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* gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778].Mark H Weaver2016-01-14
| | | | * gnu/packages/ssh.scm (openssh): Update to 7.1p2.
* gnu: Add docker-compose.David Thompson2016-01-14
| | | | * gnu/packages/docker.scm (docker-compose): New variable.
* gnu: Add python-dockerpty.David Thompson2016-01-14
| | | | * gnu/packages/docker.scm (python-dockerpty): New variable.
* gnu: Add python-docker-py.David Thompson2016-01-14
| | | | | * gnu/packages/docker.scm: New file. * Makefile.am (GNU_SYSTEM_MODULES): Add it.
* gnu: Add python-websocket-client.David Thompson2016-01-14
| | | | * gnu/packages/python.scm (python-websocket-client): New variable.
* gnu: Add python-texttable.David Thompson2016-01-14
| | | | | * gnu/packages/python.scm (python-texttable, python2-texttable): New variables.
* gnu: Update python-jsonschema to 2.5.1.David Thompson2016-01-14
| | | | | * gnu/packages/python.scm (python-jsonschema): Update to 2.5.1. [inputs]: Add python-vcversioner.
* gnu: Add python-vcversioner.David Thompson2016-01-14
| | | | | * gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New variables.
* gnu: Add version 2.7 variant of python-requests.David Thompson2016-01-14
| | | | * gnu/packages/python.scm (python-requests-2.7): New variable.
* gnu: r-go-db: Add missing input.Ricardo Wurmus2016-01-14
| | | | | * gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi".
* gnu: r-sparsem: Add missing "gfortran" input.Ricardo Wurmus2016-01-14
| | | | * gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
* gnu: bowtie: Update to 2.2.6.Ricardo Wurmus2016-01-14
| | | | | | | | | | * gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6. [source]: Remove patch; do not set CC and CPP variables. [inputs]: Add "tbb". [arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom "install" phase. * gnu/packages/patches/bowtie-fix-makefile.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove patch file.
* gnu: gnupg: Add TOFU support.Efraim Flashner2016-01-14
| | | | * gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.
* gnu: orfm: Update to 0.5.3.Ben Woodcroft2016-01-14
| | | | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas.
* gnu: Add ruby-bio-commandeer.Ben Woodcroft2016-01-14
| | | | * gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
* gnu: Add ruby-systemu.Ben Woodcroft2016-01-14
| | | | * gnu/packages/ruby.scm (ruby-systemu): New variable.
* gnu: julia: Update to 0.4.3.Ricardo Wurmus2016-01-13
| | | | | * gnu/packages/julia.scm (julia): Update to 0.4.3. (libuv-julia): Update to 07730c4bd595.
* gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].Mark H Weaver2016-01-13
| | | | * gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.
* gnu: samtools: Update to 1.3.Ricardo Wurmus2016-01-13
| | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.3. [arguments]: Enable tests for all architectures; set ncurses in configure-flags instead of make-flags; simplify "patch-tests" phase; restore "configure" phase.
* gnu: skribilo: Update to 0.9.3.Ludovic Courtès2016-01-13
| | | | | * gnu/packages/skribilo.scm (skribilo): Update to 0.9.3. [native-inputs]: New field.
* gnu: boost: Update to 1.60.0.Eric Bavier2016-01-12
| | | | | | | | | | | | | | | | | | | | | | * gnu/packages/boost.scm (boost): Update to 1.60.0. [source]: Remove patch. * gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch * gnu-system.am (dist_patch_DATA): Remove patch. Also fix dependent packages: * gnu/packages/patches/csound-header-ordering.patch: New patch. * gnu/packages/audio.scm (csound)[source]: Use it. [arguments]: Add 'set-flags phase. * gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch. * gnu/packages/libreoffice.scm (libcmis)[source]: Use it. (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags. (librevenge)[inputs]: Move boost from here... [propogated-inputs]: to here. [arguments]: Add LDFLAGS to #:configure-flags. * gnu/packages/patches/openimageio-boost-1.60.patch: New patch. * gnu/packages/graphics.scm (openimageio): Use it. * gnu-system.am (dist_patch_DATA): Add patches.
