1fa11b6237bbda9da303160c41 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 15:17:55 +0200
Subject: [PATCH 797/909] gnu: Add texlive-latex-koma-script.

* gnu/packages/tex.scm (texlive-latex-koma-script): New variable.
---
 gnu/packages/tex.scm | 60 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index 4f0201425d..6a76cbf866 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4677,3 +4677,63 @@ Its usage is similar to pstricks and the standard picture environment.  PGF
 works with plain (pdf-)TeX, (pdf-)LaTeX, and ConTeXt.  Unlike pstricks, it can
 produce either PostScript or PDF output.")
     (license license:lppl1.3c+)))
+
+(define-public texlive-latex-koma-script
+  (package
+    (name "texlive-latex-koma-script")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/tex/latex/koma-script"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1g8qg796hc6s092islnybaxs115ldsqwp2vxkk3gpy6vh7wc9r50"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (ice-9 match))
+       #:builder
+       (begin
+         (use-modules (guix build utils)
+                      (ice-9 match))
+         (let ((root (string-append (assoc-ref %outputs "out")
+                                    "/share/texmf-dist/"))
+               (pkgs '(("source" . "tex/latex/koma-script"))))
+           (for-each (match-lambda
+                       ((pkg . dir)
+                        (let ((target (string-append root dir)))
+                          (mkdir-p target)
+                          (copy-recursively (assoc-ref %build-inputs pkg)
+                                            target))))
+                     pkgs)
+           #t))))
+    (home-page "https://www.ctan.org/pkg/koma-script")
+    (synopsis "Bundle of versatile classes and packages")
+    (description
+     "The KOMA-Script bundle provides replacements for the article, report, and
+book classes with emphasis on typography and versatility.  There is also a
+letter class.
+
+The bundle also offers:
+
+@itemize
+@item a package for calculating type areas in the way laid down by the
+typographer Jan Tschichold,
+@item packages for easily changing and defining page styles,
+@item a package scrdate for getting not only the current date but also the name
+of the day, and
+@item a package scrtime for getting the current time.
+@end itemize
+
+All these packages may be used not only with KOMA-Script classes but also with
+the standard classes.
+
+Since every package has its own version number, the version number quoted only
+refers to the version of scrbook, scrreprt, scrartcl, scrlttr2 and
+typearea (which are the main parts of the bundle).")
+    (license license:lppl1.3+)))

From 99c61242292987e2eaae1ff32687ab019d225420 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Tue, 21 Aug 2018 18:25:50 +0200
Subject: [PATCH 798/909] gnu: Add cl-strings.

* gnu/packages/lisp.scm (cl-strings, sbcl-cl-strings, ecl-cl-strings): New variables.
---
 gnu/packages/lisp.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 8b8b9229b5..ef745d0ed8 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1526,3 +1526,34 @@ based on a subset of MDL.  Confusion is a MDL interpreter that works just well
 enough to play the original mainframe Zork all the way through.")
       (home-page "http://www.russotto.net/git/mrussotto/confusion/src/master/src/README")
       (license license:gpl3+))))
+
+(define-public sbcl-cl-strings
+  (let ((revision "1")
+        (commit "c5c5cbafbf3e6181d03c354d66e41a4f063f00ae"))
+    (package
+      (name "sbcl-cl-strings")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/diogoalexandrefranco/cl-strings")
+               (commit commit)))
+         (sha256
+          (base32
+           "00754mfaqallj480lwd346nkfb6ra8pa8xcxcylf4baqn604zlmv"))
+         (file-name (string-append "cl-strings-" version "-checkout"))))
+      (build-system asdf-build-system/sbcl)
+      (synopsis "Portable, dependency-free set of utilities to manipulate strings in Common Lisp")
+      (description
+       "@command{cl-strings} is a small, portable, dependency-free set of
+utilities that make it even easier to manipulate text in Common Lisp.  It has
+100% test coverage and works at least on sbcl, ecl, ccl, abcl and clisp.")
+      (home-page "https://github.com/diogoalexandrefranco/cl-strings")
+      (license license:expat))))
+
+(define-public cl-strings
+  (sbcl-package->cl-source-package sbcl-cl-strings))
+
+(define-public ecl-cl-strings
+  (sbcl-package->ecl-package sbcl-cl-strings))

From 8c661ff1ef48839de868d204487dd69eda9f5ffa Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:12:36 +0200
Subject: [PATCH 799/909] gnu: Add trivial-features.

* gnu/packages/lisp.scm (cl-trivial-features, ecl-trivial-features, sbcl-trivial-features): New variables.
---
 gnu/packages/lisp.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index ef745d0ed8..675c6dcaa4 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1557,3 +1557,30 @@ utilities that make it even easier to manipulate text in Common Lisp.  It has
 
 (define-public ecl-cl-strings
   (sbcl-package->ecl-package sbcl-cl-strings))
+
+(define-public sbcl-trivial-features
+  (package
+    (name "sbcl-trivial-features")
+    (version "0.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/trivial-features/trivial-features/archive/v"
+             version ".tar.gz"))
+       (sha256
+        (base32 "0db1awn6jyhcfhyfvpjvfziprmq85cigf19mwbvaprhblydsag3c"))
+       (file-name (string-append "trivial-features-" version ".tar.gz"))))
+    (build-system asdf-build-system/sbcl)
+    (arguments '(#:tests? #f))
+    (home-page "http://cliki.net/trivial-features")
+    (synopsis "Ensures consistency of @code{*FEATURES*} in Common Lisp")
+    (description "Trivial-features ensures that @code{*FEATURES*} is
+consistent across multiple Common Lisp implementations.")
+    (license license:expat)))
+
+(define-public cl-trivial-features
+  (sbcl-package->cl-source-package sbcl-trivial-features))
+
+(define-public ecl-trivial-features
+  (sbcl-package->ecl-package sbcl-trivial-features))

From 0cd6fb49701fcefc5e7e2d86a5bc5211b7248624 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:13:46 +0200
Subject: [PATCH 800/909] gnu: Add hu.dwim.asdf.

* gnu/packages/lisp.scm (cl-hu.dwim.asdf, ecl-hu.dwim.asdf, sbcl-hu.dwim.asdf): New variables.
---
 gnu/packages/lisp.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 675c6dcaa4..a163d2ec13 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1584,3 +1584,31 @@ consistent across multiple Common Lisp implementations.")
 
 (define-public ecl-trivial-features
   (sbcl-package->ecl-package sbcl-trivial-features))
+
+(define-public sbcl-hu.dwim.asdf
+  (let ((commit "170b0e4fdde3df0bc537327e7600575daac9e141"))
+    (package
+      (name "sbcl-hu.dwim.asdf")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri
+          (git-reference
+           (url "https://github.com/nixeagle/hu.dwim.asdf")
+           (commit commit)))
+         (sha256
+          (base32 "10ax7p8y6vjqxzcq125p62kf68zi455a65ysgk0kl1f2v839c33v"))
+         (file-name (git-file-name "hu.dwim.asdf" version))))
+      (build-system asdf-build-system/sbcl)
+      (home-page "https://hub.darcs.net/hu.dwim/hu.dwim.asdf")
+      (synopsis "Extensions to ASDF")
+      (description "Various ASDF extensions such as attached test and
+documentation system, explicit development support, etc.")
+      (license license:public-domain))))
+
+(define-public cl-hu.dwim.asdf
+  (sbcl-package->cl-source-package sbcl-hu.dwim.asdf))
+
+(define-public ecl-hu.dwim.asdf
+  (sbcl-package->ecl-package sbcl-hu.dwim.asdf))

From 4ef9ddbdaeb634948ce67687289c3d841447ec0b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:14:26 +0200
Subject: [PATCH 801/909] gnu: Add hu.dwim.stefil.

* gnu/packages/lisp.scm (cl-hu.dwim.stefil, ecl-hu.dwim.stefil, sbcl-hu.dwim.stefil): New variables.
---
 gnu/packages/lisp.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index a163d2ec13..adf91a2880 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1612,3 +1612,35 @@ documentation system, explicit development support, etc.")
 
 (define-public ecl-hu.dwim.asdf
   (sbcl-package->ecl-package sbcl-hu.dwim.asdf))
+
+(define-public sbcl-hu.dwim.stefil
+  (let ((commit "ab6d1aa8995878a1b66d745dfd0ba021090bbcf9"))
+    (package
+      (name "sbcl-hu.dwim.stefil")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri
+          (git-reference
+           (url "https://gitlab.common-lisp.net/xcvb/hu.dwim.stefil.git")
+           (commit commit)))
+         (sha256
+          (base32 "1d8yccw65zj3zh46cbi3x6nmn1dwdb76s9d0av035077mvyirqqp"))
+         (file-name (git-file-name "hu.dwim.stefil" version))))
+      (build-system asdf-build-system/sbcl)
+      (native-inputs
+       `(("asdf:cl-hu.dwim.asdf" ,sbcl-hu.dwim.asdf)))
+      (inputs
+       `(("sbcl-alexandria" ,sbcl-alexandria)))
+      (home-page "https://hub.darcs.net/hu.dwim/hu.dwim.stefil")
+      (synopsis "Simple test framework")
+      (description "Stefil is a simple test framework for Common Lisp,
+with a focus on interactive development.")
+      (license license:public-domain))))
+
+(define-public cl-hu.dwim.stefil
+  (sbcl-package->cl-source-package sbcl-hu.dwim.stefil))
+
+(define-public ecl-hu.dwim.stefil
+  (sbcl-package->ecl-package sbcl-hu.dwim.stefil))

From 2d418bfa39149df75b3975ad677d3c9b696d1954 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:16:43 +0200
Subject: [PATCH 802/909] gnu: Add babel.

* gnu/packages/lisp.scm (cl-babel, ecl-babel, sbcl-babel): New variables.
---
 gnu/packages/lisp.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index adf91a2880..f5c0b90946 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1644,3 +1644,34 @@ with a focus on interactive development.")
 
 (define-public ecl-hu.dwim.stefil
   (sbcl-package->ecl-package sbcl-hu.dwim.stefil))
+
+(define-public sbcl-babel
+  (package
+    (name "sbcl-babel")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/cl-babel/babel/archive/v"
+             version ".tar.gz"))
+       (sha256
+        (base32 "189kgbmslh36xx0d2i1g6a7mcvjryvjzkdlnhilqy5xs7hkyqirq"))
+       (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system asdf-build-system/sbcl)
+    (native-inputs
+     `(("tests:cl-hu.dwim.stefil" ,sbcl-hu.dwim.stefil)))
+    (inputs
+     `(("sbcl-alexandria" ,sbcl-alexandria)
+       ("sbcl-trivial-features" ,sbcl-trivial-features)))
+    (home-page "https://common-lisp.net/project/babel/")
+    (synopsis "Charset encoding and decoding library")
+    (description "Babel is a charset encoding and decoding library, not unlike
+GNU libiconv, but completely written in Common Lisp.")
+    (license license:expat)))
+
+(define-public cl-babel
+  (sbcl-package->cl-source-package sbcl-babel))
+
+(define-public ecl-babel
+  (sbcl-package->ecl-package sbcl-babel))

From ef091e91552dc849dcf454334449045333af9811 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:19:24 +0200
Subject: [PATCH 803/909] gnu: Add cl-yacc.

* gnu/packages/lisp.scm (cl-cl-yacc, ecl-cl-yacc, sbcl-cl-yacc): New variables.
---
 gnu/packages/lisp.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index f5c0b90946..d9a2cce260 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1675,3 +1675,38 @@ GNU libiconv, but completely written in Common Lisp.")
 
 (define-public ecl-babel
   (sbcl-package->ecl-package sbcl-babel))
+
+(define-public sbcl-cl-yacc
+  (package
+    (name "sbcl-cl-yacc")
+    (version "0.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/jech/cl-yacc")
+             (commit (string-append "cl-yacc-" version))))
+       (sha256
+        (base32
+         "16946pzf8vvadnyfayvj8rbh4zjzw90h0azz2qk1mxrvhh5wklib"))
+       (file-name (string-append "cl-yacc-" version "-checkout"))))
+    (build-system asdf-build-system/sbcl)
+    (arguments
+     `(#:asd-file "yacc.asd"
+       #:asd-system-name "yacc"))
+    (synopsis "LALR(1) parser generator for Common Lisp, similar in spirit to Yacc")
+    (description
+     "CL-Yacc is a LALR(1) parser generator for Common Lisp, similar in spirit
+to AT&T Yacc, Berkeley Yacc, GNU Bison, Zebu, lalr.cl or lalr.scm.
+
+CL-Yacc uses the algorithm due to Aho and Ullman, which is the one also used
+by AT&T Yacc, Berkeley Yacc and Zebu.  It does not use the faster algorithm due
+to DeRemer and Pennello, which is used by Bison and lalr.scm (not lalr.cl).")
+    (home-page "https://www.irif.fr/~jch//software/cl-yacc/")
+    (license license:expat)))
+
+(define-public cl-yacc
+  (sbcl-package->cl-source-package sbcl-cl-yacc))
+
+(define-public ecl-cl-yacc
+  (sbcl-package->ecl-package sbcl-cl-yacc))

From 232e1abce7f5d949256bd851b8bf0c2d0c4830fa Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:22:05 +0200
Subject: [PATCH 804/909] gnu: Add jpl-util.

* gnu/packages/lisp.scm (cl-jpl-util, ecl-jpl-util, sbcl-jpl-util): New variables.
---
 gnu/packages/lisp.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index d9a2cce260..9688e2c44d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1710,3 +1710,34 @@ to DeRemer and Pennello, which is used by Bison and lalr.scm (not lalr.cl).")
 
 (define-public ecl-cl-yacc
   (sbcl-package->ecl-package sbcl-cl-yacc))
+
+(define-public sbcl-jpl-util
+  (let ((commit "0311ed374e19a49d43318064d729fe3abd9a3b62"))
+    (package
+      (name "sbcl-jpl-util")
+      (version "20151005")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               ;; Quicklisp uses this fork.
+               (url "https://github.com/hawkir/cl-jpl-util")
+               (commit commit)))
+         (file-name
+          (git-file-name "jpl-util" version))
+         (sha256
+          (base32
+           "0nc0rk9n8grkg3045xsw34whmcmddn2sfrxki4268g7kpgz0d2yz"))))
+      (build-system asdf-build-system/sbcl)
+      (synopsis "Collection of Common Lisp utility functions and macros")
+      (description
+       "@command{cl-jpl-util} is a collection of Common Lisp utility functions
+and macros, primarily for software projects written in CL by the author.")
+      (home-page "https://www.thoughtcrime.us/software/cl-jpl-util/")
+      (license license:isc))))
+
+(define-public cl-jpl-util
+  (sbcl-package->cl-source-package sbcl-jpl-util))
+
+(define-public ecl-jpl-util
+  (sbcl-package->ecl-package sbcl-jpl-util))

From 8f41fa066ec624146ace6052d718850ccaff5bcc Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:24:21 +0200
Subject: [PATCH 805/909] gnu: Add jpl-queues.

* gnu/packages/lisp.scm (cl-jpl-queues, ecl-jpl-queues, sbcl-jpl-queues): New variables.
---
 gnu/packages/lisp.scm | 45 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 9688e2c44d..72d6a6c991 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1741,3 +1741,48 @@ and macros, primarily for software projects written in CL by the author.")
 
 (define-public ecl-jpl-util
   (sbcl-package->ecl-package sbcl-jpl-util))
+
+(define-public sbcl-jpl-queues
+  (package
+    (name "sbcl-jpl-queues")
+    (version "0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://www.thoughtcrime.us/software/jpl-queues/jpl-queues-"
+             version
+             ".tar.gz"))
+       (sha256
+        (base32
+         "1wvvv7j117h9a42qaj1g4fh4mji28xqs7s60rn6d11gk9jl76h96"))))
+    (build-system asdf-build-system/sbcl)
+    (inputs
+     `(("jpl-util" ,sbcl-jpl-util)
+       ("bordeaux-threads" ,sbcl-bordeaux-threads)))
+    (arguments
+     ;; Tests seem to be broken.
+     `(#:tests? #f))
+    (synopsis "Common Lisp library implementing a few different kinds of queues")
+    (description
+     "A Common Lisp library implementing a few different kinds of queues:
+
+@itemize
+@item Bounded and unbounded FIFO queues.
+@item Lossy bounded FIFO queues that drop elements when full.
+@item Unbounded random-order queues that use less memory than unbounded FIFO queues.
+@end itemize
+
+Additionally, a synchronization wrapper is provided to make any queue
+conforming to the @command{jpl-queues} API thread-safe for lightweight
+multithreading applications.  (See Calispel for a more sophisticated CL
+multithreaded message-passing library with timeouts and alternation among
+several blockable channels.)")
+    (home-page "https://www.thoughtcrime.us/software/jpl-queues/")
+    (license license:isc)))
+
+(define-public cl-jpl-queues
+  (sbcl-package->cl-source-package sbcl-jpl-queues))
+
+(define-public ecl-jpl-queues
+  (sbcl-package->ecl-package sbcl-jpl-queues))

From 989cd79b5ce034df08a149ac7f7ba6ece5c5afb3 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:41:45 +0200
Subject: [PATCH 806/909] gnu: Add eos.

* gnu/packages/lisp.scm (cl-eos, ecl-eos, sbcl-eos): New variables.
---
 gnu/packages/lisp.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 72d6a6c991..444a1975d0 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1786,3 +1786,33 @@ several blockable channels.)")
 
 (define-public ecl-jpl-queues
   (sbcl-package->ecl-package sbcl-jpl-queues))
+
+(define-public sbcl-eos
+  (let ((commit "b0faca83781ead9a588661e37bd47f90362ccd94"))
+    (package
+      (name "sbcl-eos")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/adlai/Eos")
+               (commit commit)))
+         (sha256
+          (base32
+           "1bq8cfg087iyxmxi1mwgx5cfgy3b8ydrf81xljcis8qbgb2vszph"))
+         (file-name (git-file-name "eos" version))))
+      (build-system asdf-build-system/sbcl)
+      (synopsis "Unit Testing for Common Lisp")
+      (description
+       "Eos was a unit testing library for Common Lisp.
+It began as a fork of FiveAM; however, FiveAM development has continued, while
+that of Eos has not.  Thus, Eos is now deprecated in favor of FiveAM.")
+      (home-page "https://github.com/adlai/Eos")
+      (license license:expat))))
+
+(define-public cl-eos
+  (sbcl-package->cl-source-package sbcl-eos))
+
+(define-public ecl-eos
+  (sbcl-package->ecl-package sbcl-eos))

From bdf83297a8cfdc83999f1511db967a3f7ff2ddbd Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:44:11 +0200
Subject: [PATCH 807/909] gnu: Add esrap.

* gnu/packages/lisp.scm (cl-esrap, ecl-esrap, sbcl-esrap): New variables.
---
 gnu/packages/lisp.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 444a1975d0..eac447d77f 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1816,3 +1816,43 @@ that of Eos has not.  Thus, Eos is now deprecated in favor of FiveAM.")
 
 (define-public ecl-eos
   (sbcl-package->ecl-package sbcl-eos))
+
+(define-public sbcl-esrap
+  (let ((commit "133be8b05c2aae48696fe5b739eea2fa573fa48d"))
+    (package
+      (name "sbcl-esrap")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/nikodemus/esrap")
+               (commit commit)))
+         (sha256
+          (base32
+           "02d5clihsdryhf7pix8c5di2571fdsffh75d40fkzhws90r5mksl"))
+         (file-name (git-file-name "esrap" version))))
+      (build-system asdf-build-system/sbcl)
+      (native-inputs
+       `(("eos" ,sbcl-eos)))            ;For testing only.
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)))
+      (synopsis "Common Lisp packrat parser")
+      (description
+       "A packrat parser for Common Lisp.
+In addition to regular Packrat / Parsing Grammar / TDPL features ESRAP supports:
+
+@itemize
+@item dynamic redefinition of nonterminals
+@item inline grammars
+@item semantic predicates
+@item introspective facilities (describing grammars, tracing, setting breaks)
+@end itemize\n")
+      (home-page "https://nikodemus.github.io/esrap/")
+      (license license:expat))))
+
+(define-public cl-esrap
+  (sbcl-package->cl-source-package sbcl-esrap))
+
+(define-public ecl-esrap
+  (sbcl-package->ecl-package sbcl-esrap))

From 141001597d10bdb2d2698398c949d46f92726f46 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:45:54 +0200
Subject: [PATCH 808/909] gnu: Add split-sequence.

* gnu/packages/lisp.scm (cl-split-sequence, ecl-split-sequence, sbcl-split-sequence): New variables.
---
 gnu/packages/lisp.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index eac447d77f..14df21d9f4 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1856,3 +1856,35 @@ In addition to regular Packrat / Parsing Grammar / TDPL features ESRAP supports:
 
 (define-public ecl-esrap
   (sbcl-package->ecl-package sbcl-esrap))
+
+(define-public sbcl-split-sequence
+  (package
+    (name "sbcl-split-sequence")
+    (version "1.4.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/sharplispers/split-sequence")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "0c3zp6b7fmmp93sfhq112ind4zkld49ycw68z409xpnz3gc0wpf0"))
+       (file-name (git-file-name "split-sequence" version))))
+    (build-system asdf-build-system/sbcl)
+    (arguments
+     ;; TODO: Tests seem to be broken.
+     ;; https://github.com/sharplispers/split-sequence/issues/8
+     `(#:tests? #f))
+    (synopsis "Member of the Common Lisp Utilities family of programs")
+    (description
+     "Splits sequence into a list of subsequences delimited by objects
+satisfying the test.")
+    (home-page "https://cliki.net/split-sequence")
+    (license license:expat)))
+
+(define-public cl-split-sequence
+  (sbcl-package->cl-source-package sbcl-split-sequence))
+
+(define-public ecl-split-sequence
+  (sbcl-package->ecl-package sbcl-split-sequence))

From 6a1761cbf66be57c028b5728d4da04752b9b2f15 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:46:45 +0200
Subject: [PATCH 809/909] gnu: Add html-encode.

* gnu/packages/lisp.scm (cl-html-encode, ecl-html-encode, sbcl-html-encode): New variables.
---
 gnu/packages/lisp.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 14df21d9f4..3c26766818 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1888,3 +1888,30 @@ satisfying the test.")
 
 (define-public ecl-split-sequence
   (sbcl-package->ecl-package sbcl-split-sequence))
+
+(define-public sbcl-html-encode
+  (package
+    (name "sbcl-html-encode")
+    (version "1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://beta.quicklisp.org/archive/html-encode/2010-10-06/html-encode-"
+             version ".tgz"))
+       (sha256
+        (base32
+         "06mf8wn95yf5swhmzk4vp0xr4ylfl33dgfknkabbkd8n6jns8gcf"))
+       (file-name (string-append "colorize" version "-checkout"))))
+    (build-system asdf-build-system/sbcl)
+    (synopsis "Common Lisp library for encoding text in various web-savvy encodings")
+    (description
+     "A library for encoding text in various web-savvy encodings.")
+    (home-page "http://quickdocs.org/html-encode/")
+    (license license:expat)))
+
+(define-public cl-html-encode
+  (sbcl-package->cl-source-package sbcl-html-encode))
+
+(define-public ecl-html-encode
+  (sbcl-package->ecl-package sbcl-html-encode))

From b4ba1c0a38ca61cecd40f9bd1ab76b1d16edc04b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:50:31 +0200
Subject: [PATCH 810/909] gnu: Add colorize.

* gnu/packages/lisp.scm (cl-colorize, ecl-colorize, sbcl-colorize): New variables.
---
 gnu/packages/lisp.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 3c26766818..d10dc7b888 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1915,3 +1915,38 @@ satisfying the test.")
 
 (define-public ecl-html-encode
   (sbcl-package->ecl-package sbcl-html-encode))
+
+(define-public sbcl-colorize
+  (let ((commit "ea676b584e0899cec82f21a9e6871172fe3c0eb5"))
+    (package
+      (name "sbcl-colorize")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/kingcons/colorize")
+               (commit commit)))
+         (sha256
+          (base32
+           "1pdg4kiaczmr3ivffhirp7m3lbr1q27rn7dhaay0vwghmi31zcw9"))
+         (file-name (git-file-name "colorize" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("split-sequence" ,sbcl-split-sequence)
+         ("html-encode" ,sbcl-html-encode)))
+      (synopsis "Common Lisp for syntax highlighting")
+      (description
+       "@command{colorize} is a Lisp library for syntax highlighting
+supporting the following languages: Common Lisp, Emacs Lisp, Scheme, Clojure,
+C, C++, Java, Python, Erlang, Haskell, Objective-C, Diff, Webkit.")
+      (home-page "https://github.com/kingcons/colorize")
+      ;; TODO: Missing license?
+      (license license:expat))))
+
+(define-public cl-colorize
+  (sbcl-package->cl-source-package sbcl-colorize))
+
+(define-public ecl-colorize
+  (sbcl-package->ecl-package sbcl-colorize))

From ef0c3e14295a2335c271f7a4e7026deb3de18a63 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:54:08 +0200
Subject: [PATCH 811/909] gnu: Add 3bmd.

