diff options
| author | Mark H Weaver <mhw@netris.org> | 2017-03-19 18:52:01 -0400 |
|---|---|---|
| committer | Mark H Weaver <mhw@netris.org> | 2017-03-19 18:52:12 -0400 |
| commit | f67337e23ec16b1e05fcdcc7953f68f13ed6770a (patch) | |
| tree | 766e98a6c4695228f0a066accf91f639791dad68 /gnu | |
| parent | b99eec83b861f6bee7afb7bd6ffcbdddd8f62b65 (diff) | |
| parent | e05fc441cd5528ba6c83b6371c27c1e87dd393e9 (diff) | |
| download | guix-f67337e23ec16b1e05fcdcc7953f68f13ed6770a.tar.gz | |
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu')
42 files changed, 2111 insertions, 596 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 9fc5953863..c92a5d09f8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -11,6 +11,7 @@ # Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> # Copyright © 2016, 2017 Alex Vong <alexvong1995@gmail.com> # Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> +# Copyright © 2017 Clément Lassieur <clement@lassieur.org> # # This file is part of GNU Guix. # @@ -680,6 +681,7 @@ dist_patch_DATA = \ %D%/packages/patches/libevent-2.0-CVE-2016-10195.patch \ %D%/packages/patches/libevent-2.0-CVE-2016-10196.patch \ %D%/packages/patches/libevent-2.0-CVE-2016-10197.patch \ + %D%/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch \ %D%/packages/patches/libevent-2.1-dns-tests.patch \ %D%/packages/patches/libevent-2.1-skip-failing-test.patch \ %D%/packages/patches/libextractor-ffmpeg-3.patch \ @@ -714,7 +716,6 @@ dist_patch_DATA = \ %D%/packages/patches/libtool-skip-tests2.patch \ %D%/packages/patches/libunwind-CVE-2015-3239.patch \ %D%/packages/patches/libvpx-CVE-2016-2818.patch \ - %D%/packages/patches/libwebp-CVE-2016-9085.patch \ %D%/packages/patches/libwmf-CAN-2004-0941.patch \ %D%/packages/patches/libwmf-CVE-2006-3376.patch \ %D%/packages/patches/libwmf-CVE-2007-0455.patch \ @@ -779,7 +780,6 @@ dist_patch_DATA = \ %D%/packages/patches/netsurf-longer-test-timeout.patch \ %D%/packages/patches/ngircd-handle-zombies.patch \ %D%/packages/patches/ngircd-no-dns-in-tests.patch \ - %D%/packages/patches/ninja-tests.patch \ %D%/packages/patches/ninja-zero-mtime.patch \ %D%/packages/patches/node-9077.patch \ %D%/packages/patches/nss-increase-test-timeout.patch \ @@ -809,6 +809,7 @@ dist_patch_DATA = \ %D%/packages/patches/ots-no-include-missing-file.patch \ %D%/packages/patches/p7zip-CVE-2016-9296.patch \ %D%/packages/patches/p7zip-remove-unused-code.patch \ + %D%/packages/patches/password-store-gnupg-compat.patch \ %D%/packages/patches/patchelf-page-size.patch \ %D%/packages/patches/patchelf-rework-for-arm.patch \ %D%/packages/patches/patchutils-xfail-gendiff-tests.patch \ @@ -878,6 +879,8 @@ dist_patch_DATA = \ %D%/packages/patches/python2-subprocess32-disable-input-test.patch \ %D%/packages/patches/qemu-CVE-2016-10155.patch \ %D%/packages/patches/qemu-CVE-2017-2615.patch \ + %D%/packages/patches/qemu-CVE-2017-2620.patch \ + %D%/packages/patches/qemu-CVE-2017-2630.patch \ %D%/packages/patches/qemu-CVE-2017-5525.patch \ %D%/packages/patches/qemu-CVE-2017-5526.patch \ %D%/packages/patches/qemu-CVE-2017-5552.patch \ @@ -965,6 +968,7 @@ dist_patch_DATA = \ %D%/packages/patches/upower-builddir.patch \ %D%/packages/patches/valgrind-enable-arm.patch \ %D%/packages/patches/vim-CVE-2017-5953.patch \ + %D%/packages/patches/virglrenderer-CVE-2017-6386.patch \ %D%/packages/patches/vorbis-tools-CVE-2014-9638+CVE-2014-9639.patch \ %D%/packages/patches/vorbis-tools-CVE-2014-9640.patch \ %D%/packages/patches/vorbis-tools-CVE-2015-6749.patch \ diff --git a/gnu/packages/apl.scm b/gnu/packages/apl.scm index 1c7d42b713..aa47edcd64 100644 --- a/gnu/packages/apl.scm +++ b/gnu/packages/apl.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> +;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,16 +31,16 @@ (define-public apl (package (name "apl") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/apl/apl-" version ".tar.gz")) (sha256 (base32 - "057zwzvvgcrrwsl52a27w86hgy31jqq6avqq629xj7yq90qah3ay")))) + "07xq8ddlmz8psvsmwr23gar108ri0lwmw0n6kpxcv8ypas1f5xlg")))) (build-system gnu-build-system) - (home-page "http://www.gnu.org/software/apl/") + (home-page "https://www.gnu.org/software/apl/") (inputs `(("gettext" ,gettext-minimal) ("lapack" ,lapack) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3387a2571a..90092ddf70 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -108,6 +108,9 @@ (base32 "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk")))) (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-nlme" ,r-nlme))) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description @@ -475,7 +478,7 @@ BED, GFF/GTF, VCF.") (inputs `(("bedtools" ,bedtools-2.18) ("samtools" ,samtools-0.1) - ("r" ,r) + ("r-minimal" ,r-minimal) ("r-foreach" ,r-foreach) ("r-xnomial" ,r-xnomial) ("r-domc" ,r-domc) @@ -1725,7 +1728,7 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.") ("python2-scipy" ,python2-scipy) ("python2-matplotlib" ,python2-matplotlib))) (propagated-inputs - `(("r" ,r) + `(("r-minimal" ,r-minimal) ("libsvm" ,libsvm) ("randomjungle" ,randomjungle))) (native-inputs @@ -4001,7 +4004,7 @@ partial genes, and identifies translation initiation sites.") ("grep" ,grep) ("sed" ,sed) ("gawk" ,gawk) - ("r" ,r) + ("r-minimal" ,r-minimal) ("r-ggplot2" ,r-ggplot2) ("coreutils" ,coreutils))) (home-page "http://sanger-pathogens.github.io/Roary") @@ -4116,7 +4119,7 @@ phylogenies.") (inputs `(("boost" ,boost) ("ncurses" ,ncurses) - ("r" ,r) + ("r-minimal" ,r-minimal) ("perl" ,perl) ("samtools" ,samtools-0.1) ("zlib" ,zlib))) @@ -4383,7 +4386,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "1.2.5") + (version "1.3.0") (source (origin (method url-fetch) @@ -4393,7 +4396,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "04y1fsmdnb5y86m3gg6f5g9wcscr6r25n7m8mdlcxy0i2q6w6cia")))) + "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -4447,7 +4450,7 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.7.0") + (version "2.8.2") (source (origin (method url-fetch) @@ -4457,67 +4460,77 @@ simultaneously.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0x1cg1x8vy0yjlkp0snc1533zcjhxqzqsaiwqk598n7vvw37n8lf")))) + "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target #:phases - (alist-replace - 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - ;; Override include path for libmagic - (substitute* "setup/package.prl" - (("name => 'magic', Include => '/usr/include'") - (string-append "name=> 'magic', Include => '" - (assoc-ref inputs "libmagic") - "/include" "'"))) - - ;; Install kdf5 library (needed by sra-tools) - (substitute* "build/Makefile.install" - (("LIBRARIES_TO_INSTALL =") - "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) - - (substitute* "build/Makefile.env" - (("CFLAGS =" prefix) - (string-append prefix "-msse2 "))) - - ;; The 'configure' script doesn't recognize things like - ;; '--enable-fast-install'. - (zero? (system* - "./configure" - (string-append "--build-prefix=" (getcwd) "/build") - (string-append "--prefix=" (assoc-ref outputs "out")) - (string-append "--debug") - (string-append "--with-xml2-prefix=" - (assoc-ref inputs "libxml2")) - (string-append "--with-ngs-sdk-prefix=" - (assoc-ref inputs "ngs-sdk")) - (string-append "--with-ngs-java-prefix=" - (assoc-ref inputs "java-ngs")) - (string-append "--with-hdf5-prefix=" - (assoc-ref inputs "hdf5")))))) - (alist-cons-after - 'install 'install-interfaces - (lambda* (#:key outputs #:allow-other-keys) - ;; Install interface libraries. On i686 the interface libraries - ;; are installed to "linux/gcc/i386", so we need to use the Linux - ;; architecture name ("i386") instead of the target system prefix - ;; ("i686"). - (mkdir (string-append (assoc-ref outputs "out") "/ilib")) - (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" - ,(system->linux-architecture - (or (%current-target-system) - (%current-system))) - "/rel/ilib") - (string-append (assoc-ref outputs "out") - "/ilib")) - ;; Install interface headers - (copy-recursively "interfaces" - (string-append (assoc-ref outputs "out") - "/include"))) - %standard-phases)))) + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + ;; Override include path for libmagic + (substitute* "setup/package.prl" + (("name => 'magic', Include => '/usr/include'") + (string-append "name=> 'magic', Include => '" + (assoc-ref inputs "libmagic") + "/include" "'"))) + + ;; Install kdf5 library (needed by sra-tools) + (substitute* "build/Makefile.install" + (("LIBRARIES_TO_INSTALL =") + "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) + + (substitute* "build/Makefile.env" + (("CFLAGS =" prefix) + (string-append prefix "-msse2 "))) + + ;; Override search path for ngs-java + (substitute* "setup/package.prl" + (("/usr/local/ngs/ngs-java") + (assoc-ref inputs "java-ngs"))) + + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (zero? (system* + "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" (assoc-ref outputs "out")) + (string-append "--debug") + (string-append "--with-xml2-prefix=" + (assoc-ref inputs "libxml2")) + (string-append "--with-ngs-sdk-prefix=" + (assoc-ref inputs "ngs-sdk")) + (string-append "--with-hdf5-prefix=" + (assoc-ref inputs "hdf5"))))))) + (add-after 'install 'install-interfaces + (lambda* (#:key outputs #:allow-other-keys) + ;; Install interface libraries. On i686 the interface libraries + ;; are installed to "linux/gcc/i386", so we need to use the Linux + ;; architecture name ("i386") instead of the target system prefix + ;; ("i686"). + (mkdir (string-append (assoc-ref outputs "out") "/ilib")) + (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" + ,(system->linux-architecture + (or (%current-target-system) + (%current-system))) + "/rel/ilib") + (string-append (assoc-ref outputs "out") + "/ilib")) + ;; Install interface headers + (copy-recursively "interfaces" + (string-append (assoc-ref outputs "out") + "/include")) + #t)) + ;; These files are needed by sra-tools. + (add-after 'install 'install-configuration-files + (lambda* (#:key outputs #:allow-other-keys) + (let ((target (string-append (assoc-ref outputs "out") "/kfg"))) + (mkdir target) + (install-file "libs/kfg/default.kfg" target) + (install-file "libs/kfg/certs.kfg" target)) + #t))))) (inputs `(("libxml2" ,libxml2) ("ngs-sdk" ,ngs-sdk) @@ -4728,7 +4741,7 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.7.0") + (version "2.8.2-1") (source (origin (method url-fetch) @@ -4738,13 +4751,19 @@ sequence itself can be retrieved from these databases.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "13paw7bq6y47d2pl0ac5gpgcqp1xsy1g7v1fwysm3hr8lb2dck17")))) + "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target #:make-flags - (list (string-append "VDB_LIBDIR=" + (list (string-append "DEFAULT_CRT=" + (assoc-ref %build-inputs "ncbi-vdb") + "/kfg/certs.kfg") + (string-append "DEFAULT_KFG=" + (assoc-ref %build-inputs "ncbi-vdb") + "/kfg/default.kfg") + (string-append "VDB_LIBDIR=" (assoc-ref %build-inputs "ncbi-vdb") ,(if (string-prefix? "x86_64" (or (%current-target-system) @@ -5337,6 +5356,7 @@ information as possible.") (propagated-inputs `(("r-cluster" ,r-cluster) ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) ("r-permute" ,r-permute))) (home-page "https://cran.r-project.org/web/packages/vegan") @@ -5418,7 +5438,8 @@ microarrays.") `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-survival" ,r-survival))) (home-page "http://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") (description @@ -5716,6 +5737,7 @@ annotation infrastructure.") ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-mass" ,r-mass) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://github.com/Kraus-Lab/groHMM") @@ -6115,7 +6137,8 @@ functionality.") (native-inputs `(("which" ,which))) (propagated-inputs - `(("r-graph" ,r-graph) + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) ("r-knitr" ,r-knitr) ("r-httr" ,r-httr) ("r-optparse" ,r-optparse) @@ -6643,6 +6666,7 @@ files.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) ("r-s4vectors" ,r-s4vectors))) (home-page "http://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") @@ -6834,8 +6858,9 @@ information about the latest version of the Gene Ontologies.") ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-go-db" ,r-go-db) - ("r-matrixstats" ,r-matrixstats) ("r-graph" ,r-graph) + ("r-lattice" ,r-lattice) + ("r-matrixstats" ,r-matrixstats) ("r-sparsem" ,r-sparsem))) (home-page "http://bioconductor.org/packages/topGO") (synopsis "Enrichment analysis for gene ontology") @@ -7611,9 +7636,9 @@ library implementing most of the pipeline's features.") `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) #t))))) (inputs - `(("r" ,r) + `(("r-minimal" ,r-minimal) ("r-rcas" ,r-rcas) - ("guile-next" ,guile-next) + ("guile-next" ,guile-2.2) ("guile-json" ,guile2.2-json) ("guile-redis" ,guile2.2-redis))) (native-inputs @@ -8227,7 +8252,8 @@ number detection tools.") "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn")))) (build-system r-build-system) (propagated-inputs - `(("r-genefilter" ,r-genefilter))) + `(("r-genefilter" ,r-genefilter) + ("r-mgcv" ,r-mgcv))) (home-page "http://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -8279,6 +8305,7 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (propagated-inputs `(("r-seqminer" ,r-seqminer) ("r-mvtnorm" ,r-mvtnorm) + ("r-mass" ,r-mass) ("r-compquadform" ,r-compquadform) ("r-getopt" ,r-getopt))) (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") @@ -8437,6 +8464,7 @@ analysis.") `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) ("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") @@ -8500,6 +8528,7 @@ specific parser.") (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") @@ -8593,6 +8622,85 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-seurat + ;; Source releases are only made for new x.0 versions. All newer versions + ;; are only released as pre-built binaries. At the time of this writing the + ;; latest binary release is 1.4.0.12, which is equivalent to this commit. + (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d") + (revision "1")) + (package + (name "r-seurat") + (version (string-append "1.4.0.12-" revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/satijalab/seurat") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl")) + ;; Delete pre-built jar. + (snippet + '(begin (delete-file "inst/java/ModularityOptimizer.jar") + #t)))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'build-jar + (lambda* (#:key inputs #:allow-other-keys) + (let ((classesdir "tmp-classes")) + (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) + (mkdir classesdir) + (and (zero? (apply system* `("javac" "-d" ,classesdir + ,@(find-files "java" "\\.java$")))) + (zero? (system* "jar" + "-cf" "inst/java/ModularityOptimizer.jar" + "-C" classesdir "."))))))))) + (native-inputs + `(("jdk" ,icedtea "jdk"))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-caret" ,r-caret) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-fastica" ,r-fastica) + ("r-fnn" ,r-fnn) + ("r-fpc" ,r-fpc) + ("r-gdata" ,r-gdata) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-lars" ,r-lars) + ("r-mixtools" ,r-mixtools) + ("r-pbapply" ,r-pbapply) + ("r-plyr" ,r-plyr) + ("r-ranger" ,r-ranger) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppprogress" ,r-rcppprogress) + ("r-reshape2" ,r-reshape2) + ("r-rocr" ,r-rocr) + ("r-rtsne" ,r-rtsne) + ("r-stringr" ,r-stringr) + ("r-tclust" ,r-tclust) + ("r-tsne" ,r-tsne) + ("r-vgam" ,r-vgam))) + (home-page "http://www.satijalab.org/seurat") + (synopsis "Seurat is an R toolkit for single cell genomics") + (description + "This package is an R package designed for QC, analysis, and +exploration of single cell RNA-seq data. It easily enables widely-used +analytical techniques, including the identification of highly variable genes, +dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering +algorithms; density clustering, hierarchical clustering, k-means, and the +discovery of differentially expressed genes and markers.") + (license license:gpl3)))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 86a776910a..5fc6bf2e29 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -259,7 +259,7 @@ tree binary files. These are board description files used by Linux and BSD.") (define u-boot (package (name "u-boot") - (version "2017.01") + (version "2017.03") (source (origin (method url-fetch) (uri (string-append @@ -267,7 +267,7 @@ tree binary files. These are board description files used by Linux and BSD.") "u-boot-" version ".tar.bz2")) (sha256 (base32 - "1wpc51jm3zyibgcr78jng2yksqvrya76bxgsr4pcyjrsz5sm2hkc")))) + "0gqihplap05dlpwdb971wsqyv01nz2vabwq5g5649gr5jczsyjzm")))) (native-inputs `(("bc" ,bc) ("dtc" ,dtc) diff --git a/gnu/packages/datastructures.scm b/gnu/packages/datastructures.scm index b9e6061238..ef249b9659 100644 --- a/gnu/packages/datastructures.scm +++ b/gnu/packages/datastructures.