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authorMarius Bakke <mbakke@fastmail.com>2018-11-09 17:02:08 +0100
committerMarius Bakke <mbakke@fastmail.com>2018-11-09 17:02:08 +0100
commit64461ba20a07a0cf3197de3e97cb44e0f66cebdc (patch)
treef48fd8e66879da30d5e2d89b16de6294ecd1192d /gnu/packages
parent55174e668f2985d1c4efda4fbf58f4061dde0db2 (diff)
parentcee9ab244f9ba9f3156b6aa50927418bae951096 (diff)
downloadguix-64461ba20a07a0cf3197de3e97cb44e0f66cebdc.tar
guix-64461ba20a07a0cf3197de3e97cb44e0f66cebdc.tar.gz
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm512
-rw-r--r--gnu/packages/c.scm5
-rw-r--r--gnu/packages/cups.scm6
-rw-r--r--gnu/packages/databases.scm4
-rw-r--r--gnu/packages/emacs.scm75
-rw-r--r--gnu/packages/gtk.scm27
-rw-r--r--gnu/packages/guile.scm6
-rw-r--r--gnu/packages/kodi.scm70
-rw-r--r--gnu/packages/maths.scm10
-rw-r--r--gnu/packages/music.scm79
-rw-r--r--gnu/packages/patches/hplip-remove-imageprocessor.patch232
-rw-r--r--gnu/packages/patches/vsearch-unbundle-cityhash.patch6
-rw-r--r--gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch26
-rw-r--r--gnu/packages/python.scm29
-rw-r--r--gnu/packages/statistics.scm17
-rw-r--r--gnu/packages/xml.scm38
16 files changed, 769 insertions, 373 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1fac960eff..8820ba0d8e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -753,15 +753,15 @@ e.g. microbiome samples, genomes, metagenomes.")
(package
(inherit base)
(arguments
- `(#:phases
- (modify-phases %standard-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))))))
+ (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)))))))))
(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.
- "-genome=./example/NC_000913.fna"
- "-out=./test2"
- "-complete=1"
- "-train=complete"))
- (file-exists? "test2.faa")
- (file-exists? "test2.ffn")
- (file-exists? "test2.gff")
- (file-exists? "test2.out")
- (zero? (system* ; Test incomplete sequences.
- frag
- "-genome=./example/NC_000913-fgs.ffn"
- "-out=out"
- "-complete=0"
- "-train=454_30")))))))))
+ ;; Test complete genome.
+ (invoke frag
+ "-genome=./example/NC_000913.fna"
+ "-out=./test2"
+ "-complete=1"
+ "-train=complete")
+ (unless (and (file-exists? "test2.faa")
+ (file-exists? "test2.ffn")
+ (file-exists? "test2.gff")
+ (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")
+ #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"
- "-classpath" "classes"
- "-d" "lib/"
- "net.sf.samtools.util.zip.IntelDeflater"))
- (with-directory-excursion "src/c/inteldeflater"
- (zero? (system* "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"
- "-o" "../../../lib/jni/libIntelDeflater.so"
- "IntelDeflater.o" "-lz" "-lstdc++"))))))
+ (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")
+ (with-directory-excursion "src/c/inteldeflater"
+ (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")
+ (invoke "gcc" "-shared"
+ "-o" "../../../lib/jni/libIntelDeflater.so"
+ "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)
- (display file)(display "\n")
- (not (zero? (system* "perl" file))))
- (find-files "t" ".*\\.t$"))))))
+ (for-each (lambda (file)
+ (display file)(display "\n")
+ (invoke "perl" file))
+ (find-files "t" ".*\\.t$"))
+ #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)
- (with-directory-excursion (string-append "tools/" dir)
- (zero? (apply system* "make" make-flags))))
- dirs)))
+ (for-each (lambda (dir)
+ (with-directory-excursion (string-append "tools/" dir)
+ (apply invoke "make" make-flags)))
+ dirs)
+ #t))
(add-after 'install 'install-additional-tools
(lambda* (#:key make-flags #:allow-other-keys)
- (fold (lambda (dir result)
- (with-directory-excursion (string-append "tools/" dir)
- (and result
- (zero? (apply system*
- `("make" ,@make-flags "install"))))))
- #t dirs)))))))
+ (for-each (lambda (dir)
+ (with-directory-excursion (string-append "tools/" dir)
+ (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"))
- (sha256
- (base32
- "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40"))))
+ (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
+ "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"
- (string-append "--build-prefix=" (getcwd) "/build")
- (string-append "--prefix=" out))))))
+ (invoke "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (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"))
- (sha256
- (base32
- "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m"))))
+ (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
+ "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"))
- (sha256
- (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/filevercmp.git")
+ (commit commit)))
+ (file-name (git-file-name name commit))
+ (sha256
