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Merge branch 'master' into core-updates

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Marius Bakke 2018-11-09 17:02:08 +01:00
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6
doc/guix.texi
View File

@ -51,6 +51,7 @@ Copyright @copyright{} 2018 Mike Gerwitz@*
Copyright @copyright{} 2018 Pierre-Antoine Rouby@*
Copyright @copyright{} 2018 Gábor Boskovits@*
Copyright @copyright{} 2018 Florian Pelz@*
Copyright @copyright{} 2018 Laura Lazzati@*
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or
@ -354,6 +355,7 @@ configuration in a transactional, reproducible, and stateless fashion
(@pxref{System Configuration}).
@cindex functional package management
@cindex isolation
Under the hood, Guix implements the @dfn{functional package management}
discipline pioneered by Nix (@pxref{Acknowledgments}).
In Guix, the package build and installation process is seen
@ -387,6 +389,7 @@ garbage collection of packages (@pxref{Features}).
@chapter Installation
@cindex installing Guix
@cindex official website
GNU Guix is available for download from its website at
@url{http://www.gnu.org/software/guix/}. This section describes the
software requirements of Guix, as well as how to install it and get
@ -398,6 +401,8 @@ instead, you want to install the complete GNU operating system,
@pxref{System Installation}.
@cindex foreign distro
@cindex directories related to foreign distro
When installed on a running GNU/Linux system---thereafter called a
@dfn{foreign distro}---GNU@tie{}Guix complements the available tools
without interference. Its data lives exclusively in two directories,
@ -420,6 +425,7 @@ Once installed, Guix can be updated by running @command{guix pull}
@section Binary Installation
@cindex installing Guix from binaries
@cindex installer script
This section describes how to install Guix on an arbitrary system from a
self-contained tarball providing binaries for Guix and for all its
dependencies. This is often quicker than installing from source, which

2
gnu/local.mk
View File

@ -813,6 +813,7 @@ dist_patch_DATA = \
%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 \
%D%/packages/patches/hplip-remove-imageprocessor.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 \
@ -1230,7 +1231,6 @@ dist_patch_DATA = \
%D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch \
%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-detect512-all-arches.patch \
%D%/packages/patches/xboing-CVE-2004-0149.patch \
%D%/packages/patches/xf86-video-ark-remove-mibstore.patch \

