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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 Pierre-Antoine Rouby@*
Copyright @copyright{} 2018 Gábor Boskovits@* Copyright @copyright{} 2018 Gábor Boskovits@*
Copyright @copyright{} 2018 Florian Pelz@* Copyright @copyright{} 2018 Florian Pelz@*
Copyright @copyright{} 2018 Laura Lazzati@*
Permission is granted to copy, distribute and/or modify this document Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3 or 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}). (@pxref{System Configuration}).
@cindex functional package management @cindex functional package management
@cindex isolation
Under the hood, Guix implements the @dfn{functional package management} Under the hood, Guix implements the @dfn{functional package management}
discipline pioneered by Nix (@pxref{Acknowledgments}). discipline pioneered by Nix (@pxref{Acknowledgments}).
In Guix, the package build and installation process is seen In Guix, the package build and installation process is seen
@ -387,6 +389,7 @@ garbage collection of packages (@pxref{Features}).
@chapter Installation @chapter Installation
@cindex installing Guix @cindex installing Guix
@cindex official website
GNU Guix is available for download from its website at GNU Guix is available for download from its website at
@url{http://www.gnu.org/software/guix/}. This section describes the @url{http://www.gnu.org/software/guix/}. This section describes the
software requirements of Guix, as well as how to install it and get 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}. @pxref{System Installation}.
@cindex foreign distro @cindex foreign distro
@cindex directories related to foreign distro
When installed on a running GNU/Linux system---thereafter called a When installed on a running GNU/Linux system---thereafter called a
@dfn{foreign distro}---GNU@tie{}Guix complements the available tools @dfn{foreign distro}---GNU@tie{}Guix complements the available tools
without interference. Its data lives exclusively in two directories, 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 @section Binary Installation
@cindex installing Guix from binaries @cindex installing Guix from binaries
@cindex installer script
This section describes how to install Guix on an arbitrary system from a This section describes how to install Guix on an arbitrary system from a
self-contained tarball providing binaries for Guix and for all its self-contained tarball providing binaries for Guix and for all its
dependencies. This is often quicker than installing from source, which 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/higan-remove-march-native-flag.patch \
%D%/packages/patches/hubbub-sort-entities.patch \ %D%/packages/patches/hubbub-sort-entities.patch \
%D%/packages/patches/hurd-fix-eth-multiplexer-dependency.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/hydra-disable-darcs-test.patch \
%D%/packages/patches/icecat-avoid-bundled-libraries.patch \ %D%/packages/patches/icecat-avoid-bundled-libraries.patch \
%D%/packages/patches/icecat-CVE-2018-12383.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-zeroed-keys.patch \
%D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch \ %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch \
%D%/packages/patches/wpa-supplicant-krack-followups.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/x265-detect512-all-arches.patch \
%D%/packages/patches/xboing-CVE-2004-0149.patch \ %D%/packages/patches/xboing-CVE-2004-0149.patch \
%D%/packages/patches/xf86-video-ark-remove-mibstore.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 (package
(inherit base) (inherit base)
(arguments (arguments
`(#:phases (substitute-keyword-arguments (package-arguments base)
(modify-phases %standard-phases ((#:phases phases)
`(modify-phases ,phases
;; Do not require the unmaintained pyqi library. ;; Do not require the unmaintained pyqi library.
(add-after 'unpack 'remove-pyqi (add-after 'unpack 'remove-pyqi
(lambda _ (lambda _
(substitute* "setup.py" (substitute* "setup.py"
(("install_requires.append\\(\"pyqi\"\\)") "pass")) (("install_requires.append\\(\"pyqi\"\\)") "pass"))
#t))) #t)))))))))
,@(package-arguments base))))))
(define-public bioperl-minimal (define-public bioperl-minimal
(let* ((inputs `(("perl-module-build" ,perl-module-build) (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/\");")))) (string-append " strcpy(train_dir, \"" share "/train/\");"))))
#t)) #t))
(replace 'build (replace 'build
(lambda _ (and (zero? (system* "make" "clean")) (lambda _
(zero? (system* "make" "fgs"))))) (invoke "make" "clean")
(invoke "make" "fgs")
#t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out"))) (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"))) (let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/")) (bin (string-append out "/bin/"))
(frag (string-append bin "run_FragGeneScan.pl"))) (frag (string-append bin "run_FragGeneScan.pl")))
(and (zero? (system* frag ; Test complete genome. ;; Test complete genome.
(invoke frag
"-genome=./example/NC_000913.fna" "-genome=./example/NC_000913.fna"
"-out=./test2" "-out=./test2"
"-complete=1" "-complete=1"
"-train=complete")) "-train=complete")
(file-exists? "test2.faa") (unless (and (file-exists? "test2.faa")
(file-exists? "test2.ffn") (file-exists? "test2.ffn")
(file-exists? "test2.gff") (file-exists? "test2.gff")
(file-exists? "test2.out") (file-exists? "test2.out"))
(zero? (system* ; Test incomplete sequences. (error "Expected files do not exist."))
frag ;; Test incomplete sequences.
(invoke frag
"-genome=./example/NC_000913-fgs.ffn" "-genome=./example/NC_000913-fgs.ffn"
"-out=out" "-out=out"
"-complete=0" "-complete=0"
"-train=454_30"))))))))) "-train=454_30")
#t))))))
(inputs (inputs
`(("perl" ,perl) `(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3. ("python" ,python-2))) ;not compatible with python 3.
@ -3471,26 +3476,28 @@ VCF.")
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "lib/jni") (mkdir-p "lib/jni")
(mkdir-p "jdk-src") (mkdir-p "jdk-src")
(and (zero? (system* "tar" "--strip-components=1" "-C" "jdk-src" (invoke "tar" "--strip-components=1" "-C" "jdk-src"
"-xf" (assoc-ref inputs "jdk-src"))) "-xf" (assoc-ref inputs "jdk-src"))
(zero? (system* "javah" "-jni" (invoke "javah" "-jni"
"-classpath" "classes" "-classpath" "classes"
"-d" "lib/" "-d" "lib/"
"net.sf.samtools.util.zip.IntelDeflater")) "net.sf.samtools.util.zip.IntelDeflater")
(with-directory-excursion "src/c/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") (string-append "-I" (assoc-ref inputs "jdk")
"/include/linux") "/include/linux")
"-I../../../jdk-src/src/share/native/common/" "-I../../../jdk-src/src/share/native/common/"
"-I../../../jdk-src/src/solaris/native/common/" "-I../../../jdk-src/src/solaris/native/common/"
"-c" "-O3" "-fPIC" "IntelDeflater.c")) "-c" "-O3" "-fPIC" "IntelDeflater.c")
(zero? (system* "gcc" "-shared" (invoke "gcc" "-shared"
"-o" "../../../lib/jni/libIntelDeflater.so" "-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. ;; We can only build everything else after building the JNI library.