* gnu/packages/lisp.scm (cl-3bmd, ecl-3bmd, sbcl-3bmd): New variables.
---
 gnu/packages/lisp.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index d10dc7b888..6feff2171c 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1950,3 +1950,39 @@ C, C++, Java, Python, Erlang, Haskell, Objective-C, Diff, Webkit.")
 
 (define-public ecl-colorize
   (sbcl-package->ecl-package sbcl-colorize))
+
+(define-public sbcl-3bmd
+  (let ((commit "192ea13435b605a96ef607df51317056914cabbd"))
+    (package
+      (name "sbcl-3bmd")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/3b/3bmd")
+               (commit commit)))
+         (sha256
+          (base32
+           "1rgv3gi7wf963ikmmpk132wgn0icddf226gq3bmcnk1fr3v9gf2f"))
+         (file-name (git-file-name "3bmd" version))))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       ;; FIXME: We need to specify the name because the build-system thinks
+       ;; "3" is a version marker.
+       `(#:asd-system-name "3bmd"))
+      (inputs
+       `(("esrap" ,sbcl-esrap)
+         ("split-sequence" ,sbcl-split-sequence)))
+      (synopsis "Markdown processor in Command Lisp using esrap parser")
+      (description
+       "Common Lisp Markdown -> HTML converter, using @command{esrap} for
+parsing, and grammar based on @command{peg-markdown}.")
+      (home-page "https://github.com/3b/3bmd")
+      (license license:expat))))
+
+(define-public cl-3bmd
+  (sbcl-package->cl-source-package sbcl-3bmd))
+
+(define-public ecl-3bmd
+  (sbcl-package->ecl-package sbcl-3bmd))

From 1a3d39c44680b811cfaf452de1b07b222c2707c7 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:58:37 +0200
Subject: [PATCH 812/909] gnu: Add 3bmd-ext-code-blocks.

* gnu/packages/lisp.scm (cl-3bmd-ext-code-blocks, ecl-3bmd-ext-code-blocks, sbcl-3bmd-ext-code-blocks): New variables.
---
 gnu/packages/lisp.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 6feff2171c..f3e3a866c2 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -1986,3 +1986,26 @@ parsing, and grammar based on @command{peg-markdown}.")
 
 (define-public ecl-3bmd
   (sbcl-package->ecl-package sbcl-3bmd))
+
+(define-public sbcl-3bmd-ext-code-blocks
+  (let ((commit "192ea13435b605a96ef607df51317056914cabbd"))
+    (package
+      (inherit sbcl-3bmd)
+      (name "sbcl-3bmd-ext-code-blocks")
+      (arguments
+       `(#:asd-system-name "3bmd-ext-code-blocks"
+         #:asd-file "3bmd-ext-code-blocks.asd"))
+      (inputs
+       `(("3bmd" ,sbcl-3bmd)
+         ("colorize" ,sbcl-colorize)))
+      (synopsis "3bmd extension which adds support for GitHub-style fenced
+code blocks")
+      (description
+       "3bmd extension which adds support for GitHub-style fenced code blocks,
+with @command{colorize} support."))))
+
+(define-public cl-3bmd-ext-code-blocks
+  (sbcl-package->cl-source-package sbcl-3bmd-ext-code-blocks))
+
+(define-public ecl-3bmd-ext-code-blocks
+  (sbcl-package->ecl-package sbcl-3bmd-ext-code-blocks))

From 1855496813bf091113484e4f1646fa5db7edb140 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 12:06:08 +0200
Subject: [PATCH 813/909] gnu: Add cl-fad.

* gnu/packages/lisp.scm (cl-fad, ecl-cl-fad, sbcl-cl-fad): New variables.
---
 gnu/packages/lisp.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index f3e3a866c2..0c04a01e66 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2009,3 +2009,36 @@ with @command{colorize} support."))))
 
 (define-public ecl-3bmd-ext-code-blocks
   (sbcl-package->ecl-package sbcl-3bmd-ext-code-blocks))
+
+(define-public sbcl-cl-fad
+  (package
+    (name "sbcl-cl-fad")
+    (version "0.7.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/edicl/cl-fad/")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "1l1qmk9z57q84bz5r04sxsksggsnd7dgkxlybzh9imz6ma7sm52m"))
+       (file-name (string-append "cl-fad" version "-checkout"))))
+    (build-system asdf-build-system/sbcl)
+    (inputs
+     `(("bordeaux-threads" ,sbcl-bordeaux-threads)))
+    (synopsis "Portable pathname library for Common Lisp")
+    (description
+     "CL-FAD (for \"Files and Directories\") is a thin layer atop Common
+Lisp's standard pathname functions.  It is intended to provide some
+unification between current CL implementations on Windows, OS X, Linux, and
+Unix.  Most of the code was written by Peter Seibel for his book Practical
+Common Lisp.")
+    (home-page "https://edicl.github.io/cl-fad/")
+    (license license:bsd-2)))
+
+(define-public cl-fad
+  (sbcl-package->cl-source-package sbcl-cl-fad))
+
+(define-public ecl-cl-fad
+  (sbcl-package->ecl-package sbcl-cl-fad))

From 5800c538a1d46d7eae5e9f55ca0bddc7f8644545 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 12:07:48 +0200
Subject: [PATCH 814/909] gnu: Add rt.

* gnu/packages/lisp.scm (cl-rt, ecl-rt, sbcl-rt): New variables.
---
 gnu/packages/lisp.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 0c04a01e66..1953cf8f9c 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2042,3 +2042,28 @@ Common Lisp.")
 
 (define-public ecl-cl-fad
   (sbcl-package->ecl-package sbcl-cl-fad))
+
+(define-public sbcl-rt
+  (package
+    (name "sbcl-rt")
+    (version "1990.12.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://beta.quicklisp.org/archive/rt/2010-10-06/rt-"
+                           "20101006-git" ".tgz"))
+       (sha256
+        (base32
+         "1jncar0xwkqk8yrc2dln389ivvgzs7ijdhhs3zpfyi5d21f0qa1v"))))
+    (build-system asdf-build-system/sbcl)
+    (synopsis "MIT Regression Tester")
+    (description
+     "RT provides a framework for writing regression test suites.")
+    (home-page "https://github.com/sharplispers/nibbles")
+    (license license:unlicense)))
+
+(define-public cl-rt
+  (sbcl-package->cl-source-package sbcl-rt))
+
+(define-public ecl-rt
+  (sbcl-package->ecl-package sbcl-rt))

From fbdd9b2c8bbcb70a6a9c05ece2d7a473c2075534 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 12:09:51 +0200
Subject: [PATCH 815/909] gnu: Add nibbles.

* gnu/packages/lisp.scm (cl-nibbles, ecl-nibbles, sbcl-nibbles): New variables.
---
 gnu/packages/lisp.scm | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 1953cf8f9c..3282c31c71 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2067,3 +2067,46 @@ Common Lisp.")
 
 (define-public ecl-rt
   (sbcl-package->ecl-package sbcl-rt))
+
+(define-public sbcl-nibbles
+  (package
+    (name "sbcl-nibbles")
+    (version "0.14")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/sharplispers/nibbles/")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "1v7qfgpvdr6nz7v63dj69d26dis0kff3rd8xamr1llfdvza2pm8f"))
+       (file-name (git-file-name "nibbles" version))))
+    (build-system asdf-build-system/sbcl)
+    (native-inputs
+     ;; Tests only.
+     `(("rt" ,sbcl-rt)))
+    (synopsis "Common Lisp library for accessing octet-addressed blocks of data")
+    (description
+     "When dealing with network protocols and file formats, it's common to
+have to read or write 16-, 32-, or 64-bit datatypes in signed or unsigned
+flavors.  Common Lisp sort of supports this by specifying :element-type for
+streams, but that facility is underspecified and there's nothing similar for
+read/write from octet vectors.  What most people wind up doing is rolling their
+own small facility for their particular needs and calling it a day.
+
+This library attempts to be comprehensive and centralize such
+facilities.  Functions to read 16-, 32-, and 64-bit quantities from octet
+vectors in signed or unsigned flavors are provided; these functions are also
+SETFable.  Since it's sometimes desirable to read/write directly from streams,
+functions for doing so are also provided.  On some implementations,
+reading/writing IEEE singles/doubles (i.e. single-float and double-float) will
+also be supported.")
+    (home-page "https://github.com/sharplispers/nibbles")
+    (license license:bsd-3)))
+
+(define-public cl-nibbles
+  (sbcl-package->cl-source-package sbcl-nibbles))
+
+(define-public ecl-nibbles
+  (sbcl-package->ecl-package sbcl-nibbles))

From e549ba059886641c1a28016822824e92be872dd8 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 12:11:21 +0200
Subject: [PATCH 816/909] gnu: Add ironclad.

* gnu/packages/lisp.scm (cl-ironclad, ecl-ironclad, sbcl-ironclad): New variables.
---
 gnu/packages/lisp.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 3282c31c71..1eff724387 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2110,3 +2110,39 @@ also be supported.")
 
 (define-public ecl-nibbles
   (sbcl-package->ecl-package sbcl-nibbles))
+
+(define-public sbcl-ironclad
+  (package
+    (name "sbcl-ironclad")
+    (version "0.42")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/sharplispers/ironclad/")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "1wjcb9vpybxjrmch7f7s78a5abxmnknbd4fl49dl5lz8a3fc8vf0"))
+       (file-name (string-append "ironblad" version "-checkout"))))
+    (build-system asdf-build-system/sbcl)
+    (native-inputs
+     ;; Tests only.
+     `(("rt" ,sbcl-rt)))
+    (inputs
+     `(("flexi-streams" ,sbcl-flexi-streams)
+       ("nibbles" ,sbcl-nibbles)))
+    (synopsis "Cryptographic toolkit written in Common Lisp")
+    (description
+     "Ironclad is a cryptography library written entirely in Common Lisp.
+It includes support for several popular ciphers, digests, MACs and public key
+cryptography algorithms.  For several implementations that support Gray
+streams, support is included for convenient stream wrappers.")
+    (home-page "https://github.com/sharplispers/ironclad")
+    (license license:bsd-3)))
+
+(define-public cl-ironclad
+  (sbcl-package->cl-source-package sbcl-ironclad))
+
+(define-public ecl-ironclad
+  (sbcl-package->ecl-package sbcl-ironclad))

From fb8c4bc6baba7a332f071183435fdb426c1365fe Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 12:30:53 +0200
Subject: [PATCH 817/909] gnu: Add named-readtables.

* gnu/packages/lisp.scm (cl-named-readtables, ecl-named-readtables, sbcl-named-readtables): New variables.

FIX named-readtables
---
 gnu/packages/lisp.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 1eff724387..2b5f240c4d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2146,3 +2146,34 @@ streams, support is included for convenient stream wrappers.")
 
 (define-public ecl-ironclad
   (sbcl-package->ecl-package sbcl-ironclad))
+
+(define-public sbcl-named-readtables
+  (let ((commit "4dfb89fa1af6b305b6492b8af042f5190c11e9fc")
+        (revision "1"))
+    (package
+      (name "sbcl-named-readtables")
+      (version (string-append "0.9-" revision "." (string-take commit 7)))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/melisgl/named-readtables.git")
+               (commit commit)))
+         (sha256
+          (base32 "083kgh5462iqbb4px6kq8s7sggvpvkm36hx4qi9rnaw53b6ilqkk"))
+         (file-name (git-file-name "named-readtables" version))))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       ;; Tests seem to be broken.
+       `(#:tests? #f))
+      (home-page "https://github.com/melisgl/named-readtables/")
+      (synopsis "Library that creates a namespace for named readtables")
+      (description "Named readtables is a library that creates a namespace for
+named readtables, which is akin to package namespacing in Common Lisp.")
+      (license license:bsd-3))))
+
+(define-public cl-named-readtables
+  (sbcl-package->cl-source-package sbcl-named-readtables))
+
+(define-public ecl-named-readtables
+  (sbcl-package->ecl-package sbcl-named-readtables))

From f07efbf1e68a26de768694fea9baa249a3183242 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 12:35:50 +0200
Subject: [PATCH 818/909] gnu: Add pythonic-string-reader.

* gnu/packages/lisp.scm (cl-pythonic-string-reader, ecl-pythonic-string-reader, sbcl-pythonic-string-reader): New variables.
---
 gnu/packages/lisp.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 2b5f240c4d..864186e080 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2177,3 +2177,34 @@ named readtables, which is akin to package namespacing in Common Lisp.")
 
 (define-public ecl-named-readtables
   (sbcl-package->ecl-package sbcl-named-readtables))
+
+(define-public sbcl-pythonic-string-reader
+  (let ((commit "47a70ba1e32362e03dad6ef8e6f36180b560f86a"))
+    (package
+      (name "sbcl-pythonic-string-reader")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/smithzvk/pythonic-string-reader/")
+               (commit commit)))
+         (sha256
+          (base32 "1b5iryqw8xsh36swckmz8rrngmc39k92si33fgy5pml3n9l5rq3j"))
+         (file-name (git-file-name "pythonic-string-reader" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("named-readtables" ,sbcl-named-readtables)))
+      (home-page "https://github.com/smithzvk/pythonic-string-reader")
+      (synopsis "Read table modification inspired by Python's three quote strings")
+      (description "This piece of code sets up some reader macros that make it
+simpler to input string literals which contain backslashes and double quotes
+This is very useful for writing complicated docstrings and, as it turns out,
+writing code that contains string literals that contain code themselves.")
+      (license license:bsd-3))))
+
+(define-public cl-pythonic-string-reader
+  (sbcl-package->cl-source-package sbcl-pythonic-string-reader))
+
+(define-public ecl-pythonic-string-reader
+  (sbcl-package->ecl-package sbcl-pythonic-string-reader))

From 8d8d1c8d6c06d777369e4680a70345ff3212e3a8 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 13:10:55 +0200
Subject: [PATCH 819/909] gnu: Add mgl-pax.

* gnu/packages/lisp.scm (cl-mgl-pax, ecl-mgl-pax, sbcl-mgl-pax): New variables.
---
 gnu/packages/lisp.scm | 50 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 864186e080..18d90d7dbf 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2208,3 +2208,53 @@ writing code that contains string literals that contain code themselves.")
 
 (define-public ecl-pythonic-string-reader
   (sbcl-package->ecl-package sbcl-pythonic-string-reader))
+
+(define-public sbcl-mgl-pax
+  (let ((commit "818448418d6b9de74620f606f5b23033c6082769"))
+    (package
+      (name "sbcl-mgl-pax")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/melisgl/mgl-pax")
+               (commit commit)))
+         (sha256
+          (base32
+           "1p97zfkh130bdxqqxwaw2j9psv58751wakx7czbfpq410lg7dd7i"))
+         (file-name (git-file-name "mgl-pax" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("3bmd" ,sbcl-3bmd)
+         ("3bmd-ext-code-blocks" ,sbcl-3bmd-ext-code-blocks)
+         ("babel" ,sbcl-babel)
+         ("cl-fad" ,sbcl-cl-fad)
+         ("ironclad" ,sbcl-ironclad)
+         ("named-readtables" ,sbcl-named-readtables)
+         ("pythonic-string-reader" ,sbcl-pythonic-string-reader)
+         ("swank" ,sbcl-slime-swank)))
+      (synopsis "Exploratory programming environment and documentation generator")
+      (description
+       "PAX provides an extremely poor man's Explorable Programming
+environment.  Narrative primarily lives in so called sections that mix markdown
+docstrings with references to functions, variables, etc, all of which should
+probably have their own docstrings.
+
+The primary focus is on making code easily explorable by using SLIME's
+@command{M-.} (@command{slime-edit-definition}).  See how to enable some
+fanciness in Emacs Integration.  Generating documentation from sections and all
+the referenced items in Markdown or HTML format is also implemented.
+
+With the simplistic tools provided, one may accomplish similar effects as with
+Literate Programming, but documentation is generated from code, not vice versa
+and there is no support for chunking yet.  Code is first, code must look
+pretty, documentation is code.")
+      (home-page "http://quotenil.com/")
+      (license license:expat))))
+
+(define-public cl-mgl-pax
+  (sbcl-package->cl-source-package sbcl-mgl-pax))
+
+(define-public ecl-mgl-pax
+  (sbcl-package->ecl-package sbcl-mgl-pax))

From a927eb3653df9097d0d6768fbfc1652221b7cdcd Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:36:22 +0200
Subject: [PATCH 820/909] gnu: Add ascii-strings.

* gnu/packages/lisp.scm (cl-ascii-strings, ecl-ascii-strings, sbcl-ascii-strings): New variables.
---
 gnu/packages/lisp.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 18d90d7dbf..139e9d2c5e 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -31,6 +31,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix hg-download)
   #:use-module (guix utils)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system asdf)
@@ -2258,3 +2259,38 @@ pretty, documentation is code.")
 
 (define-public ecl-mgl-pax
   (sbcl-package->ecl-package sbcl-mgl-pax))
+
+(define-public sbcl-ascii-strings
+  (let ((revision "1")
+        (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))
+    (package
+      (name "sbcl-ascii-strings")
+      (version (string-append "0-" revision "." (string-take changeset 7)))
+      (source
+       (origin
+         (method hg-fetch)
+         (uri (hg-reference
+               (url "https://bitbucket.org/vityok/cl-string-match/")
+               (changeset changeset)))
+         (sha256
+          (base32
+           "01wn5qx562w43ssy92xlfgv79w7p0nv0wbl76mpmba131n9ziq2y"))
+         (file-name (git-file-name "cl-string-match" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("babel" ,sbcl-babel)))
+      (arguments
+       `(#:asd-file "ascii-strings.asd"))
+      (synopsis "Operations on ASCII strings")
+      (description
+       "Operations on ASCII strings.  Essentially this can be any kind of
+single-byte encoded strings.")
+      (home-page "https://bitbucket.org/vityok/cl-string-match/")
+      (license license:bsd-3))))
+
+(define-public cl-ascii-strings
+  (sbcl-package->cl-source-package sbcl-ascii-strings))
+
+(define-public ecl-ascii-strings
+  (sbcl-package->ecl-package sbcl-ascii-strings))

From 109ce303f4f1b99a9b47ced0efbe412e68eb2eb3 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <ambrevar@gmail.com>
Date: Fri, 24 Aug 2018 11:38:00 +0200
Subject: [PATCH 821/909] gnu: Add cl-string-match.

* gnu/packages/lisp.scm (cl-string-match, ecl-cl-string-match, sbcl-cl-string-match): New variables.
---
 gnu/packages/lisp.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 139e9d2c5e..e98b937fe6 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2294,3 +2294,35 @@ single-byte encoded strings.")
 
 (define-public ecl-ascii-strings
   (sbcl-package->ecl-package sbcl-ascii-strings))
+
+(define-public sbcl-cl-string-match
+  (package
+    (inherit sbcl-ascii-strings)
+    (name "sbcl-cl-string-match")
+    (inputs
+     `(("alexandria" ,sbcl-alexandria)
+       ("ascii-strings" ,sbcl-ascii-strings)
+       ("yacc" ,sbcl-cl-yacc)
+       ("jpl-util" ,sbcl-jpl-util)
+       ("jpl-queues" ,sbcl-jpl-queues)
+       ("mgl-pax" ,sbcl-mgl-pax)
+       ("iterate" ,sbcl-iterate)))
+    ;; TODO: Tests are not evaluated properly.
+    (native-inputs
+     ;; For testing:
+     `(("lisp-unit" ,sbcl-lisp-unit)
+       ("simple-scanf" ,sbcl-simple-scanf)))
+    (arguments
+     `(#:tests? #f
+       #:asd-file "cl-string-match.asd"))
+    (synopsis "Portable, dependency-free set of utilities to manipulate strings in Common Lisp")
+    (description
+     "@command{cl-strings} is a small, portable, dependency-free set of
+utilities that make it even easier to manipulate text in Common Lisp.  It has
+100% test coverage and works at least on sbcl, ecl, ccl, abcl and clisp.")))
+
+(define-public cl-string-match
+  (sbcl-package->cl-source-package sbcl-cl-string-match))
+
+(define-public ecl-cl-string-match
+  (sbcl-package->ecl-package sbcl-cl-string-match))

From c4d4ae1e16254a96caaeb5ccb4486f301ae4f1b7 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 11 Sep 2018 22:59:35 +0200
Subject: [PATCH 822/909] gnu: Add sbcl-slime-swank.

* gnu/packages/lisp.scm (sbcl-slime-swank): New variable.
---
 gnu/packages/lisp.scm | 44 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index e98b937fe6..54beb3b25d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2210,6 +2210,50 @@ writing code that contains string literals that contain code themselves.")
 (define-public ecl-pythonic-string-reader
   (sbcl-package->ecl-package sbcl-pythonic-string-reader))
 
+(define-public sbcl-slime-swank
+  (package
+    (name "sbcl-slime-swank")
+    (version "2.22")
+    (source
+     (origin
+       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             ;; (url "https://github.com/slime/slime/")
+             ;; (commit "841f61467c03dea9f38ff9d5af0e21a8aa29e8f7")
+             ;; REVIEW: Do we need sionescu's patch to package SWANK?
+             (url "https://github.com/sionescu/slime/")
+             ;; (commit "swank-asdf")
+             (commit "2f7c3fcb3ac7d50d844d5c6ca0e89b52a45e1d3a")))
+       (sha256
+        (base32
+         ;; "065bc4y6iskazdfwlhgcjlzg9bi2hyjbhmyjw3461506pgkj08vi"
+         "0pkmg94wn4ii1zhlrncn44mdc5i6c5v0i9gbldx4dwl2yy7ibz5c"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (substitute* "contrib/swank-listener-hooks.lisp"
+             ((":compile-toplevel :load-toplevel ") ""))
+           (substitute* "contrib/swank-presentations.lisp"
+             ((":compile-toplevel :load-toplevel ") ""))
+           (substitute* "swank.asd"
+             ((":file \"packages\".*" all)
+              (string-append all "(:file \"swank-loader-asdf\")\n")))
+           (substitute* "swank-loader-asdf.lisp"
+             ((":common-lisp" all) (string-append all " #:asdf")))
+           #t))))
+    (build-system asdf-build-system/sbcl)
+    (arguments
+     `(#:asd-file "swank.asd"
+       #:asd-system-name "swank"))
+    (home-page "https://github.com/slime/slime")
+    (synopsis "Common Lisp Swank server")
+    (description
+     "This is only useful if you want to start a Swank server in a Lisp
+processes that doesn't run under Emacs.  Lisp processes created by
+@command{M-x slime} automatically start the server.")
+    (license (license (list license:gpl2+ license:public-domain)))))
+
 (define-public sbcl-mgl-pax
   (let ((commit "818448418d6b9de74620f606f5b23033c6082769"))
     (package

From 19a1c3be9773a6c6accee9e4e1d7f6319c49dfed Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:27:37 +0200
Subject: [PATCH 823/909] gnu: Add lisp-unit.

* gnu/packages/lisp.scm (cl-lisp-unit, ecl-lisp-unit, sbcl-lisp-unit): New variables.
---
 gnu/packages/lisp.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 54beb3b25d..5c25daff52 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2304,6 +2304,35 @@ pretty, documentation is code.")
 (define-public ecl-mgl-pax
   (sbcl-package->ecl-package sbcl-mgl-pax))
 
+(define-public sbcl-lisp-unit
+  (let ((commit "89653a232626b67400bf9a941f9b367da38d3815"))
+    (package
+      (name "sbcl-lisp-unit")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/OdonataResearchLLC/lisp-unit")
+               (commit commit)))
+         (sha256
+          (base32
+           "0p6gdmgr7p383nvd66c9y9fp2bjk4jx1lpa5p09g43hr9y9pp9ry"))
+         (file-name (git-file-name "lisp-unit" version))))
+      (build-system asdf-build-system/sbcl)
+      (synopsis "Common Lisp Test framework inspired by JUnit to be simple of use")
+      (description
+       "@command{lisp-unit} is a Common Lisp library that supports unit
+testing.  It is an extension of the library written by Chris Riesbeck.")
+      (home-page "https://github.com/OdonataResearchLLC/lisp-unit")
+      (license license:expat))))
+
+(define-public cl-lisp-unit
+  (sbcl-package->cl-source-package sbcl-lisp-unit))
+
+(define-public ecl-lisp-unit
+  (sbcl-package->ecl-package sbcl-lisp-unit))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 9f3000cc11c0b0bb3c8da5dc5f4390243f1e0321 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:28:56 +0200
Subject: [PATCH 824/909] gnu: Add anaphora.

* gnu/packages/lisp.scm (cl-anaphora, ecl-anaphora, sbcl-anaphora): New variables.
---
 gnu/packages/lisp.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 5c25daff52..967b648506 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2333,6 +2333,37 @@ testing.  It is an extension of the library written by Chris Riesbeck.")
 (define-public ecl-lisp-unit
   (sbcl-package->ecl-package sbcl-lisp-unit))
 
+(define-public sbcl-anaphora
+  (package
+    (name "sbcl-anaphora")
+    (version "0.9.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/tokenrove/anaphora")
+             (commit version)))
+       (sha256
+        (base32
+         "19wfrk3asimznkli0x2rfy637hwpdgqyvwj3vhq9x7vjvyf5vv6x"))
+       (file-name (git-file-name "anaphora" version))))
+    (build-system asdf-build-system/sbcl)
+    (native-inputs
+     `(("rt" ,sbcl-rt)))
+    (synopsis "The anaphoric macro collection from Hell")
+    (description
+     "Anaphora is the anaphoric macro collection from Hell: it includes many
+new fiends in addition to old friends like @command{aif} and
+@command{awhen}.")
+    (home-page "https://github.com/tokenrove/anaphora")
+    (license license:public-domain)))
+
+(define-public cl-anaphora
+  (sbcl-package->cl-source-package sbcl-anaphora))
+
+(define-public ecl-anaphora
+  (sbcl-package->ecl-package sbcl-anaphora))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 5b8a801d164634e1b34eb49a29c96bc7a1d1fac4 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:29:24 +0200
Subject: [PATCH 825/909] gnu: Add lift.

