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2016-10-26gnu: r-topgo: Update to 2.26.0.•••* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0. [propagated-inputs]: Add r-dbi. Ricardo Wurmus
2016-10-26gnu: r-graph: Update to 1.52.0.•••* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0. Ricardo Wurmus
2016-10-26gnu: r-go-db: Update to 3.4.0.•••* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0. Ricardo Wurmus
2016-10-26gnu: r-genomicfeatures: Update to 1.26.0.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0. Ricardo Wurmus
2016-10-26gnu: r-rtracklayer: Update to 1.34.0.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0. Ricardo Wurmus
2016-10-26gnu: r-genomicalignments: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.0. Ricardo Wurmus
2016-10-26gnu: r-summarizedexperiment: Update to 1.4.0.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.4.0. Ricardo Wurmus
2016-10-26gnu: r-rsamtools: Update to 1.26.1.•••* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1. Ricardo Wurmus
2016-10-26gnu: r-biostrings: Update to 2.42.0.•••* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0. Ricardo Wurmus
2016-10-26gnu: r-biocparallel: Update to 1.8.0.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0. Ricardo Wurmus
2016-10-26gnu: r-biomart: Update to 2.30.0.•••* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0. Ricardo Wurmus
2016-10-26gnu: r-annotationdbi: Update to 1.36.0.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0. Ricardo Wurmus
2016-10-26gnu: r-biobase: Update to 2.34.0.•••* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0. Ricardo Wurmus
2016-10-26gnu: r-genomicranges: Update to 1.26.1.•••* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1. [propagated-inputs]: Add r-iranges, r-s4vectors. Ricardo Wurmus
2016-10-26gnu: r-xvector: Update to 0.14.0.•••* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0. Ricardo Wurmus
2016-10-26gnu: r-limma: Update to 3.30.0.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0. Ricardo Wurmus
2016-10-26gnu: r-variantannotation: Update to 1.20.0.•••* 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. Ricardo Wurmus
2016-10-26gnu: r-edger: Update to 3.16.0.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit. Ricardo Wurmus
2016-10-26gnu: r-genomeinfodb: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0. Ricardo Wurmus
2016-10-26gnu: r-iranges: Update to 2.8.0.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0. Ricardo Wurmus
2016-10-26gnu: r-s4vectors: Update to 0.12.0.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0. Ricardo Wurmus
2016-10-26gnu: r-dnacopy: Update to 1.48.0.•••* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0. Ricardo Wurmus
2016-10-26gnu: r-biocinstaller: Update to 1.24.0.•••* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0. Ricardo Wurmus
2016-10-26gnu: r-biocgenerics: Update to 0.20.0.•••* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0. Ricardo Wurmus
2016-10-26gnu: r-grohmm: Update to 1.8.0.•••* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0. Ricardo Wurmus
2016-10-26gnu: r-systempiper: Update to 1.8.1.•••* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1. Ricardo Wurmus
2016-10-26gnu: r-shortread: Update to 1.32.0.•••* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0. Ricardo Wurmus
2016-10-26gnu: r-gostats: Update to 2.40.0.•••* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0. Ricardo Wurmus
2016-10-26gnu: r-category: Update to 2.40.0.•••* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0. Ricardo Wurmus
2016-10-26gnu: r-gseabase: Update to 1.36.0.•••* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0. Ricardo Wurmus
2016-10-26gnu: r-rbgl: Update to 1.50.0.•••* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0. Ricardo Wurmus
2016-10-26gnu: r-annotationforge: Update to 1.16.0.•••* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0. [propagated-inputs]: Add r-rcurl. Ricardo Wurmus
2016-10-26gnu: r-deseq2: Update to 1.14.0.•••* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0. Ricardo Wurmus
2016-10-26gnu: r-genefilter: Update to 1.56.0.•••* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0. Ricardo Wurmus
2016-10-26gnu: r-geneplotter: Update to 1.52.0.•••* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0. Ricardo Wurmus
2016-10-26gnu: r-annotate: Update to 1.52.0.•••* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0. Ricardo Wurmus
2016-10-26gnu: Add r-kernsmooth.•••* gnu/packages/statistics.scm (r-kernsmooth): New variable. Ricardo Wurmus
2016-10-26gnu: emacs-emms-player-mpv: Update to 0.0.10.•••* gnu/packages/emacs.scm (emacs-emms-player-mpv): Update to 0.0.10. Ricardo Wurmus
2016-10-26import cran: Use URL for Bioconductor 3.4.•••* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.4. Ricardo Wurmus
2016-10-25gnu: elfutils: Update to 0.167.•••* gnu/packages/elf.scm (elfutils): Update to 0.167. Leo Famulari
2016-10-25gnu: gtk+-2: Update to 2.24.31 [fixes CVE-2013-7447].•••* gnu/packages/gtk.scm (gtk+-2): Update to 2.24.31. Leo Famulari
2016-10-25gnu: mupdf: Fix CVE-2016-8674.•••* 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. Kei Kebreau
2016-10-25gnu: coda: Remove bundled libraries.•••* 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> Thomas Danckaert
2016-10-25build: 'guilemoduledir' honors $GUILE_EFFECTIVE_VERSION.•••* configure.ac: Define 'guilemoduledir' as a function of $GUILE_EFFECTIVE_VERSION. Ludovic Courtès
2016-10-25svg: Autoload Guile-RSVG and Guile-Cairo.•••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!'. Ludovic Courtès
2016-10-24gnu: linux-libre@4.1: Update to 4.1.35.•••* 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. Mark H Weaver
2016-10-24gnu: Add missing module import to (gnu packages gl).•••This is a followup to commit f1267c872fcaed6c53d43b3ff51abb726f7418d6. * gnu/packages/gl.scm: Import (gnu packages). Mark H Weaver
2016-10-24gnu: mesa: Fix 'wayland-egl-symbols-check' on MIPS.•••* gnu/packages/patches/mesa-wayland-egl-symbols-check-mips.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gl.scm (mesa)[source]: Add patch when building on MIPS. Mark H Weaver
2016-10-25system: grub: Use Guile-{RSVG,Cairo} instead of Inkscape + ImageMagick.•••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. Ludovic Courtès
2016-10-24gnu: perl-eval-closure: Update to 0.14.•••* gnu/packages/perl.scm (perl-eval-closure): Update to 0.14. Leo Famulari
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