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2016-11-28gnu: perl-dbd-mysql: Update to 4.041 [security fix].Marius Bakke
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.041. [source]: Update CPAN URI.
2016-11-28vm: Avoid needless file copy in 'load-in-linux-vm'.Ludovic Courtès
Reported by Chris Webber. * gnu/build/vm.scm (load-in-linux-vm)[image-file]: Remove. Directly refer to OUTPUT instead.
2016-11-28pull: Set '%nix-instantiate' to a sensible value.Ludovic Courtès
Reported by ng0 <ng0@libertad.pw>. Fixes <http://bugs.gnu.org/25053>. * guix/build/pull.scm (build-guix): Replace "@NIX_INSTANTIATE@" in guix/config.scm with "nix-instantiate".
2016-11-28doc: Document NSS incompatibility issues on foreign distros.Ludovic Courtès
* doc/guix.texi (Application Setup)[Name Service Switch]: New subsection.
2016-11-28gnu: Add r-gkmsvm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
2016-11-28gnu: Add r-rocr.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rocr): New variable.
2016-11-28gnu: Add r-gplots.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gplots): New variable.
2016-11-28gnu: Add r-gdata.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gdata): New variable.
2016-11-28gnu: Add r-seqgl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
2016-11-28gnu: Add r-chipkernels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
2016-11-28gnu: Add r-gtools.Ricardo Wurmus
* gnu/packages/statistics.scm (r-gtools): New variable.
2016-11-28gnu: Add r-kernlab.Ricardo Wurmus
* gnu/packages/machine-learning.scm (r-kernlab): New variable.
2016-11-28gnu: Add r-sfsmisc.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sfsmisc): New variable.
2016-11-28gnu: Add r-wgcna.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
2016-11-28gnu: Add r-fastcluster.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fastcluster): New variable.
2016-11-28gnu: Add r-preprocesscore.Ricardo Wurmus
* gnu/packages/statistics.scm (r-preprocesscore): New variable.
2016-11-28gnu: Add r-dynamictreecut.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dynamictreecut): New variable.
2016-11-28gnu: Add r-r4rna.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
2016-11-28gnu: Add r-spams.Ricardo Wurmus
* gnu/packages/statistics.scm (r-spams): New variable.
2016-11-28gnu: Add r-googlesheets.Ricardo Wurmus
* gnu/packages/statistics.scm (r-googlesheets): New variable.
2016-11-28gnu: Add r-cellranger.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cellranger): New variable.
2016-11-28gnu: Add r-rematch.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rematch): New variable.
2016-11-28doc: Suggest installing gvfs.Ricardo Wurmus
* gnu/system/examples/desktop.tmpl: Add gvfs to the system-wide list of packages.
2016-11-28gnu: lv2: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/audio.scm (lv2): Update to 1.14.0.
2016-11-28gnu: non-sequencer: Update to 1.9.5-2.a22f33f.Ricardo Wurmus
* gnu/packages/music.scm (non-sequencer): Update to 1.9.5-2.a22f33f.
2016-11-28gnu: ntp: Update to 4.2.8p9.Efraim Flashner
* gnu/packages/ntp.scm (ntp): Update to 4.2.8p9.
2016-11-28gnu: ntp: Fix indentation.Efraim Flashner
* gnu/packages/ntp.scm (ntp): Fix indentation to only use spaces.
2016-11-28gnu: Add editres.John Darrington
* gnu/packages/xorg.scm (editres): New variable.
2016-11-28gnu: Add newick-utils.Ben Woodcroft
* gnu/packages/bioinformatics.scm (newick-utils): New variable.
2016-11-27pull: Hack to allow compilation with older Guile-SSH packages.Ludovic Courtès
Reported by iyzsong@member.fsf.org (宋文武) at <https://lists.gnu.org/archive/html/guix-devel/2016-11/msg01045.html>. * build-aux/build-self.scm (build): Set 'LTDL_LIBRARY_PATH' when GUILE-SSH has a "0.9." version prefix.