* gnu/packages/lisp.scm (cl-lift, ecl-lift, sbcl-lift): New variables.
---
 gnu/packages/lisp.scm | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 967b648506..e6dc798407 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2364,6 +2364,49 @@ new fiends in addition to old friends like @command{aif} and
 (define-public ecl-anaphora
   (sbcl-package->ecl-package sbcl-anaphora))
 
+(define-public sbcl-lift
+  (let ((commit "7d49a66c62759535624037826891152223d4206c"))
+    (package
+      (name "sbcl-lift")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/gwkkwg/lift")
+               (commit commit)))
+         (sha256
+          (base32
+           "127v5avpz1i4m0lkaxqrq8hrl69rdazqaxf6s8awf0nd7wj2g4dp"))
+         (file-name (git-file-name "lift" version))))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       ;; The tests require a debugger, but we run with the debugger disabled.
+       '(#:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           ;; Do this to ensure the 'reset-gzip-timestamps phase works.
+           (add-after 'unpack 'make-gzips-writeable
+             (lambda _
+               (for-each (lambda (file)
+                           (chmod file #o755))
+                         (find-files "." "\\.gz$")))))))
+      (synopsis "LIsp Framework for Testing")
+      (description
+       "The LIsp Framework for Testing (LIFT) is a unit and system test tool for LISP.
+Though inspired by SUnit and JUnit, it's built with Lisp in mind.  In LIFT,
+testcases are organized into hierarchical testsuites each of which can have
+its own fixture.  When run, a testcase can succeed, fail, or error.  LIFT
+supports randomized testing, benchmarking, profiling, and reporting.")
+      (home-page "https://github.com/gwkkwg/lift")
+      (license license:x11-style))))
+
+(define-public cl-lift
+  (sbcl-package->cl-source-package sbcl-lift))
+
+(define-public ecl-lift
+  (sbcl-package->ecl-package sbcl-lift))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From d414223205d2007e0c08420b34fee178cb04e77b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:29:54 +0200
Subject: [PATCH 826/909] gnu: Add let-plus.

* gnu/packages/lisp.scm (cl-let-plus, ecl-let-plus, sbcl-let-plus): New variables.
---
 gnu/packages/lisp.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index e6dc798407..3e9180fc9a 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2407,6 +2407,48 @@ supports randomized testing, benchmarking, profiling, and reporting.")
 (define-public ecl-lift
   (sbcl-package->ecl-package sbcl-lift))
 
+(define-public sbcl-let-plus
+  (let ((commit "5f14af61d501ecead02ec6b5a5c810efc0c9fdbb"))
+    (package
+      (name "sbcl-let-plus")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/sharplispers/let-plus")
+               (commit commit)))
+         (sha256
+          (base32
+           "0i050ca2iys9f5mb7dgqgqdxfnc3b0rnjdwv95sqd490vkiwrsaj"))
+         (file-name (git-file-name "let-plus" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("anaphora" ,sbcl-anaphora)))
+      (native-inputs
+       `(("lift" ,sbcl-lift)))
+      (synopsis "Destructuring extension of let*")
+      (description
+       "This library implements the let+ macro, which is a dectructuring
+extension of let*.  It features:
+
+@itemize
+@item Clean, consistent syntax and small implementation (less than 300 LOC,
+not counting tests)
+@item Placeholder macros allow editor hints and syntax highlighting
+@item @command{&ign} for ignored values (in forms where that makes sense)
+@item Very easy to extend
+@end itemize\n")
+      (home-page "https://github.com/sharplispers/let-plus")
+      (license license:boost1.0))))
+
+(define-public cl-let-plus
+  (sbcl-package->cl-source-package sbcl-let-plus))
+
+(define-public ecl-let-plus
+  (sbcl-package->ecl-package sbcl-let-plus))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 8caa928dd44421322805d623fd47ecb8854345fa Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:30:21 +0200
Subject: [PATCH 827/909] gnu: Add cl-colors.

* gnu/packages/lisp.scm (cl-colors, ecl-cl-colors, sbcl-cl-colors): New variables.
---
 gnu/packages/lisp.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 3e9180fc9a..689a617850 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2449,6 +2449,47 @@ not counting tests)
 (define-public ecl-let-plus
   (sbcl-package->ecl-package sbcl-let-plus))
 
+(define-public sbcl-cl-colors
+  (let ((commit "827410584553f5c717eec6182343b7605f707f75"))
+    (package
+      (name "sbcl-cl-colors")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/tpapp/cl-colors")
+               (commit commit)))
+         (sha256
+          (base32
+           "0l446lday4hybsm9bq3jli97fvv8jb1d33abg79vbylpwjmf3y9a"))
+         (file-name (git-file-name "cl-colors" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("let-plus" ,sbcl-let-plus)))
+      (synopsis "Simple color library for Common Lisp")
+      (description
+       "This is a very simple color library for Common Lisp, providing
+
+@itemize
+@item Types for representing colors in HSV and RGB spaces.
+@item Simple conversion functions between the above types (and also
+hexadecimal representation for RGB).
+@item Some predefined colors (currently X11 color names – of course the
+library does not depend on X11).Because color in your terminal is nice.
+@end itemize
+
+This library is no longer supported by its author.")
+      (home-page "https://github.com/tpapp/cl-colors")
+      (license license:boost1.0))))
+
+(define-public cl-colors
+  (sbcl-package->cl-source-package sbcl-cl-colors))
+
+(define-public ecl-cl-colors
+  (sbcl-package->ecl-package sbcl-cl-colors))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 68a7b929f375bb11f29b822571c33ab0bdfd0187 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:30:47 +0200
Subject: [PATCH 828/909] gnu: Add cl-ansi-text.

* gnu/packages/lisp.scm (cl-ansi-text, ecl-cl-ansi-text, sbcl-cl-ansi-text): New variables.
---
 gnu/packages/lisp.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 689a617850..8402c805aa 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2490,6 +2490,44 @@ This library is no longer supported by its author.")
 (define-public ecl-cl-colors
   (sbcl-package->ecl-package sbcl-cl-colors))
 
+(define-public sbcl-cl-ansi-text
+  (let ((commit "53badf7878f27f22f2d4a2a43e6df458e43acbe9"))
+    (package
+      (name "sbcl-cl-ansi-text")
+      (version (git-version "1.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/pnathan/cl-ansi-text")
+               (commit commit)))
+         (sha256
+          (base32
+           "11i27n0dbz5lmygiw65zzr8lx0rac6b6yysqranphn31wls6ja3v"))
+         (file-name (git-file-name "cl-ansi-text" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("cl-colors" ,sbcl-cl-colors)))
+      (native-inputs
+       `(("fiveam" ,sbcl-fiveam)))
+      (synopsis "ANSI terminal color implementation for Common Lisp")
+      (description
+       "@command{cl-ansi-text} provides utilities which enable printing to an
+ANSI terminal with colored text.  It provides the macro @command{with-color}
+which causes everything printed in the body to be displayed with the provided
+color.  It further provides functions which will print the argument with the
+named color.")
+      (home-page "https://github.com/pnathan/cl-ansi-text")
+      ;; REVIEW: The actual license is LLGPL.  Should we add it to Guix?
+      (license license:lgpl3+))))
+
+(define-public cl-ansi-text
+  (sbcl-package->cl-source-package sbcl-cl-ansi-text))
+
+(define-public ecl-cl-ansi-text
+  (sbcl-package->ecl-package sbcl-cl-ansi-text))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 1a42bb80cb257aa4cec725dd2ef5c20123b8be9f Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:31:03 +0200
Subject: [PATCH 829/909] gnu: Add prove-asdf.

* gnu/packages/lisp.scm (cl-prove-asdf, ecl-prove-asdf, sbcl-prove-asdf): New variables.
---
 gnu/packages/lisp.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 8402c805aa..5f97c620fb 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2528,6 +2528,36 @@ named color.")
 (define-public ecl-cl-ansi-text
   (sbcl-package->ecl-package sbcl-cl-ansi-text))
 
+(define-public sbcl-prove-asdf
+  (let ((commit "4f9122bd393e63c5c70c1fba23070622317cfaa0"))
+    (package
+      (name "sbcl-prove-asdf")
+      (version (git-version "1.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/fukamachi/prove")
+               (commit commit)))
+         (sha256
+          (base32
+           "07sbfw459z8bbjvx1qlmfa8qk2mvbjnnzi2mi0x72blaj8bkl4vc"))
+         (file-name (git-file-name "prove" version))))
+      (build-system asdf-build-system/sbcl)
+      (arguments
+       `(#:asd-file "prove-asdf.asd"))
+      (synopsis "Test requirement for the Common Lisp 'prove' library")
+      (description
+       "Test requirement for the Common Lisp @command{prove} library.")
+      (home-page "https://github.com/fukamachi/prove")
+      (license license:expat))))
+
+(define-public cl-prove-asdf
+  (sbcl-package->cl-source-package sbcl-prove-asdf))
+
+(define-public ecl-prove-asdf
+  (sbcl-package->ecl-package sbcl-prove-asdf))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 86afb0a272dc24b68245d35825c0b7b5cc73f64a Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:31:25 +0200
Subject: [PATCH 830/909] gnu: Add prove.

* gnu/packages/lisp.scm (cl-prove, ecl-prove, sbcl-prove): New variables.
---
 gnu/packages/lisp.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 5f97c620fb..2e4725e084 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2558,6 +2558,38 @@ named color.")
 (define-public ecl-prove-asdf
   (sbcl-package->ecl-package sbcl-prove-asdf))
 
+(define-public sbcl-prove
+  (package
+    (inherit sbcl-prove-asdf)
+    (name "sbcl-prove")
+    (inputs
+     `(("alexandria" ,sbcl-alexandria)
+       ("cl-ppcre" ,sbcl-cl-ppcre)
+       ("cl-ansi-text" ,sbcl-cl-ansi-text)))
+    (native-inputs
+     `(("prove-asdf" ,sbcl-prove-asdf)))
+    (arguments
+     `(#:asd-file "prove.asd"))
+    (synopsis "Yet another unit testing framework for Common Lisp")
+    (description
+     "This project was originally called @command{cl-test-more}.
+@command{prove} is yet another unit testing framework for Common Lisp.  The
+advantages of @command{prove} are:
+
+@itemize
+@item Various simple functions for testing and informative error messages
+@item ASDF integration
+@item Extensible test reporters
+@item Colorizes the report if it's available (note for SLIME)
+@item Reports test durations
+@end itemize\n")))
+
+(define-public cl-prove
+  (sbcl-package->cl-source-package sbcl-prove))
+
+(define-public ecl-prove
+  (sbcl-package->ecl-package sbcl-prove))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 41b3b866ce1166d73b3c8530998f91730b3d48e3 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:31:46 +0200
Subject: [PATCH 831/909] gnu: Add proc-parse.

* gnu/packages/lisp.scm (cl-proc-parse, ecl-proc-parse, sbcl-proc-parse): New variables.
---
 gnu/packages/lisp.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 2e4725e084..cc3c343c81 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2590,6 +2590,45 @@ advantages of @command{prove} are:
 (define-public ecl-prove
   (sbcl-package->ecl-package sbcl-prove))
 
+(define-public sbcl-proc-parse
+  (let ((commit "ac3636834d561bdc2686c956dbd82494537285fd"))
+    (package
+      (name "sbcl-proc-parse")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/fukamachi/proc-parse")
+               (commit commit)))
+         (sha256
+          (base32
+           "06rnl0h4cx6xv2wj3jczmmcxqn2703inmmvg1s4npbghmijsybfh"))
+         (file-name (git-file-name "proc-parse" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("babel" ,sbcl-babel)))
+      (native-inputs
+       `(("prove" ,sbcl-prove)
+         ("prove-asdf" ,sbcl-prove-asdf)))
+      (arguments
+       ;; TODO: Tests don't find "proc-parse-test", why?
+       `(#:tests? #f))
+      (synopsis "Procedural vector parser")
+      (description
+       "This is a string/octets parser library for Common Lisp with speed and
+readability in mind.  Unlike other libraries, the code is not a
+pattern-matching-like, but a char-by-char procedural parser.")
+      (home-page "https://github.com/fukamachi/proc-parse")
+      (license license:bsd-2))))
+
+(define-public cl-proc-parse
+  (sbcl-package->cl-source-package sbcl-proc-parse))
+
+(define-public ecl-proc-parse
+  (sbcl-package->ecl-package sbcl-proc-parse))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From 28b52970ba097f9ff274b3484b1a353d67865968 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:31:59 +0200
Subject: [PATCH 832/909] gnu: Add parse-float.

* gnu/packages/lisp.scm (cl-parse-float, ecl-parse-float, sbcl-parse-float): New variables.
---
 gnu/packages/lisp.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index cc3c343c81..807398d508 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2629,6 +2629,45 @@ pattern-matching-like, but a char-by-char procedural parser.")
 (define-public ecl-proc-parse
   (sbcl-package->ecl-package sbcl-proc-parse))
 
+(define-public sbcl-parse-float
+  (let ((commit "2aae569f2a4b2eb3bfb5401a959425dcf151b09c"))
+    (package
+      (name "sbcl-parse-float")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/soemraws/parse-float")
+               (commit commit)))
+         (sha256
+          (base32
+           "08xw8cchhmqcc0byng69m3f5a2izc9y2290jzz2k0qrbibp1fdk7"))
+         (file-name (git-file-name "proc-parse" version))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("alexandria" ,sbcl-alexandria)
+         ("babel" ,sbcl-babel)))
+      (native-inputs
+       `(("prove" ,sbcl-prove)
+         ("prove-asdf" ,sbcl-prove-asdf)))
+      (arguments
+       ;; TODO: Tests don't find "proc-parse-test", why?
+       `(#:tests? #f))
+      (synopsis "Parse a floating point value from a string in Common Lisp")
+      (description
+       "This package exports the following function to parse floating-point
+values from a string in Common Lisp.")
+      (home-page "https://github.com/soemraws/parse-float")
+      ;; TODO: Missing license?
+      (license license:public-domain))))
+
+(define-public cl-parse-float
+  (sbcl-package->cl-source-package sbcl-parse-float))
+
+(define-public ecl-parse-float
+  (sbcl-package->ecl-package sbcl-parse-float))
+
 (define-public sbcl-ascii-strings
   (let ((revision "1")
         (changeset "5048480a61243e6f1b02884012c8f25cdbee6d97"))

From a28d00d999e7429a0be3e27c648688065089a6cb Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 15:32:42 +0200
Subject: [PATCH 833/909] gnu: Add simple-scanf.

* gnu/packages/lisp.scm (cl-simple-scanf, ecl-simple-scanf, sbcl-simple-scanf): New variables.
---
 gnu/packages/lisp.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 807398d508..7a6bf7496d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2703,6 +2703,27 @@ single-byte encoded strings.")
 (define-public ecl-ascii-strings
   (sbcl-package->ecl-package sbcl-ascii-strings))
 
+(define-public sbcl-simple-scanf
+  (package
+    (inherit sbcl-ascii-strings)
+    (name "sbcl-simple-scanf")
+    (inputs
+     `(("alexandria" ,sbcl-alexandria)
+       ("iterate" ,sbcl-iterate)
+       ("proc-parse" ,sbcl-proc-parse)
+       ("parse-float" ,sbcl-parse-float)))
+    (arguments
+     `(#:asd-file "simple-scanf.asd"))
+    (synopsis "Simple scanf-like functionality implementation")
+    (description
+     "A simple scanf-like functionality implementation.")))
+
+(define-public cl-simple-scanf
+  (sbcl-package->cl-source-package sbcl-simple-scanf))
+
+(define-public ecl-simple-scanf
+  (sbcl-package->ecl-package sbcl-simple-scanf))
+
 (define-public sbcl-cl-string-match
   (package
     (inherit sbcl-ascii-strings)

From 1de50cb73e6ba622c494200066fbd87884122f38 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 22:37:26 +0200
Subject: [PATCH 834/909] gnu: Add ptester.

* gnu/packages/lisp.scm (cl-ptester, ecl-ptester, sbcl-ptester): New variables.
---
 gnu/packages/lisp.scm | 32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 7a6bf7496d..f866255bf6 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -63,7 +63,8 @@
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages xorg)
   #:use-module (ice-9 match)
-  #:use-module (srfi srfi-1))
+  #:use-module (srfi srfi-1)
+  #:use-module (srfi srfi-19))
 
 (define (asdf-substitutions lisp)
   ;; Prepend XDG_DATA_DIRS/LISP-bundle-systems to ASDF's
@@ -2755,3 +2756,32 @@ utilities that make it even easier to manipulate text in Common Lisp.  It has
 
 (define-public ecl-cl-string-match
   (sbcl-package->ecl-package sbcl-cl-string-match))
+
+(define-public sbcl-ptester
+  (package
+    (name "sbcl-ptester")
+    (version "20160929")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://beta.quicklisp.org/archive/ptester/"
+                           (date->string (string->date version "~Y~m~d") "~Y-~m-~d")
+                           "/ptester-"
+                           version
+                           "-git.tgz"))
+       (sha256
+        (base32
+         "04rlq1zljhxc65pm31bah3sq3as24l0sdivz440s79qlnnyh13hz"))))
+    (build-system asdf-build-system/sbcl)
+    (home-page "http://quickdocs.org/ptester/")
+    (synopsis "Portable test harness package")
+    (description
+     "@command{ptester} is a portable testing framework based on Franz's
+tester module.")
+    (license license:lgpl3+)))
+
+(define-public cl-ptester
+  (sbcl-package->cl-source-package sbcl-ptester))
+
+(define-public ecl-ptester
+  (sbcl-package->ecl-package sbcl-ptester))

From 3f4c21c53e3256f8c010e6df8cf5a492965c5892 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 22:37:53 +0200
Subject: [PATCH 835/909] gnu: Add puri.

* gnu/packages/lisp.scm (cl-puri, ecl-puri, sbcl-puri): New variables.
---
 gnu/packages/lisp.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index f866255bf6..7b4b11560e 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2785,3 +2785,35 @@ tester module.")
 
 (define-public ecl-ptester
   (sbcl-package->ecl-package sbcl-ptester))
+
+(define-public sbcl-puri
+  (package
+    (name "sbcl-puri")
+    (version "20180228")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://beta.quicklisp.org/archive/puri/"
+                           (date->string (string->date version "~Y~m~d") "~Y-~m-~d")
+                           "/puri-"
+                           version
+                           "-git.tgz"))
+       (sha256
+        (base32
+         "1s4r5adrjy5asry45xbcbklxhdjydvf6n55z897nvyw33bigrnbz"))))
+    (build-system asdf-build-system/sbcl)
+    ;; REVIEW: Webiste down?
+    (native-inputs
+     `(("ptester" ,sbcl-ptester)))
+    (home-page "http://files.kpe.io/puri/")
+    (synopsis "Portable URI Library")
+    (description
+     "This is portable Universal Resource Identifier library for Common Lisp
+programs.  It parses URI according to the RFC 2396 specification")
+    (license license:lgpl3+)))
+
+(define-public cl-puri
+  (sbcl-package->cl-source-package sbcl-puri))
+
+(define-public ecl-puri
+  (sbcl-package->ecl-package sbcl-puri))

From eb766dfed01fb9e162c87d22dc746691d897688a Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 22:38:13 +0200
Subject: [PATCH 836/909] gnu: Add queues.

* gnu/packages/lisp.scm (cl-queues, ecl-queues, sbcl-queues): New variables.
---
 gnu/packages/lisp.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 7b4b11560e..cabc791bf3 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2817,3 +2817,32 @@ programs.  It parses URI according to the RFC 2396 specification")
 
 (define-public ecl-puri
   (sbcl-package->ecl-package sbcl-puri))
+
+(define-public sbcl-queues
+  (let ((commit "47d4da65e9ea20953b74aeeab7e89a831b66bc94"))
+    (package
+      (name "sbcl-queues")
+      (version (git-version "0.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/oconnore/queues")
+               (commit commit)))
+         (file-name (git-file-name "queues" version))
+         (sha256
+          (base32
+           "0wdhfnzi4v6d97pggzj2aw55si94w4327br94jrmyvwf351wqjvv"))))
+      (build-system asdf-build-system/sbcl)
+      (home-page "https://github.com/oconnore/queues")
+      (synopsis "Common Lisp queue library")
+      (description
+       "This is a simple queue library for Common Lisp with features such as
+non-consing thread safe queues and fibonacci priority queues.")
+      (license license:expat))))
+
+(define-public cl-queues
+  (sbcl-package->cl-source-package sbcl-queues))
+
+(define-public ecl-queues
+  (sbcl-package->ecl-package sbcl-queues))

From 6fef7c0ec89fac73410d0b850f4443c55e0943ef Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 22:38:31 +0200
Subject: [PATCH 837/909] gnu: Add queues.simple-queue.

* gnu/packages/lisp.scm (cl-queues.simple-queue, ecl-queues.simple-queue, sbcl-queues.simple-queue): New variables.
---
 gnu/packages/lisp.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index cabc791bf3..aecdfc5972 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2846,3 +2846,23 @@ non-consing thread safe queues and fibonacci priority queues.")
 
 (define-public ecl-queues
   (sbcl-package->ecl-package sbcl-queues))
+
+(define-public sbcl-queues.simple-queue
+  (package
+    (inherit sbcl-queues)
+    (name "sbcl-queues.simple-queue")
+    (inputs
+     `(("sbcl-queues" ,sbcl-queues)))
+    (arguments
+     `(#:asd-file "queues.simple-queue.asd"))
+    (synopsis "Simple queue implementation")
+    (description
+     "This is a simple queue library for Common Lisp with features such as
+non-consing thread safe queues and fibonacci priority queues.")
+    (license license:expat)))
+
+(define-public cl-queues.simple-queue
+  (sbcl-package->cl-source-package sbcl-queues.simple-queue))
+
+(define-public ecl-queues.simple-queue
+  (sbcl-package->ecl-package sbcl-queues.simple-queue))

From a889ba99c1d616d6ebd50e480685464fd0b236f3 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 22:38:46 +0200
Subject: [PATCH 838/909] gnu: Add queues.simple-cqueue.

* gnu/packages/lisp.scm (cl-queues.simple-cqueue, ecl-queues.simple-cqueue, sbcl-queues.simple-cqueue): New variables.
---
 gnu/packages/lisp.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index aecdfc5972..b4c9c9ebf1 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2866,3 +2866,25 @@ non-consing thread safe queues and fibonacci priority queues.")
 
 (define-public ecl-queues.simple-queue
   (sbcl-package->ecl-package sbcl-queues.simple-queue))
+
+(define-public sbcl-queues.simple-cqueue
+  (package
+    (inherit sbcl-queues)
+    (name "sbcl-queues.simple-cqueue")
+    (inputs
+     `(("sbcl-queues" ,sbcl-queues)
+       ("sbcl-queues.simple-queue" ,sbcl-queues.simple-queue)
+       ("bordeaux-threads" ,sbcl-bordeaux-threads)))
+    (arguments
+     `(#:asd-file "queues.simple-cqueue.asd"))
+    (synopsis "Thread safe queue implementation")
+    (description
+     "This is a simple queue library for Common Lisp with features such as
+non-consing thread safe queues and fibonacci priority queues.")
+    (license license:expat)))
+
+(define-public cl-queues.simple-cqueue
+  (sbcl-package->cl-source-package sbcl-queues.simple-cqueue))
+
+(define-public ecl-queues.simple-cqueue
+  (sbcl-package->ecl-package sbcl-queues.simple-cqueue))

From 144085cd69de3a16187f12ae9f436cd05db7b75a Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 22:39:02 +0200
Subject: [PATCH 839/909] gnu: Add queues.priority-queue.

* gnu/packages/lisp.scm (cl-queues.priority-queue, ecl-queues.priority-queue, sbcl-queues.priority-queue): New variables.
---
 gnu/packages/lisp.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index b4c9c9ebf1..6dc6d8081d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2888,3 +2888,23 @@ non-consing thread safe queues and fibonacci priority queues.")
 