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -19,6 +19,7 @@ (define-module (gnu packages datastructures) #:use-module (gnu packages) + #:use-module (gnu packages perl) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) @@ -92,3 +93,26 @@ hashes (CTPH), also called fuzzy checksums. It can identify similar files that have sequences of identical bytes in the same order, even though bytes in between these sequences may be different in both content and length.") (license license:gpl2+))) + +(define-public liburcu + (package + (name "liburcu") + (version "0.9.3") + (source (origin + (method url-fetch) + (uri (string-append "https://www.lttng.org/files/urcu/" + "userspace-rcu-" version ".tar.bz2")) + (sha256 + (base32 + "01j0xp3f0w147yfyzybkjvb7i67i7prsvnkssgvgwry9lvk35khv")))) + (build-system gnu-build-system) + (native-inputs + `(("perl" ,perl))) ; for tests + (home-page "http://liburcu.org/") + (synopsis "User-space RCU data synchronisation library") + (description "liburcu is a user-space @dfn{Read-Copy-Update} (RCU) data +synchronisation library. It provides read-side access that scales linearly +with the number of cores. liburcu-cds provides efficient data structures +based on RCU and lock-free algorithms. These structures include hash tables, +queues, stacks, and doubly-linked lists.") + (license license:lgpl2.1+))) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 541979f587..d09abc1366 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 John Darrington <jmd@gnu.org> ;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is> -;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. @@ -24,17 +24,25 @@ ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. (define-module (gnu packages dns) + #:use-module (gnu packages admin) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages databases) #:use-module (gnu packages crypto) + #:use-module (gnu packages datastructures) #:use-module (gnu packages glib) #:use-module (gnu packages groff) + #:use-module (gnu packages groff) + #:use-module (gnu packages libedit) #:use-module (gnu packages libevent) + #:use-module (gnu packages libidn) #:use-module (gnu packages linux) + #:use-module (gnu packages ncurses) + #:use-module (gnu packages nettle) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages tls) + #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) @@ -134,8 +142,8 @@ and BOOTP/TFTP for network booting of diskless machines.") (lambda _ (zero? (system* "make" "force-test"))))))) (synopsis "An implementation of the Domain Name System") - (description "BIND is an implementation of the Domain Name System (DNS) -protocols for the Internet. It is a reference implementation of those + (description "BIND is an implementation of the @dfn{Domain Name System} +(DNS) protocols for the Internet. It is a reference implementation of those protocols, but it is also production-grade software, suitable for use in high-volume and high-reliability applications. The name BIND stands for \"Berkeley Internet Name Domain\", because the software originated in the early @@ -298,9 +306,80 @@ asynchronous fashion.") "--disable-nsid"))) (home-page "http://www.yadifa.eu/") (synopsis "Authoritative DNS name server") - (description "YADIFA is an authorative name server for the Domain Name -System (DNS). It aims for both higher performance and a smaller memory + (description "YADIFA is an authoritative name server for the @dfn{Domain +Name System} (DNS). It aims for both higher performance and a smaller memory footprint than other implementations, while remaining fully RFC-compliant. -YADIFA supports dynamic record updates and the Domain Name System Security -Extensions (DNSSEC).") +YADIFA supports dynamic record updates and the @dfn{Domain Name System Security +Extensions} (DNSSEC).") (license license:bsd-3))) + +(define-public knot + (package + (name "knot") + (version "2.4.1") + (source (origin + (method url-fetch) + (uri (string-append "https://secure.nic.cz/files/knot-dns/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0k3hkc6vqj8yd479zdn80ki5f0vnjhrm4fka7kfj9z7mkgwxsr60")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove bundled libraries and dependencies on them. + (substitute* "configure" + (("src/contrib/dnstap/Makefile") "")) + (substitute* "src/Makefile.in" + (("contrib/dnstap ") "")) + (with-directory-excursion "src/contrib" + (for-each delete-file-recursively + (list "dnstap" "lmdb"))))))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("gnutls" ,gnutls) + ("jansson" ,jansson) + ("libcap-ng" ,libcap-ng) + ("libedit" ,libedit) + ("libidn" ,libidn) + ("liburcu" ,liburcu) + ("lmdb" ,lmdb) + ("ncurses" ,ncurses) + ("nettle" ,nettle))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'disable-directory-pre-creation + (lambda _ + ;; Don't install empty directories like ‘/etc’ outside the store. + (substitute* "src/Makefile.in" (("\\$\\(INSTALL\\) -d") "true")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (doc (string-append out "/share/doc/knot")) + (etc (string-append doc "/examples/etc"))) + (zero? + (system* "make" + (string-append "config_dir=" etc) + "install")))))) + #:configure-flags + (list "--sysconfdir=/etc" + "--localstatedir=/var" + "--enable-rosedb" ; serve static records from a database + (string-append "--with-bash-completions=" + (assoc-ref %outputs "out") + "/etc/bash_completion.d")))) + (home-page "https://www.knot-dns.cz/") + (synopsis "Authoritative DNS name server") + (description "Knot DNS is an authorative name server for the @dfn{Domain +Name System} (DNS), designed to meet the needs of root and @dfn{top-level +domain} (TLD) name servers. It is implemented as a threaded daemon and uses a +number of programming techniques to improve speed. For example, the responder +is completely lock-free, resulting in a very high response rate. Other features +include automatic @dfn{DNS Security Extensions} (DNSSEC) signing, dynamic record +synthesis, and on-the-fly re-configuration.") + (license (list license:expat ; src/contrib/{hat-trie,murmurhash3} + license:lgpl2.0+ ; parts of scr/contrib/ucw + license:gpl3+)))) ; everything else diff --git a/gnu/packages/documentation.scm b/gnu/packages/documentation.scm index 792e70ecdd..ba8eea3931 100644 --- a/gnu/packages/documentation.scm +++ b/gnu/packages/documentation.scm @@ -85,8 +85,17 @@ release/xsl/current") (string-append (assoc-ref inputs "docbook-xsl") "/xml/xsl/docbook-xsl-" ,(package-version docbook-xsl))))) + #t)) + ;; Do the same for docbook-xml. + (add-before 'install 'make-local-docbook-xml + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "docbook45.conf" + (("http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd") + (string-append (assoc-ref inputs "docbook-xml") + "/xml/dtd/docbook/docbookx.dtd"))) #t))))) (inputs `(("python" ,python-2) + ("docbook-xml" ,docbook-xml) ("docbook-xsl" ,docbook-xsl) ("libxml2" ,libxml2) ("libxslt" ,libxslt))) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index c6e62acb7a..b84faaff07 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -2179,7 +2179,7 @@ in @code{html-mode}.") (define-public emacs-slime (package (name "emacs-slime") - (version "2.18") + (version "2.19") (source (origin (file-name (string-append name "-" version ".tar.gz")) @@ -2189,7 +2189,7 @@ in @code{html-mode}.") version ".tar.gz")) (sha256 (base32 - "146avwbwr6mw0nmgyihx8gkr0mv6al7a73igzxvysj62000cqvlj")))) + "1jhaq5cn89k45nzyl0jd12gmjxnh1bq9jlfwrxba342agxsscb0p")))) (build-system emacs-build-system) (native-inputs `(("texinfo" ,texinfo))) @@ -2924,7 +2924,7 @@ E-Prime forbids the use of the \"to be\" form to strengthen your writing.") (string-append "SHELL = " (which "sh"))))))))) (inputs `(("emacs" ,emacs-minimal) - ("r" ,r))) + ("r-minimal" ,r-minimal))) (native-inputs `(("perl" ,perl) ("texinfo" ,texinfo) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index af95f149f7..97fddc2a84 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -350,7 +350,13 @@ standards.") (mozilla-patch "icecat-bug-1341137-pt3.patch" "69f3d44bdb48" "1ad7rw6nmg3c49ylqxlqqkb6cm2f0ygfzrigs6b60a2zkjqhbl0h") (mozilla-patch "icecat-bug-1341137-pt4.patch" "22546e2cee64" "0gbwxa3p7qkq53hwnvxcqhx8h34qmnjdxy0h3ajik4mw76vrna9s") (mozilla-patch "icecat-bug-1341137-pt5.patch" "e5083d8a855a" "1247vbpqzf007nigbxxqd6nwgr1dxd4p8cd0dr45afqh19vhlapj") - (mozilla-patch "icecat-bug-1339122.patch" "b0d156c7445e" "026jp5bb565yvhkmmicgygcn1lmak85p0466yl1vnjlx1rc8n724"))) + (mozilla-patch "icecat-bug-1339122.patch" "b0d156c7445e" "026jp5bb565yvhkmmicgygcn1lmak85p0466yl1vnjlx1rc8n724") + (mozilla-patch "icecat-bug-1319087.patch" "9cd44507fd65" "0mcfvby53r2150libazgrgaqrdyvl0g6cr1f01dsya3cgmc9mkcn") + (mozilla-patch "icecat-bug-1342661.patch" "d449995ef7d9" "1kz8k2jxvhqpjgrsj7r0kqq79036lrkfnx5pvdnsl59np9128j81") + (mozilla-patch "icecat-bug-1343261.patch" "9b5374019b58" "0v5w50r5ys4jjy1lpks280cq8paw7wdy9mrk7szzq7nlcxz90is7") + (mozilla-patch "icecat-bug-1343552-pt1.patch" "08bc7a3330e4" "1hsvffscqc4zflni866ilylgi3a13wz0n882z85xplbhwhc9lcfj") + (mozilla-patch "icecat-bug-1343552-pt2.patch" "8c61ebe37f1b" "1fjsr6bzfyd1zqzz2pglwh2ckys95h21wy3j4rlwkz66057z53qq") + (mozilla-patch "icecat-bug-1340718.patch" "bfa75fc20c2b" "08gksd06lwbb5ykdrk9gh2cb9bximwxhbxl3rprz64jj2bnmd3dq"))) (modules '((guix build utils))) (snippet '(begin diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 59de06b62f..b621d8274d 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -217,9 +217,9 @@ without requiring the source code to be rewritten.") (properties '((hidden? . #t))) ;people should install 'guile-2.0' (replacement #f))) -(define-public guile-next +(define-public guile-2.2 (package (inherit guile-2.0) - (name "guile-next") + (name "guile") (version "2.2.0") (replacement #f) (source (origin @@ -236,12 +236,8 @@ without requiring the source code to be rewritten.") ;; times (almost 3 hours on a 4-core Intel i5). (snippet '(for-each delete-file (find-files "prebuilt" "\\.go$"))))) - (synopsis "Snapshot of what will become version 2.2 of GNU Guile") (properties '((timeout . 72000) ;20 hours - (max-silent-time . 10800) ;3 hours (needed on ARM) - (upstream-name . "guile") - (ftp-server . "alpha.gnu.org") - (ftp-directory . "/gnu/guile"))) + (max-silent-time . 10800))) ;3 hours (needed on ARM) (native-search-paths (list (search-path-specification (variable "GUILE_LOAD_PATH") @@ -251,23 +247,28 @@ without requiring the source code to be rewritten.") (files '("lib/guile/2.2/site-ccache" "share/guile/site/2.2"))))))) -(define (guile-2.2-package-name name) - "Return NAME with a \"guile2.2-\" prefix instead of \"guile-\", when -applicable." - (if (string-prefix? "guile-" name) - (string-append "guile2.2-" - (string-drop name - (string-length "guile-"))) - name)) +(define (guile-variant-package-name prefix) + (lambda (name) + "Return NAME with PREFIX instead of \"guile-\", when applicable." + (if (string-prefix? "guile-" name) + (string-append prefix "-" + (string-drop name + (string-length "guile-"))) + name))) (define package-for-guile-2.2 ;; A procedure that rewrites the dependency tree of the given package to use - ;; GUILE-NEXT instead of GUILE-2.0. - (package-input-rewriting `((,guile-2.0 . ,guile-next)) - guile-2.2-package-name)) + ;; GUILE-2.2 instead of GUILE-2.0. + (package-input-rewriting `((,guile-2.0 . ,guile-2.2)) + (guile-variant-package-name "guile2.2"))) + +(define package-for-guile-2.0 + ;; Likewise, but the other way around. :-) + (package-input-rewriting `((,guile-2.2 . ,guile-2.0)) + (guile-variant-package-name "guile2.0"))) (define-public guile-for-guile-emacs - (package (inherit guile-next) + (package (inherit guile-2.2) (name "guile-for-guile-emacs") (version "20150510.d8d9a8d") (source (origin @@ -282,7 +283,7 @@ applicable." (substitute-keyword-arguments `(;; Tests aren't passing for now. ;; Obviously we should re-enable this! #:tests? #f - ,@(package-arguments guile-next)) + ,@(package-arguments guile-2.2)) ((#:phases phases) `(modify-phases ,phases (add-after 'unpack 'autogen @@ -300,7 +301,7 @@ applicable." ("flex" ,flex) ("texinfo" ,texinfo) ("gettext" ,gettext-minimal) - ,@(package-native-inputs guile-next))) + ,@(package-native-inputs guile-2.2))) ;; Same as in guile-2.0 (native-search-paths (list (search-path-specification @@ -441,7 +442,7 @@ more.") (build-system gnu-build-system) (native-inputs `(("pkgconfig" ,pkg-config) ("gperf" ,gperf))) - (inputs `(("guile" ,guile-2.0))) + (inputs `(("guile" ,guile-2.2))) (synopsis "Framework for building readers for GNU Guile") (description "Guile-Reader is a simple framework for building readers for GNU Guile. @@ -458,8 +459,10 @@ many readers as needed).") (home-page "http://www.nongnu.org/guile-reader/") (license license:gpl3+))) +(define-public guile2.0-reader + (package-for-guile-2.0 guile-reader)) (define-public guile2.2-reader - (package-for-guile-2.2 guile-reader)) + (deprecated-package "guile2.2-reader" guile-reader)) (define-public guile-ncurses (package @@ -1042,7 +1045,7 @@ Guile's foreign function interface.") `(("pkg-config" ,pkg-config) ("texinfo" ,texinfo))) (inputs - `(("guile" ,guile-2.0))) + `(("guile" ,guile-2.2))) (propagated-inputs `(("guile-reader" ,guile-reader) ("guile-commonmark" ,guile-commonmark))) @@ -1053,9 +1056,11 @@ interface for reading articles in any format.") (home-page "http://haunt.dthompson.us") (license license:gpl3+))) +(define-public guile2.0-haunt + (package-for-guile-2.0 + (package (inherit haunt) (name "guile2.0-haunt")))) (define-public guile2.2-haunt - (package-for-guile-2.2 - (package (inherit haunt) (name "guile2.2-haunt")))) + (deprecated-package "guile2.2-haunt" haunt)) (define-public guile-config (package @@ -1413,7 +1418,7 @@ you send to a FIFO file.") "/site/@GUILE_EFFECTIVE_VERSION@")))))) (build-system gnu-build-system) (inputs - `(("guile" ,guile-2.0))) + `(("guile" ,guile-2.2))) (synopsis "CommonMark parser for Guile") (description "guile-commonmark is a library for parsing CommonMark, a fully specified @@ -1424,8 +1429,10 @@ is no support for parsing block and inline level HTML.") (home-page "https://github.com/OrangeShark/guile-commonmark") (license license:lgpl3+))) +(define-public guile2.0-commonmark + (package-for-guile-2.0 guile-commonmark)) (define-public guile2.2-commonmark - (package-for-guile-2.2 guile-commonmark)) + (deprecated-package "guile2.2-commonmark" guile-commonmark)) (define-public guile-bytestructures (package @@ -1616,18 +1623,18 @@ and then run @command{scm example.scm}.") (define-public guile-8sync (package (name "guile-8sync") - (version "0.4.1") + (version "0.4.