2016-11-27gnu: jasper: Update to 2.0.0 [fixes security issues].Efraim Flashner
* gnu/packages/image.scm (jasper): Update to 2.0.0. [build-system]: Switch to cmake-build-system.
2016-11-27gnu: gphoto2: Update to 2.5.11.Tobias Geerinckx-Rice
* gnu/packages/photo.scm (gphoto2): Update to 2.5.11.
2016-11-27gnu: libgphoto2: Update to 2.5.11.Tobias Geerinckx-Rice
* gnu/packages/photo.scm (libgphoto2): Update to 2.5.11.
2016-11-27gnu: beets: Update to 1.4.1.Leo Famulari
* gnu/packages/music.scm (beets): Update to 1.4.1. [inputs]: Add python2-discogs-client.
2016-11-27gnu: Add python-discogs-client.Leo Famulari
* gnu/packages/music.scm (python-discogs-client, python2-discogs-client): New variables.
2016-11-27gnu: python-rarfile: Update to 2.8.Leo Famulari
* gnu/packages/python.scm (python-rarfile, python2-rarfile): Update to 2.8. [source]: Remove obsolete patch. * gnu/packages/patches/python-rarfile-fix-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
2016-11-27gnu: python-jellyfish: Update to 0.5.6.Leo Famulari
* gnu/packages/python.scm (python-jellyfish, python2-jellyfish): Update to 0.5.6.
2016-11-27gnu: python-pylast: Update 1.6.0.Leo Famulari
* gnu/packages/music.scm (python-pylast, python2-pylast): Update to 1.6.0.
2016-11-27gnu: python-musicbrainzngs: Update to 0.6.Leo Famulari
* gnu/packages/music.scm (python-musicbrainzngs, python2-musicbrainzngs): Update to 0.6. [arguments]: Disable the test suites.
2016-11-27gnu: python-munkres: Update to 1.0.8.Leo Famulari
* gnu/packages/python.scm (python-munkres, python2-munkres): Update to 1.0.8.
2016-11-27gnu: python-mutagen: Update to 1.35.1.Leo Famulari
* gnu/packages/music.scm (python-mutagen, python2-mutagen): Update to 1.35.1. [native-inputs]: Add python-pytest.
2016-11-27gnu: gcj: Inherit source field from "gcc".Ricardo Wurmus
* gnu/packages/gcc.scm (gcj)[source]: Inherit source from "gcc" package.
2016-11-27gnu: gcj: Correct paths in ARM patch.Ricardo Wurmus
* gnu/packages/patches/gcj-arm-mode.patch: Strip directories.
2016-11-27gnu: notmuch: Update to 0.23.3.Marius Bakke
* gnu/packages/mail.scm (notmuch): Update to 0.23.3. [arguments]: Re-enable previously failing tests.
2016-11-27gnu: gcj: Fix typo in patch filename.Leo Famulari
This is a followup to commit dbf8f84f15fb80fa41caeed073460853083e48d3. Reported by quigonjinn on #guix. * gnu/packages/gcc.scm (gcj)[source]: Fix typo.
2016-11-27gnu: python2-flask: Pick up python-flask's native-inputs.Danny Milosavljevic
* gnu/packages/python.scm (python2-flask)[native-inputs]: Pick up python-flask's native-inputs. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-27gnu: udisks: Update to 2.1.8.Marius Bakke
* gnu/packages/freedesktop.scm (udisks): Update to 2.1.8. [home-page]: Use HTTPS.
2016-11-27gnu: udisks: Add manpages.Maxim Cournoyer
* gnu/packages/freedesktop.scm (udisks)[native-inputs]: Add docbook-xml and docbook-xsl. [arguments]: Add #:make-flags to specify XML catalog files for manuals. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-27gnu: gcj: Fix build on armhf.Ricardo Wurmus
* gnu/packages/patches/gcj-arm-mode.patch: New file. * gnu/local.mk (dist_patch_DATA): Add patch. * gnu/packages/gcc.scm (gcj): Add patch. [arguments]: Delete failing tests.
2016-11-27gnu: Add biber-2.5.Ricardo Wurmus
* gnu/packages/tex.scm (biber-2.5): New variable.
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