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* gnu: r-rsamtools: Update to 1.26.1.•••* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1. Ricardo Wurmus2016-10-26
* gnu: r-biostrings: Update to 2.42.0.•••* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0. Ricardo Wurmus2016-10-26
* gnu: r-biocparallel: Update to 1.8.0.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0. Ricardo Wurmus2016-10-26
* gnu: r-biomart: Update to 2.30.0.•••* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0. Ricardo Wurmus2016-10-26
* gnu: r-annotationdbi: Update to 1.36.0.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0. Ricardo Wurmus2016-10-26
* gnu: r-biobase: Update to 2.34.0.•••* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0. Ricardo Wurmus2016-10-26
* gnu: 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 Wurmus2016-10-26
* gnu: r-xvector: Update to 0.14.0.•••* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0. Ricardo Wurmus2016-10-26
* gnu: r-limma: Update to 3.30.0.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0. Ricardo Wurmus2016-10-26
* gnu: 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 Wurmus2016-10-26
* gnu: r-edger: Update to 3.16.0.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit. Ricardo Wurmus2016-10-26
* gnu: r-genomeinfodb: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0. Ricardo Wurmus2016-10-26
* gnu: r-iranges: Update to 2.8.0.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0. Ricardo Wurmus2016-10-26
* gnu: r-s4vectors: Update to 0.12.0.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0. Ricardo Wurmus2016-10-26
* gnu: r-dnacopy: Update to 1.48.0.•••* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0. Ricardo Wurmus2016-10-26
* gnu: r-biocinstaller: Update to 1.24.0.•••* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0. Ricardo Wurmus2016-10-26
* gnu: r-biocgenerics: Update to 0.20.0.•••* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0. Ricardo Wurmus2016-10-26
* gnu: r-grohmm: Update to 1.8.0.•••* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0. Ricardo Wurmus2016-10-26
* gnu: r-systempiper: Update to 1.8.1.•••* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1. Ricardo Wurmus2016-10-26
* gnu: r-shortread: Update to 1.32.0.•••* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0. Ricardo Wurmus2016-10-26
* gnu: r-gostats: Update to 2.40.0.•••* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0. Ricardo Wurmus2016-10-26
* gnu: r-category: Update to 2.40.0.•••* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0. Ricardo Wurmus2016-10-26
* gnu: r-gseabase: Update to 1.36.0.•••* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0. Ricardo Wurmus2016-10-26
* gnu: r-rbgl: Update to 1.50.0.•••* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0. Ricardo Wurmus2016-10-26
* gnu: r-annotationforge: Update to 1.16.0.•••* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0. [propagated-inputs]: Add r-rcurl. Ricardo Wurmus2016-10-26
* gnu: r-deseq2: Update to 1.14.0.•••* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0. Ricardo Wurmus2016-10-26
* gnu: r-genefilter: Update to 1.56.0.•••* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0. Ricardo Wurmus2016-10-26
* gnu: r-geneplotter: Update to 1.52.0.•••* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0. Ricardo Wurmus2016-10-26
* gnu: r-annotate: Update to 1.52.0.•••* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0. Ricardo Wurmus2016-10-26
* gnu: Add r-kernsmooth.•••* gnu/packages/statistics.scm (r-kernsmooth): New variable. Ricardo Wurmus2016-10-26
* gnu: emacs-emms-player-mpv: Update to 0.0.10.•••* gnu/packages/emacs.scm (emacs-emms-player-mpv): Update to 0.0.10. Ricardo Wurmus2016-10-26
* gnu: elfutils: Update to 0.167.•••* gnu/packages/elf.scm (elfutils): Update to 0.167. Leo Famulari2016-10-25
* gnu: gtk+-2: Update to 2.24.31 [fixes CVE-2013-7447].•••* gnu/packages/gtk.scm (gtk+-2): Update to 2.24.31. Leo Famulari2016-10-25
* gnu: 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 Kebreau2016-10-25
* gnu: 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 Danckaert2016-10-25
* gnu: 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 Weaver2016-10-24
* gnu: Add coda.•••* gnu/packages/maths.scm (coda): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Thomas Danckaert2016-10-24
* gnu: Add hdf-eos2.•••* 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> Thomas Danckaert2016-10-24
* gnu: Add guile-bytestructures•••* gnu/packages/guile.scm (guile-bytestructures): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Amirouche2016-10-24
* gnu: efl: Update to 1.18.2.•••* gnu/packages/enlightenment.scm (efl): Update to 1.18.2. Efraim Flashner2016-10-24
* gnu: red-eclipse: Update to 1.5.6.•••* gnu/packages/games.scm (red-eclipse): Update to 1.5.6. [arguments]: Adjust phases. Kei Kebreau2016-10-24
* gnu: Add whois.•••* gnu/packages/networking.scm (whois): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> ng02016-10-24
* gnu: gnumeric: Use 'glib-or-gtk-build-system'.•••Reported by Pjotr Prins <pjotr.public12@thebird.nl>. * gnu/packages/gnome.scm (gnumeric)[build-systems]: Switch to GLIB-OR-GTK-BUILD-SYSTEM. 宋文武2016-10-24
* gnu: musl: Fix CVE-2016-8859.•••* gnu/packages/patches/musl-CVE-2016-8859.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/musl.scm (musl)[source]: Use it. Leo Famulari2016-10-23
* gnu: windowmaker: Update to 0.95.7.•••* gnu/packages/gnustep.scm (windowmaker): Update to 0.95.7. Kei Kebreau2016-10-23
* gnu: gajim: Update to 0.16.6.•••* gnu/packages/messaging.scm (gajim): Update to 0.16.6. Signed-off-by: Leo Famulari <leo@famulari.name> Arun Isaac2016-10-23
* gnu: gajim: License is "version 3 only".•••* gnu/packages/messaging.scm (gajim)[license]: Change to GPL3. Signed-off-by: Leo Famulari <leo@famulari.name> Arun Isaac2016-10-23
* gnu: weechat: Update to 1.6.•••* gnu/packages/irc.scm (weechat): Update to 1.6. Signed-off-by: Leo Famulari <leo@famulari.name> ng02016-10-23
* gnu: Add python-flask-sqlalchemy.•••* gnu/packages/python.scm (python-flask-sqlalchemy): New variable. Danny Milosavljevic2016-10-23
* gnu: Add python-flask-basicauth.•••* gnu/packages/python.scm (python-flask-basicauth): New variable. Danny Milosavljevic2016-10-23
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