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* gnu: r-rtracklayer: Update to 1.34.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
* gnu: r-genomicalignments: Update to 1.10.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.0.
* gnu: r-summarizedexperiment: Update to 1.4.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.4.0.
* gnu: r-rsamtools: Update to 1.26.1.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
* gnu: r-biostrings: Update to 2.42.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
* gnu: r-biocparallel: Update to 1.8.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
* gnu: r-biomart: Update to 2.30.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
* gnu: r-annotationdbi: Update to 1.36.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
* gnu: r-biobase: Update to 2.34.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
* gnu: r-genomicranges: Update to 1.26.1.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1. [propagated-inputs]: Add r-iranges, r-s4vectors.
* gnu: r-xvector: Update to 0.14.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
* gnu: r-limma: Update to 3.30.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
* gnu: r-variantannotation: Update to 1.20.0.Ricardo Wurmus2016-10-26
| | | | | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.0. [propagated-inputs]: Add r-biobase, r-biostrings, r-iranges, r-rtracklayer, r-s4vectors, r-xvector.
* gnu: r-edger: Update to 3.16.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit.
* gnu: r-genomeinfodb: Update to 1.10.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
* gnu: r-iranges: Update to 2.8.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
* gnu: r-s4vectors: Update to 0.12.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
* gnu: r-dnacopy: Update to 1.48.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
* gnu: r-biocinstaller: Update to 1.24.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
* gnu: r-biocgenerics: Update to 0.20.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0.
* gnu: r-grohmm: Update to 1.8.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0.
* gnu: r-systempiper: Update to 1.8.1.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1.
* gnu: r-shortread: Update to 1.32.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0.
* gnu: r-gostats: Update to 2.40.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0.
* gnu: r-category: Update to 2.40.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0.
* gnu: r-gseabase: Update to 1.36.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0.
* gnu: r-rbgl: Update to 1.50.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0.
* gnu: r-annotationforge: Update to 1.16.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0. [propagated-inputs]: Add r-rcurl.
* gnu: r-deseq2: Update to 1.14.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0.
* gnu: r-genefilter: Update to 1.56.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0.
* gnu: r-geneplotter: Update to 1.52.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0.
* gnu: r-annotate: Update to 1.52.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0.
* gnu: Add r-kernsmooth.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/statistics.scm (r-kernsmooth): New variable.
* gnu: emacs-emms-player-mpv: Update to 0.0.10.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/emacs.scm (emacs-emms-player-mpv): Update to 0.0.10.
* import cran: Use URL for Bioconductor 3.4.Ricardo Wurmus2016-10-26
| | | | | * guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.4.
* gnu: elfutils: Update to 0.167.Leo Famulari2016-10-25
| | | | * gnu/packages/elf.scm (elfutils): Update to 0.167.
* gnu: gtk+-2: Update to 2.24.31 [fixes CVE-2013-7447].Leo Famulari2016-10-25
| | | | * gnu/packages/gtk.scm (gtk+-2): Update to 2.24.31.
* gnu: mupdf: Fix CVE-2016-8674.Kei Kebreau2016-10-25
| | | | | | * gnu/packages/patches/mupdf-CVE-2016-8674.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/pdf.scm (mupdf): Use it.
* gnu: coda: Remove bundled libraries.Thomas Danckaert2016-10-25
| | | | | | | | | | * gnu/packages/maths.scm (coda): Remove bundled libraries. [source]: Add patch and snippet to remove bundled zlib, pcre and expat. [inputs]: Add system zlib, pcre and expat. * gnu/packages/patches/coda-use-system-libs.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* build: 'guilemoduledir' honors $GUILE_EFFECTIVE_VERSION.Ludovic Courtès2016-10-25
| | | | | * configure.ac: Define 'guilemoduledir' as a function of $GUILE_EFFECTIVE_VERSION.
* svg: Autoload Guile-RSVG and Guile-Cairo.Ludovic Courtès2016-10-25
| | | | | | | Fixes compilation by 'guix pull' where Guile-{RSVG,Cairo} are missing. Reported by Efraim Flashner. * gnu/build/svg.scm: Use 'module-autoload!' rather than 'module-use!'.
* gnu: linux-libre@4.1: Update to 4.1.35.Mark H Weaver2016-10-24
| | | | | | | * gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.35. Remove patch. * gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* system: grub: Use Guile-{RSVG,Cairo} instead of Inkscape + ImageMagick.Ludovic Courtès2016-10-25
| | | | | | | | | | | | Based on a suggestion by Andy Wingo at <https://lists.gnu.org/archive/html/guix-devel/2015-08/msg00753.html>. * gnu/build/svg.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/system/grub.scm (svg->png): Add #:width and #:height. Rewrite to use (gnu build svg). (resize-image): Remove. (grub-background-image): Adjust accordingly.
* gnu: Add coda.Thomas Danckaert2016-10-24
| | | | | | * gnu/packages/maths.scm (coda): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add hdf-eos2.Thomas Danckaert2016-10-24
| | | | | | | | | | * gnu/packages/maths.scm (hdf-eos2): New variable. * gnu/packages/patches/hdf-eos2-build-shared.patch: New file. * gnu/packages/patches/hdf-eos2-remove-gctp.patch: New file. * gnu/packages/patches/hdf-eos2-fortrantests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add patches. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add guile-bytestructuresAmirouche2016-10-24
| | | | | | * gnu/packages/guile.scm (guile-bytestructures): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: nginx: Virtual hosts are first-class configuration items.Julien Lepiller2016-10-24
| | | | | | | | | | | | | * gnu/services/web.scm (<nginx-vhost-configuration>): New record type. (config-domain-strings): New procedure. (config-index-strings): New procedure. (default-nginx-vhost-config): New procedure. (default-nginx-config): Add vhost support and temporary directories (nginx-activation): Create temporary directories (nginx-service): Add vhost-list key. * doc/guix.texi (Web Services): Document 'nginx-vhost-configuration'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: efl: Update to 1.18.2.Efraim Flashner2016-10-24
| | | | * gnu/packages/enlightenment.scm (efl): Update to 1.18.2.
* gnu: red-eclipse: Update to 1.5.6.Kei Kebreau2016-10-24
| | | | | * gnu/packages/games.scm (red-eclipse): Update to 1.5.6. [arguments]: Adjust phases.
* gnu: Add whois.ng02016-10-24
| | | | | | * gnu/packages/networking.scm (whois): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
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