446
gnu/packages/bioinformatics.scm
View File

@ -753,15 +753,15 @@ e.g. microbiome samples, genomes, metagenomes.")
(package
(inherit base)
(arguments
`(#:phases
(modify-phases %standard-phases
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
`(modify-phases ,phases
;; Do not require the unmaintained pyqi library.
(add-after 'unpack 'remove-pyqi
(lambda _
(substitute* "setup.py"
(("install_requires.append\\(\"pyqi\"\\)") "pass"))
#t)))
,@(package-arguments base))))))
#t)))))))))
(define-public bioperl-minimal
(let* ((inputs `(("perl-module-build" ,perl-module-build)
@ -2716,8 +2716,10 @@ Illumina, Roche 454, and the SOLiD platform.")
(string-append " strcpy(train_dir, \"" share "/train/\");"))))
#t))
(replace 'build
(lambda _ (and (zero? (system* "make" "clean"))
(zero? (system* "make" "fgs")))))
(lambda _
(invoke "make" "clean")
(invoke "make" "fgs")
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
@ -2734,21 +2736,24 @@ Illumina, Roche 454, and the SOLiD platform.")
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/"))
(frag (string-append bin "run_FragGeneScan.pl")))
(and (zero? (system* frag ; Test complete genome.
;; Test complete genome.
(invoke frag
"-genome=./example/NC_000913.fna"
"-out=./test2"
"-complete=1"
"-train=complete"))
(file-exists? "test2.faa")
"-train=complete")
(unless (and (file-exists? "test2.faa")
(file-exists? "test2.ffn")
(file-exists? "test2.gff")
(file-exists? "test2.out")
(zero? (system* ; Test incomplete sequences.
frag
(file-exists? "test2.out"))
(error "Expected files do not exist."))
;; Test incomplete sequences.
(invoke frag
"-genome=./example/NC_000913-fgs.ffn"
"-out=out"
"-complete=0"
"-train=454_30")))))))))
"-train=454_30")
#t))))))
(inputs
`(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3.
@ -3471,26 +3476,28 @@ VCF.")
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "lib/jni")
(mkdir-p "jdk-src")
(and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src"
"-xf" (assoc-ref inputs "jdk-src")))
(zero? (system* "javah" "-jni"
(invoke "tar" "--strip-components=1" "-C" "jdk-src"
"-xf" (assoc-ref inputs "jdk-src"))
(invoke "javah" "-jni"
"-classpath" "classes"
"-d" "lib/"
"net.sf.samtools.util.zip.IntelDeflater"))
"net.sf.samtools.util.zip.IntelDeflater")
(with-directory-excursion "src/c/inteldeflater"
(zero? (system* "gcc" "-I../../../lib" "-I."
(invoke "gcc" "-I../../../lib" "-I."
(string-append "-I" (assoc-ref inputs "jdk")
"/include/linux")
"-I../../../jdk-src/src/share/native/common/"
"-I../../../jdk-src/src/solaris/native/common/"
"-c" "-O3" "-fPIC" "IntelDeflater.c"))
(zero? (system* "gcc" "-shared"
"-c" "-O3" "-fPIC" "IntelDeflater.c")
(invoke "gcc" "-shared"
"-o" "../../../lib/jni/libIntelDeflater.so"
"IntelDeflater.o" "-lz" "-lstdc++"))))))
"IntelDeflater.o" "-lz" "-lstdc++"))
#t))
;; We can only build everything else after building the JNI library.
(add-after 'build-jni 'build-rest
(lambda* (#:key make-flags #:allow-other-keys)
(zero? (apply system* `("ant" "all" ,@make-flags)))))
(apply invoke `("ant" "all" ,@make-flags))
#t))
(add-before 'build 'set-JAVA6_HOME
(lambda _
(setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
@ -3977,16 +3984,16 @@ sequences).")
(define-public mash
(package
(name "mash")
(version "2.0")
(version "2.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/marbl/mash/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/marbl/mash.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
"049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
(modules '((guix build utils)))
(snippet
'(begin
@ -4011,9 +4018,7 @@ sequences).")
"src/mash/CommandScreen.cpp")
(("^#include \"kseq\\.h\"")
"#include \"htslib/kseq.h\""))
#t))
(add-after 'fix-includes 'autoconf
(lambda _ (zero? (system* "autoconf")))))))
#t)))))
(native-inputs
`(("autoconf" ,autoconf)
;; Capnproto and htslib are statically embedded in the final
@ -4040,13 +4045,14 @@ form of assemblies or reads.")
(version "2.12.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://bitbucket.org/berkeleylab/metabat.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
"0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
(patches (search-patches "metabat-fix-compilation.patch"))))
(build-system scons-build-system)
(arguments
@ -4109,16 +4115,16 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
(define-public minced
(package
(name "minced")
(version "0.2.0")
(version "0.3.2")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/ctSkennerton/minced/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/ctSkennerton/minced.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1"))))
"1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
@ -4230,12 +4236,13 @@ that a read originated from a particular isoform.")
(delete 'configure)
(replace 'check
;; There are no tests, so just test if it runs.
(lambda _ (zero? (system* "./muscle" "-version"))))
(lambda _ (invoke "./muscle" "-version") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(install-file "muscle" bin)))))))
(install-file "muscle" bin)
#t))))))
(home-page "http://www.drive5.com/muscle")
(synopsis "Multiple sequence alignment program")
(description
@ -4260,11 +4267,6 @@ program for nucleotide and protein sequences.")
(base32
"1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autoconf
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
(inputs
;; XXX: TODO: Enable Lua and Guile bindings.
;; https://github.com/tjunier/newick_utils/issues/13
@ -4309,19 +4311,20 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
(license license:lgpl3+)))
(define-public pplacer
(let ((commit "g807f6f3"))
(let ((commit "807f6f3"))
(package
(name "pplacer")
;; The commit should be updated with each version change.
(version "1.1.alpha19")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/matsen/pplacer/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/matsen/pplacer.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f"))))
(base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
(build-system ocaml-build-system)
(arguments
`(#:ocaml ,ocaml-4.01
@ -4338,11 +4341,12 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
(local-dir "cddlib_guix"))
(mkdir local-dir)
(with-directory-excursion local-dir
(system* "tar" "xvf" cddlib-src))
(invoke "tar" "xvf" cddlib-src))
(let ((cddlib-src-folder
(string-append local-dir "/"
(list-ref (scandir local-dir) 2)
"/lib-src")))
(for-each make-file-writable (find-files "cdd_src" ".*"))
(for-each
(lambda (file)
(copy-file file
@ -4406,8 +4410,7 @@ downstream analysis.")
(add-after 'unpack 'enter-scripts-dir
(lambda _ (chdir "scripts")))
(replace 'check
(lambda _
(zero? (system* "python" "-m" "unittest" "discover" "-v"))))
(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
(add-after 'install 'wrap-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -4667,13 +4670,14 @@ large-scale data and can be applied to hundreds of species at once.")
(version "2.0.7")
(source
(origin
(method url-fetch)
(uri (string-append "https://bitbucket.org/regulatorygenomicsupf/"
"pyicoteo/get/v" version ".tar.bz2"))
(file-name (string-append name "-" version ".tar.bz2"))
(method git-fetch)
(uri (git-reference
(url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa"))))
"0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; does not work with Python 3
@ -4757,10 +4761,11 @@ partial genes, and identifies translation initiation sites.")
(getenv "PATH")))
(setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
(getenv "PERL5LIB")))
(zero? (length (filter (lambda (file)
(for-each (lambda (file)
(display file)(display "\n")
(not (zero? (system* "perl" file))))
(find-files "t" ".*\\.t$"))))))
(invoke "perl" file))
(find-files "t" ".*\\.t$"))
#t))
(replace 'install
;; There is no 'install' target in the Makefile.
(lambda* (#:key outputs #:allow-other-keys)
@ -4849,18 +4854,17 @@ extremely diverse sets of genomes.")
(define-public raxml
(package
(name "raxml")
(version "8.2.10")
(version "8.2.12")
(source
(origin
(method url-fetch)
(uri
(string-append
"https://github.com/stamatak/standard-RAxML/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/stamatak/standard-RAxML.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
"1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests.
@ -5053,21 +5057,24 @@ distribution, coverage uniformity, strand specificity, etc.")
(modify-phases %standard-phases
(replace 'bootstrap
(lambda _
(invoke "bash" "gen_auto")))
(substitute* "gen_tools_am"
(("/usr/bin/env.*") (which "perl")))
(invoke "bash" "gen_auto")
#t))
(add-after 'build 'build-additional-tools
(lambda* (#:key make-flags #:allow-other-keys)
(every (lambda (dir)
(for-each (lambda (dir)
(with-directory-excursion (string-append "tools/" dir)
(zero? (apply system* "make" make-flags))))
dirs)))
(apply invoke "make" make-flags)))
dirs)
#t))
(add-after 'install 'install-additional-tools
(lambda* (#:key make-flags #:allow-other-keys)
(fold (lambda (dir result)
(for-each (lambda (dir)
(with-directory-excursion (string-append "tools/" dir)
(and result
(zero? (apply system*
`("make" ,@make-flags "install"))))))
#t dirs)))))))
(apply invoke `("make" ,@make-flags "install"))))
dirs)
#t))))))
(inputs
`(("gsl" ,gsl)
("boost" ,boost)
@ -5233,17 +5240,16 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
(define-public ngs-sdk
(package
(name "ngs-sdk")
(version "1.3.0")
(source
(origin
(method url-fetch)
(uri
(string-append "https://github.com/ncbi/ngs/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(version "2.9.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ncbi/ngs.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
"17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
@ -5259,9 +5265,10 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system* "./configure"
(invoke "./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" out))))))
(string-append "--prefix=" out))
#t)))
(add-after 'unpack 'enter-dir
(lambda _ (chdir "ngs-sdk") #t)))))
(native-inputs `(("perl" ,perl)))
@ -5299,23 +5306,24 @@ simultaneously.")
(define-public ncbi-vdb
(package
(name "ncbi-vdb")
(version "2.8.2")
(source
(origin
(method url-fetch)
(uri
(string-append "https://github.com/ncbi/ncbi-vdb/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(version "2.9.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ncbi/ncbi-vdb.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
"1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'make-files-writable
(lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
(add-before 'configure 'set-perl-search-path
(lambda _
;; Work around "dotless @INC" build failure.
@ -5349,8 +5357,7 @@ simultaneously.")
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system*
"./configure"
(invoke "./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug")
@ -5359,7 +5366,8 @@ simultaneously.")
(string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk"))
(string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5")))))))
(assoc-ref inputs "hdf5")))
#t)))
(add-after 'install 'install-interfaces
(lambda* (#:key outputs #:allow-other-keys)
;; Install interface libraries. On i686 the interface libraries
@ -5464,12 +5472,13 @@ subsequent visualization, annotation and storage of results.")
(version "1.90b4")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/chrchang/plink-ng/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/chrchang/plink-ng.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a"))))
(base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
@ -5551,14 +5560,14 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
(define-public preseq
(package
(name "preseq")
(version "2.0")
(version "2.0.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/smithlabcode/"
"preseq/archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(uri (string-append "https://github.com/smithlabcode/preseq/"
"releases/download/v" version
"/preseq_v" version ".tar.bz2"))
(sha256
(base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq"))
(base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
(modules '((guix build utils)))
(snippet '(begin
;; Remove bundled samtools.
@ -5648,17 +5657,17 @@ sequence itself can be retrieved from these databases.")
(define-public sra-tools
(package
(name "sra-tools")
(version "2.8.2-1")
(version "2.9.3")
(source
(origin
(method url-fetch)
(uri
(string-append "https://github.com/ncbi/sra-tools/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/ncbi/sra-tools.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g"))))
"0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
@ -5708,8 +5717,7 @@ sequence itself can be retrieved from these databases.")
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system*
"./configure"
(invoke "./configure"
(string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug")
@ -5727,18 +5735,7 @@ sequence itself can be retrieved from these databases.")
(string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk"))
(string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5"))))))
;; This version of sra-tools fails to build with glibc because of a
;; naming conflict. glibc-2.25/include/bits/mathcalls.h already
;; contains a definition of "canonicalize", so we rename it.
;;
;; See upstream bug report:
;; https://github.com/ncbi/sra-tools/issues/67
(add-after 'unpack 'patch-away-glibc-conflict
(lambda _
(substitute* "tools/bam-loader/bam.c"
(("canonicalize\\(" line)
(string-append "sra_tools_" line)))
(assoc-ref inputs "hdf5")))
#t)))))
(native-inputs `(("perl" ,perl)))
(inputs
@ -5865,24 +5862,16 @@ is one that takes arguments.")
(define-public seqtk
(package
(name "seqtk")
(version "1.2")
(version "1.3")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/lh3/seqtk/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/lh3/seqtk.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove extraneous header files, as is done in the seqtk
;; master branch.
(for-each (lambda (file) (delete-file file))
(list "ksort.h" "kstring.h" "kvec.h"))
#t))))
"1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@ -5890,11 +5879,12 @@ is one that takes arguments.")
(delete 'configure)
(replace 'check
;; There are no tests, so we just run a sanity check.
(lambda _ (zero? (system* "./seqtk" "seq"))))
(lambda _ (invoke "./seqtk" "seq") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(install-file "seqtk" bin)))))))
(install-file "seqtk" bin)
#t))))))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/lh3/seqtk")
@ -5910,20 +5900,20 @@ optionally compressed by gzip.")
(name "snap-aligner")
(version "1.0beta.18")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/amplab/snap/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/amplab/snap.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
"01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8"))))
(build-system gnu-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'check (lambda _ (zero? (system* "./unit_tests"))))
(replace 'check (lambda _ (invoke "./unit_tests") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -5952,14 +5942,14 @@ of these reads to align data quickly through a hash-based indexing scheme.")
(version "2.1b")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/biocore/sortmerna/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/biocore/sortmerna.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"))))
"0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf"))))
(build-system gnu-build-system)
(outputs '("out" ;for binaries
"db")) ;for sequence databases
@ -6205,8 +6195,7 @@ Cuffdiff or Ballgown programs.")
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
(lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
(propagated-inputs
`(("python-sqlalchemy" ,python2-sqlalchemy)
("python-decorator" ,python2-decorator)
@ -6839,17 +6828,17 @@ SELECT or UPDATE queries to an end-point.")
(define-public vsearch
(package
(name "vsearch")
(version "2.8.0")
(version "2.9.1")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/torognes/vsearch/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/torognes/vsearch.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
"0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
@ -6860,11 +6849,6 @@ SELECT or UPDATE queries to an end-point.")
(delete-file "src/city.cc")
#t))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
(inputs
`(("zlib" ,zlib)
("bzip2" ,bzip2)
@ -8874,13 +8858,14 @@ Sequences.")
(version "1.1.4")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/ManuSetty/SeqGL/"
"archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/ManuSetty/SeqGL.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
"1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
@ -9042,7 +9027,7 @@ AM_CONDITIONAL(AMPNG, true)"))
(("\\$\\(bindir\\)/embossupdate") ""))
#t))
(add-after 'disable-update-check 'autogen
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
(lambda _ (invoke "autoreconf" "-vif") #t)))))
(inputs
`(("perl" ,perl)
("libpng" ,libpng)
@ -9215,12 +9200,14 @@ group or two ChIP groups run under different conditions.")
(name "filevercmp")
(version (string-append "0-1." (string-take commit 7)))
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/ekg/filevercmp/archive/"
commit ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/filevercmp.git")
(commit commit)))
(file-name (git-file-name name commit))
(sha256
(base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
(base32
"1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests to run.
@ -9230,7 +9217,8 @@ group or two ChIP groups run under different conditions.")
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "filevercmp" bin)))))))
(install-file "filevercmp" bin)
#t))))))
(home-page "https://github.com/ekg/filevercmp")
(synopsis "This program compares version strings")
(description "This program compares version strings. It intends to be a
@ -11259,16 +11247,16 @@ sort, markdup, and depth.")
(define-public ritornello
(package
(name "ritornello")
(version "1.0.0")
(version "2.0.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/KlugerLab/"
"Ritornello/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/KlugerLab/Ritornello.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38"))))
"1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
@ -11277,7 +11265,7 @@ sort, markdup, and depth.")
(add-after 'unpack 'patch-samtools-references
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("src/SamStream.h"
"src/BufferedGenomeReader.h")
"src/FLD.cpp")
(("<sam.h>") "<samtools/sam.h>"))
#t))
(delete 'configure)
@ -11503,15 +11491,16 @@ applications for tackling some common problems in a user-friendly way.")
(define-public tadbit
(package
(name "tadbit")
(version "0.2")
(version "0.2.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/3DGenomes/TADbit/"
"archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/3DGenomes/TADbit.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f"))))
"07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
(build-system python-build-system)
(arguments
`(;; Tests are included and must be run after installation, but
@ -11566,13 +11555,14 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
(version "302.0.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/ENCODE-DCC/kentUtils/"
"archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/ENCODE-DCC/kentUtils.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
"0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
(modules '((guix build utils)
(srfi srfi-26)
(ice-9 ftw)))
@ -11623,6 +11613,8 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-permissions
(lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
(add-after 'unpack 'fix-paths
(lambda _
(substitute* "Makefile"
@ -11918,14 +11910,14 @@ accurate as existing quantification tools.")
(name "libgff")
(version "1.0")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/Kingsford-Group/"
"libgff/archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/Kingsford-Group/libgff.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
"0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps"))))
(build-system cmake-build-system)
(arguments `(#:tests? #f)) ; no tests included
(home-page "https://github.com/Kingsford-Group/libgff")
@ -11970,14 +11962,14 @@ bytes of memory space, where n is the length of the string.")
(name "sailfish")
(version "0.10.1")
(source (origin
(method url-fetch)
(uri
(string-append "https://github.com/kingsfordgroup/"
"sailfish/archive/v" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/kingsfordgroup/sailfish.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
"1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
(modules '((guix build utils)))
(snippet
'(begin
@ -12025,7 +12017,7 @@ bytes of memory space, where n is the length of the string.")
(include "external/install/include/rapmap/")
(rapmap (assoc-ref inputs "rapmap")))
(mkdir-p "/tmp/rapmap")
(system* "tar" "xf"
(invoke "tar" "xf"
(assoc-ref inputs "rapmap")
"-C" "/tmp/rapmap"
"--strip-components=1")