 (define-public ecl-queues.simple-cqueue
   (sbcl-package->ecl-package sbcl-queues.simple-cqueue))
+
+(define-public sbcl-queues.priority-queue
+  (package
+    (inherit sbcl-queues)
+    (name "sbcl-queues.priority-queue")
+    (inputs
+     `(("sbcl-queues" ,sbcl-queues)))
+    (arguments
+     `(#:asd-file "queues.priority-queue.asd"))
+    (synopsis "Priority queue (Fibonacci) implementation")
+    (description
+     "This is a simple queue library for Common Lisp with features such as
+non-consing thread safe queues and fibonacci priority queues.")
+    (license license:expat)))
+
+(define-public cl-queues.priority-queue
+  (sbcl-package->cl-source-package sbcl-queues.priority-queue))
+
+(define-public ecl-queues.priority-queue
+  (sbcl-package->ecl-package sbcl-queues.priority-queue))

From 92b1d09b68a4d8226163a93874ff8c4d4a9a1e84 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Mon, 1 Oct 2018 22:39:18 +0200
Subject: [PATCH 840/909] gnu: Add queues.priority-cqueue.

* gnu/packages/lisp.scm (cl-queues.priority-cqueue, ecl-queues.priority-cqueue, sbcl-queues.priority-cqueue): New variables.
---
 gnu/packages/lisp.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 6dc6d8081d..fb4b8d73ac 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2908,3 +2908,25 @@ non-consing thread safe queues and fibonacci priority queues.")
 
 (define-public ecl-queues.priority-queue
   (sbcl-package->ecl-package sbcl-queues.priority-queue))
+
+(define-public sbcl-queues.priority-cqueue
+  (package
+    (inherit sbcl-queues)
+    (name "sbcl-queues.priority-cqueue")
+    (inputs
+     `(("sbcl-queues" ,sbcl-queues)
+       ("sbcl-queues.priority-queue" ,sbcl-queues.priority-queue)
+       ("bordeaux-threads" ,sbcl-bordeaux-threads)))
+    (arguments
+     `(#:asd-file "queues.priority-cqueue.asd"))
+    (synopsis "Thread safe fibonacci priority queue implementation")
+    (description
+     "This is a simple queue library for Common Lisp with features such as
+non-consing thread safe queues and fibonacci priority queues.")
+    (license license:expat)))
+
+(define-public cl-queues.priority-cqueue
+  (sbcl-package->cl-source-package sbcl-queues.priority-cqueue))
+
+(define-public ecl-queues.priority-cqueue
+  (sbcl-package->ecl-package sbcl-queues.priority-cqueue))

From 5d9bf76235aaaf4c17356957a8a2e957fa4e6185 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 2 Oct 2018 19:58:33 +0200
Subject: [PATCH 841/909] gnu: Add sbcl-cffi-bootstrap.

* gnu/packages/lisp.scm (sbcl-cffi-bootstrap): New variable.
---
 gnu/packages/lisp.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index fb4b8d73ac..fe1b7cb056 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2930,3 +2930,45 @@ non-consing thread safe queues and fibonacci priority queues.")
 
 (define-public ecl-queues.priority-cqueue
   (sbcl-package->ecl-package sbcl-queues.priority-cqueue))
+
+(define sbcl-cffi-bootstrap
+  (package
+    (name "sbcl-cffi-bootstrap")
+    (version "0.19.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/cffi/cffi/archive/v"
+                           version ".tar.gz"))
+       (sha256
+        (base32 "07bc3c1fbfx17wgrvx6bh9byilfzfwv5n597cfdllm0vzwvbmiyk"))
+       (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system asdf-build-system/sbcl)
+    (inputs
+     `(("libffi" ,libffi)
+       ("alexandria" ,sbcl-alexandria)
+       ("babel" ,sbcl-babel)
+       ("trivial-features" ,sbcl-trivial-features)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "libffi/libffi.lisp"
+               (("libffi.so.6" all) (string-append
+                                     (assoc-ref inputs "libffi")
+                                     "/lib/" all)))
+             (substitute* "toolchain/c-toolchain.lisp"
+               (("\"cc\"") (format #f "~S" (which "gcc")))))))
+       #:asd-system-name "cffi"
+       #:tests? #f))
+    (home-page "https://common-lisp.net/project/cffi/")
+    (synopsis "Common Foreign Function Interface for Common Lisp")
+    (description "The Common Foreign Function Interface (CFFI)
+purports to be a portable foreign function interface for Common Lisp.
+The CFFI library is composed of a Lisp-implementation-specific backend
+in the CFFI-SYS package, and a portable frontend in the CFFI
+package.")
+    (license license:expat)))

From 99b3d203fb5426a53fb6cdd171cf903a69949fce Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 2 Oct 2018 19:58:49 +0200
Subject: [PATCH 842/909] gnu: Add sbcl-cffi-toolchain.

* gnu/packages/lisp.scm (sbcl-cffi-toolchain): New variable.
---
 gnu/packages/lisp.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index fe1b7cb056..72aa166e54 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2972,3 +2972,15 @@ The CFFI library is composed of a Lisp-implementation-specific backend
 in the CFFI-SYS package, and a portable frontend in the CFFI
 package.")
     (license license:expat)))
+
+(define-public sbcl-cffi-toolchain
+  (package
+    (inherit sbcl-cffi-bootstrap)
+    (name "sbcl-cffi-toolchain")
+    (inputs
+     `(("libffi" ,libffi)
+       ("sbcl-cffi" ,sbcl-cffi-bootstrap)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-cffi-bootstrap)
+       ((#:asd-system-name _) #f)
+       ((#:tests? _) #t)))))

From 9eea4e03028f0aaed9ef4a0d371601fff622ebd4 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 2 Oct 2018 19:59:05 +0200
Subject: [PATCH 843/909] gnu: Add sbcl-cffi-libffi.

* gnu/packages/lisp.scm (sbcl-cffi-libffi): New variable.
---
 gnu/packages/lisp.scm | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 72aa166e54..6608413fd0 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2984,3 +2984,13 @@ package.")
      (substitute-keyword-arguments (package-arguments sbcl-cffi-bootstrap)
        ((#:asd-system-name _) #f)
        ((#:tests? _) #t)))))
+
+(define-public sbcl-cffi-libffi
+  (package
+    (inherit sbcl-cffi-toolchain)
+    (name "sbcl-cffi-libffi")
+    (inputs
+     `(("cffi" ,sbcl-cffi-bootstrap)
+       ("cffi-grovel" ,sbcl-cffi-grovel)
+       ("trivial-features" ,sbcl-trivial-features)
+       ("libffi" ,libffi)))))

From d3142f2ffbb53f511538d3b1517f34b0e17d6414 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 2 Oct 2018 19:59:19 +0200
Subject: [PATCH 844/909] gnu: Add sbcl-cffi-grovel.

* gnu/packages/lisp.scm (sbcl-cffi-grovel): New variable.
---
 gnu/packages/lisp.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 6608413fd0..c2ec5e5acc 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2994,3 +2994,23 @@ package.")
        ("cffi-grovel" ,sbcl-cffi-grovel)
        ("trivial-features" ,sbcl-trivial-features)
        ("libffi" ,libffi)))))
+
+(define-public sbcl-cffi-grovel
+  (package
+    (inherit sbcl-cffi-toolchain)
+    (name "sbcl-cffi-grovel")
+    (inputs
+     `(("libffi" ,libffi)
+       ("cffi" ,sbcl-cffi-bootstrap)
+       ("cffi-toolchain" ,sbcl-cffi-toolchain)
+       ("alexandria" ,sbcl-alexandria)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sbcl-cffi-toolchain)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'build 'install-headers
+             (lambda* (#:key outputs #:allow-other-keys)
+               (install-file "grovel/common.h"
+                             (string-append
+                              (assoc-ref outputs "out")
+                              "/include/grovel"))))))))))

From 41123072682e4adefd200d76c594a1a529400a11 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 2 Oct 2018 19:59:29 +0200
Subject: [PATCH 845/909] gnu: Add sbcl-cffi.

* gnu/packages/lisp.scm (sbcl-cffi): New variable.
---
 gnu/packages/lisp.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index c2ec5e5acc..7a5fcfe4dc 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3014,3 +3014,15 @@ package.")
                              (string-append
                               (assoc-ref outputs "out")
                               "/include/grovel"))))))))))
+
+(define-public sbcl-cffi
+  (package
+    (inherit sbcl-cffi-toolchain)
+    (name "sbcl-cffi")
+    (inputs (package-inputs sbcl-cffi-bootstrap))
+    (native-inputs
+     `(("cffi-grovel" ,sbcl-cffi-grovel)
+       ("cffi-libffi" ,sbcl-cffi-libffi)
+       ("rt" ,sbcl-rt)
+       ("bordeaux-threads" ,sbcl-bordeaux-threads)
+       ,@(package-native-inputs sbcl-cffi-bootstrap)))))

From 8f065b47c7b8db82544e85fd26c833ef01e0f036 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 3 Oct 2018 20:18:13 +0200
Subject: [PATCH 846/909] gnu: Add sbcl-cl-sqlite.

* gnu/packages/lisp.scm (sbcl-cl-sqlite): New variable.
---
 gnu/packages/lisp.scm | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 7a5fcfe4dc..c83348d902 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -62,6 +62,7 @@
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages xorg)
+  #:use-module (gnu packages databases)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-19))
@@ -3026,3 +3027,44 @@ package.")
        ("rt" ,sbcl-rt)
        ("bordeaux-threads" ,sbcl-bordeaux-threads)
        ,@(package-native-inputs sbcl-cffi-bootstrap)))))
+
+(define-public sbcl-cl-sqlite
+  (let ((commit "c738e66d4266ef63a1debc4ef4a1b871a068c112"))
+    (package
+      (name "sbcl-cl-sqlite")
+      (version (git-version "0.2" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/dmitryvk/cl-sqlite")
+               (commit commit)))
+         (file-name (git-file-name "cl-sqlite" version))
+         (sha256
+          (base32
+           "1ng45k1hdb84sqjryrfx93g66bsbybmpy301wd0fdybnc5jzr36q"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("iterate" ,sbcl-iterate)
+         ("cffi" ,sbcl-cffi)
+         ("sqlite" ,sqlite)))
+      (native-inputs
+       `(("fiveam" ,sbcl-fiveam)
+         ("bordeaux-threads" ,sbcl-bordeaux-threads)))
+      (arguments
+       `(#:tests? #f                    ; Upstream seems to have issues with tests: https://github.com/dmitryvk/cl-sqlite/issues/7
+         #:asd-file "sqlite.asd"
+         #:asd-system-name "sqlite"
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-paths
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "sqlite-ffi.lisp"
+                 (("libsqlite3" all) (string-append
+                                      (assoc-ref inputs "sqlite")"/lib/" all))))))))
+      (home-page "https://common-lisp.net/project/cl-sqlite/")
+      (synopsis "Common Lisp binding for SQLite")
+      (description
+       "The @command{cl-sqlite} package is an interface to the SQLite embedded
+relational database engine.")
+      (license license:public-domain))))

From 4624d2e2b446d7b2ad663e6cd377314cefe0776d Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 5 Oct 2018 16:14:30 +0200
Subject: [PATCH 847/909] gnu: Add parenscript.

* gnu/packages/lisp.scm (cl-parenscript, ecl-parenscript, sbcl-parenscript): New variables.
---
 gnu/packages/lisp.scm | 60 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index c83348d902..1315edc39f 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3068,3 +3068,63 @@ package.")
        "The @command{cl-sqlite} package is an interface to the SQLite embedded
 relational database engine.")
       (license license:public-domain))))
+
+(define-public sbcl-parenscript
+  (let ((commit "061d8e286c81c3f45c84fb2b11ee7d83f590a8f8"))
+    (package
+      (name "sbcl-parenscript")
+      (version (git-version "2.6" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.common-lisp.net/parenscript/parenscript")
+               (commit commit)))
+         (file-name (git-file-name "parenscript" version))
+         (sha256
+          (base32
+           "1kbhgsjbikc73m5cwdp4d4fdafyqcr1b7b630qjrziql0nh6mi3k"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("cl-ppcre" ,sbcl-cl-ppcre)
+         ("anaphora" ,sbcl-anaphora)
+         ("named-readtables" ,sbcl-named-readtables)))
+      (home-page "https://common-lisp.net/project/parenscript/")
+      (synopsis "Translator from a subset of Common Lisp to JavaScript")
+      (description
+       "Parenscript is a translator from an extended subset of Common Lisp to
+JavaScript.  Parenscript code can run almost identically on both the
+browser (as JavaScript) and server (as Common Lisp).
+
+Parenscript code is treated the same way as Common Lisp code, making the full
+power of Lisp macros available for JavaScript.  This provides a web
+development environment that is unmatched in its ability to reduce code
+duplication and provide advanced meta-programming facilities to web
+developers.
+
+At the same time, Parenscript is different from almost all other \"language
+X\" to JavaScript translators in that it imposes almost no overhead:
+
+@itemize
+@item No run-time dependencies: Any piece of Parenscript code is runnable
+as-is.  There are no JavaScript files to include.
+@item Native types: Parenscript works entirely with native JavaScript data
+types.  There are no new types introduced, and object prototypes are not
+touched.
+@item Native calling convention: Any JavaScript code can be called without the
+need for bindings.  Likewise, Parenscript can be used to make efficient,
+self-contained JavaScript libraries.
+@item Readable code: Parenscript generates concise, formatted, idiomatic
+JavaScript code.  Identifier names are preserved.  This enables seamless
+debugging in tools like Firebug.
+@item Efficiency: Parenscript introduces minimal overhead for advanced Common
+Lisp features.  The generated code is almost as fast as hand-written
+JavaScript.
+@end itemize\n")
+      (license license:bsd-3))))
+
+(define-public cl-parenscript
+  (sbcl-package->cl-source-package sbcl-parenscript))
+
+(define-public ecl-parenscript
+  (sbcl-package->ecl-package sbcl-parenscript))

From dedbf37e5d158bdc78d1fdff2c4c5151e6d32473 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 9 Oct 2018 11:59:30 +0200
Subject: [PATCH 848/909] gnu: Add cl-json.

* gnu/packages/lisp.scm (cl-json, ecl-cl-json, sbcl-cl-json): New variables.
---
 gnu/packages/lisp.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 1315edc39f..959298f316 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3128,3 +3128,37 @@ JavaScript.
 
 (define-public ecl-parenscript
   (sbcl-package->ecl-package sbcl-parenscript))
+
+(define-public sbcl-cl-json
+  (let ((commit "6dfebb9540bfc3cc33582d0c03c9ec27cb913e79"))
+    (package
+      (name "sbcl-cl-json")
+      (version (git-version "0.5" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/hankhero/cl-json")
+               (commit commit)))
+         (file-name (git-file-name "cl-json" version))
+         (sha256
+          (base32
+           "0fx3m3x3s5ji950yzpazz4s0img3l6b3d6l3jrfjv0lr702496lh"))))
+      (build-system asdf-build-system/sbcl)
+      (native-inputs
+       `(("fiveam" ,sbcl-fiveam)))
+      (home-page "https://github.com/hankhero/cl-json")
+      (synopsis "JSON encoder and decoder for Common-Lisp")
+      (description
+       "@command{cl-json} provides an encoder of Lisp objects to JSON format
+and a corresponding decoder of JSON data to Lisp objects.  Both the encoder
+and the decoder are highly customizable; at the same time, the default
+settings ensure a very simple mode of operation, similar to that provided by
+@command{yason} or @command{st-json}.")
+      (license license:expat))))
+
+(define-public cl-json
+  (sbcl-package->cl-source-package sbcl-cl-json))
+
+(define-public ecl-cl-json
+  (sbcl-package->ecl-package sbcl-cl-json))

From 2cc931db448430433b89326fce3a9815c63775df Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 9 Oct 2018 12:05:23 +0200
Subject: [PATCH 849/909] gnu: Add cl-unix-opts.

* gnu/packages/lisp.scm (cl-unix-opts, ecl-unix-opts, sbcl-unix-opts): New variables.
---
 gnu/packages/lisp.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 959298f316..de50eb43de 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3162,3 +3162,36 @@ settings ensure a very simple mode of operation, similar to that provided by
 
 (define-public ecl-cl-json
   (sbcl-package->ecl-package sbcl-cl-json))
+
+(define-public sbcl-unix-opts
+  (package
+    (name "sbcl-unix-opts")
+    (version "0.1.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/libre-man/unix-opts")
+             (commit version)))
+       (file-name (git-file-name "unix-opts" version))
+       (sha256
+        (base32
+         "08djdi1ard09fijb7w9bdmhmwd98b1hzmcnjw9fqjiqa0g3b44rr"))))
+    (build-system asdf-build-system/sbcl)
+    (home-page "https://github.com/hankhero/cl-json")
+    (synopsis "Unix-style command line options parser")
+    (description
+     "This is a minimalistic parser of command line options.  The main
+advantage of the library is the ability to concisely define command line
+options once and then use this definition for parsing and extraction of
+command line arguments, as well as printing description of command line
+options (you get --help for free).  This way you don't need to repeat
+yourself.  Also, @command{unix-opts} doesn't depend on anything and allows to
+precisely control behavior of the parser via Common Lisp restarts.")
+    (license license:expat)))
+
+(define-public cl-unix-opts
+  (sbcl-package->cl-source-package sbcl-unix-opts))
+
+(define-public ecl-unix-opts
+  (sbcl-package->ecl-package sbcl-unix-opts))

From 4aa2342008df3e2eaa861d14c208c8c625077f82 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 11:15:17 +0200
Subject: [PATCH 850/909] gnu: Add trivial-garbage.

* gnu/packages/lisp.scm (cl-trivial-garbage, ecl-trivial-garbage, sbcl-trivial-garbage): New variables.
---
 gnu/packages/lisp.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index de50eb43de..d636c0d9b3 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3195,3 +3195,32 @@ precisely control behavior of the parser via Common Lisp restarts.")
 
 (define-public ecl-unix-opts
   (sbcl-package->ecl-package sbcl-unix-opts))
+
+(define-public sbcl-trivial-garbage
+  (package
+    (name "sbcl-trivial-garbage")
+    (version "0.21")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/trivial-garbage/trivial-garbage/archive/v"
+             version ".tar.gz"))
+       (sha256
+        (base32 "0b244nlszkrqawsnp568clnx32xmvjmbbagbz7625w9n0yq7396y"))
+       (file-name (string-append "trivial-garbage-" version ".tar.gz"))))
+    (build-system asdf-build-system/sbcl)
+    (native-inputs
+     `(("rt" ,sbcl-rt)))
+    (home-page "https://common-lisp.net/project/trivial-garbage/")
+    (synopsis "Portable GC-related APIs for Common Lisp")
+    (description "@command{trivial-garbage} provides a portable API to
+finalizers, weak hash-tables and weak pointers on all major implementations of
+the Common Lisp programming language.")
+    (license license:public-domain)))
+
+(define-public cl-trivial-garbage
+  (sbcl-package->cl-source-package sbcl-trivial-garbage))
+
+(define-public ecl-trivial-garbage
+  (sbcl-package->ecl-package sbcl-trivial-garbage))

From 85be9191ee8737b5d021f1126a826727fb8fea1b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 11:22:51 +0200
Subject: [PATCH 851/909] gnu: Add closer-mop.

* gnu/packages/lisp.scm (cl-closer-mop, ecl-closer-mop, sbcl-closer-mop): New variables.
---
 gnu/packages/lisp.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index d636c0d9b3..cc4b5a026d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3224,3 +3224,31 @@ the Common Lisp programming language.")
 
 (define-public ecl-trivial-garbage
   (sbcl-package->ecl-package sbcl-trivial-garbage))
+
+(define-public sbcl-closer-mop
+  (let ((commit "fac29ce90e3a46e1fc6cf182190e193526fa9dbc"))
+    (package
+      (name "sbcl-closer-mop")
+      (version (git-version  "1.0.0" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/pcostanza/closer-mop")
+               (commit commit)))
+         (sha256
+          (base32 "0hvh77y869h8fg9di5snyg85fxq6fdh9gj1igmx1g6j6j5x915dl"))
+         (file-name (git-file-name "closer-mop" version ))))
+      (build-system asdf-build-system/sbcl)
+      (home-page "https://github.com/pcostanza/closer-mop")
+      (synopsis "Rectifies absent or incorrect CLOS MOP features")
+      (description "Closer to MOP is a compatibility layer that rectifies many
+of the absent or incorrect CLOS MOP features across a broad range of Common
+Lisp implementations.")
+      (license license:expat))))
+
+(define-public cl-closer-mop
+  (sbcl-package->cl-source-package sbcl-closer-mop))
+
+(define-public ecl-closer-mop
+  (sbcl-package->ecl-package sbcl-closer-mop))

From c88985d9b062790be45b588bf65d4876c2ad96ac Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Tue, 9 Oct 2018 21:38:43 +0200
Subject: [PATCH 852/909] gnu: Add sbcl-cl-cffi-gtk.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk): New variable.
---
 gnu/packages/lisp.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index cc4b5a026d..a4b64fc0fe 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3252,3 +3252,30 @@ Lisp implementations.")
 
 (define-public ecl-closer-mop
   (sbcl-package->ecl-package sbcl-closer-mop))
+
+(define sbcl-cl-cffi-gtk-boot0
+  (let ((commit "29443c5aaca975709df8025c4649366d882033cb"))
+    (package
+      (name "sbcl-cl-cffi-gtk-boot0")
+      (version (git-version "0.11.2" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/Ferada/cl-cffi-gtk/")
+               (commit commit)))
+         (file-name (git-file-name "cl-cffi-gtk" version))
+         (sha256
+          (base32
+           "0f6s92sf8xyzh1yksqx8bsy1sv0zmy0c13j3b8bavaba5hlxpxah"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("iterate" ,sbcl-iterate)
+         ("cffi" ,sbcl-cffi)
+         ("trivial-features" ,sbcl-trivial-features)))
+      (home-page "https://github.com/Ferada/cl-cffi-gtk/")
+      (synopsis "Common Lisp binding for GTK+3")
+      (description
+       "@command{cl-cffi-gtk} is a Lisp binding to GTK+ 3 (GIMP Toolkit) which
+is a library for creating graphical user interfaces.")
+      (license license:lgpl3))))

From 64dcf7d99b09805b8e8888051fe47a981ff9dba6 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:52:22 +0200
Subject: [PATCH 853/909] gnu: Add sbcl-cl-cffi-gtk-glib.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk-glib): New variable.
---
 gnu/packages/lisp.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index a4b64fc0fe..6ba678961c 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -63,6 +63,7 @@
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages gtk)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-19))
@@ -3279,3 +3280,20 @@ Lisp implementations.")
        "@command{cl-cffi-gtk} is a Lisp binding to GTK+ 3 (GIMP Toolkit) which
 is a library for creating graphical user interfaces.")
       (license license:lgpl3))))
+
+(define-public sbcl-cl-cffi-gtk-glib
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk-glib")
+    (inputs
+     `(("glib" ,glib)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (arguments
+     `(#:asd-file "glib/cl-cffi-gtk-glib.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "glib/glib.init.lisp"
+               (("libglib|libgthread" all) (string-append
+                                            (assoc-ref inputs "glib") "/lib/" all))))))))))

From 77a5461c31c5e53f23a9a3e90fd77d814fa24be6 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:52:59 +0200
Subject: [PATCH 854/909] gnu: Add sbcl-cl-cffi-gtk-gobject.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk-gobject): New variable.
---
 gnu/packages/lisp.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 6ba678961c..6d945da557 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3297,3 +3297,24 @@ is a library for creating graphical user interfaces.")
              (substitute* "glib/glib.init.lisp"
                (("libglib|libgthread" all) (string-append
                                             (assoc-ref inputs "glib") "/lib/" all))))))))))
+
+(define-public sbcl-cl-cffi-gtk-gobject
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk-gobject")
+    (inputs
+     `(("glib" ,glib)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
+       ("trivial-garbage" ,sbcl-trivial-garbage)
+       ("bordeaux-threads" ,sbcl-bordeaux-threads)
+       ("closer-mop" ,sbcl-closer-mop)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (arguments
+     `(#:asd-file "gobject/cl-cffi-gtk-gobject.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "gobject/gobject.init.lisp"
+               (("libgobject" all) (string-append
+                                    (assoc-ref inputs "glib") "/lib/" all))))))))))

From 867b3f4780e293585d30585bb49473d7309b66ac Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:53:16 +0200
Subject: [PATCH 855/909] gnu: Add sbcl-cl-cffi-gtk-gio.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk-gio): New variable.
---
 gnu/packages/lisp.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 6d945da557..70282e4cb5 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3318,3 +3318,23 @@ is a library for creating graphical user interfaces.")
              (substitute* "gobject/gobject.init.lisp"
                (("libgobject" all) (string-append
                                     (assoc-ref inputs "glib") "/lib/" all))))))))))
+
+(define-public sbcl-cl-cffi-gtk-gio
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk-gio")
+    (inputs
+     `(("glib" ,glib)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
+       ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (arguments
+     `(#:asd-file "gio/cl-cffi-gtk-gio.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "gio/gio.init.lisp"
+               (("libgio" all)
+                (string-append
+                 (assoc-ref inputs "glib") "/lib/" all))))))))))