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/8sync/8sync-" version ".tar.gz")) (sha256 (base32 - "1fvf8d2s3vvg4nyskbqaiqmlm2x571hv7hizcnmny45zvalydr9h")))) + "031wm13srak3wsnll7j2mbbi29g1pcm4swdb71ds9yn567pn20qw")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) - ("guile" ,guile-next) + ("guile" ,guile-2.2) ("pkg-config" ,pkg-config) ("texinfo" ,texinfo))) (arguments @@ -1643,7 +1650,7 @@ and then run @command{scm example.scm}.") "GNU 8sync (pronounced \"eight-sync\") is an asynchronous programming library for GNU Guile based on the actor model. -Note that 8sync is only available for Guile 2.2 (guile-next in Guix).") +Note that 8sync is only available for Guile 2.2.") (license license:lgpl3+))) (define-public guile-fibers @@ -1662,7 +1669,7 @@ Note that 8sync is only available for Guile 2.2 (guile-next in Guix).") `(("texinfo" ,texinfo) ("pkg-config" ,pkg-config))) (inputs - `(("guile" ,guile-next))) + `(("guile" ,guile-2.2))) (synopsis "Lightweight concurrency facility for Guile") (description "Fibers is a Guile library that implements a a lightweight concurrency diff --git a/gnu/packages/hurd.scm b/gnu/packages/hurd.scm index ba91b60bea..2d7b7b2ac0 100644 --- a/gnu/packages/hurd.scm +++ b/gnu/packages/hurd.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com> +;;; Copyright © 2014, 2015, 2016, 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -210,3 +210,35 @@ Library for GNU/Hurd.") Hurd-minimal package which are needed for both glibc and GCC.") (home-page (package-home-page hurd-headers)) (license (package-license hurd-headers)))) + +(define-public gnumach + (package + (name "gnumach") + (version "1.8") + (source (origin + (method url-fetch) + (uri (gnumach-source-url version)) + (sha256 + (base32 + "02hygsfpd2dljl5lg1vjjg9pizi9jyxd4aiiqzjshz6jax62jm9f")))) + (build-system gnu-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (add-after 'install 'produce-image + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (boot (string-append out "/boot"))) + (and (zero? (system* "make" "gnumach.gz")) + (begin + (install-file "gnumach.gz" boot) + #t)))))))) + (native-inputs + `(("mig" ,mig) + ("perl" ,perl))) + (supported-systems (cons "i686-linux" %hurd-systems)) + (home-page + "https://www.gnu.org/software/hurd/microkernel/mach/gnumach.html") + (synopsis "Microkernel of the GNU system") + (description + "GNU Mach is the microkernel upon which a GNU Hurd system is based.") + (license gpl2+))) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index fd2eefab0d..2989ea006f 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -3,10 +3,10 @@ ;;; Copyright © 2013, 2015, 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2014, 2015 Alex Kost <alezost@gmail.com> -;;; Copyright © 2014, 2016 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2015 Amirouche Boubekki <amirouche@hypermove.net> -;;; Copyright © 2014 John Darrington <jmd@gnu.org> +;;; Copyright © 2014, 2017 John Darrington <jmd@gnu.org> ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016, 2017 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> @@ -14,6 +14,7 @@ ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org> +;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -90,6 +91,52 @@ library. It supports almost all PNG features and is extensible.") (license license:zlib) (home-page "http://www.libpng.org/pub/png/libpng.html"))) +(define-public libpng-apng + (package + (inherit libpng) + (replacement #f) ;libpng's replacement doesn't apply here + (name "libpng-apng") + (version (package-version libpng)) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-apng + (lambda* (#:key inputs #:allow-other-keys) + (define (apply-patch file) + (zero? (system* "patch" "-p1" "--force" + "--input" file))) + (let ((apng.gz (assoc-ref inputs "apng"))) + (format #t "Applying APNG patch '~a'...~%" + apng.gz) + (system (string-append "gunzip < " apng.gz " > the-patch")) + (and (apply-patch "the-patch") + (for-each apply-patch + (find-files "\\.patch")))) + #t)) + (add-before 'configure 'no-checks + (lambda _ + (substitute* "Makefile.in" + (("^scripts/symbols.chk") "") + (("check: scripts/symbols.chk") "")) + #t))))) + (inputs + `(("apng" ,(origin + (method url-fetch) + (uri + (string-append "mirror://sourceforge/libpng-apng/libpng16/" + version "/libpng-" version "-apng.patch.gz")) + (sha256 + (base32 + "026r0gbkf6d6v54wca02cdxln8sj4m2c1yk62sj2aasv2ki2ffh5")))))) + (native-inputs + `(("libtool" ,libtool))) + (synopsis "APNG patch for libpng") + (description + "APNG (Animated Portable Network Graphics) is an unofficial +extension of the APNG (Portable Network Graphics) format. +APNG patch provides APNG support to libpng.") + (home-page "https://sourceforge.net/projects/libpng-apng/"))) + (define-public libpng-1.2 (package (inherit libpng) @@ -721,17 +768,16 @@ multi-dimensional image processing.") (define-public libwebp (package (name "libwebp") - (version "0.5.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (string-append "http://downloads.webmproject.org/releases/webp/libwebp-" version ".tar.gz")) - (patches (search-patches "libwebp-CVE-2016-9085.patch")) (sha256 (base32 - "1pqki1g8nzi8qgciysypd5r38zccv81np1dn43g27830rmpnrmka")))) + "0h1brwkyxc7lb8lc53aacdks5vc1y9hzngqi41gg7y6l56912a69")))) (build-system gnu-build-system) (inputs `(("freeglut" ,freeglut) @@ -1081,3 +1127,47 @@ interface. It supports color space extensions that allow it to compress from and decompress to 32-bit and big-endian pixel buffers (RGBX, XBGR, etc.).") (license (list license:bsd-3 ; jsimd*.[ch] and most of simd/ license:ijg)))) ; the rest + +(define-public niftilib + (package + (name "niftilib") + (version "2.0.0") + (source (origin + (method url-fetch) + (uri (list (string-append "mirror://sourceforge/niftilib/" + "nifticlib/nifticlib_" + (string-join (string-split version #\.) "_") + "/nifticlib-" version ".tar.gz"))) + (sha256 + (base32 "123z9bwzgin5y8gi5ni8j217k7n683whjsvg0lrpii9flgk8isd3")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ; there is no test target + #:parallel-build? #f ; not supported + #:make-flags + (list "SHELL=bash" + (string-append "ZLIB_INC=" + (assoc-ref %build-inputs "zlib") "/include") + ;; Append "-fPIC" to CFLAGS. + (string-append "CFLAGS=" + "-Wall -ansi -pedantic -fPIC")) + #:phases + (modify-phases %standard-phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each + (lambda (dir) + (copy-recursively dir (string-append out "/" dir))) + '("bin" "lib" "include"))) + #t)) + (delete 'configure)))) + (inputs + `(("zlib" ,zlib))) + (synopsis "Library for reading and writing files in the nifti-1 format") + (description "Niftilib is a set of i/o libraries for reading and writing +files in the nifti-1 data format - a binary file format for storing +medical image data, e.g. magnetic resonance image (MRI) and functional MRI +(fMRI) brain images.") + (home-page "http://niftilib.sourceforge.net") + (license license:public-domain))) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index 3d06df9ed8..f4ff7fcbef 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -298,14 +298,14 @@ and extensible with plugins and scripts.") (define-public limnoria (package (name "limnoria") - (version "2016.08.07") + (version "2017.01.10") (source (origin (method url-fetch) (uri (pypi-uri "limnoria" version)) (sha256 (base32 - "0w1d98hfhn4iqrczam7zahhqsvxa79n3xfcrm4jwkg5lba4f9ccm")))) + "0va7iiwkrd5miibpaphfm2jlfsmaazbqb8izkmlnlzkqnskhz1ff")))) (build-system python-build-system) (inputs `(("python-pytz" ,python-pytz) diff --git a/gnu/packages/libevent.scm b/gnu/packages/libevent.scm index 551fbf7206..1bfdefd7b5 100644 --- a/gnu/packages/libevent.scm +++ b/gnu/packages/libevent.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> -;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> +;;; Copyright © 2015, 2017 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr> ;;; Copyright © 2016 David Thompson <davet@gnu.org> ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com> @@ -74,18 +74,20 @@ loop.") (inherit libevent) (version "2.0.22") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/libevent/libevent/releases/download/release-" - version "-stable/libevent-" version "-stable.tar.gz")) - (sha256 - (base32 - "18qz9qfwrkakmazdlwxvjmw8p76g70n3faikwvdwznns1agw9hki")) - (patches (search-patches - "libevent-dns-tests.patch" - "libevent-2.0-CVE-2016-10195.patch" - "libevent-2.0-CVE-2016-10196.patch" - "libevent-2.0-CVE-2016-10197.patch")))))) + (method url-fetch) + (uri (string-append + "https://github.com/libevent/libevent/releases/download/release-" + version "-stable/libevent-" version "-stable.tar.gz")) + (sha256 + (base32 + "18qz9qfwrkakmazdlwxvjmw8p76g70n3faikwvdwznns1agw9hki")) + (patches + (search-patches + "libevent-dns-tests.patch" + "libevent-2.0-CVE-2016-10195.patch" + "libevent-2.0-CVE-2016-10196.patch" + "libevent-2.0-CVE-2016-10197.patch" + "libevent-2.0-evbuffer-add-use-last-with-datap.patch")))))) (define-public libev (package diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 62b1971f02..8f13a38b5f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -348,8 +348,8 @@ It has been modified to remove all non-free binary blobs.") (define %intel-compatible-systems '("x86_64-linux" "i686-linux")) -(define %linux-libre-version "4.10.2") -(define %linux-libre-hash "01kinnv40lqsk6fyz1k7hkx2diyg4mgp28bwraar5sii1gqmcw7k") +(define %linux-libre-version "4.10.4") +(define %linux-libre-hash "0cmz4y8pb3sdag32bsrn7vg1i8v9rymfspg85ipkbamm53c7v54g") (define-public linux-libre (make-linux-libre %linux-libre-version @@ -358,14 +358,14 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.14" - "104715z772if18qi61jbyhvidfh6qnwkiy0m9aa8irxgzs1pk9mn" + (make-linux-libre "4.9.16" + "0n7y7h7ps4l1pr9d0m75hkw41jnfyw301r343dsaznwc0lpq3ch7" %intel-compatible-systems #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.53" - "07sfg4i506f3hmd9k4iimnq1w3x0980qxnh649d1sldqxbmhdgjs" + (make-linux-libre "4.4.55" + "1m4h3wi4j573hny1yfi9qwkiicx2bx3gwy52zpr8bhxpyqz0d2dl" %intel-compatible-systems #:configuration-file kernel-config)) @@ -2764,7 +2764,7 @@ and copy/paste text in the console and in xterm.") (define-public btrfs-progs (package (name "btrfs-progs") - (version "4.10") + (version "4.10.1") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/kernel/" @@ -2772,7 +2772,7 @@ and copy/paste text in the console and in xterm.") "btrfs-progs-v" version ".tar.xz")) (sha256 (base32 - "1njw2nrm51380d8arvqfmspa3app9353yd7hiddas3gpkaiwrjs4")))) + "06hs20jwa15xybbmlalba8wvhv3slq1g0wrqrgyh7ll5y11bc5kc")))) (build-system gnu-build-system) (outputs '("out" "static")) ; static versions of binaries in "out" (~16MiB!) @@ -2807,9 +2807,9 @@ and copy/paste text in the console and in xterm.") ("which" ,which))) (home-page "https://btrfs.wiki.kernel.org/") (synopsis "Create and manage btrfs copy-on-write file systems") - (description "Btrfs is a copy-on-write (CoW) file system for Linux aimed at -implementing advanced features while focusing on fault tolerance, repair and -easy administration.") + (description "Btrfs is a @dfn{copy-on-write} (CoW) file system for Linux +aimed at implementing advanced features while focusing on fault tolerance, +repair and easy administration.") ;; GPL2+: crc32.c, radix-tree.c, raid6.c, rbtree.c. ;; GPL2: Everything else. (license (list license:gpl2 license:gpl2+)))) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 7bad833b38..30f005a331 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -26,6 +26,7 @@ #:use-module (guix svn-download) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system ocaml) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages autotools) @@ -35,6 +36,7 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages image) #:use-module (gnu packages maths) + #:use-module (gnu packages ocaml) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -239,6 +241,39 @@ networks) based on simulation of (stochastic) flow in graphs.") ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html (license license:gpl3))) +(define-public ocaml-mcl + (package + (name "ocaml-mcl") + (version "12-068oasis4") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/fhcrc/mcl/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110")))) + (build-system ocaml-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'patch-paths + (lambda _ + (substitute* "configure" + (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh")))) + (substitute* "setup.ml" + (("LDFLAGS=-fPIC") + (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))) + #t))))) + (home-page "https://github.com/fhcrc/mcl") + (synopsis "OCaml wrappers around MCL") + (description + "This package provides OCaml bindings for the MCL graph clustering +algorithm.") + (license license:gpl3))) + (define-public randomjungle (package (name "randomjungle") @@ -402,7 +437,7 @@ sample proximities between pairs of cases.") (inputs `(("python" ,python) ("numpy" ,python-numpy) - ("r" ,r) + ("r-minimal" ,r-minimal) ("octave" ,octave) ("swig" ,swig) ("hdf5" ,hdf5) @@ -460,25 +495,6 @@ adaptive sparsity and the Wong algorithm for adaptively sparse gaussian geometric models.") (license license:lgpl3+))) -(define-public r-nnet - (package - (name "r-nnet") - (version "7.3-12") - (source - (origin - (method url-fetch) - (uri (cran-uri "nnet" version)) - (sha256 - (base32 - "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7")))) - (build-system r-build-system) - (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") - (synopsis "Feed-forward neural networks and multinomial log-linear models") - (description - "This package provides functions for feed-forward neural networks with a -single hidden layer, and for multinomial log-linear models.") - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-kernlab (package (name "r-kernlab") diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 03567ba083..ed13556cb4 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> -;;; Copyright © 2014, 2016 John Darrington <jmd@gnu.org> +;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org> ;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> @@ -17,6 +17,7 @@ ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be> ;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net> +;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -44,6 +45,7 @@ #:use-module (guix build utils) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (guix build-system ocaml) #:use-module (guix build-system r) #:use-module (gnu packages algebra) #:use-module (gnu packages bison) @@ -77,6 +79,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages netpbm) + #:use-module (gnu packages ocaml) #:use-module (gnu packages pcre) #:use-module (gnu packages popt) #:use-module (gnu packages perl) @@ -277,6 +280,30 @@ differential equations, linear algebra, Fast Fourier Transforms and random numbers.") (license license:gpl3+))) +(define-public ocaml-gsl + (package + (name "ocaml-gsl") + (version "1.19.3") + (source + (origin + (method url-fetch) + (uri + (string-append + "https://github.com/mmottl/gsl-ocaml/releases/download/v" + version"/gsl-ocaml-" version ".tar.gz")) + (sha256 + (base32 + "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh")))) + (build-system ocaml-build-system) + (inputs + `(("gsl" ,gsl))) + (home-page "https://mmottl.github.io/gsl-ocaml") + (synopsis "Bindings to the GNU Scientific Library") + (description + "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for +the OCaml language.") + (license license:gpl3+))) + (define-public glpk (package (name "glpk") @@ -734,6 +761,34 @@ Swath).") HDF5 file is encoded according to the HDF File Format Specification.") (license (license:x11-style "file://COPYING")))) +(define-public itpp + (package + (name "itpp") + (version "4.3.