5
gnu/packages/c.scm
View File

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
@ -160,8 +160,7 @@ standard.")
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(zero? (system* "make" "-C" "cc/cpp" "test")))))))
(lambda _ (invoke "make" "-C" "cc/cpp" "test") #t)))))
(native-inputs
`(("bison" ,bison)
("flex" ,flex)))

6
gnu/packages/cups.scm
View File

@ -391,9 +391,13 @@ device-specific programs to convert and print many types of files.")
(base32
"0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290"))
(modules '((guix build utils)))
(patches (search-patches "hplip-remove-imageprocessor.patch"))
(snippet
;; Fix type mismatch.
'(begin
;; Delete non-free blobs
(for-each delete-file (find-files "." "\\.so$"))
(delete-file "prnt/hpcups/ImageProcessor.h")
;; Fix type mismatch.
(substitute* "prnt/hpcups/genPCLm.cpp"
(("boolean") "bool"))
#t))))

4
gnu/packages/databases.scm
View File

@ -848,14 +848,14 @@ pictures, sounds, or video.")
(package
(inherit postgresql)
(name "postgresql")
(version "9.6.9")
(version "9.6.11")
(source (origin
(method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2"))
(sha256
(base32
"0biy8j69dbvdmrag55pdszpc0702agzqhhcwdx21xp02mzim4ydr"))))))
"0c55akrkzqd6p6a8hr0338wk246hl76r9j16p4zn3s51d7f0l99q"))))))
(define-public python-pymysql
(package