From 7176fe7c328f0b4778b5f600c563c8073d16b135 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:53:38 +0200
Subject: [PATCH 856/909] gnu: Add sbcl-cl-cffi-gtk-cairo.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk-cairo): New variable.
---
 gnu/packages/lisp.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 70282e4cb5..ac694e3e7e 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3338,3 +3338,22 @@ is a library for creating graphical user interfaces.")
                (("libgio" all)
                 (string-append
                  (assoc-ref inputs "glib") "/lib/" all))))))))))
+
+(define-public sbcl-cl-cffi-gtk-cairo
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk-cairo")
+    (inputs
+     `(("cairo" ,cairo)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (arguments
+     `(#:asd-file "cairo/cl-cffi-gtk-cairo.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "cairo/cairo.init.lisp"
+               (("libcairo" all)
+                (string-append
+                 (assoc-ref inputs "cairo") "/lib/" all))))))))))

From 9ecc457b52186fd96a63aeb1d8b9f2eda169f287 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:53:51 +0200
Subject: [PATCH 857/909] gnu: Add sbcl-cl-cffi-gtk-pango.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk-pango): New variable.
---
 gnu/packages/lisp.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index ac694e3e7e..dc0481dd95 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3357,3 +3357,24 @@ is a library for creating graphical user interfaces.")
                (("libcairo" all)
                 (string-append
                  (assoc-ref inputs "cairo") "/lib/" all))))))))))
+
+(define-public sbcl-cl-cffi-gtk-pango
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk-pango")
+    (inputs
+     `(("pango" ,pango)
+       ("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
+       ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
+       ("cl-cffi-gtk-cairo" ,sbcl-cl-cffi-gtk-cairo)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (arguments
+     `(#:asd-file "pango/cl-cffi-gtk-pango.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "pango/pango.init.lisp"
+               (("libpango" all)
+                (string-append
+                 (assoc-ref inputs "pango") "/lib/" all))))))))))

From a3bdddc359643a9a32e78e32b919390041818c49 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:54:06 +0200
Subject: [PATCH 858/909] gnu: Add sbcl-cl-cffi-gtk-gdk-pixbuf.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk-gdk-pixbuf): New variable.
---
 gnu/packages/lisp.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index dc0481dd95..b63a55f4ac 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3378,3 +3378,22 @@ is a library for creating graphical user interfaces.")
                (("libpango" all)
                 (string-append
                  (assoc-ref inputs "pango") "/lib/" all))))))))))
+
+(define-public sbcl-cl-cffi-gtk-gdk-pixbuf
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk-gdk-pixbuf")
+    (inputs
+     `(("gdk-pixbuf" ,gdk-pixbuf)
+       ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (arguments
+     `(#:asd-file "gdk-pixbuf/cl-cffi-gtk-gdk-pixbuf.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "gdk-pixbuf/gdk-pixbuf.init.lisp"
+               (("libgdk_pixbuf" all)
+                (string-append
+                 (assoc-ref inputs "gdk-pixbuf") "/lib/" all))))))))))

From 7b5b8c44050c459eb94998ac6a0ece204bcc5a04 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:54:26 +0200
Subject: [PATCH 859/909] gnu: Add sbcl-cl-cffi-gtk-gdk.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk-gdk): New variable.
---
 gnu/packages/lisp.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index b63a55f4ac..ac1d4a432f 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3397,3 +3397,30 @@ is a library for creating graphical user interfaces.")
                (("libgdk_pixbuf" all)
                 (string-append
                  (assoc-ref inputs "gdk-pixbuf") "/lib/" all))))))))))
+
+(define-public sbcl-cl-cffi-gtk-gdk
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk-gdk")
+    (inputs
+     `(("gtk" ,gtk+)
+       ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
+       ("cl-cffi-gtk-gio" ,sbcl-cl-cffi-gtk-gio)
+       ("cl-cffi-gtk-gdk-pixbuf" ,sbcl-cl-cffi-gtk-gdk-pixbuf)
+       ("cl-cffi-gtk-cairo" ,sbcl-cl-cffi-gtk-cairo)
+       ("cl-cffi-gtk-pango" ,sbcl-cl-cffi-gtk-pango)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (arguments
+     `(#:asd-file "gdk/cl-cffi-gtk-gdk.asd"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-paths
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "gdk/gdk.init.lisp"
+               (("libgdk" all)
+                (string-append
+                 (assoc-ref inputs "gtk") "/lib/" all)))
+             (substitute* "gdk/gdk.package.lisp"
+               (("libgtk" all)
+                (string-append
+                 (assoc-ref inputs "gtk") "/lib/" all))))))))))

From c80dfee9f18aaba422ba0ad45aa3aeb17b789fa1 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 16:54:46 +0200
Subject: [PATCH 860/909] gnu: Add sbcl-cl-cffi-gtk.

* gnu/packages/lisp.scm (sbcl-cl-cffi-gtk): New variable.
---
 gnu/packages/lisp.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index ac1d4a432f..68927971b5 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3424,3 +3424,22 @@ is a library for creating graphical user interfaces.")
                (("libgtk" all)
                 (string-append
                  (assoc-ref inputs "gtk") "/lib/" all))))))))))
+
+(define-public sbcl-cl-cffi-gtk
+  (package
+    (inherit sbcl-cl-cffi-gtk-boot0)
+    (name "sbcl-cl-cffi-gtk")
+    (inputs
+     `(("cl-cffi-gtk-glib" ,sbcl-cl-cffi-gtk-glib)
+       ("cl-cffi-gtk-gobject" ,sbcl-cl-cffi-gtk-gobject)
+       ("cl-cffi-gtk-gio" ,sbcl-cl-cffi-gtk-gio)
+       ("cl-cffi-gtk-gdk" ,sbcl-cl-cffi-gtk-gdk)
+       ,@(package-inputs sbcl-cl-cffi-gtk-boot0)))
+    (native-inputs
+     `(("fiveam" ,sbcl-fiveam)))
+    (arguments
+     `(#:asd-file "gtk/cl-cffi-gtk.asd"
+       #:test-asd-file "test/cl-cffi-gtk-test.asd"
+       ;; TODO: Tests fail with memory fault.
+       ;; See https://github.com/Ferada/cl-cffi-gtk/issues/24.
+       #:tests? #f))))

From 24fd7586a4d0ce7f61887fbc9341c6fcb72310a6 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 15:07:01 +0200
Subject: [PATCH 861/909] gnu: Add sbcl-cl-webkit.

* gnu/packages/lisp.scm (sbcl-cl-webkit): New variable.
---
 gnu/packages/lisp.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 68927971b5..8e201f3b13 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -64,6 +64,7 @@
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages gtk)
+  #:use-module (gnu packages webkit)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-19))
@@ -3443,3 +3444,43 @@ is a library for creating graphical user interfaces.")
        ;; TODO: Tests fail with memory fault.
        ;; See https://github.com/Ferada/cl-cffi-gtk/issues/24.
        #:tests? #f))))
+
+(define-public sbcl-cl-webkit
+  (let ((commit "cd2a9008e0c152e54755e8a7f07b050fe36bab31"))
+    (package
+      (name "sbcl-cl-webkit")
+      (version (git-version "2.4" "1" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/atlas-engineer/cl-webkit")
+               (commit commit)))
+         (file-name (git-file-name "cl-webkit" version))
+         (sha256
+          (base32
+           "0f5lyn9i7xrn3g1bddga377mcbawkbxydijpg389q4n04gqj0vwf"))))
+      (build-system asdf-build-system/sbcl)
+      (inputs
+       `(("cffi" ,sbcl-cffi)
+         ("cl-cffi-gtk" ,sbcl-cl-cffi-gtk)
+         ("webkitgtk" ,webkitgtk)))
+      (arguments
+       `(#:asd-file "webkit2/cl-webkit2.asd"
+         #:asd-system-name "cl-webkit2"
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-paths
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "webkit2/webkit2.init.lisp"
+                 (("libwebkit2gtk" all)
+                  (string-append
+                   (assoc-ref inputs "webkitgtk") "/lib/" all))))))))
+      (home-page "https://github.com/atlas-engineer/cl-webkit")
+      (synopsis "Binding to WebKitGTK+ for Common Lisp")
+      (description
+       "@command{cl-webkit} is a binding to WebKitGTK+ for Common Lisp,
+currently targeting WebKit version 2.  The WebKitGTK+ library adds web
+browsing capabilities to an application, leveraging the full power of the
+WebKit browsing engine.")
+      (license license:expat))))

From e2e5004f6ee4f210440e4c8a2466185c463b8dbb Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Wed, 10 Oct 2018 15:07:19 +0200
Subject: [PATCH 862/909] gnu: Add lparallel.

* gnu/packages/lisp.scm (cl-lparallel, ecl-lparallel, sbcl-lparallel): New variables.
---
 gnu/packages/lisp.scm | 45 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 8e201f3b13..bc6216018b 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -3484,3 +3484,48 @@ currently targeting WebKit version 2.  The WebKitGTK+ library adds web
 browsing capabilities to an application, leveraging the full power of the
 WebKit browsing engine.")
       (license license:expat))))
+
+(define-public sbcl-lparallel
+  (package
+    (name "sbcl-lparallel")
+    (version "2.8.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/lmj/lparallel/")
+             (commit (string-append "lparallel-" version))))
+       (file-name (git-file-name "lparallel" version))
+       (sha256
+        (base32
+         "0g0aylrbbrqsz0ahmwhvnk4cmc2931fllbpcfgzsprwnqqd7vwq9"))))
+    (build-system asdf-build-system/sbcl)
+    (inputs
+     `(("alexandria" ,sbcl-alexandria)
+       ("bordeaux-threads" ,sbcl-bordeaux-threads)
+       ("trivial-garbage" ,sbcl-trivial-garbage)))
+    (home-page "https://lparallel.org/")
+    (synopsis "Parallelism for Common Lisp")
+    (description
+     "@command{lparallel} is a library for parallel programming in Common
+Lisp, featuring:
+
+@itemize
+@item a simple model of task submission with receiving queue,
+@item constructs for expressing fine-grained parallelism,
+@item asynchronous condition handling across thread boundaries,
+@item parallel versions of map, reduce, sort, remove, and many others,
+@item promises, futures, and delayed evaluation constructs,
+@item computation trees for parallelizing interconnected tasks,
+@item bounded and unbounded FIFO queues,
+@item high and low priority tasks,
+@item task killing by category,
+@item integrated timeouts.
+@end itemize\n")
+    (license license:expat)))
+
+(define-public cl-lparallel
+  (sbcl-package->cl-source-package sbcl-lparallel))
+
+(define-public ecl-lparallel
+  (sbcl-package->ecl-package sbcl-lparallel))

From 3bd45f5c809a56baafb355d93c1d2a243d6dd996 Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Fri, 19 Oct 2018 18:00:14 +0200
Subject: [PATCH 863/909] gnu: emacs-slime: License is a mix of GPL2+ and
 public domain.

* gnu/packages/emacs.scm (emacs-slime)[license]: Update to (gpl2+ public-domain)
---
 gnu/packages/emacs.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 57841e86fa..6b360b5ac3 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3091,7 +3091,7 @@ an Emacs minor mode that complements the standard @command{lisp-mode}.
 While lisp-mode supports editing Lisp source files, @command{slime-mode}
 adds support for interacting with a running Common Lisp process
 for compilation, debugging, documentation lookup, and so on.")
-    (license license:gpl2+)))
+    (license (list license:gpl2+ license:public-domain))))
 
 (define-public emacs-popup
   (package

From fbdb7b9526272e1983bec1908d0704428af7c1f2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 19 Oct 2018 18:20:47 +0200
Subject: [PATCH 864/909] pack: Fix "-C none -f tarball".
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes a regression introduced in
48b444304e206c35cf2c8e0d87a4711f1aac4fd4 whereby "guix pack -C none
hello" would fail with:

  ERROR: In procedure string-join:
  In procedure string-join: Wrong type argument in position 1: #f
  builder for `/gnu/store/…-tarball-pack.tar.drv' failed with exit code 1

* guix/scripts/pack.scm (self-contained-tarball): Adjust for when
'compressor-command' returns #f.
---
 guix/scripts/pack.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm
index fb3c50521d..b7b4e22bbe 100644
--- a/guix/scripts/pack.scm
+++ b/guix/scripts/pack.scm
@@ -198,8 +198,11 @@ added to the pack."
             (with-directory-excursion %root
               (exit
                (zero? (apply system* "tar"
-                             "-I"
-                             (string-join '#+(compressor-command compressor))
+                             #+@(if (compressor-command compressor)
+                                    #~("-I"
+                                       (string-join
+                                        '#+(compressor-command compressor)))
+                                    #~())
                              "--format=gnu"
 
                              ;; Avoid non-determinism in the archive.  Use

From 19c924af4f3726688ca155a905ebf1cb9acdfca2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 19 Oct 2018 17:58:00 +0200
Subject: [PATCH 865/909] tests: Run 'guix pack' tests using the external
 store.

Fixes <https://bugs.gnu.org/32184>.

* guix/tests.scm (call-with-external-store): New procedure.
(with-external-store): New macro.
* tests/pack.scm (%store): Remove.
(test-assertm): Add 'store' parameter.
("self-contained-tarball"): Wrap in 'with-external-store'.
* tests/guix-pack.sh: Connect to the external store, if possible, by
setting NIX_STORE_DIR and GUIX_DAEMON_SOCKET.  Remove most uses of
'--bootstrap'.
---
 .dir-locals.el     |  1 +
 guix/tests.scm     | 37 ++++++++++++++++++++++-
 tests/guix-pack.sh | 30 ++++++++++++-------
 tests/pack.scm     | 75 ++++++++++++++++++++++++----------------------
 4 files changed, 95 insertions(+), 48 deletions(-)

diff --git a/.dir-locals.el b/.dir-locals.el
index 793117c0ae..1a3a05f100 100644
--- a/.dir-locals.el
+++ b/.dir-locals.el
@@ -45,6 +45,7 @@
    (eval . (put 'manifest-pattern 'scheme-indent-function 0))
    (eval . (put 'substitute-keyword-arguments 'scheme-indent-function 1))
    (eval . (put 'with-store 'scheme-indent-function 1))
+   (eval . (put 'with-external-store 'scheme-indent-function 1))
    (eval . (put 'with-error-handling 'scheme-indent-function 0))
    (eval . (put 'with-mutex 'scheme-indent-function 1))
    (eval . (put 'with-atomic-file-output 'scheme-indent-function 1))
diff --git a/guix/tests.scm b/guix/tests.scm
index 06e9f8da0b..bcf9b990e5 100644
--- a/guix/tests.scm
+++ b/guix/tests.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17,6 +17,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (guix tests)
+  #:use-module ((guix config) #:select (%storedir %localstatedir))
   #:use-module (guix store)
   #:use-module (guix derivations)
   #:use-module (guix packages)
@@ -30,6 +31,7 @@
   #:use-module (ice-9 binary-ports)
   #:use-module (web uri)
   #:export (open-connection-for-tests
+            with-external-store
             random-text
             random-bytevector
             file=?
@@ -74,6 +76,39 @@
 
       store)))
 
+(define (call-with-external-store proc)
+  "Call PROC with an open connection to the external store or #f it there is
+no external store to talk to."
+  (parameterize ((%daemon-socket-uri
+                  (string-append %localstatedir
+                                 "/guix/daemon-socket/socket"))
+                 (%store-prefix %storedir))
+    (define store
+      (catch #t
+        (lambda ()
+          (open-connection))
+        (const #f)))
+
+    (dynamic-wind
+      (const #t)
+      (lambda ()
+        ;; Since we're using a different store we must clear the
+        ;; package-derivation cache.
+        (hash-clear! (@@ (guix packages) %derivation-cache))
+
+        (proc store))
+      (lambda ()
+        (when store
+          (close-connection store))))))
+
+(define-syntax-rule (with-external-store store exp ...)
+  "Evaluate EXP with STORE bound to the external store rather than the
+temporary test store, or #f if there is no external store to talk to.
+
+This is meant to be used for tests that need to build packages that would be
+too expensive to build entirely in the test store."
+  (call-with-external-store (lambda (store) exp ...)))
+
 (define (random-seed)
   (or (and=> (getenv "GUIX_TESTS_RANDOM_SEED")
              number->string)
diff --git a/tests/guix-pack.sh b/tests/guix-pack.sh
index bf367fa429..cd721a60e9 100644
--- a/tests/guix-pack.sh
+++ b/tests/guix-pack.sh
@@ -1,5 +1,6 @@
 # GNU Guix --- Functional package management for GNU
 # Copyright © 2018 Chris Marusich <cmmarusich@gmail.com>
+# Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
 #
 # This file is part of GNU Guix.
 #
@@ -28,26 +29,33 @@ fi
 
 guix pack --version
 
-# FIXME: Starting from commit 66e9944e078cbb9e0d618377dd6df6e639640efa,
-# '--bootstrap' is mostly ineffective since 'guix pack' produces derivations
-# that refer to guile-sqlite3 and libgcrypt.  For now we just skip the test.
-exit 77
+# Starting from commit 66e9944e078cbb9e0d618377dd6df6e639640efa, 'guix pack'
+# produces derivations that refer to guile-sqlite3 and libgcrypt.  To make
+# that relatively inexpensive, run the test in the user's global store if
+# possible, on the grounds that binaries may already be there or can be built
+# or downloaded inexpensively.
 
-# Use --no-substitutes because we need to verify we can do this ourselves.
-GUIX_BUILD_OPTIONS="--no-substitutes"
-export GUIX_BUILD_OPTIONS
+NIX_STORE_DIR="`guile -c '(use-modules (guix config))(display %storedir)'`"
+localstatedir="`guile -c '(use-modules (guix config))(display %localstatedir)'`"
+GUIX_DAEMON_SOCKET="$localstatedir/guix/daemon-socket/socket"
+export NIX_STORE_DIR GUIX_DAEMON_SOCKET
+
+if ! guile -c '(use-modules (guix)) (exit (false-if-exception (open-connection)))'
+then
+    exit 77
+fi
 
 # Build a tarball with no compression.
-guix pack --compression=none --bootstrap guile-bootstrap
+guix pack --compression=none guile-bootstrap
 
 # Build a tarball (with compression).  Check that '-e' works as well.
-out1="`guix pack --bootstrap guile-bootstrap`"
-out2="`guix pack --bootstrap -e '(@ (gnu packages bootstrap) %bootstrap-guile)'`"
+out1="`guix pack guile-bootstrap`"
+out2="`guix pack -e '(@ (gnu packages bootstrap) %bootstrap-guile)'`"
 test -n "$out1"
 test "$out1" = "$out2"
 
 # Build a tarball with a symlink.
-the_pack="`guix pack --bootstrap -S /opt/gnu/bin=bin guile-bootstrap`"
+the_pack="`guix pack -S /opt/gnu/bin=bin guile-bootstrap`"
 
 # Try to extract it.  Note: we cannot test whether /opt/gnu/bin/guile itself
 # exists because /opt/gnu/bin may be an absolute symlink to a store item that
diff --git a/tests/pack.scm b/tests/pack.scm
index c57c6848ff..7f867894c2 100644
--- a/tests/pack.scm
+++ b/tests/pack.scm
@@ -29,15 +29,12 @@
   #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-64))
 
-(define %store
-  (open-connection-for-tests))
-
 ;; Globally disable grafts because they can trigger early builds.
 (%graft? #f)
 
-(define-syntax-rule (test-assertm name exp)
+(define-syntax-rule (test-assertm name store exp)
   (test-assert name
-    (run-with-store %store exp
+    (run-with-store store exp
                     #:guile-for-build (%guile-for-build))))
 
 (define %gzip-compressor
@@ -51,37 +48,43 @@
 
 (test-begin "pack")
 
-;; FIXME: The following test would rebuild the world (and likely fail) as a
-;; consequence of commit c45477d2a1a651485feede20fe0f3d15aec48b39 (and related
-;; changes) that made guile-sqlite3 a dependency of the derivation.
-;; See <https://bugs.gnu.org/32184>.
-(test-skip 1)
+;; The following test needs guile-sqlite3, libgcrypt, etc. as a consequence of
+;; commit c45477d2a1a651485feede20fe0f3d15aec48b39 and related changes.  Thus,
+;; run it on the user's store, if it's available, on the grounds that these
+;; dependencies may be already there, or we can get substitutes or build them
+;; quite inexpensively; see <https://bugs.gnu.org/32184>.
 
-(test-assertm "self-contained-tarball"
-  (mlet* %store-monad
-      ((profile (profile-derivation (packages->manifest
-                                     (list %bootstrap-guile))
-                                    #:hooks '()
-                                    #:locales? #f))
-       (tarball (self-contained-tarball "pack" profile
-                                        #:symlinks '(("/bin/Guile"
-                                                      -> "bin/guile"))
-                                        #:compressor %gzip-compressor
-                                        #:archiver %tar-bootstrap))
-       (check   (gexp->derivation
-                 "check-tarball"
-                 #~(let ((bin (string-append "." #$profile "/bin")))
-                     (setenv "PATH"
-                             (string-append #$%tar-bootstrap "/bin"))
-                     (system* "tar" "xvf" #$tarball)
-                     (mkdir #$output)
-                     (exit
-                      (and (file-exists? (string-append bin "/guile"))
-                           (string=? (string-append #$%bootstrap-guile "/bin")
-                                     (readlink bin))
-                           (string=? (string-append ".." #$profile
-                                                    "/bin/guile")
-                                     (readlink "bin/Guile"))))))))
-    (built-derivations (list check))))
+(with-external-store store
+  (unless store (tests-skip 1))
+  (test-assertm "self-contained-tarball" store
+    (mlet* %store-monad
+        ((profile (profile-derivation (packages->manifest
+                                       (list %bootstrap-guile))
+                                      #:hooks '()
+                                      #:locales? #f))
+         (tarball (self-contained-tarball "pack" profile
+                                          #:symlinks '(("/bin/Guile"
+                                                        -> "bin/guile"))
+                                          #:compressor %gzip-compressor
+                                          #:archiver %tar-bootstrap))
+         (check   (gexp->derivation
+                   "check-tarball"
+                   #~(let ((bin (string-append "." #$profile "/bin")))
+                       (setenv "PATH"
+                               (string-append #$%tar-bootstrap "/bin"))
+                       (system* "tar" "xvf" #$tarball)
+                       (mkdir #$output)
+                       (exit
+                        (and (file-exists? (string-append bin "/guile"))
+                             (string=? (string-append #$%bootstrap-guile "/bin")
+                                       (readlink bin))
+                             (string=? (string-append ".." #$profile
+                                                      "/bin/guile")
+                                       (readlink "bin/Guile"))))))))
+      (built-derivations (list check)))))
 
 (test-end)
+
+;; Local Variables:
+;; eval: (put 'test-assertm 'scheme-indent-function 2)
+;; End:

From 4680fef705d9aa37737422804dc2cc1805522647 Mon Sep 17 00:00:00 2001
From: Amirouche <amirouche@hypermove.net>
Date: Mon, 15 Oct 2018 20:54:45 +0200
Subject: [PATCH 866/909] gnu: Add wiredtiger 3.1.0
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/databases.scm (wiredtiger-3): New variable that inherits from
  wiredtiger

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/databases.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 73026c5e66..ee00f23717 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -1768,6 +1768,19 @@ trees (LSM), for sustained throughput under random insert workloads.")
     ;; configure.ac: WiredTiger requires a 64-bit build.
     (supported-systems '("x86_64-linux" "mips64el-linux" "aarch64-linux"))))
 
+(define-public wiredtiger-3
+  (package
+    (inherit wiredtiger)
+    (name "wiredtiger")
+    (version "3.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://source.wiredtiger.com/releases/wiredtiger-"
+                                  version ".tar.bz2"))
+              (sha256
+               (base32
+                "014awypv579ascg4jbx4pndj2wld337m79yyzrzyr7hxrff139jx"))))))
+
 (define-public guile-wiredtiger
   (package
     (name "guile-wiredtiger")

From b1e6b9380589a6cbbe903255390888b0540bfe8e Mon Sep 17 00:00:00 2001
From: Amirouche <amirouche@hypermove.net>
Date: Tue, 16 Oct 2018 20:45:28 +0200
Subject: [PATCH 867/909] gnu: guile-wiredtiger: Update to 0.7.0.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/databases.scm (guile-wiredtiger): Update to 0.7.0.
[inputs]: Replace wiredtiger with wiredtiger-3
[propagated-inputs]: Remove guile-lib, add guile-bytestructures
[description]: Update it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/databases.scm | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index ee00f23717..7b483a207d 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -1784,16 +1784,16 @@ trees (LSM), for sustained throughput under random insert workloads.")
 (define-public guile-wiredtiger
   (package
     (name "guile-wiredtiger")
-    (version "0.6.3")
+    (version "0.7.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://framagit.org/a-guile-mind/guile-wiredtiger.git")
-                    (commit "070ed68139d99c279f058a6c293f00292d35dbd7")))
+                    (commit "340ad4bc2ff4dcc6216a2f5c6f9172ca320ac66b")))
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "14rna97wsylajzxfif95wnblq85csgcfc666gh5dl0ssgd7x8llh"))))
+                "15j36bvxxzil7qpwlmh1rffqpva3ynvrcpqhhqbj2c9208ayz595"))))
     (build-system gnu-build-system)
     (arguments
      '(#:parallel-tests? #f  ;; tests can't be run in parallel, yet.
@@ -1801,21 +1801,19 @@ trees (LSM), for sustained throughput under random insert workloads.")
        (list (string-append "--with-libwiredtiger-prefix="
                             (assoc-ref %build-inputs "wiredtiger")))
        #:make-flags '("GUILE_AUTO_COMPILE=0")))
-    ;; TODO: Remove microkanren.scm when we have a separate package
-    ;; for it.
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("wiredtiger" ,wiredtiger)
+     `(("wiredtiger" ,wiredtiger-3)
        ("guile" ,guile-2.2)))
     (propagated-inputs
-     `(("guile-lib" ,guile-lib)))                 ;for (htmlprag)
+     `(("guile-bytestructures" ,guile-bytestructures)))
     (synopsis "WiredTiger bindings for GNU Guile")
     (description
      "This package provides Guile bindings to the WiredTiger ``NoSQL''
-database.  Various higher level database abstractions.")
+database.")
     (home-page "https://framagit.org/a-guile-mind/guile-wiredtiger")
     (license license:gpl3+)))
 

From 0ee6692a63538e874ba0b4d85584a4a73b75367c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 19 Oct 2018 18:34:07 +0200
Subject: [PATCH 868/909] gnu: sbcl-slime-swank: Remove reference to unbound
 variable.

