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* gnu: r-seqinr: Update to 3.3-3.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
* gnu: r-rcpparmadillo: Update to 0.7.500.0.0.Ricardo Wurmus2016-10-26
| | | | | | * 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.
* gnu: armadillo: Update to 7.500.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/maths.scm (armadillo): Update to 7.500.0.
* gnu: r-rmarkdown: Update to 1.1.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.1. [propagated-inputs]: Add r-evaluate, r-tibble.
* gnu: bioperl-minimal: Update to 1.7.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
* gnu: mupdf: Modify CVE-2016-8674 patch to apply to 1.9a.Marius Bakke2016-10-26
| | | | | | | | | | 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.
* gnu: python-certifi: Update to 2016.8.31.ng02016-10-26
| | | | | | * gnu/packages/python.scm (python-certifi): Update to 2016.8.31. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: security-token: Use 'license:' prefix.Marius Bakke2016-10-26
| | | | | * gnu/packages/security-token.scm (libyubikey)[license]: Add prefix. (ykclient)[license]: Add prefix.
* gnu: yubico.scm: Rename to security-token.scm.Marius Bakke2016-10-26
| | | | | | * gnu/packages/yubico.scm: Delete file. * gnu/packages/security-token.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
* gnu: offlineimap: Install documentation.Marius Bakke2016-10-26
| | | | | | | | * 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.
* gnu: notmuch: Update to 0.23.1.Marius Bakke2016-10-26
| | | | | | | * 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.
* gnu: vlc: Add x265 support.Efraim Flashner2016-10-26
| | | | * gnu/packages/video.scm (vlc)[inputs]: Add x265.
* gnu: gst-plugins-bad: Add x265 support.Efraim Flashner2016-10-26
| | | | * gnu/packages/gstreamer.scm (gst-plugins-bad)[inputs]: Add x265.
* gnu: ffmpeg: Add x265 support.Efraim Flashner2016-10-26
| | | | | * gnu/packages/video.scm (ffmpeg)[inputs]: Add x265. [arguments]: Add '--enable-libx265' flag.
* gnu: Add x265.Efraim Flashner2016-10-26
| | | | * gnu/packages/video.scm (x265): New variable.
* gnu: Add psyclpc.ng02016-10-26
| | | | | | * gnu/packages/psyc.scm (psyclpc): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: opensmtpd: Fix 'license' field.Ludovic Courtès2016-10-26
| | | | | | * gnu/packages/mail.scm (opensmtpd)[license]: Use LICENSE:OPENSSL, not OPENSSL. (opensmtpd-extras)[license]: Likewise.
* gnu: r-genomationdata: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
* gnu: r-bamsignals: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
* gnu: r-rhtslib: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0. [native-inputs]: Add autoconf.
* gnu: r-zlibbioc: Update to 1.20.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
* gnu: r-motifrg: Update to 1.18.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
* gnu: r-seqlogo: Update to 1.40.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
* gnu: r-genomation: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | | | * 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.
* gnu: r-seqpattern: Update to 1.6.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0. [propagated-inputs]: Add r-kernsmooth.
* gnu: r-impute: Update to 1.48.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
* gnu: r-bsgenome: Update to 1.42.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
* gnu: r-topgo: Update to 2.26.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0. [propagated-inputs]: Add r-dbi.
* gnu: r-graph: Update to 1.52.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
* gnu: r-go-db: Update to 3.4.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
* gnu: r-genomicfeatures: Update to 1.26.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
* gnu: r-rtracklayer: Update to 1.34.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
* gnu: r-genomicalignments: Update to 1.10.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.0.
* gnu: r-summarizedexperiment: Update to 1.4.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.4.0.
* gnu: r-rsamtools: Update to 1.26.1.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
* gnu: r-biostrings: Update to 2.42.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
* gnu: r-biocparallel: Update to 1.8.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
* gnu: r-biomart: Update to 2.30.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
* gnu: r-annotationdbi: Update to 1.36.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
* gnu: r-biobase: Update to 2.34.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
* gnu: r-genomicranges: Update to 1.26.1.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1. [propagated-inputs]: Add r-iranges, r-s4vectors.
* gnu: r-xvector: Update to 0.14.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
* gnu: r-limma: Update to 3.30.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
* gnu: r-variantannotation: Update to 1.20.0.Ricardo Wurmus2016-10-26
| | | | | | | * 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.
* gnu: r-edger: Update to 3.16.0.Ricardo Wurmus2016-10-26
| | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit.
* gnu: r-genomeinfodb: Update to 1.10.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
* gnu: r-iranges: Update to 2.8.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
* gnu: r-s4vectors: Update to 0.12.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
* gnu: r-dnacopy: Update to 1.48.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
* gnu: r-biocinstaller: Update to 1.24.0.Ricardo Wurmus2016-10-26
| | | | * gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
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