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2016-05-20gnu: r-rcpp: Update to 0.12.5.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.5.
2016-05-20gnu: r-genomicfeatures: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
2016-05-20gnu: r-summarizedexperiment: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
2016-05-20gnu: r-biocparallel: Update to 1.6.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
2016-05-20gnu: r-annotationdbi: Update to 1.34.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
2016-05-20gnu: r-variantannotation: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
2016-05-20gnu: r-genomeinfodb: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
2016-05-19gnu: btrfs-progs: Update to 4.5.3.Leo Famulari
* gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3.
2016-05-19gnu: jemalloc: Update to 4.2.0.Jelle Licht
* gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-05-19gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283.Leo Famulari
* 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.
2016-05-19gnu: flann: Do not install .a files.Ludovic Courtès
* gnu/packages/maths.scm (flann)[arguments]: Add #:phases.
2016-05-19gnu: python: Add 'python' variables for different major/minor versions.Hartmut Goebel
* 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>
2016-05-19gnu: flann: Strip .mex file.Ludovic Courtès
* gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories.
2016-05-19gnu: Add r-biased-urn.Ben Woodcroft
* gnu/packages/statistics.scm (r-biased-urn): New variable.
2016-05-19gnu: giflib: Use 'modify-phases'.Efraim Flashner
* gnu/packages/image.scm (giflib)[arguments]: Use 'modify-phases'.
2016-05-19gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555, CVE-2016-3977].Efraim Flashner
* gnu/packages/image.scm (giflib): Update to 5.1.4.
2016-05-19gnu: Add emacs-smartparens.humanitiesNerd
* gnu/packages/emacs.scm (emacs-smartparens): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-19Update name for Kei Kebreau.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>
2016-05-19gnu: octave: Update to 4.0.2.Kei Yamashita
* gnu/packages/maths.scm (octave): Update to 4.0.2. [inputs]: Added cyrus-sasl, openssl. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-05-18gnu: Add ntfs-3g.Ludovic Courtès
* gnu/packages/linux.scm (ntfs-3g): New variable.
2016-05-18gnu: wmbattery: Fix UPower-related memory leak.Kei Yamashita
* gnu/packages/gnustep.scm (wmbattery)[source](snippet): New field. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-05-18gnu: qtkeychain: Update to 0.6.2.Efraim Flashner
* gnu/packages/qt.scm (qtkeychain): Update to 0.6.2.
2016-05-18gnu: Add krona-tools.Ben Woodcroft
* gnu/packages/web.scm (krona-tools): New variable.
2016-05-18gnu: hurd-headers: Update to 0.8.Manolis Ragkousis
* gnu/packages/hurd.scm (hurd-headers): Update to version 0.8.
2016-05-18gnu: mig: Update to 1.7.Manolis Ragkousis
* gnu/packages/hurd.scm (mig): Update to version 1.7.
2016-05-18gnu: gnumach-headers: Update to 1.7.Manolis Ragkousis
* gnu/packages/hurd.scm (gnumach-headers): Update to version 1.7.
2016-05-18gnu: diamond: Do not specify target architecture.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not specify target architecture.
2016-05-18gnu: Add Piranha.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (piranha): New variable.
2016-05-18gnu: python2-pandas: Fix native-inputs.Efraim Flashner
* gnu/packages/python.scm (python2-pandas)[native-inputs]: Use python2- versions of python-panda's native-inputs, not of inputs.
2016-05-17gnu: Add signify.Leo Famulari
* gnu/packages/crypto.scm (signify): New variable.
2016-05-17gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].Leo Famulari
* gnu/packages/networking.scm (libndp): Update to 1.6.
2016-05-17gnu: Add emacs-zenburn-theme.humanitiesNerd
* gnu/packages/emacs.scm (emacs-zenburn-theme): New variable. Signed-off-by: Alex Kost <alezost@gmail.com>
2016-05-17gnu: gd: Fix-CVE-2016-3074.Leo Famulari
* gnu/packages/patches/gd-CVE-2016-3074.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gd.scm (gd)[source]: Use it.
2016-05-17gnu: gd: Specify 'cpe-name'.Ludovic Courtès
* gnu/packages/gd.scm (gd)[properties]: New field.
2016-05-17lint: Honor 'cpe-name' and 'cpe-version' package properties.Ludovic Courtès
* guix/scripts/lint.scm (package-name->cpe-name): Remove. (package-vulnerabilities): Honor 'cpe-name' and 'cpe-version' properties. * gnu/packages/grub.scm (grub)[properties]: New field. * gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and 'cpe-version'. * doc/guix.texi (Invoking guix lint): Mention 'cpe-name'.
2016-05-17gnu: emacs-constants: Remove old patch.Federico Beffa
* gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it. * gnu/local.mk (dist_patch_DATA): Remove entry for above patch.
2016-05-17gnu: emacs-constants: Update to 2.6.Federico Beffa
* gnu/packages/emacs.scm (emacs-constants): Change to versioned repository and update to 2.6.
2016-05-17gnu: sortmerna: Update to 2.1b.Ben Woodcroft
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b. [inputs]: New field.
2016-05-17gnu: vsearch: Update to 1.11.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
2016-05-17gnu: diamond: Update to 0.8.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1. [source]: Remove 'snippet'. [build-system]: Use cmake-build-system. [arguments]: Remove modifications to phases. [native-inputs]: Remove field. [inputs]: Remove 'boost'.
2016-05-17gnu: emacs-constants: Factorize home-page in source URL.Ludovic Courtès
* gnu/packages/emacs.scm (emacs-constants): Move 'home-page' above. Use it in 'uri'.
2016-05-17gnu: 'uncompressed-file-fetch' no longer depends on gzip.Ludovic Courtès
* gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on GZIP.
2016-05-17gnu: cflow: Update to 1.5.Efraim Flashner
* gnu/packages/code.scm (cflow): Update to 1.5.
2016-05-16gnu: Add geiser-next.Christopher Allan Webber
Also, I previously committed to this repository in 2015; add self to copyright headers for that year too. * gnu/packages/emacs.scm (geiser-next): New variable.
2016-05-16gnu: r-zlibbioc: Update to 1.18.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
2016-05-16gnu: r-motifrg: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
2016-05-16gnu: r-seqlogo: Update to 1.38.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
2016-05-16gnu: r-genomation: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
2016-05-16gnu: r-seqpattern: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
2016-05-16gnu: r-impute: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
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