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/itpp/itpp/" + version "/itpp-" + version ".tar.gz")) + (sha256 + (base32 + "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm")))) + (build-system cmake-build-system) + (arguments `(#:tests? #f)) ; Tests require googletest *sources* + (inputs `(("lapack" ,lapack) + ("fftw" ,fftw))) + (native-inputs `(("texlive-minimal" ,texlive-minimal) + ("doxygen" ,doxygen))) + (home-page "http://itpp.sourceforge.net") + (synopsis "C++ library of maths, signal processing and communication classes") + (description "IT++ is a C++ library of mathematical, signal processing and +communication classes and functions. Its main use is in simulation of +communication systems and for performing research in the area of +communications. The kernel of the library consists of generic vector and +matrix classes, and a set of accompanying routines. Such a kernel makes IT++ +similar to MATLAB, GNU Octave or SciPy.") + (license license:gpl3+))) + (define-public netcdf (package (name "netcdf") @@ -1083,6 +1138,30 @@ modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.") (license license:gpl2+))) +(define-public maxflow + (package + (name "maxflow") + (version "3.04") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gerddie/maxflow.git") + (commit "42401fa54823d16b9da47716f04e5d9ef1605875"))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb")))) + (build-system cmake-build-system) + (home-page "http://pub.ist.ac.at/~vnk/software.html") + (synopsis "Library implementing Maxflow algorithm") + (description "An implementation of the maxflow algorithm described in +@cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for +Energy Minimization in Computer Vision.\n +Yuri Boykov and Vladimir Kolmogorov.\n +In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n +September 2004}") + (license license:gpl3+))) + (define-public petsc (package (name "petsc") diff --git a/gnu/packages/ninja.scm b/gnu/packages/ninja.scm index 8f18eb3560..2a53a3f5b3 100644 --- a/gnu/packages/ninja.scm +++ b/gnu/packages/ninja.scm @@ -29,7 +29,7 @@ (define-public ninja (package (name "ninja") - (version "1.7.1") + (version "1.7.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/martine/ninja/" @@ -37,9 +37,8 @@ (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "06dy2dc1aafm61ynw9gzig88la3km9dsh53bxf4mnw7l7kjisn2i")) - (patches (search-patches "ninja-zero-mtime.patch" - "ninja-tests.patch")))) + "1n8n3g26ppwh7zwrc37n3alkbpbj0wki34ih53s3rkhs8ajs1p9f")) + (patches (search-patches "ninja-zero-mtime.patch")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) (arguments diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index ebc5caf254..2f22226b78 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -29,6 +29,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages curl) + #:use-module (gnu packages databases) #:use-module (gnu packages emacs) #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) @@ -971,14 +972,14 @@ GNU CC attributes. It provides also a C pretty printer as an example of use.") (define-public ocaml-qtest (package (name "ocaml-qtest") - (version "2.3") + (version "2.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/vincent-hugot/iTeML/" "archive/v" version ".tar.gz")) (sha256 (base32 - "1n7x5l6h4j44f75wzgzjsjkq349i4gj707w1hr7fx84igxxfr6vl")))) + "1hw3jqir7w79payy4knc38fa3nxcvl7ap6y6hnqavrhpi8zqb59j")))) (build-system ocaml-build-system) (native-inputs `(("findlib" ,ocaml-findlib))) @@ -1213,6 +1214,59 @@ to operate on the result type available from OCaml 4.03 in the standard library.") (license license:isc))) +(define-public ocaml-sqlite3 + (package + (name "ocaml-sqlite3") + (version "4.1.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/mmottl/sqlite3-ocaml/releases/download/v" + version "/sqlite3-ocaml-" version ".tar.gz")) + (sha256 + (base32 + "14c1nir7c6bivajg0vyx853y7la7r5d25g1v5hjb2wfi73r15p1m")))) + (build-system ocaml-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("sqlite" ,sqlite))) + (home-page "https://mmottl.github.io/sqlite3-ocaml") + (synopsis "SQLite3 Bindings for OCaml") + (description + "SQLite3-OCaml is an OCaml library with bindings to the SQLite3 client +API. Sqlite3 is a self-contained, serverless, zero-configuration, +transactional SQL database engine with outstanding performance for many use +cases. These bindings are written in a way that enables a friendly +coexistence with the old (version 2) SQLite and its OCaml wrapper +@code{ocaml-sqlite}.") + (license license:expat))) + +(define-public ocaml-csv + (package + (name "ocaml-csv") + (version "1.6") + (source + (origin + (method url-fetch) + (uri + (string-append + "http://github.com/Chris00/ocaml-csv/releases/download/" + version "/csv-" version ".tar.gz")) + (sha256 + (base32 + "0rv7x843vn6scxj87hzl01yqrl26rc27lr8s7z6rp9vs745g05zj")))) + (build-system ocaml-build-system) + (home-page "https://github.com/Chris00/ocaml-csv") + (synopsis "Pure OCaml functions to read and write CSV") + (description + "@dfn{Comma separated values} (CSV) is a simple tabular format supported +by all major spreadsheets. This library implements pure OCaml functions to +read and write files in this format as well as some convenience functions to +manipulate such data.") + (license (package-license camlp4)))) + (define-public ocaml-mtime (package (name "ocaml-mtime") diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 685636e8ba..f675e22ad9 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -147,14 +147,9 @@ ssh "/share/guile/site/2.0:" gnutls "/share/guile/site/2.0"))) - ;; Ignore user settings so that a bogus - ;; GUILE_LOAD_COMPILED_PATH does not prevent use of - ;; 'guix', notably when it contains entries pointing to - ;; incompatible .go files as reported at - ;; <https://lists.gnu.org/archive/html/guix-devel/2016-03/msg01261.html>. (wrap-program (string-append out "/bin/guix") `("GUILE_LOAD_PATH" ":" prefix (,path)) - `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))) + `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,path))) #t)))))) (native-inputs `(("pkg-config" ,pkg-config) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 811173cae4..3f125a0119 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org> ;;; Copyright © 2016 Alex Griffin <a@ajgrf.com> ;;; Copyright © 2017 Leo Famulari <leo@famulari.name> +;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -291,7 +292,8 @@ any X11 window.") name "-" version ".tar.xz")) (sha256 (base32 - "002mw7j0m33bw483rllzhcf41wp3ixka8yma6kqrfaj57jyw66hn")))) + "002mw7j0m33bw483rllzhcf41wp3ixka8yma6kqrfaj57jyw66hn")) + (patches (search-patches "password-store-gnupg-compat.patch")))) (build-system gnu-build-system) (arguments '(#:phases diff --git a/gnu/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch b/gnu/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch new file mode 100644 index 0000000000..0253700bf6 --- /dev/null +++ b/gnu/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch @@ -0,0 +1,38 @@ +From a8769ef12d7e223e33fc47bed03fba2bfa2f3536 Mon Sep 17 00:00:00 2001 +From: Marcus Sundberg <marcus@marcussundberg.com> +Date: Sat, 26 Mar 2016 20:11:43 +0100 +Subject: [PATCH] evbuffer_add: Use last_with_datap if set, not last. + +evbuffer_add() would always put data in the last chain, even if there +was available space in a previous chain, and in doing so it also +failed to update last_with_datap, causing subsequent calls to other +functions that do look at last_with_datap to add data in the middle +of the evbuffer instead of at the end. + +Fixes the evbuffer_add() part of issue #335, and the evbuffer/add2 and +evbuffer/add3 tests, and also prevents wasting space available in the +chain pointed to by last_with_datap. +--- + buffer.c | 6 +++++- + 1 file changed, 5 insertions(+), 1 deletion(-) + +diff --git a/buffer.c b/buffer.c +index 7cca0e8a..f378b731 100644 +--- a/buffer.c ++++ b/buffer.c +@@ -1732,7 +1732,11 @@ evbuffer_add(struct evbuffer *buf, const void *data_in, size_t datlen) + goto done; + } + +- chain = buf->last; ++ if (*buf->last_with_datap == NULL) { ++ chain = buf->last; ++ } else { ++ chain = *buf->last_with_datap; ++ } + + /* If there are no chains allocated for this buffer, allocate one + * big enough to hold all the data. */ +-- +2.12.0 + diff --git a/gnu/packages/patches/libwebp-CVE-2016-9085.patch b/gnu/packages/patches/libwebp-CVE-2016-9085.patch deleted file mode 100644 index e40b353303..0000000000 --- a/gnu/packages/patches/libwebp-CVE-2016-9085.patch +++ /dev/null @@ -1,144 +0,0 @@ -Fix CVE-2016-9085 (several integer overflows): - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-9085 -http://seclists.org/oss-sec/2016/q4/253 - -Patch copied from upstream source repository: - -https://chromium.googlesource.com/webm/libwebp/+/e2affacc35f1df6cc3b1a9fa0ceff5ce2d0cce83 - -From e2affacc35f1df6cc3b1a9fa0ceff5ce2d0cce83 Mon Sep 17 00:00:00 2001 -From: Pascal Massimino <pascal.massimino@gmail.com> -Date: Mon, 10 Oct 2016 11:48:39 +0200 -Subject: [PATCH] fix potential overflow when width * height * 4 >= (1<<32) - -Mostly: avoid doing calculation like: ptr + j * stride -when stride is 'int'. Rather use size_t, or pointer increments (ptr += stride) -when possible. - -BUG=webp:314 - -Change-Id: I81c684b515dd1ec4f601f32d50a6e821c4e46e20 ---- - examples/gifdec.c | 56 +++++++++++++++++++++++++++++++------------------------ - 1 file changed, 32 insertions(+), 24 deletions(-) - -diff --git a/examples/gifdec.c b/examples/gifdec.c -index 83c3d82..7df176f 100644 ---- a/examples/gifdec.c -+++ b/examples/gifdec.c -@@ -20,6 +20,7 @@ - - #include "webp/encode.h" - #include "webp/mux_types.h" -+#include "webp/format_constants.h" - - #define GIF_TRANSPARENT_COLOR 0x00000000 - #define GIF_WHITE_COLOR 0xffffffff -@@ -103,12 +104,19 @@ int GIFReadFrame(GifFileType* const gif, int transparent_index, - const GifImageDesc* const image_desc = &gif->Image; - uint32_t* dst = NULL; - uint8_t* tmp = NULL; -- int ok = 0; -- GIFFrameRect rect = { -+ const GIFFrameRect rect = { - image_desc->Left, image_desc->Top, image_desc->Width, image_desc->Height - }; -+ const uint64_t memory_needed = 4 * rect.width * (uint64_t)rect.height; -+ int ok = 0; - *gif_rect = rect; - -+ if (memory_needed != (size_t)memory_needed || -+ memory_needed > 4 * MAX_IMAGE_AREA) { -+ fprintf(stderr, "Image is too large (%d x %d).", rect.width, rect.height); -+ return 0; -+ } -+ - // Use a view for the sub-picture: - if (!WebPPictureView(picture, rect.x_offset, rect.y_offset, - rect.width, rect.height, &sub_image)) { -@@ -132,15 +140,15 @@ int GIFReadFrame(GifFileType* const gif, int transparent_index, - y += interlace_jumps[pass]) { - if (DGifGetLine(gif, tmp, rect.width) == GIF_ERROR) goto End; - Remap(gif, tmp, rect.width, transparent_index, -- dst + y * sub_image.argb_stride); -+ dst + y * (size_t)sub_image.argb_stride); - } - } - } else { // Non-interlaced image. - int y; -- for (y = 0; y < rect.height; ++y) { -+ uint32_t* ptr = dst; -+ for (y = 0; y < rect.height; ++y, ptr += sub_image.argb_stride) { - if (DGifGetLine(gif, tmp, rect.width) == GIF_ERROR) goto End; -- Remap(gif, tmp, rect.width, transparent_index, -- dst + y * sub_image.argb_stride); -+ Remap(gif, tmp, rect.width, transparent_index, ptr); - } - } - ok = 1; -@@ -216,13 +224,11 @@ int GIFReadMetadata(GifFileType* const gif, GifByteType** const buf, - - static void ClearRectangle(WebPPicture* const picture, - int left, int top, int width, int height) { -- int j; -- for (j = top; j < top + height; ++j) { -- uint32_t* const dst = picture->argb + j * picture->argb_stride; -- int i; -- for (i = left; i < left + width; ++i) { -- dst[i] = GIF_TRANSPARENT_COLOR; -- } -+ int i, j; -+ const size_t stride = picture->argb_stride; -+ uint32_t* dst = picture->argb + top * stride + left; -+ for (j = 0; j < height; ++j, dst += stride) { -+ for (i = 0; i < width; ++i) dst[i] = GIF_TRANSPARENT_COLOR; - } - } - -@@ -246,29 +252,31 @@ void GIFDisposeFrame(GIFDisposeMethod dispose, const GIFFrameRect* const rect, - if (dispose == GIF_DISPOSE_BACKGROUND) { - GIFClearPic(curr_canvas, rect); - } else if (dispose == GIF_DISPOSE_RESTORE_PREVIOUS) { -- const int src_stride = prev_canvas->argb_stride; -- const uint32_t* const src = -- prev_canvas->argb + rect->x_offset + rect->y_offset * src_stride; -- const int dst_stride = curr_canvas->argb_stride; -- uint32_t* const dst = -- curr_canvas->argb + rect->x_offset + rect->y_offset * dst_stride; -+ const size_t src_stride = prev_canvas->argb_stride; -+ const uint32_t* const src = prev_canvas->argb + rect->x_offset -+ + rect->y_offset * src_stride; -+ const size_t dst_stride = curr_canvas->argb_stride; -+ uint32_t* const dst = curr_canvas->argb + rect->x_offset -+ + rect->y_offset * dst_stride; - assert(prev_canvas != NULL); -- WebPCopyPlane((uint8_t*)src, 4 * src_stride, (uint8_t*)dst, 4 * dst_stride, -+ WebPCopyPlane((uint8_t*)src, (int)(4 * src_stride), -+ (uint8_t*)dst, (int)(4 * dst_stride), - 4 * rect->width, rect->height); - } - } - - void GIFBlendFrames(const WebPPicture* const src, - const GIFFrameRect* const rect, WebPPicture* const dst) { -- int j; -+ int i, j; -+ const size_t src_stride = src->argb_stride; -+ const size_t dst_stride = dst->argb_stride; - assert(src->width == dst->width && src->height == dst->height); - for (j = rect->y_offset; j < rect->y_offset + rect->height; ++j) { -- int i; - for (i = rect->x_offset; i < rect->x_offset + rect->width; ++i) { -- const uint32_t src_pixel = src->argb[j * src->argb_stride + i]; -+ const uint32_t src_pixel = src->argb[j * src_stride + i]; - const int src_alpha = src_pixel >> 24; - if (src_alpha != 0) { -- dst->argb[j * dst->argb_stride + i] = src_pixel; -+ dst->argb[j * dst_stride + i] = src_pixel; - } - } - } --- -2.10.1 - diff --git a/gnu/packages/patches/ninja-tests.patch b/gnu/packages/patches/ninja-tests.patch deleted file mode 100644 index f9b0d9f910..0000000000 --- a/gnu/packages/patches/ninja-tests.patch +++ /dev/null @@ -1,48 +0,0 @@ -From 67d6b9262efad99f8aad63ab81efc8e689748766 Mon Sep 17 00:00:00 2001 -From: Efraim Flashner <efraim@flashner.co.il> -Date: Sun, 3 Jul 2016 11:55:43 +0300 -Subject: [PATCH] patch - ---- - src/subprocess_test.cc | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/src/subprocess_test.cc b/src/subprocess_test.cc -index ee16190..a537c11 100644 ---- a/src/subprocess_test.cc -+++ b/src/subprocess_test.cc -@@ -72,6 +72,7 @@ TEST_F(SubprocessTest, NoSuchCommand) { - - #ifndef _WIN32 - -+#if 0 - TEST_F(SubprocessTest, InterruptChild) { - Subprocess* subproc = subprocs_.Add("kill -INT $$"); - ASSERT_NE((Subprocess *) 0, subproc); -@@ -82,6 +83,7 @@ TEST_F(SubprocessTest, InterruptChild) { - - EXPECT_EQ(ExitInterrupted, subproc->Finish()); - } -+#endif - - TEST_F(SubprocessTest, InterruptParent) { - Subprocess* subproc = subprocs_.Add("kill -INT $PPID ; sleep 1"); -@@ -217,6 +219,7 @@ TEST_F(SubprocessTest, SetWithMulti) { - // OS X's process limit is less than 1025 by default - // (|sysctl kern.maxprocperuid| is 709 on 10.7 and 10.8 and less prior to that). - #if !defined(__APPLE__) && !defined(_WIN32) -+#if 0 - TEST_F(SubprocessTest, SetWithLots) { - // Arbitrary big number; needs to be over 1024 to confirm we're no longer - // hostage to pselect. -@@ -245,6 +248,7 @@ TEST_F(SubprocessTest, SetWithLots) { - } - ASSERT_EQ(kNumProcs, subprocs_.finished_.size()); - } -+#endif - #endif // !