+ (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
@@ -12025,10 +12017,10 @@ 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"
- (assoc-ref inputs "rapmap")
- "-C" "/tmp/rapmap"
- "--strip-components=1")
+ (invoke "tar" "xf"
+ (assoc-ref inputs "rapmap")
+ "-C" "/tmp/rapmap"
+ "--strip-components=1")
(mkdir-p src)
(mkdir-p include)
(for-each (lambda (file)
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index 83268e871c..d89b6ea00d 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -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)))
diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm
index d7db5dd1fa..4343910d59 100644
--- a/gnu/packages/cups.scm
+++ b/gnu/packages/cups.scm
@@ -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))))
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 5fc3607b76..d4a1d35d95 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -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
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 4821c18f6e..c6008e6a94 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -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+)))
diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm
index b553fa19cd..66456ab1e2 100644
--- a/gnu/packages/gtk.scm
+++ b/gnu/packages/gtk.scm
@@ -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")
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 0c65f0e78d..a77cacffe1 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -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
diff --git a/gnu/packages/kodi.scm b/gnu/packages/kodi.scm
index 6729f1f322..fe7f93fa53 100644
--- a/gnu/packages/kodi.scm
+++ b/gnu/packages/kodi.scm
@@ -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
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2f5798c055..3e1fe7c2c1 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -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)))
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index fdbfab796c..89ef58e80c 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -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
- (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)))))))))
+ (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.
+ (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"
- ;; FIXME: these tests fail
- "exclude:Actions/EditStaff"
- "exclude:Formats/PowerTabOldImport/MergeMultiBarRests"
- "exclude:Score/ViewFilter/FilterRule"
- "exclude:Score/ViewFilter/ViewFilter"
- "exclude:Formats/PowerTabOldImport/Directions"
- ))))
+ (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")
+ #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
- (modify-phases %standard-phases
- (replace 'check
- (lambda _
- (and
- ;; requires network connections
- ;; (zero? (system* "tests/mbtest"))
- (zero? (system* "tests/ctest"))))))))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ ;; requires network connections
+ ;; (invoke "tests/mbtest")
+ (invoke "tests/ctest")
+ #t)))))
(inputs `(("neon" ,neon)
("libxml2" ,libxml2)))
(native-inputs `(("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/patches/hplip-remove-imageprocessor.patch b/gnu/packages/patches/hplip-remove-imageprocessor.patch
new file mode 100644
index 0000000000..cde3ecba2d
--- /dev/null
+++ b/gnu/packages/patches/hplip-remove-imageprocessor.patch
@@ -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
+
diff --git a/gnu/packages/patches/vsearch-unbundle-cityhash.patch b/gnu/packages/patches/vsearch-unbundle-cityhash.patch
index b1ecb1f063..2a2ab13a73 100644
--- a/gnu/packages/patches/vsearch-unbundle-cityhash.patch
+++ b/gnu/packages/patches/vsearch-unbundle-cityhash.patch
@@ -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
diff --git a/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch b/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
deleted file mode 100644
index 345101bd3a..0000000000
--- a/gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch
+++ /dev/null
@@ -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))
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7704a19767..d90805071b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -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)))
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bb942b4fea..9bfa4c5683 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -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)
diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index e19d03588f..7f7ff6fc38 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -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))))
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-02 12:05:42 +0000