75
gnu/packages/emacs.scm
View File

@ -12463,3 +12463,78 @@ correctly.")
@item helm-slime-repl-history: Select an input from the SLIME REPL history and insert it.
@end itemize\n")
(license license:gpl3+))))
(define-public emacs-clang-format
(let ((commit "5556c31528af2661bed3011bd63ffc0ed44e18a0"))
(package
(name "emacs-clang-format")
(version (git-version "0.0.0" "1" commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/emacsorphanage/clang-format")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0ynvnp3vrcpngmwakb23xv4xn7jbkg43s196q7pg9nkl13x4n2nq"))))
(build-system emacs-build-system)
(inputs
`(("clang" ,clang)))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'configure
(lambda* (#:key inputs #:allow-other-keys)
(let ((clang (assoc-ref inputs "clang")))
;; Repo is read-only.
(chmod "clang-format.el" #o644)
(emacs-substitute-variables "clang-format.el"
("clang-format-executable"
(string-append clang "/bin/clang-format"))))
#t)))))
(home-page "https://github.com/emacsorphanage/clang-format")
(synopsis "Format code using clang-format")
(description "This package allows to filter code through clang-format to
fix its formatting. @command{clang-format} is a tool that formats C/C++/Obj-C
code according to a set of style options, see
@url{http://clang.llvm.org/docs/ClangFormatStyleOptions.html}.")
(license license:gpl3+))))
(define-public emacs-gtk-look
(package
(name "emacs-gtk-look")
(version "29")
(source (origin
(method url-fetch)
(uri "https://download.tuxfamily.org/user42/gtk-look.el")
(sha256
(base32
"14p2nwrd51cr1v06fxbjjn6jdrkf9d6vcxhmscm0kl677s25ypsp"))))
(build-system emacs-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'configure
(lambda _
;; File is read-only.
(chmod "gtk-look.el" #o644)
(emacs-substitute-variables "gtk-look.el"
("gtk-lookup-devhelp-indices"
'(list (expand-file-name "~/.guix-profile/share/gtk-doc/html/*/*.devhelp*"))))
#t)))))
(home-page "http://user42.tuxfamily.org/gtk-look/index.html")
(synopsis "Find and display HTML documentation for GTK, GNOME and Glib")
(description "@command{gtk-look} finds and displays HTML documentation for
GTK, GNOME and Glib functions and variables in Emacs, similar to what
info-lookup-symbol does for info files (C-h S). The documentation is expected
to be devhelp indexes with HTML files. The location of the indexes can be
customized. In addition to C code development @command{gtk-look} is good for
@itemize
@item @command{perl-gtk2}, recognising class funcs like
@command{Gtk2::Label->new} and bare method names like @command{set_text}.
@item @command{guile-gnome}, recognising methods like @command{set-text} and
classes like @command{<gtk-window>}.
@end itemize\n")
(license license:gpl3+)))

27
gnu/packages/gtk.scm
View File

@ -1632,6 +1632,33 @@ it does not deal with windowing system surfaces, drawing, scene graphs, or
input.")
(license license:expat)))
(define-public spread-sheet-widget
(package
(name "spread-sheet-widget")
(version "0.3")
(source
(origin
(method url-fetch)
(uri (string-append "https://alpha.gnu.org/gnu/ssw/"
name "-" version ".tar.gz"))
(sha256
(base32 "1h93yyh2by6yrmkwqg38nd5knids05k5nqzcihc1hdwgzg3c4b8y"))))
(build-system gnu-build-system)
(native-inputs
`(("glib" ,glib "bin") ; for glib-genmarshal, etc.
("pkg-config" ,pkg-config)))
;; In 'Requires' of spread-sheet-widget.pc.
(propagated-inputs
`(("glib" ,glib)
("gtk+" ,gtk+)))
(home-page "https://www.gnu.org/software/ssw/")
(synopsis "Gtk+ widget for dealing with 2-D tabular data")
(description
"GNU Spread Sheet Widget is a library for Gtk+ which provides a widget for
viewing and manipulating 2 dimensional tabular data in a manner similar to many
popular spread sheet programs.")
(license license:gpl3+)))
(define-public yad
(package
(name "yad")

6
gnu/packages/guile.scm
View File

@ -2246,8 +2246,8 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
;; There has not been any release yet.
(define-public guile-newt
(let ((commit "596ad760bee1be419d71271732f0f30eaee55143")
(revision "0"))
(let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")
(revision "1"))
(package
(name "guile-newt")
(version (string-append "0-" revision "." (string-take commit 9)))
@ -2259,7 +2259,7 @@ tracker's SOAP service, such as @url{https://bugs.gnu.org}.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"18qqbi0bc7vp2vlrhib3p3wwgn7wrlv5728dn0avirhw4fxxivnf"))))
"0ww7jbdsmjlsxm60ym6cb5s5kc4ljz8bn4y2lvcqnap0aihqfk10"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags

70
gnu/packages/kodi.scm
View File

@ -3,6 +3,7 @@
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -48,6 +49,7 @@
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
#:use-module (gnu packages gperf)
#:use-module (gnu packages groff)
#:use-module (gnu packages gnunet)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages image)
@ -62,6 +64,7 @@
#:use-module (gnu packages python)
#:use-module (gnu packages samba)
#:use-module (gnu packages sdl)
#:use-module (gnu packages serialization)
#:use-module (gnu packages ssh)
#:use-module (gnu packages swig)
#:use-module (gnu packages textutils)
@ -75,11 +78,12 @@
#:use-module (gnu packages assembly))
(define-public crossguid
(let ((commit "8f399e8bd4252be9952f3dfa8199924cc8487ca4"))
(let ((commit "fef89a4174a7bf8cd99fa9154864ce9e8e3bf989")
(revision "2"))
(package
(name "crossguid")
(version (string-append "0.0-1." (string-take commit 7)))
;; There's no official release. Just a Git repository.
(version (string-append "0.0-" revision "." (string-take commit 7)))
;; This is the commit that Kodi wants.
(source (origin
(method git-fetch)
(uri (git-reference
@ -88,13 +92,12 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1i29y207qqddvaxbn39pk2fbh3gx8zvdprfp35wasj9rw2wjk3s9"))))
"1blrkc7zcqrqcr5msvhyhm98s2jvm9hr0isqs4288q2r4mdnrfq0"))))
(build-system gnu-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
;; There's no build system here, so we have to do it ourselves.
(replace 'build
(lambda _
(invoke "g++" "-c" "guid.cpp" "-o" "guid.o"
@ -129,7 +132,7 @@ generator library for C++.")
;; of the standard build process. To make things easier, we bootstrap
;; and patch shebangs here, so we don't have to worry about it later.
(define libdvdnav/kodi
(let ((commit "6.0.0-Leia-Alpha-1"))
(let ((commit "6.0.0-Leia-Alpha-3"))
(package
(name "libdvdnav-bootstrapped")
(version commit)
@ -141,7 +144,7 @@ generator library for C++.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1xiyfgf8v8aknlxlzsvk6pbzkhclz0hbh3s1b0w6ivkng2k310j9"))))
"0qwlf4lgahxqxk1r2pzl866mi03pbp7l1fc0rk522sc0ak2s9jhb"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
@ -164,7 +167,7 @@ generator library for C++.")
(license license:gpl2+))))
(define libdvdread/kodi
(let ((commit "6.0.0-Leia-Alpha-1"))
(let ((commit "6.0.0-Leia-Alpha-3"))
(package
(name "libdvdread-bootstrapped")
(version commit)
@ -176,7 +179,7 @@ generator library for C++.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1c3g18n2vwhgcfz3dka1pmw58bnv2ram7xjvizfiykb3sgi9zfwp"))))
"1xxn01mhkdnp10cqdr357wx77vyzfb5glqpqyg8m0skyi75aii59"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
@ -199,7 +202,7 @@ generator library for C++.")
(license (list license:gpl2+ license:lgpl2.1+)))))
(define libdvdcss/kodi
(let ((commit "1.4.1-Leia-Alpha-1"))
(let ((commit "1.4.2-Leia-Beta-5"))
(package
(name "libdvdcss-bootstrapped")
(version commit)
@ -211,7 +214,7 @@ generator library for C++.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0adafwsawxssj3nilkql447v0l4a2584rdpmy5rfjmznh91lykgh"))))
"0j41ydzx0imaix069s3z07xqw9q95k7llh06fc27dcn6f7b8ydyl"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
@ -233,28 +236,53 @@ generator library for C++.")
(description (package-description libdvdcss))
(license license:gpl2+))))
(define-public fstrcmp
(package
(name "fstrcmp")
(version "0.7.D001")
(source
(origin
(method url-fetch)
(uri (string-append "http://fstrcmp.sourceforge.net/fstrcmp-"
version ".tar.gz"))
(sha256
(base32
"0xilghiy3mz78bjmfldi39qyy7jvw5b6wafsx370lw401y2qw0g4"))))
(build-system gnu-build-system)
(home-page "http://fstrcmp.sourceforge.net/")
(arguments
'(#:configure-flags '("SH=sh")))
(native-inputs
`(("ghostscript" ,ghostscript) ; ps2pdf
("groff" ,groff)
("libtool" ,libtool)
("which" ,which)))
(synopsis "fuzzy comparison of strings")
(description
"The fstrcmp project provides a library that is used to make fuzzy
comparisons of strings and byte arrays, including multi-byte character strings.
This can be useful in error messages, enabling the suggestion of likely valid
alternatives. In compilers, this can reduce the cascade of secondary errors.")
(license license:gpl3+)))
(define-public kodi
;; We package the git version because the current released
;; version was cut while the cmake transition was in turmoil.
(let ((commit "ec16dbca4dcf2923f53f819695a6d47c52e68d74")
(revision "8"))
(package
(name "kodi")
(version (git-version "18.0_alpha" revision commit))
(version "18.0b5")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/xbmc/xbmc.git")
(commit commit)))
(commit (string-append version "-Leia"))))
(file-name (git-file-name name version))
(sha256
(base32
"1rxg752cl59124cfpfwmyjldn6qpq5jginxddpzvgagfadf10i4d"))
"042qzvhys3sajby6ywgmrsymhji37qk0iqgppznrvm53vrizwsam"))
(snippet
'(begin
(use-modules (guix build utils))
(for-each delete-file-recursively
'("project/BuildDependencies/bin/"
'("project/BuildDependencies/"
;; TODO: Purge these jars.
;;"tools/codegenerator/groovy"
;; And these sources:
@ -370,10 +398,12 @@ generator library for C++.")
("eudev" ,eudev)
("ffmpeg" ,ffmpeg)
("flac" ,flac)
("flatbuffers" ,flatbuffers)
("fmt" ,fmt)
("fontconfig" ,fontconfig)
("freetype" ,freetype)
("fribidi" ,fribidi)
("fstrcmp" ,fstrcmp)
("giflib" ,giflib)
("glew" ,glew)
("gnutls" ,gnutls)
@ -427,7 +457,7 @@ plug-in system.")
license:expat ;cpluff, dbwrappers
license:public-domain ;cpluff/examples
license:bsd-3 ;misc, gtest
license:bsd-2))))) ;xbmc/freebsd
license:bsd-2)))) ;xbmc/freebsd
(define-public kodi-cli
(let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for

10
gnu/packages/maths.scm
View File

@ -2763,18 +2763,16 @@ point numbers.")
(define-public wxmaxima
(package
(name "wxmaxima")
(version "18.02.0")
(version "18.10.1")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/andrejv/" name "/archive"
"/Version-" version ".tar.gz"))
(uri (string-append "https://github.com/wxMaxima-developers/" name
"/archive/Version-" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
(patches
(search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
"0c2blq65r0am509p3rjqpwqk6vl5r2yg1p9nh2jczf80vhi3ldas"))))
(build-system cmake-build-system)
(native-inputs
`(("gettext" ,gettext-minimal)))

53
gnu/packages/music.scm
View File

@ -309,29 +309,27 @@ playing your music.")
(name "cmus")
(version "2.7.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/" name "/" name "/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/cmus/cmus.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0raixgjavkm7hxppzsc5zqbfbh2bhjcmbiplhnsxsmyj8flafyc1"))))
"0xd96py21bl869qlv1353zw7xsgq6v5s8szr0ldr63zj5fgc2ps5"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; cmus does not include tests
#:phases
(modify-phases %standard-phases
(replace
'configure
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; It's an idiosyncratic configure script that doesn't
;; understand --prefix=..; it wants prefix=.. instead.
(zero?
(system* "./configure"
(string-append "prefix=" out)))))))))
(invoke "./configure"
(string-append "prefix=" out))
#t))))))
;; TODO: cmus optionally supports the following formats, which haven't yet
;; been added to Guix:
;;
@ -1144,14 +1142,14 @@ your own lessons.")
(name "powertabeditor")
(version "2.0.0-alpha10")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/powertab/powertabeditor/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(method git-fetch)
(uri (git-reference
(url "https://github.com/powertab/powertabeditor.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1fr14ql0yhlqvh6y08yaanszm2nvca5i50rqym396kfvga3ky18x"))
"1z4fhdp71ck9synr12rg1p6365xnypd8ih40c5icj4si36khvksk"))
(modules '((guix build utils)))
(snippet
'(begin
@ -1185,14 +1183,14 @@ add_library( rapidjson INTERFACE IMPORTED )"))
(modify-phases %standard-phases
(replace 'check
(lambda _
(zero? (system* "bin/pte_tests"
(invoke "bin/pte_tests"
;; FIXME: these tests fail
"exclude:Actions/EditStaff"
"exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
"exclude:Score/ViewFilter/FilterRule"
"exclude:Score/ViewFilter/ViewFilter"
"exclude:Formats/PowerTabOldImport/Directions"
))))
"exclude:Formats/PowerTabOldImport/Directions")
#t))
;; FIXME: This bug has been fixed upstream, but no release has been
;; made yet. See https://github.com/powertab/powertabeditor/issues/257
(add-after 'unpack 'fix-boost-bug
@ -1751,9 +1749,7 @@ export.")
(lambda _
(substitute* "tcl/pd-gui.tcl"
(("exec wish ") (string-append "exec " (which "wish8.6") " ")))
#t))
(add-after 'unpack 'autoconf
(lambda _ (zero? (system* "bash" "./autogen.sh")))))))
#t)))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
@ -4071,14 +4067,15 @@ ISRCs and the MCN (=UPC/EAN) from disc.")
(base32
"0ikb9igyyk28jm34raxfzkw2qyn4nzzwsymdyprp7cmvi6g2ajb7"))))
(build-system cmake-build-system)
(arguments `(#:phases
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(and
;; requires network connections
;; (zero? (system* "tests/mbtest"))
(zero? (system* "tests/ctest"))))))))
;; (invoke "tests/mbtest")
(invoke "tests/ctest")
#t)))))
(inputs `(("neon" ,neon)
("libxml2" ,libxml2)))
(native-inputs `(("pkg-config" ,pkg-config)))

