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2016-10-26gnu: r-rcpparmadillo: Update to 0.7.500.0.0....* 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. Ricardo Wurmus
2016-10-26gnu: armadillo: Update to 7.500.0....* gnu/packages/maths.scm (armadillo): Update to 7.500.0. Ricardo Wurmus
2016-10-26gnu: r-rmarkdown: Update to 1.1....* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.1. [propagated-inputs]: Add r-evaluate, r-tibble. Ricardo Wurmus
2016-10-26gnu: bioperl-minimal: Update to 1.7.0....* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0. Ricardo Wurmus
2016-10-26gnu: mupdf: Modify CVE-2016-8674 patch to apply to 1.9a....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. Marius Bakke
2016-10-26gnu: python-certifi: Update to 2016.8.31....* gnu/packages/python.scm (python-certifi): Update to 2016.8.31. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> ng0
2016-10-26gnu: security-token: Use 'license:' prefix....* gnu/packages/security-token.scm (libyubikey)[license]: Add prefix. (ykclient)[license]: Add prefix. Marius Bakke
2016-10-26gnu: yubico.scm: Rename to security-token.scm....* gnu/packages/yubico.scm: Delete file. * gnu/packages/security-token.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly. Marius Bakke
2016-10-26gnu: offlineimap: Install documentation....* 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. Marius Bakke
2016-10-26gnu: notmuch: Update to 0.23.1....* 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. Marius Bakke
2016-10-26gnu: vlc: Add x265 support....* gnu/packages/video.scm (vlc)[inputs]: Add x265. Efraim Flashner
2016-10-26gnu: gst-plugins-bad: Add x265 support....* gnu/packages/gstreamer.scm (gst-plugins-bad)[inputs]: Add x265. Efraim Flashner
2016-10-26gnu: ffmpeg: Add x265 support....* gnu/packages/video.scm (ffmpeg)[inputs]: Add x265. [arguments]: Add '--enable-libx265' flag. Efraim Flashner
2016-10-26gnu: Add x265....* gnu/packages/video.scm (x265): New variable. Efraim Flashner
2016-10-26gnu: Add psyclpc....* gnu/packages/psyc.scm (psyclpc): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> ng0
2016-10-26gnu: opensmtpd: Fix 'license' field....* gnu/packages/mail.scm (opensmtpd)[license]: Use LICENSE:OPENSSL, not OPENSSL. (opensmtpd-extras)[license]: Likewise. Ludovic Courtès
2016-10-26gnu: r-genomationdata: Update to 1.6.0....* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0. Ricardo Wurmus
2016-10-26gnu: r-bamsignals: Update to 1.6.0....* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0. Ricardo Wurmus
2016-10-26gnu: r-rhtslib: Update to 1.6.0....* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0. [native-inputs]: Add autoconf. Ricardo Wurmus
2016-10-26gnu: r-zlibbioc: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0. Ricardo Wurmus
2016-10-26gnu: r-motifrg: Update to 1.18.0....* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0. Ricardo Wurmus
2016-10-26gnu: r-seqlogo: Update to 1.40.0....* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0. Ricardo Wurmus
2016-10-26gnu: r-genomation: Update to 1.6.0....* 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. Ricardo Wurmus
2016-10-26gnu: r-seqpattern: Update to 1.6.0....* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0. [propagated-inputs]: Add r-kernsmooth. Ricardo Wurmus
2016-10-26gnu: r-impute: Update to 1.48.0....* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0. Ricardo Wurmus
2016-10-26gnu: r-bsgenome: Update to 1.42.0....* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0. Ricardo Wurmus
2016-10-26gnu: r-topgo: Update to 2.26.0....* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0. [propagated-inputs]: Add r-dbi. Ricardo Wurmus
2016-10-26gnu: r-graph: Update to 1.52.0....* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0. Ricardo Wurmus
2016-10-26gnu: r-go-db: Update to 3.4.0....* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0. Ricardo Wurmus
2016-10-26gnu: r-genomicfeatures: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0. Ricardo Wurmus
2016-10-26gnu: r-rtracklayer: Update to 1.34.0....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0. Ricardo Wurmus
2016-10-26gnu: r-genomicalignments: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.0. Ricardo Wurmus
2016-10-26gnu: r-summarizedexperiment: Update to 1.4.0....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.4.0. Ricardo Wurmus
2016-10-26gnu: r-rsamtools: Update to 1.26.1....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1. Ricardo Wurmus
2016-10-26gnu: r-biostrings: Update to 2.42.0....* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0. Ricardo Wurmus
2016-10-26gnu: r-biocparallel: Update to 1.8.0....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0. Ricardo Wurmus
2016-10-26gnu: r-biomart: Update to 2.30.0....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0. Ricardo Wurmus
2016-10-26gnu: r-annotationdbi: Update to 1.36.0....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0. Ricardo Wurmus
2016-10-26gnu: r-biobase: Update to 2.34.0....* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0. Ricardo Wurmus
2016-10-26gnu: 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 Wurmus
2016-10-26gnu: r-xvector: Update to 0.14.0....* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0. Ricardo Wurmus
2016-10-26gnu: r-limma: Update to 3.30.0....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0. Ricardo Wurmus
2016-10-26gnu: 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 Wurmus
2016-10-26gnu: r-edger: Update to 3.16.0....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit. Ricardo Wurmus
2016-10-26gnu: r-genomeinfodb: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0. Ricardo Wurmus
2016-10-26gnu: r-iranges: Update to 2.8.0....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0. Ricardo Wurmus
2016-10-26gnu: r-s4vectors: Update to 0.12.0....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0. Ricardo Wurmus
2016-10-26gnu: r-dnacopy: Update to 1.48.0....* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0. Ricardo Wurmus
2016-10-26gnu: r-biocinstaller: Update to 1.24.0....* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0. Ricardo Wurmus
2016-10-26gnu: r-biocgenerics: Update to 0.20.0....* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0. Ricardo Wurmus
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