diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/local.mk | 2 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 512 | ||||
| -rw-r--r-- | gnu/packages/c.scm | 5 | ||||
| -rw-r--r-- | gnu/packages/cups.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/databases.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/emacs.scm | 75 | ||||
| -rw-r--r-- | gnu/packages/gtk.scm | 27 | ||||
| -rw-r--r-- | gnu/packages/guile.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/kodi.scm | 70 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 10 | ||||
| -rw-r--r-- | gnu/packages/music.scm | 79 | ||||
| -rw-r--r-- | gnu/packages/patches/hplip-remove-imageprocessor.patch | 232 | ||||
| -rw-r--r-- | gnu/packages/patches/vsearch-unbundle-cityhash.patch | 6 | ||||
| -rw-r--r-- | gnu/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch | 26 | ||||
| -rw-r--r-- | gnu/packages/python.scm | 29 | ||||
| -rw-r--r-- | gnu/packages/statistics.scm | 17 | ||||
| -rw-r--r-- | gnu/packages/xml.scm | 38 | ||||
| -rw-r--r-- | gnu/services/desktop.scm | 8 |
18 files changed, 774 insertions, 378 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 90dbe94025..545a7d173f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -813,6 +813,7 @@ dist_patch_DATA = \ %D%/packages/patches/higan-remove-march-native-flag.patch \ %D%/packages/patches/hubbub-sort-entities.patch \ %D%/packages/patches/hurd-fix-eth-multiplexer-dependency.patch \ + %D%/packages/patches/hplip-remove-imageprocessor.patch \ %D%/packages/patches/hydra-disable-darcs-test.patch \ %D%/packages/patches/icecat-avoid-bundled-libraries.patch \ %D%/packages/patches/icecat-CVE-2018-12383.patch \ @@ -1230,7 +1231,6 @@ dist_patch_DATA = \ %D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch \ %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch \ %D%/packages/patches/wpa-supplicant-krack-followups.patch \ - %D%/packages/patches/wxmaxima-do-not-use-old-gnuplot-parameters.patch \ %D%/packages/patches/x265-detect512-all-arches.patch \ %D%/packages/patches/xboing-CVE-2004-0149.patch \ %D%/packages/patches/xf86-video-ark-remove-mibstore.patch \ 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)))) diff --git a/gnu/services/desktop.scm b/gnu/services/desktop.scm index e038f97683..47d1096c6d 100644 --- a/gnu/services/desktop.scm +++ b/gnu/services/desktop.scm @@ -672,7 +672,7 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks." ("KillUserProcesses" (yesno elogind-kill-user-processes?)) ("KillOnlyUsers" (user-name-list elogind-kill-only-users)) ("KillExcludeUsers" (user-name-list elogind-kill-exclude-users)) - ("InhibitDelayMaxSecs" (non-negative-integer elogind-inhibit-delay-max-seconds)) + ("InhibitDelayMaxSec" (non-negative-integer elogind-inhibit-delay-max-seconds)) ("HandlePowerKey" (handle-action elogind-handle-power-key)) ("HandleSuspendKey" (handle-action elogind-handle-suspend-key)) ("HandleHibernateKey" (handle-action elogind-handle-hibernate-key)) @@ -682,16 +682,16 @@ include the @command{udisksctl} command, part of UDisks, and GNOME Disks." ("SuspendKeyIgnoreInhibited" (yesno elogind-suspend-key-ignore-inhibited?)) ("HibernateKeyIgnoreInhibited" (yesno elogind-hibernate-key-ignore-inhibited?)) ("LidSwitchIgnoreInhibited" (yesno elogind-lid-switch-ignore-inhibited?)) - ("HoldoffTimeoutSecs" (non-negative-integer elogind-holdoff-timeout-seconds)) + ("HoldoffTimeoutSec" (non-negative-integer elogind-holdoff-timeout-seconds)) ("IdleAction" (handle-action elogind-idle-action)) - ("IdleActionSeconds" (non-negative-integer elogind-idle-action-seconds)) + ("IdleActionSec" (non-negative-integer elogind-idle-action-seconds)) ("RuntimeDirectorySize" (identity (lambda (config) (match (elogind-runtime-directory-size-percent config) (#f (non-negative-integer (elogind-runtime-directory-size config))) (percent (string-append (non-negative-integer percent) "%")))))) - ("RemoveIpc" (yesno elogind-remove-ipc?)) + ("RemoveIPC" (yesno elogind-remove-ipc?)) "[Sleep]" ("SuspendState" (sleep-list elogind-suspend-state)) ("SuspendMode" (sleep-list elogind-suspend-mode)) |