(add-after 'build-jni 'build-rest (add-after 'build-jni 'build-rest
(lambda* (#:key make-flags #:allow-other-keys) (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 (add-before 'build 'set-JAVA6_HOME
(lambda _ (lambda _
(setenv "JAVA6_HOME" (getenv "JAVA_HOME")) (setenv "JAVA6_HOME" (getenv "JAVA_HOME"))
@ -3977,16 +3984,16 @@ sequences).")
(define-public mash (define-public mash
(package (package
(name "mash") (name "mash")
(version "2.0") (version "2.1")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/marbl/mash/archive/v" (url "https://github.com/marbl/mash.git")
version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) "049hwcc059p2fd9vwndn63laifvvsi0wmv84i6y1fr79k15dxwy6"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
@ -4011,9 +4018,7 @@ sequences).")
"src/mash/CommandScreen.cpp") "src/mash/CommandScreen.cpp")
(("^#include \"kseq\\.h\"") (("^#include \"kseq\\.h\"")
"#include \"htslib/kseq.h\"")) "#include \"htslib/kseq.h\""))
#t)) #t)))))
(add-after 'fix-includes 'autoconf
(lambda _ (zero? (system* "autoconf")))))))
(native-inputs (native-inputs
`(("autoconf" ,autoconf) `(("autoconf" ,autoconf)
;; Capnproto and htslib are statically embedded in the final ;; Capnproto and htslib are statically embedded in the final
@ -4040,13 +4045,14 @@ form of assemblies or reads.")
(version "2.12.1") (version "2.12.1")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v" (uri (git-reference
version ".tar.gz")) (url "https://bitbucket.org/berkeleylab/metabat.git")
(file-name (string-append name "-" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73")) "0hyg2smw1nz69mfvjpk45xyyychmda92c80a0cv7baji84ri4iyn"))
(patches (search-patches "metabat-fix-compilation.patch")))) (patches (search-patches "metabat-fix-compilation.patch"))))
(build-system scons-build-system) (build-system scons-build-system)
(arguments (arguments
@ -4109,16 +4115,16 @@ probabilistic distances of genome abundance and tetranucleotide frequency.")
(define-public minced (define-public minced
(package (package
(name "minced") (name "minced")
(version "0.2.0") (version "0.3.2")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/ctSkennerton/minced/archive/" (url "https://github.com/ctSkennerton/minced.git")
version ".tar.gz")) (commit version)))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0wxmlsapxfpxfd3ps9636h7i2xy6la8i42mwh0j2lsky63h63jp1")))) "1f5h9him0gd355cnx7p6pnxpknhckd4g0v62mg8zyhfbx9as25fv"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:test-target "test" `(#:test-target "test"
@ -4230,12 +4236,13 @@ that a read originated from a particular isoform.")
(delete 'configure) (delete 'configure)
(replace 'check (replace 'check
;; There are no tests, so just test if it runs. ;; There are no tests, so just test if it runs.
(lambda _ (zero? (system* "./muscle" "-version")))) (lambda _ (invoke "./muscle" "-version") #t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))) (bin (string-append out "/bin")))
(install-file "muscle" bin))))))) (install-file "muscle" bin)
#t))))))
(home-page "http://www.drive5.com/muscle") (home-page "http://www.drive5.com/muscle")
(synopsis "Multiple sequence alignment program") (synopsis "Multiple sequence alignment program")
(description (description
@ -4260,11 +4267,6 @@ program for nucleotide and protein sequences.")
(base32 (base32
"1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb")))) "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autoconf
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
(inputs (inputs
;; XXX: TODO: Enable Lua and Guile bindings. ;; XXX: TODO: Enable Lua and Guile bindings.
;; https://github.com/tjunier/newick_utils/issues/13 ;; 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+))) (license license:lgpl3+)))
(define-public pplacer (define-public pplacer
(let ((commit "g807f6f3")) (let ((commit "807f6f3"))
(package (package
(name "pplacer") (name "pplacer")
;; The commit should be updated with each version change. ;; The commit should be updated with each version change.
(version "1.1.alpha19") (version "1.1.alpha19")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/matsen/pplacer/archive/v" (uri (git-reference
version ".tar.gz")) (url "https://github.com/matsen/pplacer.git")
(file-name (string-append name "-" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 "0z1lnd2s8sh6kpzg106wzbh2szw7h0hvq8syd5a6wv4rmyyz6x0f")))) (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
(build-system ocaml-build-system) (build-system ocaml-build-system)
(arguments (arguments
`(#:ocaml ,ocaml-4.01 `(#:ocaml ,ocaml-4.01
@ -4338,11 +4341,12 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
(local-dir "cddlib_guix")) (local-dir "cddlib_guix"))
(mkdir local-dir) (mkdir local-dir)
(with-directory-excursion local-dir (with-directory-excursion local-dir
(system* "tar" "xvf" cddlib-src)) (invoke "tar" "xvf" cddlib-src))
(let ((cddlib-src-folder (let ((cddlib-src-folder
(string-append local-dir "/" (string-append local-dir "/"
(list-ref (scandir local-dir) 2) (list-ref (scandir local-dir) 2)
"/lib-src"))) "/lib-src")))
(for-each make-file-writable (find-files "cdd_src" ".*"))
(for-each (for-each
(lambda (file) (lambda (file)
(copy-file file (copy-file file
@ -4406,8 +4410,7 @@ downstream analysis.")
(add-after 'unpack 'enter-scripts-dir (add-after 'unpack 'enter-scripts-dir
(lambda _ (chdir "scripts"))) (lambda _ (chdir "scripts")))
(replace 'check (replace 'check
(lambda _ (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
(zero? (system* "python" "-m" "unittest" "discover" "-v"))))
(add-after 'install 'wrap-executables (add-after 'install 'wrap-executables
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (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") (version "2.0.7")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" (uri (git-reference
"pyicoteo/get/v" version ".tar.bz2")) (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
(file-name (string-append name "-" version ".tar.bz2")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:python ,python-2 ; does not work with Python 3 `(#:python ,python-2 ; does not work with Python 3
@ -4757,10 +4761,11 @@ partial genes, and identifies translation initiation sites.")
(getenv "PATH"))) (getenv "PATH")))
(setenv "PERL5LIB" (string-append (getcwd) "/lib" ":" (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
(getenv "PERL5LIB"))) (getenv "PERL5LIB")))
(zero? (length (filter (lambda (file) (for-each (lambda (file)
(display file)(display "\n") (display file)(display "\n")
(not (zero? (system* "perl" file)))) (invoke "perl" file))
(find-files "t" ".*\\.t$")))))) (find-files "t" ".*\\.t$"))
#t))
(replace 'install (replace 'install
;; There is no 'install' target in the Makefile. ;; There is no 'install' target in the Makefile.