232
gnu/packages/patches/hplip-remove-imageprocessor.patch 100644
View File

@ -0,0 +1,232 @@
This patch is based heavily on the Debian patch.
https://salsa.debian.org/printing-team/hplip/raw/debian/3.18.10+dfsg0-1/debian/patches/0025-Remove-all-ImageProcessor-functionality-which-is-clo.patch
---
Makefile.am | 22 +++-------------------
Makefile.in | 33 +++++----------------------------
prnt/hpcups/HPCupsFilter.cpp | 21 ---------------------
3 files changed, 8 insertions(+), 68 deletions(-)
diff --git a/Makefile.am b/Makefile.am
index ef6480f..ecada5c 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -166,7 +166,7 @@ if !HPLIP_CLASS_DRIVER
dist_hplip_SCRIPTS = hpssd.py __init__.py hpdio.py
endif #HPLIP_CLASS_DRIVER
-dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
+dist_noinst_DATA += prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
dist_noinst_SCRIPTS += dat2drv.py install.py hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
if !HPLIP_CLASS_DRIVER
@@ -590,11 +590,10 @@ hpcups_SOURCES = prnt/hpcups/HPCupsFilter.cpp prnt/hpcups/HPCupsFilter.h prnt/hp
prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
prnt/hpcups/genPCLm.h \
common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
- prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
- prnt/hpcups/ImageProcessor.h
+ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
-hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
+hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
#else
#hpcupsdir = $(cupsfilterdir)
#hpcups_PROGRAMS = hpcups
@@ -679,21 +678,10 @@ printpluginsdir=$(cupsfilterdir)
dist_filter_DATA = hpcups hpps dat2drv
-dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
endif #HPLIP_CLASS_DRIVER
install-data-hook:
if HPLIP_BUILD
- if [ \( "$(UNAME)" = "x86_64" -a -d "$(libdir)/" \) ]; then \
- cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
- chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
- ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
- fi; \
- if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
- cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
- chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
- ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
- fi
if !HPLIP_CLASS_DRIVER
# If scanner build, add hpaio entry to sane dll.conf.
if [ "$(scan_build)" = "yes" ]; then \
@@ -874,10 +862,6 @@ if HPLIP_CLASS_DRIVER
rm -rf $(distdir)/setup.py
rm -rf $(distdir)/systray.py
rm -rf $(distdir)/timedate.py
- rm -rf $(distdir)/prnt/plugins/lj-arm32.so
- rm -rf $(distdir)/prnt/plugins/lj-arm64.so
- rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
- rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
rm -rf $(distdir)/hpijs-drv
rm -rf $(distdir)/prnt/hpcups/
rm -rf $(distdir)/prnt/ps/
diff --git a/Makefile.in b/Makefile.in
index 910a268..cd44203 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -103,7 +103,7 @@ DIST_COMMON = $(am__configure_deps) \
# ip library
@HPLIP_BUILD_TRUE@am__append_12 = libhpip.la
-@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template prnt/hpcups/libImageProcessor-x86_64.so prnt/hpcups/libImageProcessor-x86_32.so
+@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_13 = prnt/drv/hpijs.drv.in.template prnt/drv/hpcups.drv.in.template
@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@am__append_14 = dat2drv.py install.py hplip-install init-suse-firewall init-iptables-firewall class_rpm_build.sh hplipclassdriver.spec createPPD.sh Makefile_dat2drv hpijs-drv
@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@am__append_15 = scan/sane/hpaio.desc \
@FULL_BUILD_TRUE@@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@ installer/text_install.py \
@@ -500,8 +500,7 @@ am__hpcups_SOURCES_DIST = prnt/hpcups/HPCupsFilter.cpp \
prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
prnt/hpcups/genPCLm.h common/utils.c common/utils.h \
prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
- prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
- prnt/hpcups/ImageProcessor.h
+ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
@HPCUPS_INSTALL_TRUE@am_hpcups_OBJECTS = \
@HPCUPS_INSTALL_TRUE@ hpcups-HPCupsFilter.$(OBJEXT) \
@HPCUPS_INSTALL_TRUE@ hpcups-dbuscomm.$(OBJEXT) \
@@ -723,8 +722,7 @@ am__dist_locatedriver_DATA_DIST = locatedriver
am__dist_models_DATA_DIST = data/models/models.dat
am__dist_noinst_DATA_DIST = prnt/drv/hpijs.drv.in.template \
prnt/drv/hpcups.drv.in.template \
- prnt/hpcups/libImageProcessor-x86_64.so \
- prnt/hpcups/libImageProcessor-x86_32.so scan/sane/hpaio.desc \
+ scan/sane/hpaio.desc \
installer/text_install.py data/localization/hplip_de.ts \
data/localization/hplip_es.ts data/localization/hplip_fr.ts \
data/localization/hplip_it.ts data/localization/hplip_pt.ts \
@@ -1932,11 +1930,6 @@ am__dist_ppd_DATA_DIST = prnt/ps/hp-designjet_z6810ps_42in-ps.ppd.gz \
ppd/classppd/ps/hp-postscript-inkjet.ppd.gz \
ppd/classppd/ps/hp-postscript-laserjet-pro.ppd.gz \
ppd/classppd/ps/hp-postscript-laserjet.ppd.gz
-am__dist_printplugins_DATA_DIST = prnt/plugins/hbpl1-arm32.so \
- prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so \
- prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so \
- prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so \
- prnt/plugins/lj-x86_64.so
am__dist_prnt_DATA_DIST = prnt/cups.py prnt/__init__.py prnt/ldl.py \
prnt/pcl.py prnt/colorcal.py
am__dist_rules_DATA_DIST = data/rules/56-hpmud.rules \
@@ -4665,11 +4658,10 @@ libapdk_la_CFLAGS = $(libapdk_la_CXXFLAGS) -Iprnt/hpijs
@HPCUPS_INSTALL_TRUE@ prnt/hpcups/flate_colorspace.h prnt/hpcups/RunLenEncoding.h prnt/hpcups/common_defines.h \
@HPCUPS_INSTALL_TRUE@ prnt/hpcups/genPCLm.h \
@HPCUPS_INSTALL_TRUE@ common/utils.c common/utils.h prnt/hpcups/Hbpl1_Wrapper.cpp prnt/hpcups/genPCLm.cpp \
-@HPCUPS_INSTALL_TRUE@ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp \
-@HPCUPS_INSTALL_TRUE@ prnt/hpcups/ImageProcessor.h
+@HPCUPS_INSTALL_TRUE@ prnt/hpcups/genJPEGStrips.cpp prnt/hpcups/RunLenEncoding.cpp
@HPCUPS_INSTALL_TRUE@hpcups_CXXFLAGS = $(APDK_ENDIAN_FLAG) $(DBUS_CFLAGS)
-@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lImageProcessor -lcups -lcupsimage -lz $(DBUS_LIBS)
+@HPCUPS_INSTALL_TRUE@hpcups_LDADD = -L./prnt/hpcups/ -ljpeg -ldl -lcups -lcupsimage -lz $(DBUS_LIBS)
#else
#hpcupsdir = $(cupsfilterdir)
#hpcups_PROGRAMS = hpcups
@@ -4717,7 +4709,6 @@ ppddir = $(hpppddir)
@HPLIP_CLASS_DRIVER_TRUE@filterdir = $(cupsfilterdir)
@HPLIP_CLASS_DRIVER_TRUE@printpluginsdir = $(cupsfilterdir)
@HPLIP_CLASS_DRIVER_TRUE@dist_filter_DATA = hpcups hpps dat2drv
-@HPLIP_CLASS_DRIVER_TRUE@dist_printplugins_DATA = prnt/plugins/hbpl1-arm32.so prnt/plugins/hbpl1-arm64.so prnt/plugins/hbpl1-x86_32.so prnt/plugins/hbpl1-x86_64.so prnt/plugins/lj-arm32.so prnt/plugins/lj-arm64.so prnt/plugins/lj-x86_32.so prnt/plugins/lj-x86_64.so
all: all-am
.SUFFIXES:
@@ -9380,16 +9371,6 @@ uninstall-am: uninstall-apparmor_abstractionDATA \
install-data-hook:
-@HPLIP_BUILD_TRUE@ if [ \( "$(UNAME)" = "x86_64" -a -d "$(libdir)/" \) ]; then \
-@HPLIP_BUILD_TRUE@ cp prnt/hpcups/libImageProcessor-x86_64.so $(libdir)/ ; \
-@HPLIP_BUILD_TRUE@ chmod 775 $(libdir)/libImageProcessor-x86_64.so ; \
-@HPLIP_BUILD_TRUE@ ln -sf $(libdir)/libImageProcessor-x86_64.so $(libdir)/libImageProcessor.so ; \
-@HPLIP_BUILD_TRUE@ fi; \
-@HPLIP_BUILD_TRUE@ if [ \( \( "$(UNAME)" = "i686" -o "$(UNAME)" = "i386" \) -a -d "$(libdir)/" \) ]; then \
-@HPLIP_BUILD_TRUE@ cp prnt/hpcups/libImageProcessor-x86_32.so $(libdir)/ ; \
-@HPLIP_BUILD_TRUE@ chmod 775 $(libdir)/libImageProcessor-x86_32.so ; \
-@HPLIP_BUILD_TRUE@ ln -sf $(libdir)/libImageProcessor-x86_32.so $(libdir)/libImageProcessor.so ; \
-@HPLIP_BUILD_TRUE@ fi
# If scanner build, add hpaio entry to sane dll.conf.
@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@ if [ "$(scan_build)" = "yes" ]; then \
@HPLIP_BUILD_TRUE@@HPLIP_CLASS_DRIVER_FALSE@ $(mkinstalldirs) $(DESTDIR)/etc/sane.d; \
@@ -9556,10 +9537,6 @@ dist-hook:
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/setup.py
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/systray.py
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/timedate.py
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-arm32.so
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-arm64.so
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-x86_32.so
-@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/plugins/lj-x86_64.so
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/hpijs-drv
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/hpcups/
@HPLIP_CLASS_DRIVER_TRUE@ rm -rf $(distdir)/prnt/ps/
diff --git a/prnt/hpcups/HPCupsFilter.cpp b/prnt/hpcups/HPCupsFilter.cpp
index 5b282d8..0bacfaf 100644
--- a/prnt/hpcups/HPCupsFilter.cpp
+++ b/prnt/hpcups/HPCupsFilter.cpp
@@ -31,7 +31,6 @@
\*****************************************************************************/
#include "HPCupsFilter.h"
-#include "ImageProcessor.h"
#include <signal.h>
#include <sys/wait.h>
@@ -637,16 +636,10 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
sprintf(hpPreProcessedRasterFile, "%s/hp_%s_cups_SwapedPagesXXXXXX",CUPS_TMP_DIR, m_JA.user_name);
- image_processor_t* imageProcessor = imageProcessorCreate();
while (cupsRasterReadHeader2(cups_raster, &cups_header))
{
- IMAGE_PROCESSOR_ERROR result = imageProcessorStartPage(imageProcessor, &cups_header);
- if (result != IPE_SUCCESS){
- dbglog("DEBUG: imageProcessorStartPage failed result = %d\n", result);
- }
-
current_page_number++;
if (current_page_number == 1) {
@@ -745,12 +738,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
color_raster = rgbRaster;
black_raster = kRaster;
- result = imageProcessorProcessLine(imageProcessor, m_pPrinterBuffer, cups_header.cupsBytesPerLine);
- if (result != IPE_SUCCESS){
- dbglog("DEBUG: imageProcessorProcessLine failed result = %d\n", result);
- }
-
-
if ((y == 0) && !is_ljmono) {
//For ljmono, make sure that first line is not a blankRaster line.Otherwise printer
//may not skip blank lines before actual data
@@ -780,12 +767,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
}
} // for() loop end
- result = imageProcessorEndPage(imageProcessor);
- if (result != IPE_SUCCESS){
- dbglog("DEBUG: imageProcessorEndPage failed result = %d\n", result);
- }
-
-
m_Job.NewPage();
if (err != NO_ERROR) {
break;
@@ -800,8 +781,6 @@ int HPCupsFilter::processRasterData(cups_raster_t *cups_raster)
rgbRaster = NULL;
}
- imageProcessorDestroy(imageProcessor);
-
unlink(hpPreProcessedRasterFile);
return ret_status;
}
--
2.19.1