__APPLE__ && !_WIN32 - - // TODO: this test could work on Windows, just not sure how to simply --- -2.9.0 - diff --git a/gnu/packages/patches/password-store-gnupg-compat.patch b/gnu/packages/patches/password-store-gnupg-compat.patch new file mode 100644 index 0000000000..c314ba6647 --- /dev/null +++ b/gnu/packages/patches/password-store-gnupg-compat.patch @@ -0,0 +1,53 @@ +Copied from upstream mailing list: +https://lists.zx2c4.com/pipermail/password-store/2017-March/002844.html. + +The patch actually restores compatibility with GnuPG 2.1.19, the '2.2.19' in +the commit message is a typo. + +From 8723d8e8192683891904aff321446b0fac37d1ad Mon Sep 17 00:00:00 2001 +From: Andreas Stieger <astieger@suse.com> +Date: Fri, 10 Mar 2017 15:43:26 +0100 +Subject: [PATCH] Fix compatibility with GnuPG 2.2.19 + +GnuPG 2.2.19 added a warning when no command was given. + +* src/password-store.sh (reencrypt_path): Add --decrypt to --list-only +* tests/t0300-reencryption.sh (gpg_keys_from_encrypted_file): same + +https://bugs.gnupg.org/gnupg/msg9873 +http://git.gnupg.org/cgi-bin/gitweb.cgi?p=gnupg.git;a=commit;h=810adfd47801fc01e45fb71af9f05c91f7890cdb +https://bugzilla.suse.com/show_bug.cgi?id=1028867 +--- + src/password-store.sh | 2 +- + tests/t0300-reencryption.sh | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/password-store.sh b/src/password-store.sh +index 1ab6fb5..bad8d4f 100755 +--- a/src/password-store.sh ++++ b/src/password-store.sh +@@ -125,7 +125,7 @@ reencrypt_path() { + done + gpg_keys="$($GPG $PASSWORD_STORE_GPG_OPTS --list-keys --with-colons "${GPG_RECIPIENTS[@]}" | sed -n 's/sub:[^:]*:[^:]*:[^:]*:\([^:]*\):[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[a-zA-Z]*e[a-zA-Z]*:.*/\1/p' | LC_ALL=C sort -u)" + fi +- current_keys="$($GPG $PASSWORD_STORE_GPG_OPTS -v --no-secmem-warning --no-permission-warning --list-only --keyid-format long "$passfile" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u)" ++ current_keys="$($GPG $PASSWORD_STORE_GPG_OPTS -v --no-secmem-warning --no-permission-warning --decrypt --list-only --keyid-format long "$passfile" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u)" + + if [[ $gpg_keys != "$current_keys" ]]; then + echo "$passfile_display: reencrypting to ${gpg_keys//$'\n'/ }" +diff --git a/tests/t0300-reencryption.sh b/tests/t0300-reencryption.sh +index 9d46580..6d5811d 100755 +--- a/tests/t0300-reencryption.sh ++++ b/tests/t0300-reencryption.sh +@@ -10,7 +10,7 @@ canonicalize_gpg_keys() { + $GPG --list-keys --with-colons "$@" | sed -n 's/sub:[^:]*:[^:]*:[^:]*:\([^:]*\):[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[^:]*:[a-zA-Z]*e[a-zA-Z]*:.*/\1/p' | LC_ALL=C sort -u + } + gpg_keys_from_encrypted_file() { +- $GPG -v --no-secmem-warning --no-permission-warning --list-only --keyid-format long "$1" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u ++ $GPG -v --no-secmem-warning --no-permission-warning --decrypt --list-only --keyid-format long "$1" 2>&1 | cut -d ' ' -f 5 | LC_ALL=C sort -u + } + gpg_keys_from_group() { + local output="$($GPG --list-config --with-colons | sed -n "s/^cfg:group:$1:\\(.*\\)/\\1/p" | head -n 1)" +-- +2.12.0 + diff --git a/gnu/packages/patches/qemu-CVE-2017-2620.patch b/gnu/packages/patches/qemu-CVE-2017-2620.patch new file mode 100644 index 0000000000..d3111827b7 --- /dev/null +++ b/gnu/packages/patches/qemu-CVE-2017-2620.patch @@ -0,0 +1,134 @@ +Fix CVE-2017-2620: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-2620 +https://lists.gnu.org/archive/html/qemu-devel/2017-02/msg04700.html + +Both patches copied from upstream source repository: + +Fixes CVE-2017-2620: +http://git.qemu-project.org/?p=qemu.git;a=commit;h=92f2b88cea48c6aeba8de568a45f2ed958f3c298 + +The CVE-2017-2620 bug-fix depends on this earlier patch: +http://git.qemu-project.org/?p=qemu.git;a=commit;h=913a87885f589d263e682c2eb6637c6e14538061 + +From 92f2b88cea48c6aeba8de568a45f2ed958f3c298 Mon Sep 17 00:00:00 2001 +From: Gerd Hoffmann <kraxel@redhat.com> +Date: Wed, 8 Feb 2017 11:18:36 +0100 +Subject: [PATCH] cirrus: add blit_is_unsafe call to cirrus_bitblt_cputovideo + (CVE-2017-2620) + +CIRRUS_BLTMODE_MEMSYSSRC blits do NOT check blit destination +and blit width, at all. Oops. Fix it. + +Security impact: high. + +The missing blit destination check allows to write to host memory. +Basically same as CVE-2014-8106 for the other blit variants. + +Cc: qemu-stable@nongnu.org +Signed-off-by: Gerd Hoffmann <kraxel@redhat.com> +--- + hw/display/cirrus_vga.c | 8 ++++++++ + 1 file changed, 8 insertions(+) + +diff --git a/hw/display/cirrus_vga.c b/hw/display/cirrus_vga.c +index 1deb52070a..b9e7cb1df1 100644 +--- a/hw/display/cirrus_vga.c ++++ b/hw/display/cirrus_vga.c +@@ -900,6 +900,10 @@ static int cirrus_bitblt_cputovideo(CirrusVGAState * s) + { + int w; + ++ if (blit_is_unsafe(s, true)) { ++ return 0; ++ } ++ + s->cirrus_blt_mode &= ~CIRRUS_BLTMODE_MEMSYSSRC; + s->cirrus_srcptr = &s->cirrus_bltbuf[0]; + s->cirrus_srcptr_end = &s->cirrus_bltbuf[0]; +@@ -925,6 +929,10 @@ static int cirrus_bitblt_cputovideo(CirrusVGAState * s) + } + s->cirrus_srccounter = s->cirrus_blt_srcpitch * s->cirrus_blt_height; + } ++ ++ /* the blit_is_unsafe call above should catch this */ ++ assert(s->cirrus_blt_srcpitch <= CIRRUS_BLTBUFSIZE); ++ + s->cirrus_srcptr = s->cirrus_bltbuf; + s->cirrus_srcptr_end = s->cirrus_bltbuf + s->cirrus_blt_srcpitch; + cirrus_update_memory_access(s); +-- +2.12.0 + +From 913a87885f589d263e682c2eb6637c6e14538061 Mon Sep 17 00:00:00 2001 +From: Bruce Rogers <brogers@suse.com> +Date: Mon, 9 Jan 2017 13:35:20 -0700 +Subject: [PATCH] display: cirrus: ignore source pitch value as needed in + blit_is_unsafe + +Commit 4299b90 added a check which is too broad, given that the source +pitch value is not required to be initialized for solid fill operations. +This patch refines the blit_is_unsafe() check to ignore source pitch in +that case. After applying the above commit as a security patch, we +noticed the SLES 11 SP4 guest gui failed to initialize properly. + +Signed-off-by: Bruce Rogers <brogers@suse.com> +Message-id: 20170109203520.5619-1-brogers@suse.com +Signed-off-by: Gerd Hoffmann <kraxel@redhat.com> +--- + hw/display/cirrus_vga.c | 11 +++++++---- + 1 file changed, 7 insertions(+), 4 deletions(-) + +diff --git a/hw/display/cirrus_vga.c b/hw/display/cirrus_vga.c +index bdb092ee9d..379910db2d 100644 +--- a/hw/display/cirrus_vga.c ++++ b/hw/display/cirrus_vga.c +@@ -294,7 +294,7 @@ static bool blit_region_is_unsafe(struct CirrusVGAState *s, + return false; + } + +-static bool blit_is_unsafe(struct CirrusVGAState *s) ++static bool blit_is_unsafe(struct CirrusVGAState *s, bool dst_only) + { + /* should be the case, see cirrus_bitblt_start */ + assert(s->cirrus_blt_width > 0); +@@ -308,6 +308,9 @@ static bool blit_is_unsafe(struct CirrusVGAState *s) + s->cirrus_blt_dstaddr & s->cirrus_addr_mask)) { + return true; + } ++ if (dst_only) { ++ return false; ++ } + if (blit_region_is_unsafe(s, s->cirrus_blt_srcpitch, + s->cirrus_blt_srcaddr & s->cirrus_addr_mask)) { + return true; +@@ -673,7 +676,7 @@ static int cirrus_bitblt_common_patterncopy(CirrusVGAState * s, + + dst = s->vga.vram_ptr + (s->cirrus_blt_dstaddr & s->cirrus_addr_mask); + +- if (blit_is_unsafe(s)) ++ if (blit_is_unsafe(s, false)) + return 0; + + (*s->cirrus_rop) (s, dst, src, +@@ -691,7 +694,7 @@ static int cirrus_bitblt_solidfill(CirrusVGAState *s, int blt_rop) + { + cirrus_fill_t rop_func; + +- if (blit_is_unsafe(s)) { ++ if (blit_is_unsafe(s, true)) { + return 0; + } + rop_func = cirrus_fill[rop_to_index[blt_rop]][s->cirrus_blt_pixelwidth - 1]; +@@ -795,7 +798,7 @@ static int cirrus_do_copy(CirrusVGAState *s, int dst, int src, int w, int h) + + static int cirrus_bitblt_videotovideo_copy(CirrusVGAState * s) + { +- if (blit_is_unsafe(s)) ++ if (blit_is_unsafe(s, false)) + return 0; + + return cirrus_do_copy(s, s->cirrus_blt_dstaddr - s->vga.start_addr, +-- +2.12.0 + diff --git a/gnu/packages/patches/qemu-CVE-2017-2630.patch b/gnu/packages/patches/qemu-CVE-2017-2630.patch new file mode 100644 index 0000000000..b154d171f1 --- /dev/null +++ b/gnu/packages/patches/qemu-CVE-2017-2630.patch @@ -0,0 +1,47 @@ +Fix CVE-2017-2630: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-2630 +https://lists.gnu.org/archive/html/qemu-devel/2017-02/msg01246.html + +Patch copied from upstream source repository: + +http://git.qemu-project.org/?p=qemu.git;a=commit;h=2563c9c6b8670400c48e562034b321a7cf3d9a85 + +From 2563c9c6b8670400c48e562034b321a7cf3d9a85 Mon Sep 17 00:00:00 2001 +From: Vladimir Sementsov-Ogievskiy <vsementsov@virtuozzo.com> +Date: Tue, 7 Mar 2017 09:16:27 -0600 +Subject: [PATCH] nbd/client: fix drop_sync [CVE-2017-2630] +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Comparison symbol is misused. It may lead to memory corruption. +Introduced in commit 7d3123e. + +Signed-off-by: Vladimir Sementsov-Ogievskiy <vsementsov@virtuozzo.com> +Message-Id: <20170203154757.36140-6-vsementsov@virtuozzo.com> +[eblake: add CVE details, update conditional] +Signed-off-by: Eric Blake <eblake@redhat.com> +Reviewed-by: Marc-André Lureau <marcandre.lureau@redhat.com> +Message-Id: <20170307151627.27212-1-eblake@redhat.com> +Signed-off-by: Paolo Bonzini <pbonzini@redhat.com> +--- + nbd/client.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/nbd/client.c b/nbd/client.c +index 5c9dee37fa..3dc2564cd0 100644 +--- a/nbd/client.c ++++ b/nbd/client.c +@@ -94,7 +94,7 @@ static ssize_t drop_sync(QIOChannel *ioc, size_t size) + char small[1024]; + char *buffer; + +- buffer = sizeof(small) < size ? small : g_malloc(MIN(65536, size)); ++ buffer = sizeof(small) >= size ? small : g_malloc(MIN(65536, size)); + while (size > 0) { + ssize_t count = read_sync(ioc, buffer, MIN(65536, size)); + +-- +2.12.0 + diff --git a/gnu/packages/patches/virglrenderer-CVE-2017-6386.patch b/gnu/packages/patches/virglrenderer-CVE-2017-6386.patch new file mode 100644 index 0000000000..bd3bf106bf --- /dev/null +++ b/gnu/packages/patches/virglrenderer-CVE-2017-6386.patch @@ -0,0 +1,54 @@ +Fix CVE-2017-6386 (memory leak introduced by fix for CVE-2017-5994). + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5994 + +Patch copied from upstream source repository: + +https://cgit.freedesktop.org/virglrenderer/commit/?id=737c3350850ca4dbc5633b3bdb4118176ce59920 + +From 737c3350850ca4dbc5633b3bdb4118176ce59920 Mon Sep 17 00:00:00 2001 +From: Dave Airlie <airlied@redhat.com> +Date: Tue, 28 Feb 2017 14:52:09 +1000 +Subject: renderer: fix memory leak in vertex elements state create + +Reported-by: Li Qiang +Free the vertex array in error path. +This was introduced by this commit: +renderer: fix heap overflow in vertex elements state create. + +I rewrote the code to not require the allocation in the first +place if we have an error, seems nicer. + +Signed-off-by: Dave Airlie <airlied@redhat.com> + +diff --git a/src/vrend_renderer.c b/src/vrend_renderer.c +index 1bca7ad..e5d9f5c 100644 +--- a/src/vrend_renderer.c ++++ b/src/vrend_renderer.c +@@ -1648,18 +1648,19 @@ int vrend_create_vertex_elements_state(struct vrend_context *ctx, + unsigned num_elements, + const struct pipe_vertex_element *elements) + { +- struct vrend_vertex_element_array *v = CALLOC_STRUCT(vrend_vertex_element_array); ++ struct vrend_vertex_element_array *v; + const struct util_format_description *desc; + GLenum type; + int i; + uint32_t ret_handle; + +- if (!v) +- return ENOMEM; +- + if (num_elements > PIPE_MAX_ATTRIBS) + return EINVAL; + ++ v = CALLOC_STRUCT(vrend_vertex_element_array); ++ if (!v) ++ return ENOMEM; ++ + v->count = num_elements; + for (i = 0; i < num_elements; i++) { + memcpy(&v->elements[i].base, &elements[i], sizeof(struct pipe_vertex_element)); +-- +cgit v0.10.2 + diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index ef63f58f64..7f3dccc8ba 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017 Leo Famulari <leo@famulari.name> ;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com> +;;; Copyright © 2017 Rene Saavedra <rennes@openmailbox.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -45,6 +46,7 @@ #:use-module (gnu packages fontutils) #:use-module (gnu packages game-development) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages gnupg) #:use-module (gnu packages databases) #:use-module (gnu packages djvu) #:use-module (gnu packages gettext) @@ -875,3 +877,31 @@ This is much like @command{poster} does for Postscript files, but working with PDF. Since sometimes @command{poster} does not like your files converted from PDF. Indeed @command{pdfposter} was inspired by @command{poster}.") (license license:gpl3+))) + +(define-public pdfgrep + (package + (name "pdfgrep") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://pdfgrep.org/download/" + name "-" version ".tar.gz")) + (sha256 + (base32 + "07llkrkcfjwd3ybai9ad10ybhr0biffcplmy7lw4fb87nd2dfw03")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libgcrypt" ,libgcrypt) + ("pcre" ,pcre) + ("poppler" ,poppler))) + (home-page "https://pdfgrep.org") + (synopsis "Command-line utility to search text in PDF files") + (description + "Pdfgrep searches in pdf files for strings matching a regular expression. +Support some GNU grep options as file name output, page number output, +optional case insensitivity, count occurrences, color highlights and search in +multiple files.") + (license license:gpl2+))) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 00598776ab..96c4245384 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4075,7 +4075,8 @@ operators such as union, intersection, and difference.") `(("readline" ,readline) ("icu4c" ,icu4c) ("pcre" ,pcre) - ("r" ,r))) + ("r-minimal" ,r-minimal) + ("r-survival" ,r-survival))) (native-inputs `(("zlib" ,zlib))) (home-page "http://rpy.sourceforge.net/") @@ -5860,13 +5861,13 @@ of the structure, dynamics, and functions of complex networks.") (define-public snakemake (package (name "snakemake") - (version "3.9.0") + (version "3.11.2") (source (origin (method url-fetch) (uri (pypi-uri "snakemake" version)) (sha256 - (base32 "1d48ql0010v9ls6mac7fz6j391gm4h74a64hqgw89s0vfqgdyzdl")))) + (base32 "0qcp7y9csvanyzh08jppryhd5di8r1z7p0d4wkfg5591pj3bb8zp")))) (build-system python-build-system) (arguments ;; TODO: Package missing test dependencies. diff --git a/gnu/packages/qemu.scm b/gnu/packages/qemu.scm index d43593957e..aa12b2c493 100644 --- a/gnu/packages/qemu.scm +++ b/gnu/packages/qemu.scm @@ -79,6 +79,8 @@ "0qjy3rcrn89n42y5iz60kgr0rrl29hpnj8mq2yvbc1wrcizmvzfs")) (patches (search-patches "qemu-CVE-2016-10155.patch" "qemu-CVE-2017-2615.patch" + "qemu-CVE-2017-2620.patch" + "qemu-CVE-2017-2630.patch" "qemu-CVE-2017-5525.patch" "qemu-CVE-2017-5526.patch" "qemu-CVE-2017-5552.patch" diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm index fb284102da..2dedef8373 100644 --- a/gnu/packages/rust.scm +++ b/gnu/packages/rust.scm @@ -44,7 +44,7 @@ #:use-module (srfi srfi-26)) ;; Should be one less than the current released version. -(define %rust-bootstrap-binaries-version "1.13.0") +(define %rust-bootstrap-binaries-version "1.14.0") (define %rust-bootstrap-binaries (origin @@ -55,7 +55,7 @@ "-i686-unknown-linux-gnu.tar.gz")) (sha256 (base32 - "0fcl7xgm2m21sjv1f27i3v692aa91lk8r867hl8d6l377w8k95r3")))) + "0h384prpabcl08mxs1bilyb0dbk0knpdylcnz4b84ij4idr7ap4d")))) (define (increment-rust-version rust-version major patch) (match (string-split rust-version #\.) @@ -205,7 +205,7 @@ rustc-bootstrap and cargo-bootstrap packages.") "rustc-" version "-src.tar.gz")) (sha256 (base32 - "0srvmhhdbbcl21nzg9m9zni7k10h88lsy8k1ljz03g8mx79fv467")))) + "0wvn8m1nfg664b95qrdpfh72q1a6ir09rqkrnlzbkay2r7xf8mgn")))) (build-system gnu-build-system) (native-inputs `(("cmake" ,cmake) @@ -234,10 +234,13 @@ rustc-bootstrap and cargo-bootstrap packages.") (lambda _ (setenv "SHELL" (which "sh")) (setenv "CONFIG_SHELL" (which "sh")))) - (add-after 'unpack 'patch-lockfile-test - (lambda _ + (add-after 'unpack 'patch-tests + (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/tools/tidy/src/main.rs" - (("^.