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
@ -4849,18 +4854,17 @@ extremely diverse sets of genomes.")
(define-public raxml (define-public raxml
(package (package
(name "raxml") (name "raxml")
(version "8.2.10") (version "8.2.12")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (uri (git-reference
(string-append (url "https://github.com/stamatak/standard-RAxML.git")
"https://github.com/stamatak/standard-RAxML/archive/v" (commit (string-append "v" version))))
version ".tar.gz")) (file-name (git-file-name name version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8")))) "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; There are no tests. `(#:tests? #f ; There are no tests.
@ -5053,21 +5057,24 @@ distribution, coverage uniformity, strand specificity, etc.")
(modify-phases %standard-phases (modify-phases %standard-phases
(replace 'bootstrap (replace 'bootstrap
(lambda _ (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 (add-after 'build 'build-additional-tools
(lambda* (#:key make-flags #:allow-other-keys) (lambda* (#:key make-flags #:allow-other-keys)
(every (lambda (dir) (for-each (lambda (dir)
(with-directory-excursion (string-append "tools/" dir) (with-directory-excursion (string-append "tools/" dir)
(zero? (apply system* "make" make-flags)))) (apply invoke "make" make-flags)))
dirs))) dirs)
#t))
(add-after 'install 'install-additional-tools (add-after 'install 'install-additional-tools
(lambda* (#:key make-flags #:allow-other-keys) (lambda* (#:key make-flags #:allow-other-keys)
(fold (lambda (dir result) (for-each (lambda (dir)
(with-directory-excursion (string-append "tools/" dir) (with-directory-excursion (string-append "tools/" dir)
(and result (apply invoke `("make" ,@make-flags "install"))))
(zero? (apply system* dirs)
`("make" ,@make-flags "install")))))) #t))))))
#t dirs)))))))
(inputs (inputs
`(("gsl" ,gsl) `(("gsl" ,gsl)
("boost" ,boost) ("boost" ,boost)
@ -5233,17 +5240,16 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
(define-public ngs-sdk (define-public ngs-sdk
(package (package
(name "ngs-sdk") (name "ngs-sdk")
(version "1.3.0") (version "2.9.3")
(source (source (origin
(origin (method git-fetch)
(method url-fetch) (uri (git-reference
(uri (url "https://github.com/ncbi/ngs.git")
(string-append "https://github.com/ncbi/ngs/archive/" (commit version)))
version ".tar.gz")) (file-name (git-file-name name version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) "17c0v1nah3g3d2ib5bbi0vhma1ghd6vb9xycavqsh64lhp840rk3"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:parallel-build? #f ; not supported `(#: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 ;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'. ;; '--enable-fast-install'.
(zero? (system* "./configure" (invoke "./configure"
(string-append "--build-prefix=" (getcwd) "/build") (string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" out)))))) (string-append "--prefix=" out))
#t)))
(add-after 'unpack 'enter-dir (add-after 'unpack 'enter-dir
(lambda _ (chdir "ngs-sdk") #t))))) (lambda _ (chdir "ngs-sdk") #t)))))
(native-inputs `(("perl" ,perl))) (native-inputs `(("perl" ,perl)))
@ -5299,23 +5306,24 @@ simultaneously.")
(define-public ncbi-vdb (define-public ncbi-vdb
(package (package
(name "ncbi-vdb") (name "ncbi-vdb")
(version "2.8.2") (version "2.9.3")
(source (source (origin
(origin (method git-fetch)
(method url-fetch) (uri (git-reference
(uri (url "https://github.com/ncbi/ncbi-vdb.git")
(string-append "https://github.com/ncbi/ncbi-vdb/archive/" (commit version)))
version ".tar.gz")) (file-name (git-file-name name version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) "1l4ny67nxwv1lagk9wwjbrgm7ln7adci6dnpc7k1yaln6shj0qpm"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:parallel-build? #f ; not supported `(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target #:tests? #f ; no "check" target
#:phases #:phases
(modify-phases %standard-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 (add-before 'configure 'set-perl-search-path
(lambda _ (lambda _
;; Work around "dotless @INC" build failure. ;; Work around "dotless @INC" build failure.
@ -5349,8 +5357,7 @@ simultaneously.")
;; The 'configure' script doesn't recognize things like ;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'. ;; '--enable-fast-install'.
(zero? (system* (invoke "./configure"
"./configure"
(string-append "--build-prefix=" (getcwd) "/build") (string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out")) (string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug") (string-append "--debug")
@ -5359,7 +5366,8 @@ simultaneously.")
(string-append "--with-ngs-sdk-prefix=" (string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk")) (assoc-ref inputs "ngs-sdk"))
(string-append "--with-hdf5-prefix=" (string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5"))))))) (assoc-ref inputs "hdf5")))
#t)))
(add-after 'install 'install-interfaces (add-after 'install 'install-interfaces
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
;; Install interface libraries. On i686 the interface libraries ;; Install interface libraries. On i686 the interface libraries
@ -5464,12 +5472,13 @@ subsequent visualization, annotation and storage of results.")
(version "1.90b4") (version "1.90b4")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/chrchang/plink-ng/archive/v" (uri (git-reference
version ".tar.gz")) (url "https://github.com/chrchang/plink-ng.git")
(file-name (string-append name "-" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 "09ixrds009aczjswxr2alcb774mksq5g0v78dgjjn1h4dky0kf9a")))) (base32 "02npdwgkpfkdnhw819rhj5kw02a5k5m90b14zq9zzya4hyg929c0"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:tests? #f ;no "check" target '(#:tests? #f ;no "check" target
@ -5551,14 +5560,14 @@ structures, classes for genomic regions, mapped sequencing reads, etc.")
(define-public preseq (define-public preseq
(package (package
(name "preseq") (name "preseq")
(version "2.0") (version "2.0.3")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://github.com/smithlabcode/" (uri (string-append "https://github.com/smithlabcode/preseq/"
"preseq/archive/v" version ".tar.gz")) "releases/download/v" version
(file-name (string-append name "-" version ".tar.gz")) "/preseq_v" version ".tar.bz2"))
(sha256 (sha256
(base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) (base32 "149x9xmk1wy1gff85325yfzqc0qk4sgp1w6gbyj9cnji4x1dszbl"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet '(begin (snippet '(begin
;; Remove bundled samtools. ;; Remove bundled samtools.
@ -5648,17 +5657,17 @@ sequence itself can be retrieved from these databases.")