6
gnu/packages/patches/vsearch-unbundle-cityhash.patch
View File

@ -6,7 +6,7 @@ index e56a8a2..4adcc48 100644
if TARGET_PPC
AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
else
-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g
-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
+AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -lcityhash
endif
@ -39,7 +39,7 @@ index e56a8a2..4adcc48 100644
-
if TARGET_WIN
-libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g -D_MSC_VER
-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare -D_MSC_VER
-__top_builddir__bin_vsearch_LDFLAGS = -static
-__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a
+__top_builddir__bin_vsearch_LDFLAGS = -static -lcityhash
@ -47,7 +47,7 @@ index e56a8a2..4adcc48 100644
else
-libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g
-libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare
-
if TARGET_PPC
-__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu.a

26
gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
View File

@ -1,26 +0,0 @@
This fixes the wxplot2d plotting issue found at
https://github.com/andrejv/wxmaxima/issues/973.
From 5a0693c97ceaa4935b908f1e478126896952f399 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gunter=20K=C3=B6nigsmann?= <gunter@peterpall.de>
Date: Mon, 19 Feb 2018 05:37:35 +0100
Subject: [PATCH] Seems I accidentally made wxMaxima to default to parameters
for old gnuplots. Resolves #973
---
data/wxmathml.lisp.in | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/data/wxmathml.lisp.in b/data/wxmathml.lisp.in
index a32e3fc3..4e19acaf 100644
--- a/data/wxmathml.lisp.in
+++ b/data/wxmathml.lisp.in
@@ -43,7 +43,7 @@
(defvar $wxsubscripts t
"Recognize TeX-style subscripts")
(defvar $wxplot_pngcairo nil "Use gnuplot's pngcairo terminal for new plots?")
-(defmvar $wxplot_old_gnuplot t)
+(defmvar $wxplot_old_gnuplot nil)
(defun $wxstatusbar (status)
(format t "<statusbar>~a</statusbar>~%" status))

