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2017-01-01gnu: manaplus: Update to 1.6.12.24.Alex Kost
* gnu/packages/games.scm (manaplus): Update to 1.6.12.24.
2017-01-01gnu: python-dendropy: Update to 4.2.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0. [source]: Remove patch. (python2-dendropy)[source]: Use the same source as python-dendropy. * gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
2017-01-01gnu: diamond: Update to 0.8.31.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
2016-12-31gnu: nagios: Update to 4.2.4 [fixes CVE-2016-{9565,9566}].Ludovic Courtès
* gnu/packages/monitoring.scm (nagios): Update to 4.2.4. [native-inputs]: New field.
2016-12-31gnu: python-graphql-relay: Update to 0.4.5.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-graphql-relay): Update to 0.4.5.
2016-12-31gnu: python-freezegun: Update to 0.3.8.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-freezegun): Update to 0.3.8.
2016-12-31gnu: python-ply: Update to 3.9.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-ply): Update to 3.9. [source]: Use pypi-uri.
2016-12-31gnu: python-pyquery: Update to 1.2.17.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-pyquery): Update to 1.2.17.
2016-12-31gnu: python-click-log: Update to 0.1.8.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-click-log): Update to 0.1.8.
2016-12-31gnu: python-ndg-httpsclient: Update to 0.4.2.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-ndg-httpsclient): Update to 0.4.2.
2016-12-31gnu: python-ipykernel: Update to 4.5.2.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-ipykernel): Update to 4.5.2.
2016-12-31gnu: python-jupyter-core: Update to 4.2.1.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-jupyter-core): Update to 4.2.1.
2016-12-31gnu: python2-fastlmm: Update to 0.2.26.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python2-fastlmm): Update to 0.2.26.
2016-12-31gnu: python-pytz: Update to 2016.10.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-pytz): Update to 2016.10.
2016-12-31gnu: python-pyyaml: Update to 3.12.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-pyyaml): Update to 3.12. [source]: Use pypi-uri.
2016-12-31gnu: python-pygments: Update to 2.1.3.Tobias Geerinckx-Rice
* gnu/packages/python.scm (python-pygments): Update to 2.1.3.
2016-12-30gnu: tiled: Update to 0.18.0.Kei Kebreau
* gnu/packages/game-development.scm (tiled): Update to 0.18.0.
2016-12-31gnu: mc: Partially fix absolute file paths.ng0
Partially fixes <http://bugs.gnu.org/25273>. * gnu/packages/mc.scm (mc)[arguments]: Add new phase 'fix-absolutism. This substitutes absolute file paths with functional file paths. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-31gnu: pius: Update to 2.2.2-0.891687c.Troy Sankey
* gnu/packages/gnupg.scm (pius): Update to 2.2.2-0.891687c. [inputs]: Change GNUPG-2.0 to GNUPG (2.1). Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-30gnu: libtermkey: Update to 0.19.José Miguel Sánchez García
* gnu/packages/terminals.scm (libtermkey): Update to 0.19. Co-authored-by: Leo Famulari <leo@famulari.name>
2016-12-30gnu: libpng: Mention CVE-2016-10087.Leo Famulari
* gnu/packages/patches/libpng-fix-null-ptr-dereference.patch: Rename to ... * gnu/packages/patches/libpng-CVE-2016-10087.patch: ... this. * gnu/local.mk (dist_patch_DATA): Adjust. * gnu/packages/image.scm (libpng/fixed)[source]: Use renamed patch.
2016-12-30gnu: linux-libre@4.1: Update to 4.1.37.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.37.
2016-12-30gnu: multiqc: Update to 0.9.Ben Woodcroft
Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>. * gnu/packages/bioinformatics.scm (multiqc): Update to 0.9. [origin]: Add patch. * gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2016-12-29gnu: elogind: Enable ACL support.Chris Marusich
* gnu/packages/freedesktop.scm (elogind) [inputs]: Add acl. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-12-29services: Add libmtp's udev rules to '%desktop-services'.Ludovic Courtès
Suggested by Chris Marusich <cmmarusich@gmail.com>. * gnu/services/desktop.scm (%desktop-services): Add 'mtp' service via call to 'simple-service'.
2016-12-29gnu: mpd: Install systemd service files.Leo Famulari
* gnu/packages/mpd.scm (mpd)[arguments]: Add 'install-service-files' phase.
2016-12-29gnu: r-genomicfeatures: Update to 1.26.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
2016-12-29gnu: r-biostrings: Update to 2.42.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
2016-12-29gnu: r-limma: Update to 3.30.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
2016-12-29gnu: r-variantannotation: Update to 1.20.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
2016-12-29gnu: r-edger: Update to 3.16.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
2016-12-29gnu: r-genomeinfodb: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
2016-12-29gnu: r-iranges: Update to 2.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
2016-12-29gnu: r-s4vectors: Update to 0.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
2016-12-29gnu: r-biocstyle: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
2016-12-29gnu: r-deseq2: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
2016-12-29gnu: r-annotate: Update to 1.52.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1. [propagated-inputs]: Add r-rcurl.
2016-12-29gnu: khard: Update to 0.11.3.Leo Famulari
* gnu/packages/mail.scm (khard): Update to 0.11.3. [arguments]: Build with python instead of python-2. Remove 'disable-egg-compression' phase. [propagated-inputs]: Don't use python-2 variants of propagated-inputs.
2016-12-29gnu: r-rsqlite: Update to 1.1-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rsqlite): Update to 1.1-1. [propagated-inputs]: Add r-bh, r-memoise, r-plogr, and r-rcpp.
2016-12-29gnu: Add r-plogr.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plogr): New variable.
2016-12-29gnu: r-hmisc: Update to 4.0-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hmisc): Update to 4.0-1. [propagated-inputs]: Remove r-cluster, r-foreign, r-lattice, r-nnet, and r-rpart; add r-base64.
2016-12-29gnu: Add r-base64.Ricardo Wurmus
* gnu/packages/statistics.scm (r-base64): New variable.
2016-12-29gnu: r-rmarkdown: Update to 1.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.3. [propagated-inputs]: Remove r-tibble; add r-rprojroot.
2016-12-29gnu: Add r-rprojroot.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rprojroot): New variable.
2016-12-29gnu: r-rcpparmadillo: Update to 0.7.600.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.600.1.0. * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to 7.600.1.
2016-12-29gnu: armadillo: Update to 7.600.2.Ricardo Wurmus
* gnu/packages/maths.scm (armadillo): Update to 7.600.2.
2016-12-29gnu: r-zoo: Update to 1.7-14.Ricardo Wurmus
* gnu/packages/statistics.scm (r-zoo): Update to 1.7-14. [propagated-inputs]: Remove r-lattice.
2016-12-29gnu: r-fastcluster: Update to 1.1.22.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fastcluster): Update to 1.1.22.
2016-12-29gnu: r-plotly: Update to 4.5.6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotly): Update to 4.5.6.
2016-12-29gnu: r-r-rsp: Update to 0.40.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.40.0.
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