(define-public sra-tools (define-public sra-tools
(package (package
(name "sra-tools") (name "sra-tools")
(version "2.8.2-1") (version "2.9.3")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (uri (git-reference
(string-append "https://github.com/ncbi/sra-tools/archive/" (url "https://github.com/ncbi/sra-tools.git")
version ".tar.gz")) (commit version)))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) "0663gcdxkziwsmlznjxysb00621rllpbz6jwsfifq7z3dj3lwm8b"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:parallel-build? #f ; not supported `(#: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 ;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'. ;; '--enable-fast-install'.
(zero? (system* (invoke "./configure"
"./configure"
(string-append "--build-prefix=" (getcwd) "/build") (string-append "--build-prefix=" (getcwd) "/build")
(string-append "--prefix=" (assoc-ref outputs "out")) (string-append "--prefix=" (assoc-ref outputs "out"))
(string-append "--debug") (string-append "--debug")
@ -5727,18 +5735,7 @@ sequence itself can be retrieved from these databases.")
(string-append "--with-ngs-sdk-prefix=" (string-append "--with-ngs-sdk-prefix="
(assoc-ref inputs "ngs-sdk")) (assoc-ref inputs "ngs-sdk"))
(string-append "--with-hdf5-prefix=" (string-append "--with-hdf5-prefix="
(assoc-ref inputs "hdf5")))))) (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)))
#t))))) #t)))))
(native-inputs `(("perl" ,perl))) (native-inputs `(("perl" ,perl)))
(inputs (inputs
@ -5865,24 +5862,16 @@ is one that takes arguments.")
(define-public seqtk (define-public seqtk
(package (package
(name "seqtk") (name "seqtk")
(version "1.2") (version "1.3")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/lh3/seqtk/archive/v" (url "https://github.com/lh3/seqtk.git")
version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0ywdyzpmfiz2wp6ampbzqg4y8bj450nfgqarpamg045b8mk32lxx")) "1bfzlqa84b5s1qi22blmmw2s8xdyp9h9ydcq22pfjhh5gab3yz6l"))))
(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))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:phases `(#:phases
@ -5890,11 +5879,12 @@ is one that takes arguments.")
(delete 'configure) (delete 'configure)
(replace 'check (replace 'check
;; There are no tests, so we just run a sanity check. ;; There are no tests, so we just run a sanity check.
(lambda _ (zero? (system* "./seqtk" "seq")))) (lambda _ (invoke "./seqtk" "seq") #t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(install-file "seqtk" bin))))))) (install-file "seqtk" bin)
#t))))))
(inputs (inputs
`(("zlib" ,zlib))) `(("zlib" ,zlib)))
(home-page "https://github.com/lh3/seqtk") (home-page "https://github.com/lh3/seqtk")
@ -5910,20 +5900,20 @@ optionally compressed by gzip.")
(name "snap-aligner") (name "snap-aligner")
(version "1.0beta.18") (version "1.0beta.18")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/amplab/snap/archive/v" (url "https://github.com/amplab/snap.git")
version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")))) "01w3qq4wm07z73vky0cfwlmrbf50n3w722cxrlzxfi99mnb808d8"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:phases '(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(delete 'configure) (delete 'configure)
(replace 'check (lambda _ (zero? (system* "./unit_tests")))) (replace 'check (lambda _ (invoke "./unit_tests") #t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (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") (version "2.1b")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/biocore/sortmerna/archive/" (url "https://github.com/biocore/sortmerna.git")
version ".tar.gz")) (commit version)))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) "0j3mbz4n25738yijmjbr5r4fyvkgm8v5vn3sshyfvmyqf5q9byqf"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(outputs '("out" ;for binaries (outputs '("out" ;for binaries
"db")) ;for sequence databases "db")) ;for sequence databases
@ -6205,8 +6195,7 @@ Cuffdiff or Ballgown programs.")
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(replace 'check (replace 'check
(lambda _ (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
(zero? (system* "python" "-m" "unittest" "discover" "-v")))))))
(propagated-inputs (propagated-inputs
`(("python-sqlalchemy" ,python2-sqlalchemy) `(("python-sqlalchemy" ,python2-sqlalchemy)
("python-decorator" ,python2-decorator) ("python-decorator" ,python2-decorator)
@ -6839,17 +6828,17 @@ SELECT or UPDATE queries to an end-point.")
(define-public vsearch (define-public vsearch
(package (package
(name "vsearch") (name "vsearch")
(version "2.8.0") (version "2.9.1")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/torognes/vsearch/archive/v" (url "https://github.com/torognes/vsearch.git")
version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3")) "0vhrpjfdf75ba04b24xknp41790cvcgwl0vgpy7qbzj5xh2521ss"))
(patches (search-patches "vsearch-unbundle-cityhash.patch")) (patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet (snippet
'(begin '(begin
@ -6860,11 +6849,6 @@ SELECT or UPDATE queries to an end-point.")
(delete-file "src/city.cc") (delete-file "src/city.cc")
#t)))) #t))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _ (zero? (system* "autoreconf" "-vif")))))))
(inputs (inputs
`(("zlib" ,zlib) `(("zlib" ,zlib)
("bzip2" ,bzip2) ("bzip2" ,bzip2)
@ -8874,13 +8858,14 @@ Sequences.")
(version "1.1.4") (version "1.1.4")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/ManuSetty/SeqGL/" (uri (git-reference
"archive/" version ".tar.gz")) (url "https://github.com/ManuSetty/SeqGL.git")
(file-name (string-append name "-" version ".tar.gz")) (commit version)))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh")))) "1r6ywvhxl3ffv48lgj7sbd582mcc6dha3ksgc2qjlvjrnkbj3799"))))
(build-system r-build-system) (build-system r-build-system)
(propagated-inputs (propagated-inputs
`(("r-biostrings" ,r-biostrings) `(("r-biostrings" ,r-biostrings)
@ -9042,7 +9027,7 @@ AM_CONDITIONAL(AMPNG, true)"))
(("\\$\\(bindir\\)/embossupdate") "")) (("\\$\\(bindir\\)/embossupdate") ""))
#t)) #t))
(add-after 'disable-update-check 'autogen (add-after 'disable-update-check 'autogen
(lambda _ (zero? (system* "autoreconf" "-vif"))))))) (lambda _ (invoke "autoreconf" "-vif") #t)))))
(inputs (inputs
`(("perl" ,perl) `(("perl" ,perl)
("libpng" ,libpng) ("libpng" ,libpng)
@ -9215,12 +9200,14 @@ group or two ChIP groups run under different conditions.")
(name "filevercmp") (name "filevercmp")
(version (string-append "0-1." (string-take commit 7))) (version (string-append "0-1." (string-take commit 7)))
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/ekg/filevercmp/archive/" (uri (git-reference
commit ".tar.gz")) (url "https://github.com/ekg/filevercmp.git")
(file-name (string-append name "-" version ".tar.gz")) (commit commit)))
(file-name (git-file-name name commit))
(sha256 (sha256
(base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450")))) (base32
"1j9vxsy0y050v59h0q1d6501fcw1kjvj0d18l1xk2zyg0jzj247c"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; There are no tests to run. `(#:tests? #f ; There are no tests to run.