Fixes a regression introduced in commit
c4d4ae1e16254a96caaeb5ccb4486f301ae4f1b7.

* gnu/packages/lisp.scm (sbcl-slime-swank)[license]: Remove extra 'license'.
---
 gnu/packages/lisp.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index bc6216018b..89ccdb720a 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -2256,7 +2256,7 @@ writing code that contains string literals that contain code themselves.")
      "This is only useful if you want to start a Swank server in a Lisp
 processes that doesn't run under Emacs.  Lisp processes created by
 @command{M-x slime} automatically start the server.")
-    (license (license (list license:gpl2+ license:public-domain)))))
+    (license (list license:gpl2+ license:public-domain))))
 
 (define-public sbcl-mgl-pax
   (let ((commit "818448418d6b9de74620f606f5b23033c6082769"))

From be200ef316478585059041a33d8f4287017dea5a Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 19 Oct 2018 18:51:46 +0200
Subject: [PATCH 869/909] gnu: texlive-bin: Fix FTBFS on i686-linux.

* gnu/packages/tex.scm (texlive-bin)[arguments]: Add phase 'disable-failing-test'.
---
 gnu/packages/tex.scm | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index c62512b8d0..ccbdfc6f61 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -194,6 +194,14 @@
             (copy-file "texk/web2c/pdftexdir/pdftosrc-newpoppler.cc"
                        "texk/web2c/pdftexdir/pdftosrc.cc")
             #t))
+        (add-after 'unpack 'disable-failing-test
+          (lambda _
+            ;; FIXME: This test fails on 32-bit architectures since Glibc 2.28:
+            ;; <https://bugzilla.redhat.com/show_bug.cgi?id=1631847>.
+            (substitute* "texk/web2c/omegafonts/check.test"
+              (("^\\./omfonts -ofm2opl \\$srcdir/tests/check tests/xcheck || exit 1")
+               "./omfonts -ofm2opl $srcdir/tests/check tests/xcheck || exit 77"))
+            #t))
         (add-after 'install 'postint
           (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
             (let* ((out (assoc-ref outputs "out"))

From cdb84eb0e6a2c0a885c742c01615c5c0e3c04124 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 19 Oct 2018 21:58:48 +0200
Subject: [PATCH 870/909] gnu: qsynth: Update to 0.5.3.

* gnu/packages/audio.scm (qsynth): Update to 0.5.3.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 69b5d01d6f..ac41ed2dfe 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2759,7 +2759,7 @@ interface.")
 (define-public qsynth
   (package
     (name "qsynth")
-    (version "0.5.2")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
@@ -2767,7 +2767,7 @@ interface.")
                            "/qsynth-" version ".tar.gz"))
        (sha256
         (base32
-         "1rfkaxq1pyc4hv3l0i6wicianbcbm1wp53kh9i5d4jsljgisd1dv"))))
+         "1jghczmmva7cyavg1q0j8nr3hmjpzzglzi5ckg92ax4ji8gpks9c"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no "check" phase

From 58352f269e46942c34d7ee4e29f91144576ca661 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Thu, 18 Oct 2018 02:53:32 +0800
Subject: [PATCH 871/909] build-system/haskell: Use 'strip-store-file-name'.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

See the discussion at
<https://lists.gnu.org/archive/html/guix-devel/2018-10/msg00250.html>.

* guix/build/haskell-build-system.scm (package-name-version): Remove it.
(configure): Use 'strip-store-file-name' instead of 'package-name-version'.
(setup-compiler): Likewise.
(make-ghc-package-database): Likewise.
(register): Likewise.
* gnu/packages/haskell.scm (ghc-cairo)[arguments]: Likewise.
* gnu/packages/agda.scm (agda)[arguments]: Likewise.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/agda.scm               |  5 +++--
 gnu/packages/haskell.scm            |  4 ++--
 guix/build/haskell-build-system.scm | 20 +++++++++-----------
 3 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/agda.scm b/gnu/packages/agda.scm
index 6bb38aac4d..d2113555eb 100644
--- a/gnu/packages/agda.scm
+++ b/gnu/packages/agda.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2018 Alex ter Weele <alex.ter.weele@gmail.com>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -85,6 +86,7 @@
            (lambda* (#:key outputs inputs tests? (configure-flags '())
                      #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
+                    (name-version (strip-store-file-name out))
                     (input-dirs (match inputs
                                   (((_ . dir) ...)
                                    dir)
@@ -95,8 +97,7 @@
                                     `(,(string-append "--bindir=" out "/bin"))
                                     `(,(string-append
                                         "--docdir=" out
-                                        "/share/doc/" ((@@ (guix build haskell-build-system)
-                                                           package-name-version) out)))
+                                        "/share/doc/" name-version))
                                     '("--libsubdir=$compiler/$pkg-$version")
                                     '("--package-db=../package.conf.d")
                                     '("--global")
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 0a90ac523c..57435dca07 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -10619,6 +10619,7 @@ expose it from another module in the hierarchy.
            (lambda* (#:key outputs inputs tests? (configure-flags '())
                      #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
+                    (name-version (strip-store-file-name out))
                     (input-dirs (match inputs
                                   (((_ . dir) ...)
                                    dir)
@@ -10629,8 +10630,7 @@ expose it from another module in the hierarchy.
                                     `(,(string-append "--bindir=" out "/bin"))
                                     `(,(string-append
                                         "--docdir=" out
-                                        "/share/doc/" ((@@ (guix build haskell-build-system)
-                                                           package-name-version) out)))
+                                        "/share/doc/" name-version))
                                     '("--libsubdir=$compiler/$pkg-$version")
                                     '("--package-db=../package.conf.d")
                                     '("--global")
diff --git a/guix/build/haskell-build-system.scm b/guix/build/haskell-build-system.scm
index 72714a29ad..7b556f6431 100644
--- a/guix/build/haskell-build-system.scm
+++ b/guix/build/haskell-build-system.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -78,6 +79,7 @@ and parameters ~s~%"
          (doc (assoc-ref outputs "doc"))
          (lib (assoc-ref outputs "lib"))
          (bin (assoc-ref outputs "bin"))
+         (name-version (strip-store-file-name out))
          (input-dirs (match inputs
                        (((_ . dir) ...)
                         dir)
@@ -88,7 +90,7 @@ and parameters ~s~%"
                          `(,(string-append "--bindir=" (or bin out) "/bin"))
                          `(,(string-append
                              "--docdir=" (or doc out)
-                             "/share/doc/" (package-name-version out)))
+                             "/share/doc/" name-version))
                          '("--libsubdir=$compiler/$pkg-$version")
                          `(,(string-append "--package-db=" %tmp-db-dir))
                          '("--global")
@@ -127,12 +129,6 @@ and parameters ~s~%"
   "Install a given Haskell package."
   (run-setuphs "copy" '()))
 
-(define (package-name-version store-dir)
-  "Given a store directory STORE-DIR return 'name-version' of the package."
-  (let* ((base (basename store-dir)))
-    (string-drop base
-                 (+ 1 (string-index base #\-)))))
-
 (define (grep rx port)
   "Given a regular-expression RX including a group, read from PORT until the
 first match and return the content of the group."
@@ -147,7 +143,7 @@ first match and return the content of the group."
 (define* (setup-compiler #:key system inputs outputs #:allow-other-keys)
   "Setup the compiler environment."
   (let* ((haskell (assoc-ref inputs "haskell"))
-         (name-version (package-name-version haskell)))
+         (name-version (strip-store-file-name haskell)))
     (cond
      ((string-match "ghc" name-version)
       (make-ghc-package-database system inputs outputs))
@@ -164,6 +160,7 @@ first match and return the content of the group."
 (define (make-ghc-package-database system inputs outputs)
   "Generate the GHC package database."
   (let* ((haskell  (assoc-ref inputs "haskell"))
+         (name-version (strip-store-file-name haskell))
          (input-dirs (match inputs
                        (((_ . dir) ...)
                         dir)
@@ -171,7 +168,7 @@ first match and return the content of the group."
          ;; Silence 'find-files' (see 'evaluate-search-paths')
          (conf-dirs (with-null-error-port
                      (search-path-as-list
-                      `(,(string-append "lib/" (package-name-version haskell)))
+                      `(,(string-append "lib/" name-version))
                       input-dirs #:pattern ".*\\.conf.d$")))
          (conf-files (append-map (cut find-files <> "\\.conf$") conf-dirs)))
     (mkdir-p %tmp-db-dir)
@@ -231,9 +228,10 @@ given Haskell package."
 
   (let* ((out (assoc-ref outputs "out"))
          (haskell  (assoc-ref inputs "haskell"))
+         (name-verion (strip-store-file-name haskell))
          (lib (string-append out "/lib"))
-         (config-dir (string-append lib "/"
-                                    (package-name-version haskell)
+         (config-dir (string-append lib
+                                    "/" name-verion
                                     "/" name ".conf.d"))
          (id-rx (make-regexp "^id: *(.*)$"))
          (config-file (string-append out "/" name ".conf"))

From 418f1b241486ef7f98fdce1e6f8e53f2e7863fd9 Mon Sep 17 00:00:00 2001
From: Alex Vong <alexvong1995@gmail.com>
Date: Thu, 18 Oct 2018 03:08:31 +0800
Subject: [PATCH 872/909] java-utils: Use 'strip-store-file-name'.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

See the discussion at
<https://lists.gnu.org/archive/html/guix-devel/2018-10/msg00250.html>.

* guix/build/java-utils.scm (package-name-version): Remove it.
(install-javadoc): Use 'strip-store-file-name' instead of
'package-name-version'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 guix/build/java-utils.scm | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/guix/build/java-utils.scm b/guix/build/java-utils.scm
index 128be1edeb..8200638bee 100644
--- a/guix/build/java-utils.scm
+++ b/guix/build/java-utils.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,12 +24,6 @@
             install-jars
             install-javadoc))
 
-;; Copied from haskell-build-system.scm
-(define (package-name-version store-dir)
-  "Given a store directory STORE-DIR return 'name-version' of the package."
-  (let* ((base (basename store-dir)))
-    (string-drop base (+ 1 (string-index base #\-)))))
-
 (define* (ant-build-javadoc #:key (target "javadoc") (make-flags '())
                             #:allow-other-keys)
   (apply invoke `("ant" ,target ,@make-flags)))
@@ -48,8 +43,9 @@ is used in case the build.xml does not include an install target."
 install javadocs when this is not done by the install target."
   (lambda* (#:key outputs #:allow-other-keys)
     (let* ((out (assoc-ref outputs "out"))
+           (name-version (strip-store-file-name out))
            (docs (string-append (or (assoc-ref outputs "doc") out)
-                                "/share/doc/" (package-name-version out) "/")))
+                                "/share/doc/" name-version "/")))
       (mkdir-p docs)
       (copy-recursively apidoc-directory docs)
       #t)))

From bc83b2e22f39c00ab3d0072c9c8f13285f7967d6 Mon Sep 17 00:00:00 2001
From: Meiyo Peng <meiyo.peng@gmail.com>
Date: Tue, 16 Oct 2018 15:16:43 +0800
Subject: [PATCH 873/909] gnu: Add i3blocks.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/wm.scm (i3blocks): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/wm.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 7c58770de7..68d497e955 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -17,6 +17,7 @@
 ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <contact@parouby.fr>
+;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -233,6 +234,46 @@ from scratch.  i3 is primarily targeted at advanced users and
 developers.")
     (license license:bsd-3)))
 
+(define-public i3blocks
+  (let ((commit "37f23805ff886639163fbef8aedba71c8071eff8")
+        (revision "1"))
+    (package
+      (name "i3blocks")
+      (version (string-append "1.4-" revision "."
+                              (string-take commit 7)))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/vivien/i3blocks.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "15rnrcajzyrmhlz1a21qqsjlj3dkib70806dlb386fliylc2kisb"))
+                (file-name (string-append name "-" version "-checkout"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:make-flags (list "CC=gcc" (string-append "PREFIX=" %output))
+         #:phases (modify-phases %standard-phases
+                    (add-after 'unpack 'autogen
+                      (lambda _ (invoke "sh" "autogen.sh")))
+                    (add-after 'install 'install-doc
+                      (lambda* (#:key outputs #:allow-other-keys)
+                        (let* ((out (assoc-ref outputs "out"))
+                               (man1 (string-append out "/share/man/man1")))
+                          (install-file "docs/i3blocks.1" man1)
+                          #t))))))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("pkg-config" ,pkg-config)))
+      (home-page "https://github.com/vivien/i3blocks")
+      (synopsis "Minimalist scheduler for status bar scripts")
+      (description "i3blocks executes your command lines and generates a
+status line from their output.  The generated line is meant to be displayed by
+the i3 window manager through its i3bar component, as an alternative to
+i3status.")
+      (license license:gpl3+))))
+
 (define-public perl-anyevent-i3
   (package
     (name "perl-anyevent-i3")

From 64791eb7e1dceb0940cc881e84820f0170298b34 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= <ludo@gnu.org>
Date: Fri, 19 Oct 2018 22:46:23 +0200
Subject: [PATCH 874/909] services: ntp: Document 'ntp-service-type' and
 'ntp-configuration'.

* gnu/services/networking.scm (<ntp-configuration>)[servers]: Add
default value.
(ntp-service-type)[default-value]: New field.
(ntp-service): Mark as deprecated.
* gnu/services/desktop.scm (%desktop-services): Use (service
ntp-service-type) instead of calling 'ntp-service'.
* doc/guix.texi (Networking Services): Document 'ntp-service-type' and
'ntp-configuration'.
---
 doc/guix.texi               | 39 ++++++++++++++++++++++++++-----------
 gnu/services/desktop.scm    |  4 ++--
 gnu/services/networking.scm |  8 +++++---
 3 files changed, 35 insertions(+), 16 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index f4f19949f1..12346c4b8e 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -11817,20 +11817,37 @@ objects}).
 @end table
 @end deftp
 
-@cindex NTP
+@cindex NTP (Network Time Protocol), service
 @cindex real time clock
-@deffn {Scheme Procedure} ntp-service [#:ntp @var{ntp}] @
-  [#:servers @var{%ntp-servers}] @
-  [#:allow-large-adjustment? #f]
-Return a service that runs the daemon from @var{ntp}, the
-@uref{http://www.ntp.org, Network Time Protocol package}.  The daemon will
-keep the system clock synchronized with that of @var{servers}.
-@var{allow-large-adjustment?} determines whether @command{ntpd} is allowed to
-make an initial adjustment of more than 1,000 seconds.
-@end deffn
+@defvr {Scheme Variable} ntp-service-type
+This is the type of the service running the the @uref{http://www.ntp.org,
+Network Time Protocol (NTP)} daemon, @command{ntpd}.  The daemon will keep the
+system clock synchronized with that of the specified NTP servers.
+
+The value of this service is an @code{ntpd-configuration} object, as described
+below.
+@end defvr
+
+@deftp {Data Type} ntp-configuration
+This is the data type for the NTP service configuration.
+
+@table @asis
+@item @code{servers} (default: @code{%ntp-servers})
+This is the list of servers (host names) with which @command{ntpd} will be
+synchronized.
+
+@item @code{allow-large-adjustment?} (default: @code{#f})
+This determines whether @command{ntpd} is allowed to make an initial
+adjustment of more than 1,000 seconds.
+
+@item @code{ntp} (default: @code{ntp})
+The NTP package to use.
+@end table
+@end deftp
 
 @defvr {Scheme Variable} %ntp-servers
-List of host names used as the default NTP servers.
+List of host names used as the default NTP servers.  These are servers of the
+@uref{https://www.ntppool.org/en/, NTP Pool Project}.
 @end defvr
 
 @cindex OpenNTPD
diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm
index 1e8c02c02a..e038f97683 100644
--- a/gnu/services/desktop.scm
+++ b/gnu/services/desktop.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Sou Bunnbu <iyzsong@gmail.com>
@@ -996,7 +996,7 @@ as expected.")))
          (elogind-service)
          (dbus-service)
 
-         (ntp-service)
+         (service ntp-service-type)
 
          x11-socket-directory-service
 
diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm
index b764cde5ac..bfa6e297e6 100644
--- a/gnu/services/networking.scm
+++ b/gnu/services/networking.scm
@@ -297,7 +297,8 @@ Protocol (DHCP) client, on all the non-loopback network interfaces."
   ntp-configuration?
   (ntp      ntp-configuration-ntp
             (default ntp))
-  (servers  ntp-configuration-servers)
+  (servers  ntp-configuration-servers
+            (default %ntp-servers))
   (allow-large-adjustment? ntp-allow-large-adjustment?
                            (default #f)))
 
@@ -370,9 +371,10 @@ restrict -6 ::1\n"))
                 (description
                  "Run the @command{ntpd}, the Network Time Protocol (NTP)
 daemon of the @uref{http://www.ntp.org, Network Time Foundation}.  The daemon
-will keep the system clock synchronized with that of the given servers.")))
+will keep the system clock synchronized with that of the given servers.")
+                (default-value (ntp-configuration))))
 
-(define* (ntp-service #:key (ntp ntp)
+(define* (ntp-service #:key (ntp ntp)             ;deprecated
                       (servers %ntp-servers)
                       allow-large-adjustment?)
   "Return a service that runs the daemon from @var{ntp}, the

From b5a927b3baa10d4eade7e7194db6c2b5b7d8c6b6 Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Tue, 16 Oct 2018 14:18:14 +0200
Subject: [PATCH 875/909] gnu: Add enchive.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/crypto.scm (enchive): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/crypto.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index 33f4abb5ae..77b4dba6d4 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -10,6 +10,7 @@
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2018 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -854,3 +855,36 @@ public-key cryptography.  Asignify is designed to be portable and self-contained
 with zero external dependencies.  Asignify can verify OpenBSD signatures, but it
 cannot sign messages in OpenBSD format yet.")
       (license license:bsd-2))))
+
+(define-public enchive
+  (package
+    (name "enchive")
+    (version "3.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/skeeto/" name "/archive/"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "17hrxpp4cpn10bk48sfvfjc8hghky34agsnypam1v9f36kbalqfk"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f                      ; no check target         '
+       #:make-flags (list "CC=gcc" "PREFIX=$(out)")
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)
+                  (add-after 'install 'post-install
+                    (lambda _
+                      (let* ((out (assoc-ref %outputs "out"))
+                             (lisp (string-append out "/share/emacs/site-lisp")))
+                        (install-file "enchive-mode.el" lisp)
+                        #t))))))
+    (synopsis "Encrypted personal archives")
+    (description
+     "Enchive is a tool to encrypt files to yourself for long-term
+archival.  It's a focused, simple alternative to more complex solutions such as
+GnuPG or encrypted filesystems.  Enchive has no external dependencies and is
+trivial to build for local use.  Portability is emphasized over performance.")
+    (home-page "https://github.com/skeeto/enchive")
+    (license license:unlicense)))

From 0d3f17086480ad13d2c993022c1b8b5304e327d2 Mon Sep 17 00:00:00 2001
From: Christopher Baines <mail@cbaines.net>
Date: Sun, 14 Oct 2018 21:17:28 +0100
Subject: [PATCH 876/909] gnu: Add soundconverter.

* gnu/packages/gnome.scm (soundconverter): New variable.
* gnu/packages/patches/soundconverter-remove-gconf-dependency.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                  |  1 +
 gnu/packages/gnome.scm                        | 65 +++++++++++++++
 ...undconverter-remove-gconf-dependency.patch | 83 +++++++++++++++++++
 3 files changed, 149 insertions(+)
 create mode 100644 gnu/packages/patches/soundconverter-remove-gconf-dependency.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 402505e229..71aa115621 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1150,6 +1150,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/slim-reset.patch				\
   %D%/packages/patches/slim-login.patch				\
   %D%/packages/patches/sooperlooper-build-with-wx-30.patch 	\
+  %D%/packages/patches/soundconverter-remove-gconf-dependency.patch	\
   %D%/packages/patches/soundtouch-CVE-2018-14044-14045.patch 	\
   %D%/packages/patches/soundtouch-CVE-2018-1000223.patch 	\
   %D%/packages/patches/steghide-fixes.patch			\
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index de938e4b14..7b04716fa2 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -7220,6 +7220,71 @@ It supports ripping to any audio codec supported by a GStreamer plugin, such as
 mp3, Ogg Vorbis and FLAC")
     (license license:gpl2+)))
 
+(define-public soundconverter
+  (package
+    (name "soundconverter")
+    (version "3.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://launchpad.net/soundconverter/trunk/"
+                           version "/+download/"
+                           "soundconverter-" version ".tar.xz"))
+
+       (sha256
+        (base32
+         "1wrxf5py54xplrf97qp24pzbis0cvax5c6k0c7vr3z3ry8r7gd7c"))
+       (patches
+        (search-patches
+         "soundconverter-remove-gconf-dependency.patch"))))
+    (build-system glib-or-gtk-build-system)
+    (arguments
+     `(#:imported-modules ((guix build python-build-system)
+                           (guix build glib-or-gtk-build-system)
+                           ,@%gnu-build-system-modules)
+
+       #:modules ((guix build glib-or-gtk-build-system)
+                  (guix build utils)
+                  ((guix build gnu-build-system) #:prefix gnu:)
+                  ((guix build python-build-system) #:prefix python:))
+
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-POTFILES.in
+           (lambda _
+             (substitute* "po/POTFILES.in"
+               ;; This file doesn't exist, so without removing it, the 'check
+               ;; phase fails for the po directory
+               (("soundconverter/gconfstore\\.py") ""))))
+         (add-after 'install 'wrap-soundconverter-for-python
+           (assoc-ref python:%standard-phases 'wrap))
+         (add-after 'install 'wrap-soundconverter
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out               (assoc-ref outputs "out"))
+                   (gi-typelib-path   (getenv "GI_TYPELIB_PATH"))
+                   (gst-plugin-path   (getenv "GST_PLUGIN_SYSTEM_PATH")))
+               (wrap-program (string-append out "/bin/soundconverter")
+                 `("GI_TYPELIB_PATH"        ":" prefix (,gi-typelib-path))
+                 `("GST_PLUGIN_SYSTEM_PATH" ":" prefix (,gst-plugin-path))))
+             #t)))))
+    (native-inputs
+     `(("intltool" ,intltool)
+       ("pkg-config" ,pkg-config)
+       ("glib:bin" ,glib "bin")))
+    (inputs
+     `(("gtk+" ,gtk+)
+       ("python" ,python)
+       ("python-pygobject" ,python-pygobject)
+       ("gstreamer" ,gstreamer)
+       ("gst-plugins-base" ,gst-plugins-base)))
+    (home-page "http://soundconverter.org/")
+    (synopsis "Convert between audio formats with a graphical interface")
+    (description
+     "SoundConverter supports converting between many audio formats including
+Opus, Ogg Vorbis, FLAC and more.  It supports parallel conversion, and
+configurable file renaming. ")
+    (license license:gpl3)))
+
 (define-public workrave
   (let ((commit "v1_10_21"))
     (package
diff --git a/gnu/packages/patches/soundconverter-remove-gconf-dependency.patch b/gnu/packages/patches/soundconverter-remove-gconf-dependency.patch
new file mode 100644
index 0000000000..f065b9a3d4
--- /dev/null
+++ b/gnu/packages/patches/soundconverter-remove-gconf-dependency.patch
@@ -0,0 +1,83 @@
+From: Sebastian Ramacher <sebastian@ramacher.at>
+Date: Fri, 6 Apr 2018 13:25:35 +0200
+Subject: Only fetch profiles if GConf is still available
+
+---
+ bin/soundconverter.py       |  1 -
+ soundconverter/gstreamer.py | 44 ++++++++++++++++++++++++--------------------
+ 2 files changed, 24 insertions(+), 21 deletions(-)
+
+diff --git a/bin/soundconverter.py b/bin/soundconverter.py
+index 39055ce..5198443 100644
+--- a/bin/soundconverter.py
++++ b/bin/soundconverter.py
+@@ -66,7 +66,6 @@ def _check_libs():
+         import gi
+         gi.require_version('Gst', '1.0')
+         gi.require_version('Gtk', '3.0')
+-        gi.require_version('GConf', '2.0')
+         from gi.repository import GObject
+         # force GIL creation - see https://bugzilla.gnome.org/show_bug.cgi?id=710447
+         import threading
+diff --git a/soundconverter/gstreamer.py b/soundconverter/gstreamer.py
+index 23aaa9b..211b052 100644
+--- a/soundconverter/gstreamer.py
++++ b/soundconverter/gstreamer.py
+@@ -25,7 +25,7 @@ from urllib.parse import urlparse
+ from gettext import gettext as _
+ 
+ import gi
+-from gi.repository import Gst, Gtk, GObject, GConf, Gio
++from gi.repository import Gst, Gtk, GObject, Gio
+ 
+ from soundconverter.fileoperations import vfs_encode_filename, file_encode_filename
+ from soundconverter.fileoperations import unquote_filename, vfs_makedirs, vfs_unlink
+@@ -66,25 +66,29 @@ _GCONF_PROFILE_LIST_PATH = "/system/gstreamer/1.0/audio/global/profile_list"
+ audio_profiles_list = []
+ audio_profiles_dict = {}
+ 
+-_GCONF = GConf.Client.get_default()
+-profiles = _GCONF.all_dirs(_GCONF_PROFILE_LIST_PATH)
+-for name in profiles:
+-    if _GCONF.get_bool(_GCONF_PROFILE_PATH + name + "/active"):
+-        # get profile
+-        description = _GCONF.get_string(_GCONF_PROFILE_PATH + name + "/name")
+-        extension = _GCONF.get_string(_GCONF_PROFILE_PATH + name + "/extension")
+-        pipeline = _GCONF.get_string(_GCONF_PROFILE_PATH + name + "/pipeline")
+-        # check profile validity
+-        if not extension or not pipeline:
+-            continue
+-        if not description:
+-            description = extension
+-        if description in audio_profiles_dict:
+-            continue
+-            # store
+-        profile = description, extension, pipeline
+-        audio_profiles_list.append(profile)
+-        audio_profiles_dict[description] = profile
++try:
++    from gi.repository import GConf
++    _GCONF = GConf.Client.get_default()
++    profiles = _GCONF.all_dirs(_GCONF_PROFILE_LIST_PATH)
++    for name in profiles:
++        if _GCONF.get_bool(_GCONF_PROFILE_PATH + name + "/active"):
++            # get profile
++            description = _GCONF.get_string(_GCONF_PROFILE_PATH + name + "/name")
++            extension = _GCONF.get_string(_GCONF_PROFILE_PATH + name + "/extension")
++            pipeline = _GCONF.get_string(_GCONF_PROFILE_PATH + name + "/pipeline")
++            # check profile validity
++            if not extension or not pipeline:
++                continue
++            if not description:
++                description = extension
++            if description in audio_profiles_dict:
++                continue
++                # store
++            profile = description, extension, pipeline
++            audio_profiles_list.append(profile)
++            audio_profiles_dict[description] = profile
++except ImportError:
++    pass
+ 
+ required_elements = ('decodebin', 'fakesink', 'audioconvert', 'typefind', 'audiorate')
+ for element in required_elements:

From 42f9ebdc77693f78030c0251e3ffde863542fcc6 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:37:32 +0300
Subject: [PATCH 877/909] gnu: emacs-which-key: Update to 3.3.0.

