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2016-10-26gnu: r-matrix: Update to 1.2-7.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-7.1.
2016-10-26gnu: r-colorspace: Update to 1.2-7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-colorspace): Update to 1.2-7.
2016-10-26gnu: r-jsonlite: Update to 1.1.Ricardo Wurmus
* gnu/packages/web.scm (r-jsonlite): Update to 1.1.
2016-10-26gnu: r-curl: Update to 2.2.Ricardo Wurmus
* gnu/packages/web.scm (r-curl): Update to 2.2.
2016-10-26gnu: r-seqinr: Update to 3.3-3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
2016-10-26gnu: r-rcpparmadillo: Update to 0.7.500.0.0.Ricardo Wurmus
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to 7.500.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.500.0.0.
2016-10-26gnu: armadillo: Update to 7.500.0.Ricardo Wurmus
* gnu/packages/maths.scm (armadillo): Update to 7.500.0.
2016-10-26gnu: r-rmarkdown: Update to 1.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.1. [propagated-inputs]: Add r-evaluate, r-tibble.
2016-10-26gnu: bioperl-minimal: Update to 1.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
2016-10-26gnu: mupdf: Modify CVE-2016-8674 patch to apply to 1.9a.Marius Bakke
The fix from upstream did not apply cleanly due to many context changes. This was adapted by cloning mupdf 1.9a from git and fixing conflicts after applying our patches and cherry-picking upstream commit 1e03c06. This is a follow-up to 47a04fca999b91309d196afc9ebf4d8ac6f2083f. * gnu/packages/patches/mupdf-CVE-2016-8674.patch: Adapt to 1.9a.
2016-10-26gnu: python-certifi: Update to 2016.8.31.ng0
* gnu/packages/python.scm (python-certifi): Update to 2016.8.31. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-10-26gnu: security-token: Use 'license:' prefix.Marius Bakke
* gnu/packages/security-token.scm (libyubikey)[license]: Add prefix. (ykclient)[license]: Add prefix.
2016-10-26gnu: yubico.scm: Rename to security-token.scm.Marius Bakke
* gnu/packages/yubico.scm: Delete file. * gnu/packages/security-token.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
2016-10-26gnu: offlineimap: Install documentation.Marius Bakke
* gnu/packages/mail.scm (offlineimap)[native-inputs]: Add asciidoc and libxslt. [arguments]: Add phases 'build-documentation' and 'install-documentation' to build and install manpages. Also remove unneeded key 'inputs' from 'wrap-binary' phase.
2016-10-26gnu: notmuch: Update to 0.23.1.Marius Bakke
* gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/mail.scm (notmuch): Update to 0.23.1. Remove patch.
2016-10-26gnu: vlc: Add x265 support.Efraim Flashner
* gnu/packages/video.scm (vlc)[inputs]: Add x265.
2016-10-26gnu: gst-plugins-bad: Add x265 support.Efraim Flashner
* gnu/packages/gstreamer.scm (gst-plugins-bad)[inputs]: Add x265.
2016-10-26gnu: ffmpeg: Add x265 support.Efraim Flashner
* gnu/packages/video.scm (ffmpeg)[inputs]: Add x265. [arguments]: Add '--enable-libx265' flag.
2016-10-26gnu: Add x265.Efraim Flashner
* gnu/packages/video.scm (x265): New variable.
2016-10-26gnu: Add psyclpc.ng0
* gnu/packages/psyc.scm (psyclpc): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-10-26gnu: opensmtpd: Fix 'license' field.Ludovic Courtès
* gnu/packages/mail.scm (opensmtpd)[license]: Use LICENSE:OPENSSL, not OPENSSL. (opensmtpd-extras)[license]: Likewise.
2016-10-26gnu: r-genomationdata: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
2016-10-26gnu: r-bamsignals: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
2016-10-26gnu: r-rhtslib: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0. [native-inputs]: Add autoconf.
2016-10-26gnu: r-zlibbioc: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
2016-10-26gnu: r-motifrg: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
2016-10-26gnu: r-seqlogo: Update to 1.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
2016-10-26gnu: r-genomation: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0. [propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors. [inputs]: Add zlib.
2016-10-26gnu: r-seqpattern: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0. [propagated-inputs]: Add r-kernsmooth.
2016-10-26gnu: r-impute: Update to 1.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
2016-10-26gnu: r-bsgenome: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
2016-10-26gnu: r-topgo: Update to 2.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0. [propagated-inputs]: Add r-dbi.
2016-10-26gnu: r-graph: Update to 1.52.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
2016-10-26gnu: r-go-db: Update to 3.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
2016-10-26gnu: r-genomicfeatures: Update to 1.26.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
2016-10-26gnu: r-rtracklayer: Update to 1.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
2016-10-26gnu: r-genomicalignments: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.0.
2016-10-26gnu: r-summarizedexperiment: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.4.0.
2016-10-26gnu: r-rsamtools: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
2016-10-26gnu: r-biostrings: Update to 2.42.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
2016-10-26gnu: r-biocparallel: Update to 1.8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
2016-10-26gnu: r-biomart: Update to 2.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
2016-10-26gnu: r-annotationdbi: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
2016-10-26gnu: r-biobase: Update to 2.34.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
2016-10-26gnu: r-genomicranges: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1. [propagated-inputs]: Add r-iranges, r-s4vectors.
2016-10-26gnu: r-xvector: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
2016-10-26gnu: r-limma: Update to 3.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
2016-10-26gnu: r-variantannotation: Update to 1.20.0.Ricardo Wurmus
* 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.
2016-10-26gnu: r-edger: Update to 3.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit.
2016-10-26gnu: r-genomeinfodb: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
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