@ -9230,7 +9217,8 @@ group or two ChIP groups run under different conditions.")
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (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") (home-page "https://github.com/ekg/filevercmp")
(synopsis "This program compares version strings") (synopsis "This program compares version strings")
(description "This program compares version strings. It intends to be a (description "This program compares version strings. It intends to be a
@ -11259,16 +11247,16 @@ sort, markdup, and depth.")
(define-public ritornello (define-public ritornello
(package (package
(name "ritornello") (name "ritornello")
(version "1.0.0") (version "2.0.1")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/KlugerLab/" (uri (git-reference
"Ritornello/archive/v" (url "https://github.com/KlugerLab/Ritornello.git")
version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38")))) "1xahvq215qld7x1w8vpa5zbrsj6p9crb9shqa2x89sb0aaxa02jk"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; there are no tests `(#:tests? #f ; there are no tests
@ -11277,7 +11265,7 @@ sort, markdup, and depth.")
(add-after 'unpack 'patch-samtools-references (add-after 'unpack 'patch-samtools-references
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(substitute* '("src/SamStream.h" (substitute* '("src/SamStream.h"
"src/BufferedGenomeReader.h") "src/FLD.cpp")
(("<sam.h>") "<samtools/sam.h>")) (("<sam.h>") "<samtools/sam.h>"))
#t)) #t))
(delete 'configure) (delete 'configure)
@ -11503,15 +11491,16 @@ applications for tackling some common problems in a user-friendly way.")
(define-public tadbit (define-public tadbit
(package (package
(name "tadbit") (name "tadbit")
(version "0.2") (version "0.2.0")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/3DGenomes/TADbit/" (uri (git-reference
"archive/v" version ".tar.gz")) (url "https://github.com/3DGenomes/TADbit.git")
(file-name (string-append name "-" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f")))) "07g3aj648prmsvxp9caz5yl41k0y0647vxh0f5p3w8376mfiljd0"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(;; Tests are included and must be run after installation, but `(;; 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") (version "302.0.0")
(source (source
(origin (origin
(method url-fetch) (method git-fetch)
(uri (string-append "https://github.com/ENCODE-DCC/kentUtils/" (uri (git-reference
"archive/v" version ".tar.gz")) (url "https://github.com/ENCODE-DCC/kentUtils.git")
(file-name (string-append name "-" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm")) "0n1wbyjpzii2b9qhyp9r1q76j623cggpg3y8fmw78ld3z4y7ivha"))
(modules '((guix build utils) (modules '((guix build utils)
(srfi srfi-26) (srfi srfi-26)
(ice-9 ftw))) (ice-9 ftw)))
@ -11623,6 +11613,8 @@ models. TADbit is complemented by TADkit for visualizing 3D models.")
#:tests? #f #:tests? #f
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'fix-permissions
(lambda _ (make-file-writable "src/inc/localEnvironment.mk") #t))
(add-after 'unpack 'fix-paths (add-after 'unpack 'fix-paths
(lambda _ (lambda _
(substitute* "Makefile" (substitute* "Makefile"
@ -11918,14 +11910,14 @@ accurate as existing quantification tools.")
(name "libgff") (name "libgff")
(version "1.0") (version "1.0")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/Kingsford-Group/" (url "https://github.com/Kingsford-Group/libgff.git")
"libgff/archive/v" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls")))) "0n6vfjnq7a2mianipscbshrvbncss8z4zkgkbjw754p9043nfkps"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments `(#:tests? #f)) ; no tests included (arguments `(#:tests? #f)) ; no tests included
(home-page "https://github.com/Kingsford-Group/libgff") (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") (name "sailfish")
(version "0.10.1") (version "0.10.1")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (uri (git-reference
(string-append "https://github.com/kingsfordgroup/" (url "https://github.com/kingsfordgroup/sailfish.git")
"sailfish/archive/v" version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0")) "1amcc5hqvsl42hg4x19bi9vy47cl874s0lw1fmi0hwsdk9i8c03v"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
@ -12025,7 +12017,7 @@ bytes of memory space, where n is the length of the string.")
(include "external/install/include/rapmap/") (include "external/install/include/rapmap/")
(rapmap (assoc-ref inputs "rapmap"))) (rapmap (assoc-ref inputs "rapmap")))
(mkdir-p "/tmp/rapmap") (mkdir-p "/tmp/rapmap")
(system* "tar" "xf" (invoke "tar" "xf"
(assoc-ref inputs "rapmap") (assoc-ref inputs "rapmap")
"-C" "/tmp/rapmap" "-C" "/tmp/rapmap"
"--strip-components=1") "--strip-components=1")

5
gnu/packages/c.scm
View File

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org> ;;; 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 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz> ;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; ;;;
@ -160,8 +160,7 @@ standard.")
`(#:phases `(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(replace 'check (replace 'check
(lambda _ (lambda _ (invoke "make" "-C" "cc/cpp" "test") #t)))))
(zero? (system* "make" "-C" "cc/cpp" "test")))))))
(native-inputs (native-inputs
`(("bison" ,bison) `(("bison" ,bison)
("flex" ,flex))) ("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 (base32
"0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290")) "0g3q5mm2crjyc1z4z6gv4lam6sc5d3diz704djrnpqadk4q3h290"))
(modules '((guix build utils))) (modules '((guix build utils)))
(patches (search-patches "hplip-remove-imageprocessor.patch"))
(snippet (snippet
;; Fix type mismatch.
'(begin '(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" (substitute* "prnt/hpcups/genPCLm.cpp"
(("boolean") "bool")) (("boolean") "bool"))
#t)))) #t))))

4
gnu/packages/databases.scm
View File

@ -848,14 +848,14 @@ pictures, sounds, or video.")
(package (package
(inherit postgresql) (inherit postgresql)
(name "postgresql") (name "postgresql")
(version "9.6.9") (version "9.6.11")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://ftp.postgresql.org/pub/source/v" (uri (string-append "https://ftp.postgresql.org/pub/source/v"
version "/postgresql-" version ".tar.bz2")) version "/postgresql-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"0biy8j69dbvdmrag55pdszpc0702agzqhhcwdx21xp02mzim4ydr")))))) "0c55akrkzqd6p6a8hr0338wk246hl76r9j16p4zn3s51d7f0l99q"))))))
(define-public python-pymysql (define-public python-pymysql
(package (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. @item helm-slime-repl-history: Select an input from the SLIME REPL history and insert it.
@end itemize\n") @end itemize\n")
(license license:gpl3+)))) (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.") input.")
(license license:expat))) (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 (define-public yad
(package (package
(name "yad") (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. ;; There has not been any release yet.