* gnu/packages/emacs.scm (emacs-which-key): Update to 3.3.0.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 6b360b5ac3..2c6aeca058 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -7243,7 +7243,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.")
 (define-public emacs-which-key
   (package
     (name "emacs-which-key")
-    (version "3.0.2")
+    (version "3.3.0")
     (source
      (origin
        (method url-fetch)
@@ -7252,7 +7252,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.")
              version ".tar.gz"))
        (sha256
         (base32
-         "1xvd70cwq9n31f28viyjxmr3nn8l153gsy6scpszvgvjxkiikv24"))
+         "1lsj314111cp2hjjwnv3f46ws1za6bm39rgy3l19044xf6a68j5w"))
        (file-name (string-append name "-" version ".tar.gz"))))
     (build-system emacs-build-system)
     (arguments

From 83246854f32ccb30bb4dfa7e8d4aeb4689b8a372 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:46:43 +0300
Subject: [PATCH 878/909] gnu: emacs-ggtags: Update to 0.8.13.

* gnu/packages/emacs.scm (emacs-ggtags): Update to 0.8.13.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 2c6aeca058..25bb3bd5bc 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -1376,7 +1376,7 @@ environment set through Direnv.")
 (define-public emacs-ggtags
   (package
     (name "emacs-ggtags")
-    (version "0.8.12")
+    (version "0.8.13")
     (source
      (origin
        (method url-fetch)
@@ -1384,7 +1384,7 @@ environment set through Direnv.")
                            version ".el"))
        (sha256
         (base32
-         "0ny3llk021g6r0s75xdm4hzpbxv393ddm2r6f2xdk8kqnq4gnirp"))))
+         "1qa7lcrcmf76sf6dy8sxbg4adq7rg59fm0n5848w3qxgsr0h45fg"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/leoliu/ggtags")
     (synopsis "Frontend to the GNU Global source code tagging system")

From 9137596179193434c3ddde3f4ee41552c3db6f13 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:47:13 +0300
Subject: [PATCH 879/909] gnu: emacs-fill-column-indicator: Update to 1.89.

* gnu/packages/emacs.scm (emacs-fill-column-indicator): Update to 1.89.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 25bb3bd5bc..24736fd6e7 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -2162,7 +2162,7 @@ keep pressing the key until it selects what you want.  There's also
 (define-public emacs-fill-column-indicator
   (package
     (name "emacs-fill-column-indicator")
-    (version "1.81")
+    (version "1.89")
     (source
      (origin
        (method url-fetch)
@@ -2171,7 +2171,7 @@ keep pressing the key until it selects what you want.  There's also
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1xwyqbjbbicmvhlb85vg4j5snwy1vd7rfk89ws4viws5ljkhhyg8"))))
+         "09ab01np14bdcsr38xf95kpnvxzqr46mdjmphg3pigwnx39a3jvg"))))
     (build-system emacs-build-system)
     (home-page "https://www.emacswiki.org/emacs/FillColumnIndicator")
     (synopsis "Graphically indicate the fill column")

From 45dcdf53491209da56e4f9154cbc63efad39bd86 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:47:46 +0300
Subject: [PATCH 880/909] gnu: emacs-smart-mode-line: Update to 2.12.0.

* gnu/packages/emacs.scm (emacs-smart-mode-line): Update to 2.12.0.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 24736fd6e7..8fdf4b43be 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -2512,7 +2512,7 @@ snippets for yasnippet.")
 (define-public emacs-smart-mode-line
   (package
     (name "emacs-smart-mode-line")
-    (version "2.10.1")
+    (version "2.12.0")
     (source
      (origin
        (method url-fetch)
@@ -2521,7 +2521,7 @@ snippets for yasnippet.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0i9wajabrrsjzwd842q0m2611kf0q31p9hg1pdj81177gynkw8l8"))))
+         "1hn8s6laijmg7w1bgwdfrki6h9vxkbgr8rmmssvd5yqyad5w2sba"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-rich-minority" ,emacs-rich-minority)))

From 2f1dacc281b49436868e7905d0cc25f451a4d984 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:48:07 +0300
Subject: [PATCH 881/909] gnu: emacs-rainbow-mode: Update to 1.0.1.

* gnu/packages/emacs.scm (emacs-rainbow-mode): Update to 1.0.1.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 8fdf4b43be..24e198465b 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -4757,14 +4757,14 @@ of its name.")
 (define-public emacs-rainbow-mode
   (package
     (name "emacs-rainbow-mode")
-    (version "0.13")
+    (version "1.0.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
                     "http://elpa.gnu.org/packages/rainbow-mode-" version ".el"))
               (sha256
                (base32
-                "1d3aamx6qgqqpqijwsr02ggwrh67gfink1bir0692alfkm3zdddl"))))
+                "0cpga4ax635rfpj7y2vmh7ank0yw00dcy20gjg1mj74r97by8csf"))))
     (build-system emacs-build-system)
     (home-page "http://elpa.gnu.org/packages/rainbow-mode.html")
     (synopsis "Colorize color names in buffers")

From 292d637b9eb20364c10610e5587c076f6a0cce72 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:48:28 +0300
Subject: [PATCH 882/909] gnu: emacs-nginx-mode: Update to 1.1.9.

* gnu/packages/emacs.scm (emacs-nginx-mode): Update to 1.1.9.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 24e198465b..ec55018ad4 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5599,7 +5599,7 @@ This package contains the library runtime.")
 (define-public emacs-nginx-mode
   (package
     (name "emacs-nginx-mode")
-    (version "1.1.4")
+    (version "1.1.9")
     (source
      (origin
        (method url-fetch)
@@ -5609,7 +5609,7 @@ This package contains the library runtime.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1lvkj07kq0jkskr2f61vqb5rlrbnaz9a76ikq40w6925i2r970rr"))))
+         "0bzyrj6zz1hm67bkhw23bam7qc869s3zg7m1rb1c3aa4n0aw90cq"))))
     (build-system emacs-build-system)
     (home-page "https://github.com/ajc/nginx-mode")
     (synopsis "Emacs major mode for editing nginx config files")

From 91c5e6a69d1c073459e1f26b94bf803dcd85414c Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:48:36 +0300
Subject: [PATCH 883/909] gnu: emacs-yasnippet: Update to 0.13.0.

* gnu/packages/emacs.scm (emacs-yasnippet): Update to 0.13.0.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index ec55018ad4..13d8dd99dc 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -5814,7 +5814,7 @@ mode-line.")
 (define-public emacs-yasnippet
   (package
     (name "emacs-yasnippet")
-    (version "0.12.2")
+    (version "0.13.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/joaotavora/yasnippet/"
@@ -5822,7 +5822,7 @@ mode-line.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "01jabaz0g67bsziayrxgv74px55fx4nlrcl0csl8f1by2102pwc5"))
+                "12ls2x17agzbrj1xynjbmfa11igqxia4hj4fv6fpr66yci2r1plc"))
               (modules '((guix build utils)))
               (snippet
                '(begin

From e661dca879796e7b209446e63faf94ba9cce91d9 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:48:49 +0300
Subject: [PATCH 884/909] gnu: emacs-erc-hl-nicks: Update to 1.3.3.

* gnu/packages/emacs.scm (emacs-erc-hl-nicks): Update to 1.3.3.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 13d8dd99dc..539b1bf46a 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -7421,7 +7421,7 @@ created by @code{git format-patch}, from @code{magit}, @code{dired} and
 (define-public emacs-erc-hl-nicks
   (package
     (name "emacs-erc-hl-nicks")
-    (version "1.3.2")
+    (version "1.3.3")
     (source
      (origin
        (method url-fetch)
@@ -7430,7 +7430,7 @@ created by @code{git format-patch}, from @code{magit}, @code{dired} and
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "01svpl9bps5kx4y1wnymakxya2cznqmlynvqv2r500wpnbxczrbs"))))
+         "1a1r2kc3688g8c2ybkpwh88kgmnqhg3h3032g2yn4zr9m0n3vpkr"))))
     (build-system emacs-build-system)
     (synopsis "Nickname highlighting for Emacs ERC")
     (description "@code{erc-hl-nicks} highlights nicknames in ERC, an IRC

From 67fd64a490f549a08f2eaa869915c37836f8c9f3 Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 17:48:58 +0300
Subject: [PATCH 885/909] gnu: emacs-hy-mode: Update to 1.0.3.

* gnu/packages/emacs.scm (emacs-hy-mode): Update to 1.0.3.
---
 gnu/packages/emacs.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 539b1bf46a..1069b9e3c3 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -9736,7 +9736,7 @@ documentation.")
 (define-public emacs-hy-mode
   (package
     (name "emacs-hy-mode")
-    (version "1.0.2")
+    (version "1.0.3")
     (source
      (origin
        (method url-fetch)
@@ -9745,7 +9745,7 @@ documentation.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0sbga36zkyhzrzcczsyjzll7b9qsa215pnlw51m4li2irm23jh17"))))
+         "0b4pvbr2hf77bq2vsyfsv653q0dab7qzq85wc7kdziw7687jdf2z"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-dash" ,emacs-dash)

From 227da3a4c5e8420927c1f69c6c87d7d2a62040fe Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 20 Oct 2018 18:24:23 +0300
Subject: [PATCH 886/909] gnu: python-glances: Update to 3.0.2.

* gnu/packages/python.scm (python-glances): Update to 3.0.2.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index e3a04b0344..29ce213afb 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -10246,14 +10246,14 @@ functionality in the command line.")
 (define-public python-glances
   (package
   (name "python-glances")
-  (version "2.7.1")
+  (version "3.0.2")
   (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "Glances" version))
       (sha256
         (base32
-          "11jbq40g8alsbirnd4kiagznqg270247i0m8qhi48ldf2i5xppxg"))))
+          "09fxysfp1n16csqvzvawy74qm6a94nvwjf3vcf5gkqp4i6k4vjjy"))))
   (build-system python-build-system)
   (propagated-inputs
    `(("python-psutil" ,python-psutil)))

From 82cbe4e0467304e5d8f5931ca4d70617a0e323ba Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sun, 14 Oct 2018 13:55:10 -0400
Subject: [PATCH 887/909] gnu: maxima: Update to 5.42.0.

* gnu/packages/maths.scm (maxima): Update to 5.42.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d4128f55c4..48bfcba35a 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2659,7 +2659,7 @@ to BMP, JPEG or PNG image formats.")
 (define-public maxima
   (package
     (name "maxima")
-    (version "5.41.0")
+    (version "5.42.0")
     (source
      (origin
        (method url-fetch)
@@ -2667,7 +2667,7 @@ to BMP, JPEG or PNG image formats.")
                            version "-source/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
+         "0d5pdihvcbwb7r4i4qs5qqgsz46hxlq33qj8is053llrgn9ylpyn"))
        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
     (build-system gnu-build-system)
     (inputs

From bfa47f14b1a19150d6ddf149597d16493f69ae6d Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Sat, 20 Oct 2018 14:37:24 -0400
Subject: [PATCH 888/909] gnu: cataclysm-dda: Update snapshot.

* gnu/packages/games.scm (cataclysm-dda): Update snapshot to 0b2c194e5.
---
 gnu/packages/games.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index e2d1a5d6a8..c3067c5684 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -246,8 +246,8 @@ canyons and wait for the long I-shaped block to clear four rows at a time.")
     (license license:gpl3+)))
 
 (define-public cataclysm-dda
-  (let ((commit "ad3b0c3d521292d119f97a83390e7acfe9e9e7f7")
-        (revision "1"))
+  (let ((commit "0b2c194e5c6a06f4fbf14a0ec1260e0f3cf2567c")
+        (revision "2"))
     (package
       (name "cataclysm-dda")
       ;; This denotes the version released after the 0.C release.
@@ -260,7 +260,7 @@ canyons and wait for the long I-shaped block to clear four rows at a time.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "1kdgbl8zqd53f5yilm2c9nyq3w6585yxl5jvgxy65dlpzxcqqj7y"))
+                  "1yzsn0y2g27bvbxjvivjyjhkmf2w5na1qqw5qfkswcfqqwym2y33"))
                 (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments

From 129363b762ad235fe729fdce6c1120f143d0620f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 18:12:21 +0200
Subject: [PATCH 889/909] gnu: Add bedtools-2.26.

* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
---
 gnu/packages/bioinformatics.scm | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 91bb94c549..c5abe6755e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -453,6 +453,20 @@ BED, GFF/GTF, VCF.")
                          (find-files "bin" ".*")))
              #t)))))))
 
+;; Needed for pybedtools.
+(define-public bedtools-2.26
+  (package (inherit bedtools)
+    (name "bedtools")
+    (version "2.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/arq5x/bedtools2/releases/"
+                                  "download/v" version "/"
+                                  "bedtools-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5"))))))
+
 (define-public ribotaper
   (package
     (name "ribotaper")

From 895cf8278abab83032b1efb9e050134639491624 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 19:29:37 +0200
Subject: [PATCH 890/909] gnu: python-pybedtools: Update to 0.7.10.

* gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10.
[arguments]: Disable broken tests.
[propagated-inputs]: Replace bedtools with bedtools-2.26; add
python-matplotlib, python-pysam, and python-pyyaml.
[native-inputs]: Remove python-pyyaml; add kentutils, python-numpy,
python-pandas, and python-six.
(python-pybedtools): New variable.
---
 gnu/packages/bioinformatics.scm | 85 +++++++++++++++++++++++++++------
 1 file changed, 70 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c5abe6755e..bb9bf00499 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -596,29 +596,54 @@ input/output delimiter.  When the new functionality is not used, bioawk is
 intended to behave exactly the same as the original BWK awk.")
     (license license:x11)))
 
-(define-public python2-pybedtools
+(define-public python-pybedtools
   (package
-    (name "python2-pybedtools")
-    (version "0.6.9")
+    (name "python-pybedtools")
+    (version "0.7.10")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
-                    version ".tar.gz"))
+              (uri (pypi-uri "pybedtools" version))
               (sha256
                (base32
-                "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
+                "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji"))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2)) ; no Python 3 support
-    (inputs
-     `(("python-matplotlib" ,python2-matplotlib)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; See https://github.com/daler/pybedtools/issues/261
+         (add-after 'unpack 'disable-broken-tests
+           (lambda _
+             ;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a
+             ;; graphical environment.
+             (substitute* "pybedtools/test/test_scripts.py"
+               (("def test_venn_mpl")
+                "def _do_not_test_venn_mpl"))
+             ;; Requires internet access.
+             (substitute* "pybedtools/test/test_helpers.py"
+               (("def test_chromsizes")
+                "def _do_not_test_chromsizes"))
+             ;; FIXME: these two fail for no good reason.
+             (substitute* "pybedtools/test/test1.py"
+               (("def test_issue_157")
+                "def _do_not_test_issue_157")
+               (("def test_to_dataframe")
+                "def _do_not_test_to_dataframe"))
+             #t)))))
     (propagated-inputs
-     `(("bedtools" ,bedtools)
-       ("samtools" ,samtools)))
+     ;; Tests don't pass with Bedtools 2.27.1.
+     ;; See https://github.com/daler/pybedtools/issues/260
+     `(("bedtools" ,bedtools-2.26)
+       ("samtools" ,samtools)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-pysam" ,python-pysam)
+       ("python-pyyaml" ,python-pyyaml)))
     (native-inputs
-     `(("python-cython" ,python2-cython)
-       ("python-pyyaml" ,python2-pyyaml)
-       ("python-nose" ,python2-nose)))
+     `(("python-numpy" ,python-numpy)
+       ("python-pandas" ,python-pandas)
+       ("python-cython" ,python-cython)
+       ("python-nose" ,python-nose)
+       ("kentutils" ,kentutils) ; for bedGraphToBigWig
+       ("python-six" ,python-six)))
     (home-page "https://pythonhosted.org/pybedtools/")
     (synopsis "Python wrapper for BEDtools programs")
     (description
@@ -628,6 +653,36 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
 Python.")
     (license license:gpl2+)))
 
+(define-public python2-pybedtools
+  (let ((pkg (package-with-python2 python-pybedtools)))
+    (package (inherit pkg)
+      (arguments
+       `(#:modules ((ice-9 ftw)
+                    (srfi srfi-1)
+                    (srfi srfi-26)
+                    (guix build utils)
+                    (guix build python-build-system))
+         ;; See https://github.com/daler/pybedtools/issues/192
+         ,@(substitute-keyword-arguments (package-arguments pkg)
+             ((#:phases phases)
+              `(modify-phases ,phases
+                 (replace 'check
+                   (lambda _
+                     (let ((cwd (getcwd)))
+                       (setenv "PYTHONPATH"
+                               (string-append cwd "/build/"
+                                              (find (cut string-prefix? "lib" <>)
+                                                    (scandir (string-append cwd "/build")))
+                                              ":" (getenv "PYTHONPATH"))))
+                     ;; The tests need to be run from elsewhere...
+                     (mkdir-p "/tmp/test")
+                     (copy-recursively "pybedtools/test" "/tmp/test")
+                     (with-directory-excursion "/tmp/test"
+                       (invoke "nosetests"
+                               ;; This test fails for unknown reasons
+                               "--exclude=.*test_getting_example_beds"))
+                     #t))))))))))
+
 (define-public python-biom-format
   (package
    (name "python-biom-format")

From 8b4102b9038f394749463d002572a730a44b78ef Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 21:31:56 +0200
Subject: [PATCH 891/909] gnu: clipper: Update to 1.2.1.

* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Add fix-typo phase.
---
 gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++------------
 1 file changed, 18 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bb9bf00499..3f50ce0737 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1707,29 +1707,35 @@ databases.")
 (define-public clipper
   (package
     (name "clipper")
-    (version "1.1")
+    (version "1.2.1")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/YeoLab/clipper/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/YeoLab/clipper.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0pflmsvhbf8izbgwhbhj1i7349sw1f55qpqj8ljmapp16hb0p0qi"))
+                "0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb"))
               (modules '((guix build utils)))
               (snippet
                '(begin
                   ;; remove unnecessary setup dependency
                   (substitute* "setup.py"
                     (("setup_requires = .*") ""))
-                  (for-each delete-file
-                            '("clipper/src/peaks.so"
-                              "clipper/src/readsToWiggle.so"))
-                  (delete-file-recursively "dist/")
                   #t))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2)) ; only Python 2 is supported
+    (arguments
+     `(#:python ,python-2 ; only Python 2 is supported
+       #:phases
+       (modify-phases %standard-phases
+         ;; This is fixed in upstream commit
+         ;; f6c2990198f906bf97730d95695b4bd5a6d01ddb.
+         (add-after 'unpack 'fix-typo
+           (lambda _
+             (substitute* "clipper/src/readsToWiggle.pyx"
+               (("^sc.*") ""))
+             #t)))))
     (inputs
      `(("htseq" ,python2-htseq)
        ("python-pybedtools" ,python2-pybedtools)

From 95758e2faf7bb96d8df270d37bf71d52cbd4270c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 21:34:20 +0200
Subject: [PATCH 892/909] gnu: aragorn: Use invoke and simplify.

* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
---
 gnu/packages/bioinformatics.scm | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3f50ce0737..56a566f1ef 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -136,24 +136,23 @@
        (modify-phases %standard-phases
          (delete 'configure)
          (replace 'build
-                  (lambda _
-                    (zero? (system* "gcc"
-                                    "-O3"
-                                    "-ffast-math"
-                                    "-finline-functions"
-                                    "-o"
-                                    "aragorn"
-                                    (string-append "aragorn" ,version ".c")))))
+           (lambda _
+             (invoke "gcc"
+                     "-O3"
+                     "-ffast-math"
+                     "-finline-functions"
+                     "-o"
+                     "aragorn"
+                     (string-append "aragorn" ,version ".c"))
+             #t))
          (replace 'install
-                  (lambda* (#:key outputs #:allow-other-keys)
-                    (let* ((out (assoc-ref outputs "out"))
-                           (bin (string-append out "/bin"))
-                           (man (string-append out "/share/man/man1")))
-                      (mkdir-p bin)
-                      (install-file "aragorn" bin)
-                      (mkdir-p man)
-                      (install-file "aragorn.1" man))
-                    #t)))))
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man/man1")))
+               (install-file "aragorn" bin)
+               (install-file "aragorn.1" man))
+             #t)))))
     (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
     (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
     (description

From c793f4d8fb25044994b2694632c6d6f3d40b49b7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 22:03:02 +0200
Subject: [PATCH 893/909] gnu: bamm: Fetch from git and use INVOKE.

* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 56a566f1ef..4192a6c61b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -167,15 +167,16 @@ structure of the predicted RNA.")
     (name "bamm")
     (version "1.7.3")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
               ;; BamM is not available on pypi.
-              (uri (string-append
-                    "https://github.com/Ecogenomics/BamM/archive/"
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (uri (git-reference
+                    (url "https://github.com/Ecogenomics/BamM.git")
+                    (commit version)
+                    (recursive? #t)))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "1f35yxp4pc8aadsvbpg6r4kg2jh4fkjci0iby4iyljm6980sac0s"))
+                "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
               (modules '((guix build utils)))
               (snippet
                `(begin
@@ -197,11 +198,12 @@ structure of the predicted RNA.")
            (lambda _
              (with-directory-excursion "c"
                (let ((sh (which "sh")))
+                 (for-each make-file-writable (find-files "." ".*"))
                  ;; Use autogen so that 'configure' works.
                  (substitute* "autogen.sh" (("/bin/sh") sh))
                  (setenv "CONFIG_SHELL" sh)
-                 (substitute* "configure" (("/bin/sh") sh))
-                 (zero? (system* "./autogen.sh"))))))
+                 (invoke "./autogen.sh")))
+             #t))
          (delete 'build)
          ;; Run tests after installation so compilation only happens once.
          (delete 'check)
@@ -229,7 +231,8 @@ structure of the predicted RNA.")
              ;; There are 2 errors printed, but they are safe to ignore:
              ;; 1) [E::hts_open_format] fail to open file ...
              ;; 2) samtools view: failed to open ...
-             (zero? (system* "nosetests")))))))
+             (invoke "nosetests")
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)

From 337d72fb4410d0ed255b032ca55d2d9dd3dd3065 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 22:05:10 +0200
Subject: [PATCH 894/909] gnu: bedops: Use INVOKE.

* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4192a6c61b..ef1f1ae0c2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -367,9 +367,9 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
 
              ;; Unpack the tarballs to benefit from shebang patching.
              (with-directory-excursion "third-party"
-               (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
-                    (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
-                    (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
+               (invoke "tar" "xvf" "jansson-2.6.tar.bz2")
+               (invoke "tar" "xvf" "zlib-1.2.7.tar.bz2")
+               (invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2"))
              ;; Disable unpacking of tarballs in Makefile.
              (substitute* "system.mk/Makefile.linux"
                (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")

From f8b697a3855adbf583fedd970fe8bc3ab5a8d3f1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 22:17:44 +0200
Subject: [PATCH 895/909] gnu: bedops: Update to 2.4.35.

* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
---
 gnu/packages/bioinformatics.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef1f1ae0c2..a77eaead7e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -337,15 +337,16 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
 (define-public bedops
   (package
     (name "bedops")
-    (version "2.4.33")
+    (version "2.4.35")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/bedops/bedops/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/bedops/bedops.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
+                "0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f

From f45093429c8319475b22c5478ea6b719b7c97cb8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 22:22:28 +0200
Subject: [PATCH 896/909] gnu: blast+: Use INVOKE and return #T
 unconditionally.

* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
---
 gnu/packages/bioinformatics.scm | 59 ++++++++++++++++-----------------
 1 file changed, 28 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a77eaead7e..66e06869c4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1071,15 +1071,12 @@ package provides command line tools using the Bio++ library.")
        #:parallel-build? #f ; not supported
        #:phases
        (modify-phases %standard-phases
-         (add-before
-          'configure 'set-HOME
+         (add-before 'configure 'set-HOME
           ;; $HOME needs to be set at some point during the configure phase
           (lambda _ (setenv "HOME" "/tmp") #t))
-         (add-after
-          'unpack 'enter-dir
+         (add-after 'unpack 'enter-dir
           (lambda _ (chdir "c++") #t))
-         (add-after
-          'enter-dir 'fix-build-system
+         (add-after 'enter-dir 'fix-build-system
           (lambda _
             (define (which* cmd)
               (cond ((string=? cmd "date")
@@ -1127,31 +1124,31 @@ package provides command line tools using the Bio++ library.")
               (("action=/bin/") "action=")
               (("export PATH") ":"))
             #t))
-         (replace
-          'configure
-          (lambda* (#:key inputs outputs #:allow-other-keys)
-            (let ((out     (assoc-ref outputs "out"))
-                  (lib     (string-append (assoc-ref outputs "lib") "/lib"))
-                  (include (string-append (assoc-ref outputs "include")
-                                          "/include/ncbi-tools++")))
-              ;; The 'configure' script doesn't recognize things like
-              ;; '--enable-fast-install'.
-              (zero? (system* "./configure.orig"
-                              (string-append "--with-build-root=" (getcwd) "/build")
-                              (string-append "--prefix=" out)
-                              (string-append "--libdir=" lib)
-                              (string-append "--includedir=" include)
-                              (string-append "--with-bz2="
-                                             (assoc-ref inputs "bzip2"))
-                              (string-append "--with-z="
-                                             (assoc-ref inputs "zlib"))
-                              (string-append "--with-pcre="
-                                             (assoc-ref inputs "pcre"))
-                              ;; Each library is built twice by default, once
-                              ;; with "-static" in its name, and again
-                              ;; without.
-                              "--without-static"
-                              "--with-dll"))))))))
+         (replace 'configure
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out     (assoc-ref outputs "out"))
+                   (lib     (string-append (assoc-ref outputs "lib") "/lib"))
+                   (include (string-append (assoc-ref outputs "include")
+                                           "/include/ncbi-tools++")))
+               ;; The 'configure' script doesn't recognize things like
+               ;; '--enable-fast-install'.
+               (invoke "./configure.orig"
+                       (string-append "--with-build-root=" (getcwd) "/build")
+                       (string-append "--prefix=" out)
+                       (string-append "--libdir=" lib)
+                       (string-append "--includedir=" include)
+                       (string-append "--with-bz2="
+                                      (assoc-ref inputs "bzip2"))
+                       (string-append "--with-z="
+                                      (assoc-ref inputs "zlib"))
+                       (string-append "--with-pcre="
+                                      (assoc-ref inputs "pcre"))
+                       ;; Each library is built twice by default, once
+                       ;; with "-static" in its name, and again
+                       ;; without.
+                       "--without-static"
+                       "--with-dll")
+               #t))))))
     (outputs '("out"       ;  21 MB
                "lib"       ; 226 MB
                "include")) ;  33 MB

From 21c837405a7d46590fbe1d9e45e16a56f182e451 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 20 Oct 2018 23:04:02 +0200
Subject: [PATCH 897/909] gnu: bowtie: Update to 2.3.4.3.

* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
---
 gnu/packages/bioinformatics.scm | 41 ++++++++++++++++++---------------
 1 file changed, 22 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 66e06869c4..7c58ab2455 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1273,15 +1273,16 @@ errors at the end of reads.")
 (define-public bowtie
   (package
     (name "bowtie")
-    (version "2.3.2")
+    (version "2.3.4.3")
     (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
-                                  version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/BenLangmead/bowtie2.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90"))
+                "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1291,14 +1292,6 @@ errors at the end of reads.")
                     (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
                   #t))))
     (build-system gnu-build-system)
-    (inputs
-     `(("perl" ,perl)
-       ("perl-clone" ,perl-clone)
-       ("perl-test-deep" ,perl-test-deep)
-       ("perl-test-simple" ,perl-test-simple)
-       ("python" ,python-2)
-       ("tbb" ,tbb)
-       ("zlib" ,zlib)))
     (arguments
      '(#:make-flags
        (list "allall"
@@ -1308,11 +1301,21 @@ errors at the end of reads.")
        (modify-phases %standard-phases
          (delete 'configure)
          (replace 'check
-           (lambda* (#:key outputs #:allow-other-keys)
-             (zero? (system* "perl"
-                             "scripts/test/simple_tests.pl"
-                             "--bowtie2=./bowtie2"
-                             "--bowtie2-build=./bowtie2-build")))))))
+           (lambda _
+             (invoke "perl"
+                     "scripts/test/simple_tests.pl"
+                     "--bowtie2=./bowtie2"
+                     "--bowtie2-build=./bowtie2-build")
+             #t)))))
+    (inputs
+     `(("tbb" ,tbb)
+       ("zlib" ,zlib)
+       ("python" ,python-wrapper)))
+    (native-inputs
+     `(("perl" ,perl)
+       ("perl-clone" ,perl-clone)
+       ("perl-test-deep" ,perl-test-deep)
+       ("perl-test-simple" ,perl-test-simple)))
     (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
     (synopsis "Fast and sensitive nucleotide sequence read aligner")
     (description

From 617c478506888daea35dceeda3679196eb8a5177 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sun, 21 Oct 2018 22:31:56 +1000
Subject: [PATCH 898/909] gnu: python2-dendropy: Disable failing test.

* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
---
 gnu/packages/bioinformatics.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7c58ab2455..1e04081ceb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2063,7 +2063,21 @@ trees (phylogenies) and characters.")
     (license license:bsd-3)))
 
 (define-public python2-dendropy
-  (package-with-python2 python-dendropy))
+  (let ((base (package-with-python2 python-dendropy)))
+    (package
+      (inherit base)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'remove-failing-test
+             (lambda _
+               ;; This test fails when the full test suite is run, as documented
+               ;; at https://github.com/jeetsukumaran/DendroPy/issues/74
+               (substitute* "tests/test_dataio_nexml_reader_tree_list.py"
+                 (("test_collection_comments_and_annotations")
+                  "do_not_test_collection_comments_and_annotations"))
+               #t)))
+         ,@(package-arguments base))))))
 
 (define-public python-py2bit
   (package

From 2c17bd7b2955beef4130d11b33e07e4fb3b234dc Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 21 Oct 2018 12:06:13 +0300
Subject: [PATCH 899/909] gnu: kodi: Disable version checker.

Fixes bug#32997.

* gnu/packages/kodi.scm (kodi)[arguments]: Add substitution to remove
the version checking configuration option.
---
 gnu/packages/kodi.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 86ce914d53..21e7b12d3e 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -317,6 +317,11 @@ generator library for C++.")
                 (string-append (assoc-ref inputs "tzdata")
                                "/share/zoneinfo")))
 
+             ;; Don't phone home to check for updates.¬
+             (substitute* "system/addon-manifest.xml"¬
+               (("<addon optional=\\\"true\\\">service.xbmc.versioncheck</addon>")
+                ""))
+
              ;; Let's disable some tests that are known not to work here.
              ;; Doing this later while in the cmake "../build" directory
              ;; is trickier.

From 8eadc552029a6ec6385d28aaa687f0208aad26c3 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 20 Oct 2018 17:23:45 +0200
Subject: [PATCH 900/909] gnu: openal: Update to 1.19.1.

* gnu/packages/audio.scm (openal): Update to 1.19.1.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index ac41ed2dfe..5ec10b370e 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1910,7 +1910,7 @@ lv2-c++-tools.")
 (define-public openal
   (package
     (name "openal")
-    (version "1.19.0")
+    (version "1.19.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1918,7 +1918,7 @@ lv2-c++-tools.")
                     version ".tar.bz2"))
               (sha256
                (base32
-                "1mhf5bsb58s1xk6hvxl7ly7rd4rpl9z8h07xl1q94brywykg7bgi"))))
+                "1sdjhkz2gd6lbnwphi1b6aw3br4wv2lik5vnqh6mxfc8a7zqfbsw"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f  ; no check target

From 8941b4ab3d41ff2ca036c2ec6aa762fe78516c4b Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 20 Oct 2018 17:24:12 +0200
Subject: [PATCH 901/909] gnu: appstream-glib: Update to 0.7.14.

* gnu/packages/glib.scm (appstream-glib): Update to 0.7.14.
---
 gnu/packages/glib.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index 14d2a8b315..703cd3f74e 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -787,7 +787,7 @@ programming langauage.  It also contains the utility
 (define-public appstream-glib
   (package
     (name "appstream-glib")
-    (version "0.7.12")
+    (version "0.7.14")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://people.freedesktop.org/~hughsient/"
@@ -795,7 +795,7 @@ programming langauage.  It also contains the utility
                                   "appstream-glib-" version ".tar.xz"))
               (sha256
                (base32
-                "1jcb2bggcic3iczr2hn8zp8a3c2hl1xjij0aawr7kwqmzh9b3jms"))))
+                "0n0s99jmx2sx5895lcvmfjwa9r0f06i71495dpn9v9frz4asvk3d"))))
     (build-system meson-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)

From ab5e4be647613e7b3d741b4cabf682cc96514658 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 20 Oct 2018 17:24:34 +0200
Subject: [PATCH 902/909] gnu: libgphoto2: Update to 2.5.19.

* gnu/packages/photo.scm (libgphoto2): Update to 2.5.19.
---
 gnu/packages/photo.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm
index 7bdf04cb49..db7a9f9d45 100644
--- a/gnu/packages/photo.scm
+++ b/gnu/packages/photo.scm
@@ -131,14 +131,14 @@ data as produced by digital cameras.")
 (define-public libgphoto2
   (package
     (name "libgphoto2")
-    (version "2.5.18")
+    (version "2.5.19")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/gphoto/libgphoto/"
                                   version "/libgphoto2-" version ".tar.bz2"))
               (sha256
                (base32
-                "1v57ayp17j88bj79nl7rf4iyajbxx00kgb4l5k3kbv50gjfvh5sv"))))
+                "0qrcc6kajbfb237paxrl904vvwl7hd8mnqvjw00j6m5qwd93wlk2"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs

From 920de4286adb1b4afe2ce48bac1bbef57f1c2cba Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 20 Oct 2018 17:24:55 +0200
Subject: [PATCH 903/909] gnu: re2: Update to 2018-10-01.

* gnu/packages/regex.scm (re2): Update to 2018-10-01.
---
 gnu/packages/regex.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm
index c9d9e8a359..c05d819d65 100644
--- a/gnu/packages/regex.scm
+++ b/gnu/packages/regex.scm
@@ -29,7 +29,7 @@
 (define-public re2
    (package
      (name "re2")
-     (version "2018-09-01")
+     (version "2018-10-01")
      (home-page "https://github.com/google/re2")
      (source (origin
                (method url-fetch)
@@ -37,7 +37,7 @@
                (file-name (string-append name "-" version ".tar.gz"))
                (sha256
                 (base32
-                 "0hygr88hvy7if1i45m5r6x60zf73439j2fwzw7wwcw9gb01v690l"))))
+                 "10fsxsj3yip34hp2zl5rw8h2x2lgnp83fwrh7m0qfd9m99qrf4x3"))))
      (build-system gnu-build-system)
      (arguments
       `(#:modules ((guix build gnu-build-system)

From c8d62d936e23ed6c3aee0d7cbfca16e66e0de9cb Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 20 Oct 2018 17:36:13 +0200
Subject: [PATCH 904/909] gnu: libgxps: Propagate required inputs.

* gnu/packages/gnome.scm (libgxps)[inputs]: Move CAIRO, GLIB and LIBARCHIVE ...
[propagated-inputs]: ... here.  New field.
---
 gnu/packages/gnome.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 7b04716fa2..4251d5cf8f 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -412,13 +412,16 @@ access the common Google services, and has full asynchronous support.")
      `(("gobject-introspection" ,gobject-introspection)
        ("pkg-config" ,pkg-config)))
     (inputs
-     `(("cairo" ,cairo)
-       ("glib" ,glib)
-       ("libarchive" ,libarchive)
+     `(("gtk+" ,gtk+)
        ("libjpeg" ,libjpeg)
        ("lcms" ,lcms)
        ("libtiff" ,libtiff)
        ("nettle" ,nettle)))
+    (propagated-inputs
+     ;; In Requires of libgxps.pc.
+     `(("cairo" ,cairo)
+       ("glib" ,glib)
+       ("libarchive" ,libarchive)))
     (home-page "https://wiki.gnome.org/Projects/libgxps")
     (synopsis "GObject-based library for handling and rendering XPS documents")
     (description

From b6b3e5120ad3badba4f55af45b02667b662c1362 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sat, 20 Oct 2018 17:43:47 +0200
Subject: [PATCH 905/909] gnu: libgxps: Update to 0.3.0.

* gnu/packages/gnome.scm (libgxps): Update to 0.3.0.
[source](patches): Remove.
[build-system]: Switch to MESON-BUILD-SYSTEM.
[inputs]: Change LIBJPEG to LIBJPEG-TURBO.
* gnu/packages/patches/libgxps-CVE-2017-11590.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
---
 gnu/local.mk                                  |  1 -
 gnu/packages/gnome.scm                        |  9 ++--
 .../patches/libgxps-CVE-2017-11590.patch      | 48 -------------------
 3 files changed, 4 insertions(+), 54 deletions(-)
 delete mode 100644 gnu/packages/patches/libgxps-CVE-2017-11590.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 71aa115621..1c48fd3d6e 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -883,7 +883,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libgnome-encoding.patch			\
   %D%/packages/patches/libgnomeui-utf8.patch			\
   %D%/packages/patches/libgpg-error-aarch64-logging-fix.patch	\
-  %D%/packages/patches/libgxps-CVE-2017-11590.patch		\
   %D%/packages/patches/libffi-3.2.1-complex-alpha.patch		\
   %D%/packages/patches/libjxr-fix-function-signature.patch	\
   %D%/packages/patches/libjxr-fix-typos.patch			\
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 4251d5cf8f..7d2742f08d 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -397,23 +397,22 @@ access the common Google services, and has full asynchronous support.")
 (define-public libgxps
   (package
     (name "libgxps")
-    (version "0.2.5")
+    (version "0.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
                                   (version-major+minor version) "/"
                                   name "-" version ".tar.xz"))
-              (patches (search-patches "libgxps-CVE-2017-11590.patch"))
               (sha256
                (base32
-                "184r06s8g20cfigg7m169n42jjsc9wmzzlycr4g1fxxhr72r8x9y"))))
-    (build-system gnu-build-system)
+                "1bhgrpb6ndlp11qwr95g9piklmjcsca7bi04f8gy9ziipm1i6as1"))))
+    (build-system meson-build-system)
     (native-inputs
      `(("gobject-introspection" ,gobject-introspection)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("gtk+" ,gtk+)
-       ("libjpeg" ,libjpeg)
+       ("libjpeg" ,libjpeg-turbo)
        ("lcms" ,lcms)
        ("libtiff" ,libtiff)
        ("nettle" ,nettle)))
diff --git a/gnu/packages/patches/libgxps-CVE-2017-11590.patch b/gnu/packages/patches/libgxps-CVE-2017-11590.patch
deleted file mode 100644
index 9caa79b6f0..0000000000
--- a/gnu/packages/patches/libgxps-CVE-2017-11590.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-Fix CVE-2017-11590:
-
-https://bugzilla.gnome.org/show_bug.cgi?id=785479
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-11590
-
-Patch copied from upstream source repository:
-
-https://git.gnome.org/browse/libgxps/commit/?id=9d5d292055250ed298f3b89dc332d6db4003a031
-
-From 9d5d292055250ed298f3b89dc332d6db4003a031 Mon Sep 17 00:00:00 2001
-From: Marek Kasik <mkasik@redhat.com>
-Date: Wed, 26 Jul 2017 16:23:37 +0200
-Subject: archive: Check for pathname being NULL before dereferencing
-
-Check whether "archive_entry_pathname ()" returns a non-NULL pathname
-before using it to avoid a NULL pointer being dereferenced.
-
-https://bugzilla.gnome.org/show_bug.cgi?id=785479
----
- libgxps/gxps-archive.c | 5 ++++-
- 1 file changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/libgxps/gxps-archive.c b/libgxps/gxps-archive.c
-index acf8d7d..e763773 100644
---- a/libgxps/gxps-archive.c
-+++ b/libgxps/gxps-archive.c
-@@ -257,6 +257,7 @@ gxps_archive_initable_init (GInitable     *initable,
- 	GXPSArchive          *archive;
- 	ZipArchive           *zip;
- 	struct archive_entry *entry;
-+	const gchar          *pathname;
- 
- 	archive = GXPS_ARCHIVE (initable);
- 
-@@ -281,7 +282,9 @@ gxps_archive_initable_init (GInitable     *initable,
- 
-         while (gxps_zip_archive_iter_next (zip, &entry)) {
-                 /* FIXME: We can ignore directories here */
--                g_hash_table_add (archive->entries, g_strdup (archive_entry_pathname (entry)));
-+                pathname = archive_entry_pathname (entry);
-+                if (pathname != NULL)
-+                        g_hash_table_add (archive->entries, g_strdup (pathname));
-                 archive_read_data_skip (zip->archive);
-         }
- 
--- 
-cgit v0.12
-

From 9b6dc31b6d0fa56e005c928453a6bc72cff9ae73 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 21 Oct 2018 17:47:35 +0200
Subject: [PATCH 906/909] gnu: fluidsynth: Update to 2.0.1.

* gnu/packages/audio.scm (fluidsynth): Update to 2.0.1.
(fluidsynth-1): New public variable.
* gnu/packages/games.scm (gzdoom)[inputs]: Change FLUIDSYNTH to FLUIDSYNTH-1.
* gnu/packages/music.scm (lmms)[inputs]: Likewise.
---
 gnu/packages/audio.scm | 21 +++++++++++++++++++--
 gnu/packages/games.scm |  2 +-
 gnu/packages/music.scm |  2 +-
 3 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 5ec10b370e..a1745bb7a6 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2018 Brett Gilio <brettg@posteo.net>
+;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1041,7 +1042,7 @@ follower.")
 (define-public fluidsynth
   (package
     (name "fluidsynth")
-    (version "1.1.11")
+    (version "2.0.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1050,7 +1051,7 @@ follower.")
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0n75jq3xgq46hfmjkaaxz3gic77shs4fzajq40c8gk043i84xbdh"))))
+                "1mqyym5qkh8xd1rqj3yhfxbw5dxjcrljb6nkfqzvcarlv4h6rjn7"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f                      ; no check target
@@ -1082,6 +1083,22 @@ device.  It is the software analogue of a MIDI synthesizer.  FluidSynth can
 also play midifiles using a Soundfont.")
     (license license:lgpl2.1+)))
 
+;; gzdoom@3.3.0 and lmms@1.1.3 requires this version.  Remove once no longer
+;; needed.
+(define-public fluidsynth-1
+  (package
+    (inherit fluidsynth)
+    (version "1.1.11")
+    (source (origin
+              (inherit (package-source fluidsynth))
+              (uri (git-reference
+                    (url "https://github.com/FluidSynth/fluidsynth")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name "fluidsynth" version))
+              (sha256
+               (base32
+                "0n75jq3xgq46hfmjkaaxz3gic77shs4fzajq40c8gk043i84xbdh"))))))
+
 (define-public faad2
   (package
     (name "faad2")
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index c3067c5684..bb96bbe68a 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -5355,7 +5355,7 @@ You can save humanity and get programming skills!")
     (build-system cmake-build-system)
     (inputs `(("bzip2" ,bzip2)
               ("fluid-3" ,fluid-3)
-              ("fluidsynth" ,fluidsynth)
+              ("fluidsynth" ,fluidsynth-1)      ;XXX: try using 2.x when updating
               ("gtk+3" ,gtk+)
               ("libgme" ,libgme)
               ("libjpeg" ,libjpeg)
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 13a6ecc36f..cdd06647e1 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -3567,7 +3567,7 @@ are a C compiler and glib.  Full API documentation and examples are included.")
        ("fltk" ,fltk)
        ("libogg" ,libogg)
        ("libsamplerate" ,libsamplerate)
-       ("fluidsynth" ,fluidsynth)
+       ("fluidsynth" ,fluidsynth-1)         ;XXX: try using 2.x when updating
        ("libvorbis" ,libvorbis)
        ("alsa-lib" ,alsa-lib)
        ("portaudio" ,portaudio)

From 3a69b59332f02805fde2aee22b8f622c651f7007 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 21 Oct 2018 17:51:42 +0200
Subject: [PATCH 907/909] gnu: rng-tools: Update to 6.6.

* gnu/packages/linux.scm (rng-tools): Update to 6.6.
---
 gnu/packages/linux.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 6a89caf277..2aeddc2a34 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -3671,7 +3671,7 @@ The collection contains a set of bandwidth and latency benchmark such as:
   (package
     (name "rng-tools")
     (home-page "https://github.com/nhorman/rng-tools")
-    (version "6.5")
+    (version "6.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference (url home-page)
@@ -3679,7 +3679,7 @@ The collection contains a set of bandwidth and latency benchmark such as:
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "11kw1rcgzmgzwk7g1w2g0nzjraqb0pf24gxpy50k4ls2qxslw3rk"))))
+                "0c32sxfvngdjzfmxn5ngc5yxwi8ij3yl216nhzyz9r31qi3m14v7"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Avoid using OpenSSL, curl, and libxml2, reducing the closure by 166 MiB.

From ecc604baf0357fa32e5e0c983193573eab3cd9d3 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 19 Oct 2018 19:17:54 +0200
Subject: [PATCH 908/909] gnu: klick: Use scons-python2 for building.

* gnu/packages/music.scm (klick)[arguments]: Add #:scons.
---
 gnu/packages/music.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 13a6ecc36f..1bd9972862 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -718,6 +718,7 @@ audio and video).")
     (build-system scons-build-system)
     (arguments
      `(#:scons-flags (list (string-append "PREFIX=" %output))
+       #:scons ,scons-python2
        #:tests? #f)) ;no "check" target
     (inputs
      `(("boost" ,boost)

From e381ae317c054a8ac52037c3f0df72ca3c96b91f Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Fri, 19 Oct 2018 21:29:51 +0200
Subject: [PATCH 909/909] gnu: python2-bz2file: Inherit arguments from
 python-bzfile.

* gnu/packages/python.scm (python-bz2file)[properties]: Remove field.
(python2-bz2file): Use PACKAGE-WITH-PYTHON2.
---
 gnu/packages/python.scm | 17 ++---------------
 1 file changed, 2 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 63cf440014..c2987207f4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8806,23 +8806,10 @@ LDFLAGS and parse the output to build extensions with setup.py.")
 files.  It contains a drop-in replacement for the I/O interface in the
 standard library's @code{bz2} module, including features from the latest
 development version of CPython that are not available in older releases.")
-    (license license:asl2.0)
-    (properties `((python2-variant . ,(delay python2-bz2file))))))
+    (license license:asl2.0)))
 
 (define-public python2-bz2file
-  (let ((base (package-with-python2
-               (strip-python2-variant python-bz2file))))
-    (package
-      (inherit base)
-      (arguments
-       `(#:python ,python-2
-         #:phases
-         (modify-phases %standard-phases
-           ;; 'python setup.py test' does not work as of 0.98.
-           ;; There is only the one test file, so we run it directly.
-           (replace 'check
-                    (lambda _ (zero? (system* "python"
-                                              "test_bz2file.py"))))))))))
+  (package-with-python2 python-bz2file))
 
 (define-public python-future
   (package