*cargo.*::check.*$") "")))) + (("^.*cargo.*::check.*$") "")) + (substitute* "src/libstd/process.rs" + (("\"/bin/sh\"") (string-append "\"" (assoc-ref inputs "bash") "/bin/sh\""))) + #t)) (replace 'configure (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -260,7 +263,7 @@ rustc-bootstrap and cargo-bootstrap packages.") "--release-channel=stable" "--enable-rpath" "--enable-local-rust" - ;;"--enable-rustbuild" + "--disable-rustbuild" ; use Makefiles "--disable-manage-submodules"))) ;; Rust uses a custom configure script (no autoconf). (zero? (apply system* "./configure" flags))))) @@ -288,15 +291,12 @@ safety and thread safety guarantees.") (version (cargo-version (rustc-version %rust-bootstrap-binaries-version))) (source (origin (method url-fetch) - ;; Use a cargo tarball with vendored dependencies and a cargo - ;; config file. - (uri (string-append - "https://github.com/dvc94ch/cargo" - "/archive/" version "-cargo-vendor.tar.gz")) + (uri (string-append "https://github.com/rust-lang/cargo/archive/" + version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0hpix5hwz10pm1wh65gimhsy9nxjvy7yikgbpw8afwglqr3bl856")))) + "194i06y9nql0p93gahh0vm4qwv6c1kpd9rprpf22w5gav9lpcyjz")))) (build-system cargo-build-system) (propagated-inputs `(("cmake" ,cmake) @@ -308,6 +308,483 @@ safety and thread safety guarantees.") ("openssl" ,openssl) ("python-2" ,python-2) ("zlib" ,zlib))) + (native-inputs + `(("rust-openssl" + ,(origin + (method url-fetch) + (uri (crate-uri "openssl" "0.9.1")) + (sha256 + (base32 + "1m2mhiar87qnw4gxci286q9g85ljafbc41salbj2hmcgh8aagchy")))) + ("rust-strsim" + ,(origin + (method url-fetch) + (uri (crate-uri "strsim" "0.5.1")) + (sha256 + (base32 + "0bj4fsm1l2yqbfpspyvjf9m3m50pskapcddzm0ji9c74jbgnkh2h")))) + ("rust-libc" + ,(origin + (method url-fetch) + (uri (crate-uri "libc" "0.2.18")) + (sha256 + (base32 + "0w5cghr0wx3hi2sclk8r9iyzlbxsakil87ada40q2ykyhky24655")))) + ("rust-bitflags" + ,(origin + (method url-fetch) + (uri (crate-uri "bitflags" "0.7.0")) + (sha256 + (base32 + "0v8hh6wdkpk9my8z8442g4hqrqf05h0qj53dsay6mv18lqvqklda")))) + ("rust-unicode-normalization" + ,(origin + (method url-fetch) + (uri (crate-uri "unicode-normalization" "0.1.2")) + (sha256 + (base32 + "0whi4xxqcjfsz6ywyrfd5lhgk1a44c86qwgvfqcmzidshcpklr16")))) + ("rust-rand" + ,(origin + (method url-fetch) + (uri (crate-uri "rand" "0.3.14")) + (sha256 + (base32 + "1984zvj8572ig28fz6idc4r96fx39h4lzmr07yf7kb7gdn6di497")))) + ("rust-gcc" + ,(origin + (method url-fetch) + (uri (crate-uri "gcc" "0.3.39")) + (sha256 + (base32 + "1q0idjvmhp6shkb9hqabh51rgfr8dqpi1xfmyzq7q8vgzybll7kp")))) + ("rust-tempdir" + ,(origin + (method url-fetch) + (uri (crate-uri "tempdir" "0.3.5")) + (sha256 + (base32 + "1mij45kgzflkja0h8q9avrik76h5a0b60m9hfd6k9yqxbiplm5w7")))) + ("rust-memchr" + ,(origin + (method url-fetch) + (uri (crate-uri "memchr" "0.1.11")) + (sha256 + (base32 + "084d85hjfa3xf5kwdms2mhbkh78m1gl2254cp5swcxj3a7xjkdnq")))) + ("rust-rustc-serialize" + ,(origin + (method url-fetch) + (uri (crate-uri "rustc-serialize" "0.3.21")) + (sha256 + (base32 + "064qmyr2508qf78dwcpiv25rfjp9h9vd0wrj4mmwgppjg4fgrydz")))) + ("rust-cmake" + ,(origin + (method url-fetch) + (uri (crate-uri "cmake" "0.1.19")) + (sha256 + (base32 + "0am8c8ns1h6b1a5x9z2r1m3rszvya5nccl2pzszzjv5aiiaydgcf")))) + ("rust-matches" + ,(origin + (method url-fetch) + (uri (crate-uri "matches" "0.1.4")) + (sha256 + (base32 + "1c8190j84hbicy8jwscw5icfam12j6lcxi02lvmadq9260p65mzg")))) + ("rust-winapi" + ,(origin + (method url-fetch) + (uri (crate-uri "winapi" "0.2.8")) + (sha256 + (base32 + "0yh816lh6lf56dpsgxy189c2ai1z3j8mw9si6izqb6wsjkbcjz8n")))) + ("rust-pkg-config" + ,(origin + (method url-fetch) + (uri (crate-uri "pkg-config" "0.3.8")) + (sha256 + (base32 + "1ypj4nj2z9z27qg06v3g40jyhw685i3l2wi098d21bvyri781vlc")))) + ("rust-libssh2-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "libssh2-sys" "0.2.4")) + (sha256 + (base32 + "1pmmh0hcx14856wg9bp740yf618qfl2765vhf67sfs5lmf39227d")))) + ("rust-libz-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "libz-sys" "1.0.10")) + (sha256 + (base32 + "1rl85x045sk5d345hgcahx99plpbdg2a3bx5vjfxig30qah74p4h")))) + ("rust-curl-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "curl-sys" "0.3.6")) + (sha256 + (base32 + "0fi8kjz3f8m8vfazycs3ddm0h6j3x78hw78gwbvybx71129192i1")))) + ("rust-openssl-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "openssl-sys" "0.9.1")) + (sha256 + (base32 + "1sdhgalfm2zdqf144xhdnxdha7ifjgsfbmlrqbx0j9f3mh4gpscm")))) + ("rust-fs2" + ,(origin + (method url-fetch) + (uri (crate-uri "fs2" "0.3.0")) + (sha256 + (base32 + "0lg57mgcm1r0m8jm4nqpcrl6lmxg8lj854k2h0r7qp46pphh2034")))) + ("rust-log" + ,(origin + (method url-fetch) + (uri (crate-uri "log" "0.3.6")) + (sha256 + (base32 + "0m40hgs3cg57dd5kk1mabfk6gk8z6l1cihar8akx4kmzz1xlk0xb")))) + ("rust-filetime" + ,(origin + (method url-fetch) + (uri (crate-uri "filetime" "0.1.10")) + (sha256 + (base32 + "08p9scgv30i1141cnp5xi4pqlnkfci455nrpca55df1r867anqsk")))) + ("rust-tar" + ,(origin + (method url-fetch) + (uri (crate-uri "tar" "0.4.9")) + (sha256 + (base32 + "1vi3nl8s3jjf5l20ni47gmh1p4bdjfh7q50fbg7izzqrf7i4i40c")))) + ("rust-glob" + ,(origin + (method url-fetch) + (uri (crate-uri "glob" "0.2.11")) + (sha256 + (base32 + "1ysvi72slkw784fcsymgj4308c3y03gwjjzqxp80xdjnkbh8vqcb")))) + ("rust-cfg-if" + ,(origin + (method url-fetch) + (uri (crate-uri "cfg-if" "0.1.0")) + (sha256 + (base32 + "137qikjcal4h75frzcn6mknygqk8vy5bva7w851aydb5gc6pc7ny")))) + ("rust-winapi-build" + ,(origin + (method url-fetch) + (uri (crate-uri "winapi-build" "0.1.1")) + (sha256 + (base32 + "1g4rqsgjky0a7530qajn2bbfcrl2v0zb39idgdws9b1l7gp5wc9d")))) + ("rust-advapi32-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "advapi32-sys" "0.2.0")) + (sha256 + (base32 + "16largvlrd1800vvdchml0ngnszjlnpqm01rcz5hm7di1h48hrg0")))) + ("rust-gdi32-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "gdi32-sys" "0.2.0")) + (sha256 + (base32 + "0605d4ngjsspghwjv4jicajich1gnl0aik9f880ajjzjixd524h9")))) + ("rust-ws2_32-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "ws2_32-sys" "0.2.1")) + (sha256 + (base32 + "0ppscg5qfqaw0gzwv2a4nhn5bn01ff9iwn6ysqnzm4n8s3myz76m")))) + ("rust-user32-sys" + ,(origin + (method url-fetch) + (uri (crate-uri "user32-sys" "0.2.0")) + (sha256 + (base32 + 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+ ,(origin + (method url-fetch) + (uri (crate-uri "libgit2-sys" "0.6.5")) + (sha256 + (base32 + "0yl80n12ih4jh1halpbj3zqlqvw5zxdr6m6xdcvdz67svjy50bjh")))) + ("rust-env_logger" + ,(origin + (method url-fetch) + (uri (crate-uri "env_logger" "0.3.5")) + (sha256 + (base32 + "0bvcjgkw4s3k1rd7glpflgc8s9a393zjd6jfdgvs8gjvwj0dgaqm")))) + ("rust-openssl-probe" + ,(origin + (method url-fetch) + (uri (crate-uri "openssl-probe" "0.1.0")) + (sha256 + (base32 + "0689h6rhzy6dypqr90lsxnf108nsnh952wsx7ggs70s48b44jvbm")))) + ("rust-lazy_static" + ,(origin + (method url-fetch) + (uri (crate-uri "lazy_static" "0.2.2")) + (sha256 + (base32 + "16z1h7w702sxnscak38jykxlhxq0b5ip4mndlb46pkaqwzi0xgka")))) + ("rust-semver-parser" + ,(origin + (method url-fetch) + (uri (crate-uri "semver-parser" "0.6.1")) + (sha256 + (base32 + "1s8s7a7yg8xhgci17y0xhyyncg229byivhpr0wbs3ljdlyjl73p8")))) + ("rust-semver" + ,(origin + (method url-fetch) + (uri (crate-uri "semver" "0.5.1")) + (sha256 + (base32 + 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(base32 + "0kk6abp1qbpv44hkq1yjp7xgpzjzafs83i1l26ycr0aph1gbwig9")))) + ("rust-git2-curl" + ,(origin + (method url-fetch) + (uri (crate-uri "git2-curl" "0.7.0")) + (sha256 + (base32 + "13mzqp4rd81zp78261rlq23iw9aaysdr56484y1yy2xzhk3nnrv8")))) + ("rust-bufstream" + ,(origin + (method url-fetch) + (uri (crate-uri "bufstream" "0.1.2")) + (sha256 + (base32 + "0x6h27md1fwabbhbycfldj0wklrpjr520z9p0cpzm60fzzidnj3v")))) + ("rust-hamcrest" + ,(origin + (method url-fetch) + (uri (crate-uri "hamcrest" "0.1.1")) + (sha256 + (base32 + "1m49rf7bnkx0qxja56slrjh44zi4z5bjz5x4pblqjw265828y25z")))) + ("rust-num" + ,(origin + (method url-fetch) + (uri (crate-uri "num" "0.1.36")) + (sha256 + (base32 + "081i1r3mdz6jasqd7qwraqqfqa3sdpvdvxl1xq0s7ip714xw1rxx")))) + ("rust-num-traits" + ,(origin + (method url-fetch) + (uri (crate-uri "num-traits" "0.1.36")) + (sha256 + (base32 + "07688sp4z40p14lh5ywvrpm4zq8kcxzhjks8sg33jsr5da2l4sm1")))) + ("rust-num-integer" + ,(origin + (method url-fetch) + (uri (crate-uri "num-integer" "0.1.32")) + (sha256 + (base32 + "14pvaaawl0pgdcgh4dfdd67lz58yxlfl95bry86h28pjnfzxj97v")))) + ("rust-num-bigint" + ,(origin + (method url-fetch) + (uri (crate-uri "num-bigint" "0.1.35")) + (sha256 + (base32 + "0jayfkdm33p4zvcahlv46zdfhlzg053mpw32abf2lz0z8xw47cc8")))) + ("rust-num-rational" + ,(origin + (method url-fetch) + (uri (crate-uri "num-rational" "0.1.35")) + (sha256 + (base32 + "1bwaygv64qg7i78yqg0v4d0amfhamj598rpy4yxjz9rlhcxn1zsl")))) + ("rust-num-iter" + ,(origin + (method url-fetch) + (uri (crate-uri "num-iter" "0.1.32")) + (sha256 + (base32 + "0p74nj5c1mc33h9lx4wpmlmggmn5lnkhxv1225g0aix8d6ciqyi8")))) + ("rust-num-complex" + ,(origin + (method url-fetch) + (uri (crate-uri "num-complex" "0.1.35")) + (sha256 + (base32 + "0bzrjfppnnzf9vmkpklhp2dw9sb1lqzydb8r6k83z76i9l2qxizh")))))) (arguments `(#:cargo ,cargo-bootstrap #:tests? #f ; FIXME @@ -317,12 +794,41 @@ safety and thread safety guarantees.") (delete 'patch-source-shebangs) (delete 'patch-generated-file-shebangs) (delete 'patch-usr-bin-file) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((unpack (lambda (source target) + (mkdir-p target) + (with-directory-excursion target + (zero? (system* "tar" "xf" + source + "--strip-components=1")))))) + (mkdir "vendor") + (for-each (lambda (p) + (let ((name (car p))) + (if (string-prefix? "rust-" name) + (let ((rsrc (string-append "vendor/" + (string-drop name + (string-length "rust-"))))) + (unpack (assoc-ref inputs name) rsrc) + (system* "touch" (string-append rsrc "/.cargo-ok")) + (generate-checksums rsrc (assoc-ref inputs name)))))) inputs)))) ;; Set CARGO_HOME to use the vendored dependencies. (add-after 'unpack 'set-cargo-home (lambda* (#:key inputs #:allow-other-keys) (let* ((gcc (assoc-ref inputs "gcc")) (cc (string-append gcc "/bin/gcc"))) + (mkdir "cargohome") (setenv "CARGO_HOME" (string-append (getcwd) "/cargohome")) + (call-with-output-file "cargohome/config" + (lambda (p) + (format p " +[source.crates-io] +registry = 'https://github.com/rust-lang/crates.io-index' +replace-with = 'vendored-sources' + +[source.vendored-sources] +directory = 'vendor' +"))) (setenv "CMAKE_C_COMPILER" cc) (setenv "CC" cc)) #t))))) diff --git a/gnu/packages/skribilo.scm b/gnu/packages/skribilo.scm index 52ed1c34e3..78b4806c8c 100644 --- a/gnu/packages/skribilo.scm +++ b/gnu/packages/skribilo.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -73,7 +73,7 @@ ;; The 'skribilo' command needs them, and for people using Skribilo as a ;; library, these inputs are needed as well. - (propagated-inputs `(("guile-reader" ,guile-reader) + (propagated-inputs `(("guile-reader" ,guile2.0-reader) ("guile-lib" ,guile-lib))) (home-page "http://www.nongnu.org/skribilo/") diff --git a/gnu/packages/spice.scm b/gnu/packages/spice.scm index 363a5e8fc5..838db4b35d 100644 --- a/gnu/packages/spice.scm +++ b/gnu/packages/spice.scm @@ -102,6 +102,7 @@ (uri (string-append "https://www.freedesktop.org/software/virgl/" "virglrenderer-" version ".tar.bz2")) + (patches (search-patches "virglrenderer-CVE-2017-6386.patch")) (sha256 (base32 "06kf0q4l52gzx5p63l8850hff8pmhp7xv1hk8zgx2apbw18y6jd5")))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 49bb24e594..d0bed4dd7f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -31,6 +31,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system r) #:use-module (guix build-system python) + #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages compression) #:use-module (gnu packages curl) @@ -99,9 +100,12 @@ can be imported from spreadsheets, text files and database sources and it can be output in text, PostScript, PDF or HTML.") (license license:gpl3+))) -(define-public r +;; Update this package together with the set of recommended packages: r-boot, +;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, +;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. +(define-public r-minimal (package - (name "r") + (name "r-minimal") (version "3.3.3") (source (origin (method url-fetch) @@ -129,17 +133,46 @@ be output in text, PostScript, PDF or HTML.") (substitute* "src/scripts/R.sh.in" (("uname") uname-bin))) #t)) - (add-after 'unpack 'build-recommended-packages-reproducibly + (add-after 'unpack 'build-reproducibly (lambda _ - (substitute* "src/library/Recommended/Makefile.in" - (("INSTALL_OPTS =(.