(define-public guile-newt (define-public guile-newt
(let ((commit "596ad760bee1be419d71271732f0f30eaee55143") (let ((commit "4eaa3cf84b9b426cc0ff7bec48b76cca6ca3ec83")
(revision "0")) (revision "1"))
(package (package
(name "guile-newt") (name "guile-newt")
(version (string-append "0-" revision "." (string-take commit 9))) (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")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"18qqbi0bc7vp2vlrhib3p3wwgn7wrlv5728dn0avirhw4fxxivnf")))) "0ww7jbdsmjlsxm60ym6cb5s5kc4ljz8bn4y2lvcqnap0aihqfk10"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:make-flags '(#:make-flags

70
gnu/packages/kodi.scm
View File

@ -3,6 +3,7 @@
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com> ;;; Copyright © 2017 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
;;; ;;;
@ -48,6 +49,7 @@
#:use-module (gnu packages gl) #:use-module (gnu packages gl)
#:use-module (gnu packages glib) #:use-module (gnu packages glib)
#:use-module (gnu packages gperf) #:use-module (gnu packages gperf)
#:use-module (gnu packages groff)
#:use-module (gnu packages gnunet) #:use-module (gnu packages gnunet)
#:use-module (gnu packages gnupg) #:use-module (gnu packages gnupg)
#:use-module (gnu packages image) #:use-module (gnu packages image)
@ -62,6 +64,7 @@
#:use-module (gnu packages python) #:use-module (gnu packages python)
#:use-module (gnu packages samba) #:use-module (gnu packages samba)
#:use-module (gnu packages sdl) #:use-module (gnu packages sdl)
#:use-module (gnu packages serialization)
#:use-module (gnu packages ssh) #:use-module (gnu packages ssh)
#:use-module (gnu packages swig) #:use-module (gnu packages swig)
#:use-module (gnu packages textutils) #:use-module (gnu packages textutils)
@ -75,11 +78,12 @@
#:use-module (gnu packages assembly)) #:use-module (gnu packages assembly))
(define-public crossguid (define-public crossguid
(let ((commit "8f399e8bd4252be9952f3dfa8199924cc8487ca4")) (let ((commit "fef89a4174a7bf8cd99fa9154864ce9e8e3bf989")
(revision "2"))
(package (package
(name "crossguid") (name "crossguid")
(version (string-append "0.0-1." (string-take commit 7))) (version (string-append "0.0-" revision "." (string-take commit 7)))
;; There's no official release. Just a Git repository. ;; This is the commit that Kodi wants.
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -88,13 +92,12 @@
(file-name (string-append name "-" version "-checkout")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"1i29y207qqddvaxbn39pk2fbh3gx8zvdprfp35wasj9rw2wjk3s9")))) "1blrkc7zcqrqcr5msvhyhm98s2jvm9hr0isqs4288q2r4mdnrfq0"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:phases '(#:phases
(modify-phases %standard-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 (replace 'build
(lambda _ (lambda _
(invoke "g++" "-c" "guid.cpp" "-o" "guid.o" (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 ;; 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. ;; and patch shebangs here, so we don't have to worry about it later.
(define libdvdnav/kodi (define libdvdnav/kodi
(let ((commit "6.0.0-Leia-Alpha-1")) (let ((commit "6.0.0-Leia-Alpha-3"))
(package (package
(name "libdvdnav-bootstrapped") (name "libdvdnav-bootstrapped")
(version commit) (version commit)
@ -141,7 +144,7 @@ generator library for C++.")
(file-name (string-append name "-" version "-checkout")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"1xiyfgf8v8aknlxlzsvk6pbzkhclz0hbh3s1b0w6ivkng2k310j9")))) "0qwlf4lgahxqxk1r2pzl866mi03pbp7l1fc0rk522sc0ak2s9jhb"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:tests? #f '(#:tests? #f
@ -164,7 +167,7 @@ generator library for C++.")
(license license:gpl2+)))) (license license:gpl2+))))
(define libdvdread/kodi (define libdvdread/kodi
(let ((commit "6.0.0-Leia-Alpha-1")) (let ((commit "6.0.0-Leia-Alpha-3"))
(package (package
(name "libdvdread-bootstrapped") (name "libdvdread-bootstrapped")
(version commit) (version commit)
@ -176,7 +179,7 @@ generator library for C++.")
(file-name (string-append name "-" version "-checkout")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"1c3g18n2vwhgcfz3dka1pmw58bnv2ram7xjvizfiykb3sgi9zfwp")))) "1xxn01mhkdnp10cqdr357wx77vyzfb5glqpqyg8m0skyi75aii59"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:tests? #f '(#:tests? #f
@ -199,7 +202,7 @@ generator library for C++.")
(license (list license:gpl2+ license:lgpl2.1+))))) (license (list license:gpl2+ license:lgpl2.1+)))))
(define libdvdcss/kodi (define libdvdcss/kodi
(let ((commit "1.4.1-Leia-Alpha-1")) (let ((commit "1.4.2-Leia-Beta-5"))
(package (package
(name "libdvdcss-bootstrapped") (name "libdvdcss-bootstrapped")
(version commit) (version commit)
@ -211,7 +214,7 @@ generator library for C++.")
(file-name (string-append name "-" version "-checkout")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"0adafwsawxssj3nilkql447v0l4a2584rdpmy5rfjmznh91lykgh")))) "0j41ydzx0imaix069s3z07xqw9q95k7llh06fc27dcn6f7b8ydyl"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:tests? #f '(#:tests? #f
@ -233,28 +236,53 @@ generator library for C++.")
(description (package-description libdvdcss)) (description (package-description libdvdcss))
(license license:gpl2+)))) (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 (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 (package
(name "kodi") (name "kodi")
(version (git-version "18.0_alpha" revision commit)) (version "18.0b5")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/xbmc/xbmc.git") (url "https://github.com/xbmc/xbmc.git")
(commit commit))) (commit (string-append version "-Leia"))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1rxg752cl59124cfpfwmyjldn6qpq5jginxddpzvgagfadf10i4d")) "042qzvhys3sajby6ywgmrsymhji37qk0iqgppznrvm53vrizwsam"))
(snippet (snippet
'(begin '(begin
(use-modules (guix build utils)) (use-modules (guix build utils))
(for-each delete-file-recursively (for-each delete-file-recursively
'("project/BuildDependencies/bin/" '("project/BuildDependencies/"
;; TODO: Purge these jars. ;; TODO: Purge these jars.
;;"tools/codegenerator/groovy" ;;"tools/codegenerator/groovy"
;; And these sources: ;; And these sources:
@ -370,10 +398,12 @@ generator library for C++.")
