gnu: r-summarizedexperiment: Update to 1.2.2. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
gnu: r-biocparallel: Update to 1.6.2. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
gnu: r-annotationdbi: Update to 1.34.2. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
gnu: r-variantannotation: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
gnu: r-genomeinfodb: Update to 1.8.1. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
gnu: btrfs-progs: Update to 4.5.3. * gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3.
gnu: jemalloc: Update to 4.2.0. * gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283. * gnu/packages/patches/expat-CVE-2015-1283-refix.patch, gnu/packages/patches/expat-CVE-2016-0718.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/xml.scm (expat)[replacement]: New field. (expat/fixed): New variable. [source]: Use new patches.
gnu: flann: Do not install .a files. * gnu/packages/maths.scm (flann)[arguments]: Add #:phases.
gnu: python: Add 'python' variables for different major/minor versions. * gnu/packages/python.scm (python-2): Rename variable to... (python-2.7): ...this. (python-2): Refer to "python-2.7". (python): Rename variable to... (python-3.4): ...this. (python-3): Refer to "python-3.4". (python): Refer to "python-3". Signed-off-by: Ludovic Courtès <ludo@gnu.org>
gnu: flann: Strip .mex file. * gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories.
gnu: Add r-biased-urn. * gnu/packages/statistics.scm (r-biased-urn): New variable.
gnu: giflib: Use 'modify-phases'. * gnu/packages/image.scm (giflib)[arguments]: Use 'modify-phases'.
gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555, CVE-2016-3977]. * gnu/packages/image.scm (giflib): Update to 5.1.4.
gnu: Add emacs-smartparens. * gnu/packages/emacs.scm (emacs-smartparens): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
Update name for Kei Kebreau. * .mailmap: Add Kei Kebreau. * gnu/local.mk: Replace "Kei Yamashita" with "Kei Kebreau". * gnu/packages/calendar.scm: Likewise. * gnu/packages/dillo.scm: Likewise. * gnu/packages/fltk.scm: Likewise. * gnu/packages/game-development.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/gnome.scm: Likewise. * gnu/packages/gtk.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/xfce.scm: Likewise. Signed-off-by: Alex Kost <alezost@gmail.com>
gnu: octave: Update to 4.0.2. * gnu/packages/maths.scm (octave): Update to 4.0.2. [inputs]: Added cyrus-sasl, openssl. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
gnu: Add ntfs-3g. * gnu/packages/linux.scm (ntfs-3g): New variable.
gnu: wmbattery: Fix UPower-related memory leak. * gnu/packages/gnustep.scm (wmbattery)[source](snippet): New field. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
gnu: qtkeychain: Update to 0.6.2. * gnu/packages/qt.scm (qtkeychain): Update to 0.6.2.