*)" line rest ) - (string-append "INSTALL_OPTS = --built-timestamp=1970-01-01" - rest))) - ;; Ensure that gzipped files are reproducible + ;; The documentation contains time stamps to demonstrate + ;; documentation generation in different phases. + (substitute* "src/library/tools/man/Rd2HTML.Rd" + (("\\\\%Y-\\\\%m-\\\\%d at \\\\%H:\\\\%M:\\\\%S") + "(removed for reproducibility)")) + + ;; Remove timestamp from tracing environment. This fixes + ;; reproducibility of "methods.rd{b,x}". + (substitute* "src/library/methods/R/trace.R" + (("dateCreated = Sys.time\\(\\)") + "dateCreated = as.POSIXct(\"1970-1-1 00:00:00\", tz = \"UTC\")")) + + ;; Ensure that gzipped files are reproducible. (substitute* '("src/library/grDevices/Makefile.in" "doc/manual/Makefile.in") (("R_GZIPCMD\\)" line) (string-append line " -n"))) + + ;; The "srcfile" procedure in "src/library/base/R/srcfile.R" + ;; queries the mtime of a given file and records it in an object. + ;; This is acceptable at runtime to detect stale source files, + ;; but it destroys reproducibility at build time. + ;; + ;; Instead of disabling this feature, which may have unexpected + ;; consequences, we reset the mtime of generated files before + ;; passing them to the "srcfile" procedure. + (substitute* "src/library/Makefile.in" + (("@\\(cd base && \\$\\(MAKE\\) mkdesc\\)" line) + (string-append line "\n find $(top_builddir)/library/tools | xargs touch -d '1970-01-01'; \n")) + (("@\\$\\(MAKE\\) Rdobjects" line) + (string-append "@find $(srcdir)/tools | xargs touch -d '1970-01-01'; \n " + line))) + (substitute* "src/library/tools/Makefile.in" + (("@\\$\\(INSTALL_DATA\\) all.R \\$\\(top_builddir\\)/library/\\$\\(pkg\\)/R/\\$\\(pkg\\)" line) + (string-append + line + "\n find $(srcdir)/$(pkg) $(top_builddir)/library/$(pkg) | xargs touch -d \"1970-01-01\"; \n"))) + ;; This library is installed using "install_package_description", ;; so we need to pass the "builtStamp" argument. (substitute* "src/library/tools/Makefile.in" @@ -163,7 +196,12 @@ be output in text, PostScript, PDF or HTML.") (add-after 'build 'install-info (lambda _ (zero? (system* "make" "install-info"))))) #:configure-flags - '("--with-cairo" + '(;; Do not build the recommended packages. The build system creates + ;; random temporary directories and embeds their names in some + ;; package files. We build these packages with the r-build-system + ;; instead. + "--without-recommended-packages" + "--with-cairo" "--with-blas=-lopenblas" "--with-libpng" "--with-jpeglib" @@ -221,6 +259,343 @@ publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.") (license license:gpl3+))) +(define-public r-boot + (package + (name "r-boot") + (version "1.3-18") + (source + (origin + (method url-fetch) + (uri (cran-uri "boot" version)) + (sha256 + (base32 + "0pi348vvgzn1ny54yxhw6kq6nl7rx9bpr9ji1a6wqs8ah5zj7z8j")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/boot") + (synopsis "Bootstrap functions for R") + (description + "This package provides functions and datasets for bootstrapping from the +book \"Bootstrap Methods and Their Application\" by A.C. Davison and +D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.") + ;; Unlimited distribution + (license (license:non-copyleft "file://R/bootfuns.q")))) + +(define-public r-mass + (package + (name "r-mass") + (version "7.3-45") + (source + (origin + (method url-fetch) + (uri (cran-uri "MASS" version)) + (sha256 + (base32 + "13lp5919h2bnpmf8rbmkar8a41yx62fnx66pkvljvqf60wa29qsx")))) + (properties `((upstream-name . "MASS"))) + (build-system r-build-system) + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") + (synopsis "Support functions and datasets for Venables and Ripley's MASS") + (description + "This package provides functions and datasets for the book \"Modern +Applied Statistics with S\" (4th edition, 2002) by Venables and Ripley.") + ;; Either version may be picked. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-class + (package + (name "r-class") + (version "7.3-14") + (source + (origin + (method url-fetch) + (uri (cran-uri "class" version)) + (sha256 + (base32 + "173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") + (synopsis "R functions for classification") + (description + "This package provides various functions for classification, including +k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.") + ;; Either of the two versions can be picked. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-cluster + (package + (name "r-cluster") + (version "2.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "cluster" version)) + (sha256 + (base32 + "1bkvqmv8h2c423q9ag2afb6s9j2vcdlxsf559zzbimraphrr2c2b")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/cluster") + (synopsis "Methods for cluster analysis") + (description + "This package provides methods for cluster analysis. It is a much +extended version of the original from Peter Rousseeuw, Anja Struyf and Mia +Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") + (license license:gpl2+))) + +(define-public r-codetools + (package + (name "r-codetools") + (version "0.2-15") + (source + (origin + (method url-fetch) + (uri (cran-uri "codetools" version)) + (sha256 + (base32 + "0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/codetools") + (synopsis "Code analysis tools for R") + (description "This package provides code analysis tools for R.") + ;; Any version of the GPL. + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-foreign + (package + (name "r-foreign") + (version "0.8-67") + (source + (origin + (method url-fetch) + (uri (cran-uri "foreign" version)) + (sha256 + (base32 + "1mcrm2pydimbyjhkrw5h380bifj1jhwzifph1xgh90asf3lvd1xd")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/foreign") + (synopsis "Read data stored by other statistics software") + (description + "This package provides functions for reading and writing data stored by +some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and +for reading and writing some dBase files.") + (license license:gpl2+))) + +(define-public r-kernsmooth + (package + (name "r-kernsmooth") + (version "2.23-15") + (source + (origin + (method url-fetch) + (uri (cran-uri "KernSmooth" version)) + (sha256 + (base32 + "1xhha8kw10jv8pv8b61hb5in9qiw3r2a9kdji3qlm991s4zd4wlb")))) + (properties `((upstream-name . "KernSmooth"))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/KernSmooth") + (synopsis "Functions for kernel smoothing") + (description + "This package provides functions for kernel smoothing (and density +estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) +\"Kernel Smoothing\".") + ;; Unlimited distribution + (license (license:non-copyleft "file://LICENCE.note")))) + +(define-public r-lattice + (package + (name "r-lattice") + (version "0.20-34") + (source (origin + (method url-fetch) + (uri (cran-uri "lattice" version)) + (sha256 + (base32 + "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) + (build-system r-build-system) + (home-page "http://lattice.r-forge.r-project.org/") + (synopsis "High-level data visualization system") + (description + "The lattice package provides a powerful and elegant high-level data +visualization system inspired by Trellis graphics, with an emphasis on +multivariate data. Lattice is sufficient for typical graphics needs, and is +also flexible enough to handle most nonstandard requirements.") + (license license:gpl2+))) + +(define-public r-matrix + (package + (name "r-matrix") + (version "1.2-7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "Matrix" version)) + (sha256 + (base32 + "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) + (properties `((upstream-name . "Matrix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "http://Matrix.R-forge.R-project.org/") + (synopsis "Sparse and dense matrix classes and methods") + (description + "This package provides classes and methods for dense and sparse matrices +and operations on them using LAPACK and SuiteSparse.") + (license license:gpl2+))) + +(define-public r-nlme + (package + (name "r-nlme") + (version "3.1-131") + (source + (origin + (method url-fetch) + (uri (cran-uri "nlme" version)) + (sha256 + (base32 + "0k2nvdzhic6bzhfsbq6la6q6a1i5nlj4pnh6lpdxiiwvxdks3nkr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/nlme") + (synopsis "Linear and nonlinear mixed effects models") + (description + "This package provides tools to fit and compare Gaussian linear and +nonlinear mixed-effects models.") + (license license:gpl2+))) + +(define-public r-mgcv + (package + (name "r-mgcv") + (version "1.8-16") + (source + (origin + (method url-fetch) + (uri (cran-uri "mgcv" version)) + (sha256 + (base32 + "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix) + ("r-nlme" ,r-nlme))) + (home-page "http://cran.r-project.org/web/packages/mgcv") + (synopsis "Mixed generalised additive model computation") + (description + "GAMs, GAMMs and other generalized ridge regression with multiple smoothing +parameter estimation by GCV, REML or UBRE/AIC. The library includes a +@code{gam()} function, a wide variety of smoothers, JAGS support and +distributions beyond the exponential family.") + (license license:gpl2+))) + +(define-public r-nnet + (package + (name "r-nnet") + (version "7.3-12") + (source + (origin + (method url-fetch) + (uri (cran-uri "nnet" version)) + (sha256 + (base32 + "17amqnw9dpap2w8ivx53hxha2xrm0drwfnj32li0xk41hlz548r7")))) + (build-system r-build-system) + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") + (synopsis "Feed-forward neural networks and multinomial log-linear models") + (description + "This package provides functions for feed-forward neural networks with a +single hidden layer, and for multinomial log-linear models.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-rpart + (package + (name "r-rpart") + (version "4.1-10") + (source + (origin + (method url-fetch) + (uri (cran-uri "rpart" version)) + (sha256 + (base32 + "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/rpart") + (synopsis "Recursive partitioning and regression trees") + (description + "This package provides recursive partitioning functions for +classification, regression and survival trees.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-spatial + (package + (name "r-spatial") + (version "7.3-11") + (source + (origin + (method url-fetch) + (uri (cran-uri "spatial" version)) + (sha256 + (base32 + "04aw8j533sn63ybyrf4hyhrqm4058vfcb7yhjy07kq92mk94hi32")))) + (build-system r-build-system) + (home-page "http://www.stats.ox.ac.uk/pub/MASS4/") + (synopsis "Functions for kriging and point pattern analysis") + (description + "This package provides functions for kriging and point pattern +analysis.") + ;; Either version may be picked. + (license (list license:gpl2 license:gpl3)))) + +(define-public r-survival + (package + (name "r-survival") + (version "2.40-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "survival" version)) + (sha256 + (base32 + "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) + (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) + (home-page "https://github.com/therneau/survival") + (synopsis "Survival analysis") + (description + "This package contains the core survival analysis routines, including +definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) +curves, Cox models, and parametric accelerated failure time models.") + (license license:lgpl2.0+))) + +(define-public r + (package (inherit r-minimal) + (name "r") + (source #f) + (build-system trivial-build-system) + (arguments '(#:builder (mkdir %output))) + (propagated-inputs + `(("r-minimal" ,r-minimal) + ("r-boot" ,r-boot) + ("r-class" ,r-class) + ("r-cluster" ,r-cluster) + ("r-codetools" ,r-codetools) + ("r-foreign" ,r-foreign) + ("r-kernsmooth" ,r-kernsmooth) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-nlme" ,r-nlme) + ("r-nnet" ,r-nnet) + ("r-rpart" ,r-rpart) + ("r-spatial" ,r-spatial) + ("r-survival" ,r-survival))))) + (define-public r-bit (package (name "r-bit") @@ -460,49 +835,6 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation(\"Rcpp\")' for details on these last two.") (license license:gpl2+))) -(define-public r-matrix - (package - (name "r-matrix") - (version "1.2-7.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "Matrix" version)) - (sha256 - (base32 - "09rd51na9spz0lm1lylkfhw43w7c922b83m4jsggmpg3pbd6dssa")))) - (properties `((upstream-name . "Matrix"))) - (build-system r-build-system) - (propagated-inputs - `(("r-lattice" ,r-lattice))) - (home-page "http://Matrix.R-forge.R-project.org/") - (synopsis "Sparse and dense matrix classes and methods") - (description - "This package provides classes and methods for dense and sparse matrices -and operations on them using LAPACK and SuiteSparse.") - (license license:gpl2+))) - -(define-public r-mgcv - (package - (name "r-mgcv") - (version "1.8-16") - (source - (origin - (method url-fetch) - (uri (cran-uri "mgcv" version)) - (sha256 - (base32 - "0pj31gdwra7nv8spys4pfcbmsik99q1y1d0d2g37ywc3sz5s0rlj")))) - (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/mgcv") - (synopsis "Mixed generalised additive model computation") - (description - "GAMs, GAMMs and other generalized ridge regression with multiple smoothing -parameter estimation by GCV, REML or UBRE/AIC. The library includes a -@code{gam()} function, a wide variety of smoothers, JAGS support and -distributions beyond the exponential family.") - (license license:gpl2+))) - (define-public r-permute (package (name "r-permute") @@ -722,6 +1054,7 @@ legends.") ("r-gtable" ,r-gtable) ("r-plyr" ,r-plyr) ("r-lazyeval" ,r-lazyeval) + ("r-mass" ,r-mass) ("r-tibble" ,r-tibble) ("r-reshape2" ,r-reshape2) ("r-scales" ,r-scales) @@ -1342,6 +1675,8 @@ side.") (base32 "0lafrmq1q7x026m92h01hc9cjjiximqqi3v1g2hw7ai9vf7i897m")))) (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) (home-page "http://cran.r-project.org/web/packages/locfit") (synopsis "Local regression, likelihood and density estimation") (description @@ -1519,6 +1854,8 @@ inference for statistical models.") (base32 "14a4a8df4ygj05h37chmdn8kzcqs07fpbflxfrq530563mrza7yl")))) (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) (home-page "http://cran.r-project.org/web/packages/coda") (synopsis "This is a package for Output Analysis and Diagnostics for MCMC") (description "This package provides functions for summarizing and plotting @@ -2028,26 +2365,6 @@ scaling functions for R.") "This package provides an integration of base and grid graphics for R.") (license license:gpl2+))) -(define-public r-lattice - (package - (name "r-lattice") - (version "0.20-34") - (source (origin - (method url-fetch) - (uri (cran-uri "lattice" version)) - (sha256 - (base32 - "0615h69czr73k47whhzimf1qxv5qk0cabcrkljwhyrn6m6piq6ja")))) - (build-system r-build-system) - (home-page "http://lattice.r-forge.r-project.org/") - (synopsis "High-level data visualization system") - (description - "The lattice package provides a powerful and elegant high-level data -visualization system inspired by Trellis graphics, with an emphasis on -multivariate data. Lattice is sufficient for typical graphics needs, and is -also flexible enough to handle most nonstandard requirements.") - (license license:gpl2+))) - (define-public r-latticeextra (package (name "r-latticeextra") @@ -2687,6 +3004,8 @@ flexible than the orphaned \"base64\" package.") (base32 "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) (home-page "http://cran.r-project.org/web/packages/irlba") (synopsis "Methods for eigendecomposition of large matrices") (description @@ -2707,10 +3026,11 @@ analysis of large sparse or dense matrices.") (base32 "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) (build-system r-build-system) - (inputs - `(("gfortran" ,gfortran))) + (inputs + `(("gfortran" ,gfortran))) (propagated-inputs - `(("r-foreach" ,r-foreach))) + `(("r-foreach" ,r-foreach) + ("r-matrix" ,r-matrix))) (home-page "http://www.jstatsoft.org/v33/i01") (synopsis "Lasso and elastic-net regularized generalized linear models") (description @@ -2828,6 +3148,8 @@ Stochastic Neighbor Embedding using a Barnes-Hut implementation.") (base32 "1069qwj9gsjq6par2cgfah8nn5x2w38830761x1f7mqpmk0gnj3h")))) (build-system r-build-system) + (propagated-inputs + `(("r-class" ,r-class))) (home-page "http://cran.r-project.org/web/packages/e1071") (synopsis "Miscellaneous functions for probability theory") (description @@ -3439,6 +3761,9 @@ from within R.") (("if isnan\\(lambda\\) \\{") "if (isnan(lambda)) {")) #t))))) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-matrix" ,r-matrix))) (home-page "http://spams-devel.gforge.inria.fr") (synopsis "Toolbox for solving sparse estimation problems") (description "SPAMS (SPArse Modeling Software) is an optimization toolbox @@ -3456,45 +3781,6 @@ following problems: @end enumerate\n") (license