("eudev" ,eudev) ("eudev" ,eudev)
("ffmpeg" ,ffmpeg) ("ffmpeg" ,ffmpeg)
("flac" ,flac) ("flac" ,flac)
("flatbuffers" ,flatbuffers)
("fmt" ,fmt) ("fmt" ,fmt)
("fontconfig" ,fontconfig) ("fontconfig" ,fontconfig)
("freetype" ,freetype) ("freetype" ,freetype)
("fribidi" ,fribidi) ("fribidi" ,fribidi)
("fstrcmp" ,fstrcmp)
("giflib" ,giflib) ("giflib" ,giflib)
("glew" ,glew) ("glew" ,glew)
("gnutls" ,gnutls) ("gnutls" ,gnutls)
@ -427,7 +457,7 @@ plug-in system.")
license:expat ;cpluff, dbwrappers license:expat ;cpluff, dbwrappers
license:public-domain ;cpluff/examples license:public-domain ;cpluff/examples
license:bsd-3 ;misc, gtest license:bsd-3 ;misc, gtest
license:bsd-2))))) ;xbmc/freebsd license:bsd-2)))) ;xbmc/freebsd
(define-public kodi-cli (define-public kodi-cli
(let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for (let ((commit "104dc23b2a993c8e6db8c46f4f8bec24b146549b") ; Add support for

10
gnu/packages/maths.scm
View File

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

53
gnu/packages/music.scm
View File

@ -309,29 +309,27 @@ playing your music.")
(name "cmus") (name "cmus")
(version "2.7.1") (version "2.7.1")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/" name "/" name "/archive/v" (url "https://github.com/cmus/cmus.git")
version ".tar.gz")) (commit (string-append "v" version))))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0raixgjavkm7hxppzsc5zqbfbh2bhjcmbiplhnsxsmyj8flafyc1")))) "0xd96py21bl869qlv1353zw7xsgq6v5s8szr0ldr63zj5fgc2ps5"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:tests? #f ; cmus does not include tests `(#:tests? #f ; cmus does not include tests
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(replace (replace 'configure
'configure
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))) (let ((out (assoc-ref outputs "out")))
;; It's an idiosyncratic configure script that doesn't ;; It's an idiosyncratic configure script that doesn't
;; understand --prefix=..; it wants prefix=.. instead. ;; understand --prefix=..; it wants prefix=.. instead.
(zero? (invoke "./configure"
(system* "./configure" (string-append "prefix=" out))
(string-append "prefix=" out))))))))) #t))))))
;; TODO: cmus optionally supports the following formats, which haven't yet ;; TODO: cmus optionally supports the following formats, which haven't yet
;; been added to Guix: ;; been added to Guix:
;; ;;
@ -1144,14 +1142,14 @@ your own lessons.")
(name "powertabeditor") (name "powertabeditor")
(version "2.0.0-alpha10") (version "2.0.0-alpha10")
(source (origin (source (origin
(method url-fetch) (method git-fetch)
(uri (string-append (uri (git-reference
"https://github.com/powertab/powertabeditor/archive/" (url "https://github.com/powertab/powertabeditor.git")
version ".tar.gz")) (commit version)))
(file-name (string-append name "-" version ".tar.gz")) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"1fr14ql0yhlqvh6y08yaanszm2nvca5i50rqym396kfvga3ky18x")) "1z4fhdp71ck9synr12rg1p6365xnypd8ih40c5icj4si36khvksk"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(begin '(begin
@ -1185,14 +1183,14 @@ add_library( rapidjson INTERFACE IMPORTED )"))
(modify-phases %standard-phases (modify-phases %standard-phases
(replace 'check (replace 'check
(lambda _ (lambda _
(zero? (system* "bin/pte_tests" (invoke "bin/pte_tests"
;; FIXME: these tests fail ;; FIXME: these tests fail
"exclude:Actions/EditStaff" "exclude:Actions/EditStaff"
"exclude:Formats/PowerTabOldImport/MergeMultiBarRests" "exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
"exclude:Score/ViewFilter/FilterRule" "exclude:Score/ViewFilter/FilterRule"
"exclude:Score/ViewFilter/ViewFilter" "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 ;; FIXME: This bug has been fixed upstream, but no release has been
;; made yet. See https://github.com/powertab/powertabeditor/issues/257 ;; made yet. See https://github.com/powertab/powertabeditor/issues/257
(add-after 'unpack 'fix-boost-bug (add-after 'unpack 'fix-boost-bug
@ -1751,9 +1749,7 @@ export.")
(lambda _ (lambda _
(substitute* "tcl/pd-gui.tcl" (substitute* "tcl/pd-gui.tcl"
(("exec wish ") (string-append "exec " (which "wish8.6") " "))) (("exec wish ") (string-append "exec " (which "wish8.6") " ")))
#t)) #t)))))
(add-after 'unpack 'autoconf
(lambda _ (zero? (system* "bash" "./autogen.sh")))))))
(native-inputs (native-inputs
`(("autoconf" ,autoconf) `(("autoconf" ,autoconf)
("automake" ,automake) ("automake" ,automake)
@ -4071,14 +4067,15 @@ ISRCs and the MCN (=UPC/EAN) from disc.")