29
gnu/packages/python.scm
View File

@ -10530,6 +10530,31 @@ useful as a validator for JSON data.")
(define-public python2-validictory
(package-with-python2 python-validictory))
(define-public python-pyelftools
(package
(name "python-pyelftools")
(version "0.25")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyelftools" version))
(sha256
(base32
"090vdksbz341f7ljvr0zswblw4lspa8qaiikzyjkf318arpxmil9"))))
(build-system python-build-system)
;; Test suite requires python-setuptools
(native-inputs
`(("python-setuptools" ,python-setuptools)))
(home-page
"https://github.com/eliben/pyelftools")
(synopsis
"Analyze binary and library file information")
(description "This Python library provides interfaces for parsing and
analyzing two binary and library file formats; the Executable and Linking
Format (ELF), and debugging information in the Debugging With Attributed
Record Format (DWARF).")
(license license:public-domain)))
(define-public python-pyev
(package
(name "python-pyev")
@ -14532,14 +14557,14 @@ run on top of the dynamic task schedulers. ")
(define-public python-ilinkedlist
(package
(name "python-ilinkedlist")
(version "0.2.0")
(version "0.3.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ilinkedlist" version))
(sha256
(base32
"0klb846q5vs62d8f89my7wan1sji4yjj6pjhjch9dha3p8vlncd2"))))
"04wpv7km8jggrngc4bjg3nm615czd3bjdvpsy2icg6c1c8162zyg"))))
(build-system python-build-system)
(native-inputs `(("python-pytest" ,python-pytest)))
(inputs `(("python" ,python)))

17
gnu/packages/statistics.scm
View File

@ -39,6 +39,7 @@
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bash)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
@ -75,7 +76,7 @@
(define-public pspp
(package
(name "pspp")
(version "1.0.1")
(version "1.2.0")
(source
(origin
(method url-fetch)
@ -83,7 +84,7 @@
version ".tar.gz"))
(sha256
(base32
"1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s"))))
"07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
(build-system gnu-build-system)
(inputs
`(("cairo" ,cairo)
@ -94,11 +95,15 @@
("readline" ,readline)
("gtk" ,gtk+)
("gtksourceview" ,gtksourceview)
("spread-sheet-widget" ,spread-sheet-widget)
("zlib" ,zlib)))
(native-inputs
`(("glib" ,glib "bin") ;for glib-genmarshal
`(("autoconf" ,autoconf) ;for tests
("glib" ,glib "bin") ;for glib-genmarshal
("perl" ,perl)
("pkg-config" ,pkg-config)))
("pkg-config" ,pkg-config)
("python" ,python-2) ;for tests
("texinfo" ,texinfo)))
(home-page "https://www.gnu.org/software/pspp/")
(synopsis "Statistical analysis")
(description
@ -116,7 +121,7 @@ be output in text, PostScript, PDF or HTML.")
(define r-with-tests
(package
(name "r-with-tests")
(version "3.5.0")
(version "3.5.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://cran/src/base/R-"
@ -124,7 +129,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz"))
(sha256
(base32
"0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx"))))
"1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4"))))
(build-system gnu-build-system)
(arguments
`(#:disallowed-references (,tzdata-for-tests)

38
gnu/packages/xml.scm
View File

@ -19,6 +19,7 @@
;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2017 Petter <petter@mykolab.ch>
;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
@ -39,6 +40,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages java)
#:use-module (gnu packages gnuzilla)
@ -2111,3 +2113,39 @@ derivations of regular expressions.")
"The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
introduces a more general approach for processing XML with Haskell.")
(license license:expat)))
(define-public xmlrpc-c
(package
(name "xmlrpc-c")
(version "1.43.08")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/xmlrpc-c/Xmlrpc-c%20Super%20Stable/"
version "/xmlrpc-c-" version ".tgz"))
(sha256
(base32
"18zwbj6i2hpcn5riiyp8i6rml0sfv60dd7phw1x8g4r4lj2bbxf9"))))
(build-system gnu-build-system)
(inputs
`(("curl" ,curl)))
(native-inputs
`(;; For tools, if ever needed.
("perl" ,perl)))
(arguments
`(#:make-flags ; Add $libdir to the RUNPATH of all the executables.
(list (string-append "LDFLAGS_PERSONAL=-Wl,-rpath=" %output "/lib"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-/bin/sh-in-tests
(lambda _
(substitute* "GNUmakefile"
(("#! /bin/sh") (which "sh")))
#t)))))
(home-page "http://xmlrpc-c.sourceforge.net/")
(synopsis "Lightweight RPC library based on XML and HTTP")
(description
"XML-RPC is a quick-and-easy way to make procedure calls over the Internet.
It converts the procedure call into an XML document, sends it to a remote
server using HTTP, and gets back the response as XML. This library provides a
modular implementation of XML-RPC for C and C++.")
(license (list license:psfl license:expat))))

8
gnu/services/desktop.scm
View File

@ -672,7 +672,7 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks."
("KillUserProcesses" (yesno elogind-kill-user-processes?))
("KillOnlyUsers" (user-name-list elogind-kill-only-users))
("KillExcludeUsers" (user-name-list elogind-kill-exclude-users))
("InhibitDelayMaxSecs" (non-negative-integer elogind-inhibit-delay-max-seconds))
("InhibitDelayMaxSec" (non-negative-integer elogind-inhibit-delay-max-seconds))
("HandlePowerKey" (handle-action elogind-handle-power-key))
("HandleSuspendKey" (handle-action elogind-handle-suspend-key))
("HandleHibernateKey" (handle-action elogind-handle-hibernate-key))
@ -682,16 +682,16 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks."
("SuspendKeyIgnoreInhibited" (yesno elogind-suspend-key-ignore-inhibited?))
("HibernateKeyIgnoreInhibited" (yesno elogind-hibernate-key-ignore-inhibited?))
("LidSwitchIgnoreInhibited" (yesno elogind-lid-switch-ignore-inhibited?))
("HoldoffTimeoutSecs" (non-negative-integer elogind-holdoff-timeout-seconds))
("HoldoffTimeoutSec" (non-negative-integer elogind-holdoff-timeout-seconds))
("IdleAction" (handle-action elogind-idle-action))
("IdleActionSeconds" (non-negative-integer elogind-idle-action-seconds))
("IdleActionSec" (non-negative-integer elogind-idle-action-seconds))
("RuntimeDirectorySize"
(identity
(lambda (config)
(match (elogind-runtime-directory-size-percent config)
(#f (non-negative-integer (elogind-runtime-directory-size config)))
(percent (string-append (non-negative-integer percent) "%"))))))
("RemoveIpc" (yesno elogind-remove-ipc?))
("RemoveIPC" (yesno elogind-remove-ipc?))
"[Sleep]"
("SuspendState" (sleep-list elogind-suspend-state))
("SuspendMode" (sleep-list elogind-suspend-mode))

2
guix/scripts/pull.scm
View File

@ -177,7 +177,7 @@ true, display what would be built without actually building it."
(update-profile profile manifest
#:dry-run? dry-run?)
(munless dry-run?
(display-profile-news profile)))))
(return (display-profile-news profile))))))
(define (honor-lets-encrypt-certificates! store)
"Tell Guile-Git to use the Let's Encrypt certificates."