license:gpl3+))) -(define-public r-rpart - (package - (name "r-rpart") - (version "4.1-10") - (source - (origin - (method url-fetch) - (uri (cran-uri "rpart" version)) - (sha256 - (base32 - "119dvh2cpab4vq9blvbkil5hgq6w018amiwlda3ii0fki39axpf5")))) - (build-system r-build-system) - (home-page "http://cran.r-project.org/web/packages/rpart") - (synopsis "Recursive partitioning and regression trees") - (description - "This package provides recursive partitioning functions for -classification, regression and survival trees.") - (license (list license:gpl2+ license:gpl3+)))) - -(define-public r-survival - (package - (name "r-survival") - (version "2.40-1") - (source - (origin - (method url-fetch) - (uri (cran-uri "survival" version)) - (sha256 - (base32 - "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci")))) - (build-system r-build-system) - (home-page "https://github.com/therneau/survival") - (synopsis "Survival analysis") - (description - "This package contains the core survival analysis routines, including -definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) -curves, Cox models, and parametric accelerated failure time models.") - (license license:lgpl2.0+))) - (define-public r-base64 (package (name "r-base64") @@ -3536,17 +3822,20 @@ package instead.") `(("r-acepack" ,r-acepack) ("r-base64" ,r-base64) ("r-base64enc" ,r-base64enc) + ("r-cluster" ,r-cluster) ("r-data-table" ,r-data-table) + ("r-foreign" ,r-foreign) ("r-formula" ,r-formula) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtable" ,r-gtable) - ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival - ;; package that comes with R 3.3.2. - ("r-survival" ,r-survival) + ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-htmltable" ,r-htmltable) ("r-htmltools" ,r-htmltools) + ("r-nnet" ,r-nnet) + ("r-rpart" ,r-rpart) + ("r-survival" ,r-survival) ("r-viridis" ,r-viridis))) (home-page "http://biostat.mc.vanderbilt.edu/Hmisc") (synopsis "Miscellaneous data analysis and graphics functions") @@ -3831,6 +4120,8 @@ estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) (base32 "167m142rwwfy8b9hnfc3fi28dcsdjk61g1crqhll6sh5xmgnfn28")))) (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) (home-page "http://zoo.R-Forge.R-project.org/") (synopsis "S3 infrastructure for regular and irregular time series") (description "This package contains an S3 class with methods for totally @@ -4097,7 +4388,9 @@ letters, as is often required for scientific publications.") "133rr17ywmlhsc6457hs8qxi8ng443ql9ashxpwc8875gjhv1x32")))) (build-system r-build-system) (propagated-inputs - `(("r-segmented" ,r-segmented))) + `(("r-boot" ,r-boot) + ("r-mass" ,r-mass) + ("r-segmented" ,r-segmented))) (home-page "http://cran.r-project.org/web/packages/mixtools") (synopsis "Tools for analyzing finite mixture models") (description @@ -4227,7 +4520,9 @@ to change in the future.") "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z")))) (build-system r-build-system) (propagated-inputs - `(("r-modeltools" ,r-modeltools))) + `(("r-lattice" ,r-lattice) + ("r-modeltools" ,r-modeltools) + ("r-nnet" ,r-nnet))) (home-page "http://cran.r-project.org/web/packages/flexmix") (synopsis "Flexible mixture modeling") (description @@ -4274,7 +4569,8 @@ and resampling-based inference.") "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1")))) (build-system r-build-system) (propagated-inputs - `(("r-mclust" ,r-mclust))) + `(("r-mass" ,r-mass) + ("r-mclust" ,r-mclust))) (home-page "https://cran.r-project.org/web/packages/prabclus") (synopsis "Parametric bootstrap tests for spatial neighborhood clustering") (description @@ -4363,9 +4659,12 @@ of the points.") "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx")))) (build-system r-build-system) (propagated-inputs - `(("r-diptest" ,r-diptest) + `(("r-class" ,r-class) + ("r-cluster" ,r-cluster) + ("r-diptest" ,r-diptest) ("r-flexmix" ,r-flexmix) ("r-kernlab" ,r-kernlab) + ("r-mass" ,r-mass) ("r-mclust" ,r-mclust) ("r-mvtnorm" ,r-mvtnorm) ("r-prabclus" ,r-prabclus) @@ -4484,7 +4783,8 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-rcpp" ,r-rcpp) + ("r-matrix" ,r-matrix))) (home-page "http://eigen.tuxfamily.org") (synopsis "Rcpp integration for the Eigen templated linear algebra library") (description @@ -4529,6 +4829,8 @@ metrics for evaluating models.") "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy")))) (properties `((upstream-name . "MatrixModels"))) (build-system r-build-system) + (propagated-inputs + `(("r-matrix" ,r-matrix))) (home-page "https://cran.r-project.org/web/packages/MatrixModels") (synopsis "Modelling with sparse and dense matrices") (description @@ -4606,7 +4908,9 @@ algorithms.") ("r-rcppeigen" ,r-rcppeigen))) (propagated-inputs `(("r-minqa" ,r-minqa) - ("r-nloptr" ,r-nloptr))) + ("r-nloptr" ,r-nloptr) + ("r-mass" ,r-mass) + ("r-nlme" ,r-nlme))) (home-page "http://cran.r-project.org/web/packages/lme4") (synopsis "Linear mixed-effects models using eigen and S4") (description @@ -4629,7 +4933,9 @@ C++ library for numerical linear algebra and RcppEigen glue.") "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x")))) (build-system r-build-system) (propagated-inputs - `(("r-lme4" ,r-lme4))) + `(("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix))) (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/") (synopsis "Methods for linear mixed model comparison") (description @@ -4651,7 +4957,10 @@ bootstrap test for generalized linear mixed models.") "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx")))) (build-system r-build-system) (propagated-inputs - `(("r-pbkrtest" ,r-pbkrtest) + `(("r-mass" ,r-mass) + ("r-mgcv" ,r-mgcv) + ("r-nnet" ,r-nnet) + ("r-pbkrtest" ,r-pbkrtest) ("r-quantreg" ,r-quantreg))) (home-page "https://r-forge.r-project.org/projects/car/") (synopsis "Companion to applied regression") @@ -4790,7 +5099,8 @@ multivariate case.") "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp")))) (build-system r-build-system) (propagated-inputs - `(("r-mclust" ,r-mclust) + `(("r-cluster" ,r-cluster) + ("r-mclust" ,r-mclust) ("r-mvtnorm" ,r-mvtnorm) ("r-sn" ,r-sn))) (home-page "http://cran.r-project.org/web/packages/tclust") diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 9796c18c7d..2aecc5fd12 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -222,7 +222,7 @@ required structures.") (substitute-keyword-arguments (package-arguments gnutls) ((#:configure-flags flags) `(cdr ,flags)))) - (inputs `(("guile" ,guile-next) + (inputs `(("guile" ,guile-2.2) ,@(alist-delete "guile" (package-inputs gnutls)))))) (define-public openssl diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 2988773398..9fa7b8544d 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -220,14 +220,14 @@ television and DVD. It is also known as AC-3.") (define-public libx264 (package (name "libx264") - (version "20170224-2245") + (version "20170316-2245") (source (origin (method url-fetch) (uri (string-append "https://download.videolan.org/pub/x264/snapshots/" "x264-snapshot-" version ".tar.bz2")) (sha256 (base32 - "0paw8vzsy2qh5jf6xg2i1risjwyvmxgfnivly4gh0bib62cp4vib")))) + "1s1nnvl3axz38sv4g09skijl6k9mbbngbb1nsh26w4dr2w2gyzad")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -980,7 +980,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2017.03.15") + (version "2017.03.16") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -988,7 +988,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "0h561pbphdkfalir9awp0k4fmsnzdf6kx56adb9bb0v9pfsb1y0f")))) + "14nlgl0kh4mwl7sx58vd7nxr5iklxi00612lmydy91ngm6ykrpsm")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion @@ -1022,7 +1022,7 @@ YouTube.com and a few more sites.") (define-public libbluray (package (name "libbluray") - (version "0.9.3") + (version "1.0.0") (source (origin (method url-fetch) (uri (string-append "https://download.videolan.org/videolan/" @@ -1030,7 +1030,7 @@ YouTube.com and a few more sites.") name "-" version ".tar.bz2")) (sha256 (base32 - "1q1whviqv5sr9nr372h31zwid1rvbfbx3z4lzr8lnj25xha6cdm6")))) + "1k3lag4lxi2jjd3zh4wcb5l3hadzm54j5kagh92yzfy76p9svqzp")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--disable-bdjava") diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm index 40e1dd5cfc..4f6e76d58e 100644 --- a/gnu/packages/wine.scm +++ b/gnu/packages/wine.scm @@ -54,14 +54,14 @@ (define-public wine (package (name "wine") - (version "2.3") + (version "2.4") (source (origin (method url-fetch) (uri (string-append "https://dl.winehq.org/wine/source/2.x" "/wine-" version ".tar.xz")) (sha256 (base32 - "0zh6kvs4d6d99x5qgxbb5jq2wilwzifhmib2nhq0g3ychxx5rjdg")))) + "13klfadvd44zdfrzh38al99s53i02x3mlhcj5z7fq7vqwh3xzdc7")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) ("gettext" ,gettext-minimal) diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 5298a11f63..dad1911d31 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -274,7 +274,8 @@ FILE-SYSTEM." (options (file-system-options file-system)) (check? (file-system-check? file-system)) (create? (file-system-create-mount-point? file-system)) - (dependencies (file-system-dependencies file-system))) + (dependencies (file-system-dependencies file-system)) + (packages (file-system-packages (list file-system)))) (and (file-system-mount? file-system) (with-imported-modules '((gnu build file-systems) (guix build bournish)) @@ -284,7 +285,7 @@ FILE-SYSTEM." ,@(map dependency->shepherd-service-name dependencies))) (documentation "Check, mount, and unmount the given file system.") (start #~(lambda args - #$(if create? + #$(if create? #~(mkdir-p #$target) #t) @@ -292,11 +293,12 @@ FILE-SYSTEM." ;; Make sure fsck.ext2 & co. can be found. (dynamic-wind (lambda () - (setenv "PATH" - (string-append - #$e2fsprogs "/sbin:" - "/run/current-system/profile/sbin:" - $PATH))) + ;; Don’t display the PATH settings. + (with-output-to-port (%make-void-port "w") + (lambda () + (set-path-environment-variable "PATH" + '("bin" "sbin") + '#$packages)))) (lambda () (mount-file-system `(#$device #$title #$target #$type #$flags diff --git a/gnu/services/networking.scm b/gnu/services/networking.scm index 18bce2a2b8..9b8e5b36b1 100644 --- a/gnu/services/networking.scm +++ b/gnu/services/networking.scm @@ -80,7 +80,10 @@ network-manager-configuration-dns network-manager-service-type - connman-service + connman-configuration + connman-configuration? + connman-service-type + wpa-supplicant-service-type openvswitch-service-type @@ -822,45 +825,54 @@ dns=" dns " ;;; Connman ;;; -(define %connman-activation - ;; Activation gexp for Connman. - #~(begin - (use-modules (guix build utils)) - (mkdir-p "/var/lib/connman/") - (mkdir-p "/var/lib/connman-vpn/"))) - -(define (connman-shepherd-service connman) +(define-record-type* <connman-configuration> + connman-configuration make-connman-configuration + connman-configuration? + (connman connman-configuration-connman + (default connman)) + (disable-vpn? connman-configuration-disable-vpn? + (default #f))) + +(define (connman-activation config) + (let ((disable-vpn? (connman-configuration-disable-vpn? config))) + (with-imported-modules '((guix build utils)) + #~(begin + (use-modules (guix build utils)) + (mkdir-p "/var/lib/connman/") + (unless #$disable-vpn? + (mkdir-p "/var/lib/connman-vpn/")))))) + +(define (connman-shepherd-service config) "Return a shepherd service for Connman" - (list (shepherd-service - (documentation "Run Connman") - (provision '(networking)) - (requirement '(user-processes dbus-system loopback wpa-supplicant)) - (start #~(make-forkexec-constructor - (list (string-append #$connman - "/sbin/connmand") - "-n" "-r"))) - (stop #~(make-kill-destructor))))) + (and + (connman-configuration? config) + (let ((connman (connman-configuration-connman config)) + (disable-vpn? (connman-configuration-disable-vpn? config))) + (list (shepherd-service + (documentation "Run Connman") + (provision '(networking)) + (requirement + '(user-processes dbus-system loopback wpa-supplicant)) + (start #~(make-forkexec-constructor + (list (string-append #$connman + "/sbin/connmand") + "-n" "-r" + #$@(if disable-vpn? '("--noplugin=vpn") '())))) + (stop #~(make-kill-destructor))))))) (define connman-service-type - (service-type (name 'connman) - (extensions - (list (service-extension shepherd-root-service-type - connman-shepherd-service) - (service-extension dbus-root-service-type list) - (service-extension activation-service-type - (const %connman-activation)) - ;; Add connman to the system profile. - (service-extension profile-service-type list))))) - -(define* (connman-service #:key (connman connman)) - "Return a service that runs @url{https://01.org/connman,Connman}, a network -connection manager. - -This service adds the @var{connman} package to the global profile, providing -several the @command{connmanctl} command to interact with the daemon and -configure networking." - (service connman-service-type connman)) - + (let ((connman-package (compose list connman-configuration-connman))) + (service-type (name 'connman) + (extensions + (list (service-extension shepherd-root-service-type + connman-shepherd-service) + (service-extension dbus-root-service-type + connman-package) + (service-extension activation-service-type + connman-activation) + ;; Add connman to the system profile. + (service-extension profile-service-type + connman-package)))))) ;;; diff --git a/gnu/system/file-systems.scm b/gnu/system/file-systems.scm index 7011a279d3..8107722c74 100644 --- a/gnu/system/file-systems.scm +++ b/gnu/system/file-systems.scm @@ -22,6 +22,8 @@ #:use-module (guix records) #:use-module ((gnu build file-systems) #:select (string->uuid uuid->string)) + #:use-module (gnu packages linux) + #:use-module (gnu packages disk) #:re-export (string->uuid uuid->string) #:export (<file-system> @@ -65,6 +67,8 @@ file-system-mapping->bind-mount + file-system-packages + %store-mapping %network-configuration-files %network-file-mappings)) @@ -411,4 +415,26 @@ a bind mount." (writable? (string=? file "/etc/resolv.conf")))) %network-configuration-files)) +(define (file-system-type-predicate type) + (lambda (fs) + (string=? (file-system-type fs) type))) + +(define* (file-system-packages file-systems #:key (volatile-root? #f)) + `(,@(if (find (lambda (fs) + (string-prefix? "ext" (file-system-type fs))) + file-systems) + (list e2fsck/static) + '()) + ,@(if (find (lambda (fs) + (string-suffix? "fat" (file-system-type fs))) + file-systems) + (list fatfsck/static) + '()) + ,@(if (find (file-system-type-predicate "btrfs") file-systems) + (list btrfs-progs/static) + '()) + ,@(if volatile-root? + (list unionfs-fuse/static) + '()))) + ;;; file-systems.scm ends here diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index 81c1278c0c..1f1c306828 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -272,23 +272,7 @@ loaded at boot time in the order in which they appear." ,@extra-modules)) (define helper-packages - ;; Packages to be copied on the initrd. - `(,@(if (find (lambda (fs) - (string-prefix? "ext" (file-system-type fs))) - file-systems) - (list e2fsck/static) - '()) - ,@(if (find (lambda (fs) - (string-suffix? "fat" (file-system-type fs))) - file-systems) - (list fatfsck/static) - '()) - ,@(if (find (file-system-type-predicate "btrfs") file-systems) - (list btrfs-progs/static) - '()) - ,@(if volatile-root? - (list unionfs-fuse/static) - '()))) + (file-system-packages file-systems #:volatile-root? volatile-root?)) (raw-initrd file-systems #:linux linux |