(base32 (base32
"0ikb9igyyk28jm34raxfzkw2qyn4nzzwsymdyprp7cmvi6g2ajb7")))) "0ikb9igyyk28jm34raxfzkw2qyn4nzzwsymdyprp7cmvi6g2ajb7"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments `(#:phases (arguments
`(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(replace 'check (replace 'check
(lambda _ (lambda _
(and
;; requires network connections ;; requires network connections
;; (zero? (system* "tests/mbtest")) ;; (invoke "tests/mbtest")
(zero? (system* "tests/ctest")))))))) (invoke "tests/ctest")
#t)))))
(inputs `(("neon" ,neon) (inputs `(("neon" ,neon)
("libxml2" ,libxml2))) ("libxml2" ,libxml2)))
(native-inputs `(("pkg-config" ,pkg-config))) (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 if TARGET_PPC
AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8 AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
else 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 +AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -lcityhash
endif endif
@ -39,7 +39,7 @@ index e56a8a2..4adcc48 100644
- -
if TARGET_WIN 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_LDFLAGS = -static
-__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a -__top_builddir__bin_vsearch_LDADD = libregex.a libcityhash.a libcpu_ssse3.a libcpu_sse2.a
+__top_builddir__bin_vsearch_LDFLAGS = -static -lcityhash +__top_builddir__bin_vsearch_LDFLAGS = -static -lcityhash
@ -47,7 +47,7 @@ index e56a8a2..4adcc48 100644
else else
-libcityhash_a_CXXFLAGS = -Wall -Wno-sign-compare -O3 -g -libcityhash_a_CXXFLAGS = $(AM_CXXFLAGS) -Wno-sign-compare
- -
if TARGET_PPC if TARGET_PPC
-__top_builddir__bin_vsearch_LDADD = libcityhash.a libcpu.a -__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 (define-public python2-validictory
(package-with-python2 python-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 (define-public python-pyev
(package (package
(name "python-pyev") (name "python-pyev")
@ -14532,14 +14557,14 @@ run on top of the dynamic task schedulers. ")
(define-public python-ilinkedlist (define-public python-ilinkedlist
(package (package
(name "python-ilinkedlist") (name "python-ilinkedlist")
(version "0.2.0") (version "0.3.1")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "ilinkedlist" version)) (uri (pypi-uri "ilinkedlist" version))
(sha256 (sha256
(base32 (base32
"0klb846q5vs62d8f89my7wan1sji4yjj6pjhjch9dha3p8vlncd2")))) "04wpv7km8jggrngc4bjg3nm615czd3bjdvpsy2icg6c1c8162zyg"))))
(build-system python-build-system) (build-system python-build-system)
(native-inputs `(("python-pytest" ,python-pytest))) (native-inputs `(("python-pytest" ,python-pytest)))
(inputs `(("python" ,python))) (inputs `(("python" ,python)))

17
gnu/packages/statistics.scm
View File

@ -39,6 +39,7 @@
#:use-module (guix build-system trivial) #:use-module (guix build-system trivial)
#:use-module (gnu packages) #:use-module (gnu packages)
#:use-module (gnu packages algebra) #:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module (gnu packages bash) #:use-module (gnu packages bash)
#:use-module (gnu packages check) #:use-module (gnu packages check)
#:use-module (gnu packages compression) #:use-module (gnu packages compression)
@ -75,7 +76,7 @@
(define-public pspp (define-public pspp
(package (package
(name "pspp") (name "pspp")
(version "1.0.1") (version "1.2.0")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -83,7 +84,7 @@
version ".tar.gz")) version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1r8smr5057993h90nx0mdnff8nxw9x546zzh6qpy4h3xblp1la5s")))) "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs (inputs
`(("cairo" ,cairo) `(("cairo" ,cairo)
@ -94,11 +95,15 @@
("readline" ,readline) ("readline" ,readline)
("gtk" ,gtk+) ("gtk" ,gtk+)
("gtksourceview" ,gtksourceview) ("gtksourceview" ,gtksourceview)
("spread-sheet-widget" ,spread-sheet-widget)
("zlib" ,zlib))) ("zlib" ,zlib)))
(native-inputs (native-inputs
`(("glib" ,glib "bin") ;for glib-genmarshal `(("autoconf" ,autoconf) ;for tests
("glib" ,glib "bin") ;for glib-genmarshal
("perl" ,perl) ("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/") (home-page "https://www.gnu.org/software/pspp/")
(synopsis "Statistical analysis") (synopsis "Statistical analysis")
(description (description
@ -116,7 +121,7 @@ be output in text, PostScript, PDF or HTML.")
(define r-with-tests (define r-with-tests
(package (package
(name "r-with-tests") (name "r-with-tests")
(version "3.5.0") (version "3.5.1")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "mirror://cran/src/base/R-" (uri (string-append "mirror://cran/src/base/R-"
@ -124,7 +129,7 @@ be output in text, PostScript, PDF or HTML.")
version ".tar.gz")) version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx")))) "1vap2k8kj5icy9naw61f9zyphf4rs0c9rxvil0zxkwx0xvsvyqq4"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:disallowed-references (,tzdata-for-tests) `(#: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 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2017 Petter <petter@mykolab.ch> ;;; Copyright © 2017 Petter <petter@mykolab.ch>
;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at> ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
;;; ;;;
@ -39,6 +40,7 @@
#:use-module (gnu packages) #:use-module (gnu packages)
#:use-module (gnu packages autotools) #:use-module (gnu packages autotools)
#:use-module (gnu packages compression) #:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages gnupg) #:use-module (gnu packages gnupg)
#:use-module (gnu packages java) #:use-module (gnu packages java)
#:use-module (gnu packages gnuzilla) #: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 "The Haskell XML Toolbox bases on the ideas of HaXml and HXML, but
introduces a more general approach for processing XML with Haskell.") introduces a more general approach for processing XML with Haskell.")
(license license:expat))) (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?)) ("KillUserProcesses" (yesno elogind-kill-user-processes?))
("KillOnlyUsers" (user-name-list elogind-kill-only-users)) ("KillOnlyUsers" (user-name-list elogind-kill-only-users))
("KillExcludeUsers" (user-name-list elogind-kill-exclude-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)) ("HandlePowerKey" (handle-action elogind-handle-power-key))
("HandleSuspendKey" (handle-action elogind-handle-suspend-key)) ("HandleSuspendKey" (handle-action elogind-handle-suspend-key))
("HandleHibernateKey" (handle-action elogind-handle-hibernate-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?)) ("SuspendKeyIgnoreInhibited" (yesno elogind-suspend-key-ignore-inhibited?))
("HibernateKeyIgnoreInhibited" (yesno elogind-hibernate-key-ignore-inhibited?)) ("HibernateKeyIgnoreInhibited" (yesno elogind-hibernate-key-ignore-inhibited?))
("LidSwitchIgnoreInhibited" (yesno elogind-lid-switch-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)) ("IdleAction" (handle-action elogind-idle-action))
("IdleActionSeconds" (non-negative-integer elogind-idle-action-seconds)) ("IdleActionSec" (non-negative-integer elogind-idle-action-seconds))
("RuntimeDirectorySize" ("RuntimeDirectorySize"
(identity (identity
(lambda (config) (lambda (config)
(match (elogind-runtime-directory-size-percent config) (match (elogind-runtime-directory-size-percent config)
(#f (non-negative-integer (elogind-runtime-directory-size config))) (#f (non-negative-integer (elogind-runtime-directory-size config)))
(percent (string-append (non-negative-integer percent) "%")))))) (percent (string-append (non-negative-integer percent) "%"))))))
("RemoveIpc" (yesno elogind-remove-ipc?)) ("RemoveIPC" (yesno elogind-remove-ipc?))
"[Sleep]" "[Sleep]"
("SuspendState" (sleep-list elogind-suspend-state)) ("SuspendState" (sleep-list elogind-suspend-state))
("SuspendMode" (sleep-list elogind-suspend-mode)) ("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 (update-profile profile manifest
#:dry-run? dry-run?) #:dry-run? dry-run?)
(munless dry-run? (munless dry-run?
(display-profile-news profile))))) (return (display-profile-news profile))))))
(define (honor-lets-encrypt-certificates! store) (define (honor-lets-encrypt-certificates! store)
"Tell Guile-Git to use the Let's Encrypt certificates." "Tell Guile-Git to use the Let's Encrypt certificates."