* gnu: boost: Use modify-phases.Eric Bavier2016-01-12
| | | | * gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
* gnu: sudo: Add fix for CVE-2015-5602.Mark H Weaver2016-01-12
| | | | | | * gnu/packages/patches/sudo-CVE-2015-5602.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/admin.scm (sudo)[source]: Add patch.
* gnu: global: Use modify-phases syntax.Efraim Flashner2016-01-12
| | | | * gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
* gnu: global: Update to 6.5.2.Efraim Flashner2016-01-12
| | | | * gnu/packages/code.scm (global): Update to 6.5.2.
* gnu: icedtea-6: Fix directory name in "unpack" phase.Ricardo Wurmus2016-01-12
| | | | | * gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-".
* gnu: linux-libre: Update to 4.4.Mark H Weaver2016-01-11
| | | | | | | * gnu/packages/linux.scm (linux-libre): Update to 4.4. * gnu/packages/linux-libre-i686.conf, gnu/packages/linux-libre-x86_64.conf: Update from <https://jxself.org/git/kernel-configs.git>.
* gnu: Add fxtract.Ben Woodcroft2016-01-12
| | | | * gnu/packages/bioinformatics.scm (fxtract): New variable.
* gnu: youtube-dl: Update to 2016.01.09.Efraim Flashner2016-01-11
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
* gnu: gp2c: Update to 0.0.9pl5.Andreas Enge2016-01-11
| | | | * gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
* gnu: texlive: Use modify-phases syntax.Andreas Enge2016-01-11
| | | | | * gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax.
* gnu: man-pages: Update to 4.04.Efraim Flashner2016-01-11
| | | | | * gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location.
* gnu: bedtools: Update to 2.25.0.Ben Woodcroft2016-01-11
| | | | | | | | | * gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
* gnu: bedtools: Use modify-phases.Ben Woodcroft2016-01-11
| | | | * gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
* gnu: r: Update to 3.2.3.Andreas Enge2016-01-09
| | | | * gnu/packages/statistics.scm (r): Update to 3.2.3.
* gnu: icecat: Update to 38.5.2-gnu1.Andreas Enge2016-01-09
| | | | * gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
* gnu: ruby-2.1: Update to 2.1.8.Ben Woodcroft2016-01-09
| | | | * gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.
* gnu: i2c-tools: Update source and home-page URLs.Leo Famulari2016-01-08
| | | | | * gnu/packages/linux.scm (i2c-tools)[source]: Update URL. [home-page]: Update URL.
* gnu: lm-sensors: Update source and home-page URLs.Leo Famulari2016-01-08
| | | | | * gnu/packages/linux.scm (lm-sensors)[source]: Update URL. [home-page]: Update URL.
* gnu: nss: Update to 3.21 [fixes CVE-2015-7575].Mark H Weaver2016-01-08
| | | | | | * gnu/packages/gnuzilla.scm (nss): Update to 3.21. [arguments]: In configure phase, setenv CC=gcc. * gnu/packages/patches/nss-pkgconfig.patch: Adapt to NSS 3.21.
* gnu: Add missing (gnu packages gcc) import.Mathieu Lirzin2016-01-08
| | | | | * gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'.
* gnu: xterm: Update to 322.Mathieu Lirzin2016-01-08
| | | | * gnu/packages/xorg.scm (xterm): Update to 322.
* gnu: epiphany: Update to 3.18.2.宋文武2016-01-08
| | | | * gnu/packages/gnome.scm (epiphany): Update to 3.18.2.
* gnu: webkitgtk: Update to 2.10.4.宋文武2016-01-08
| | | | * gnu/packages/webkit.scm (webkitgtk): Update to 2.10.4.
* gnu: Add Pfff.Pjotr Prins2016-01-07
| | | | * gnu/packages/textutils.scm (pfff): New variable.
* gnu: mpv: Remove 'samba' input.Alex Kost2016-01-07
| | | | | | | This is a heavy-weight and uncommon feature. See <http://lists.gnu.org/archive/html/guix-devel/2015-12/msg00701.html>. * gnu/packages/video.scm (mpv)[inputs]: Remove 'samba'.
* gnu: Add genomation.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomation): New variable.
* gnu: Add seqPattern.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
* gnu: Add impute.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-impute): New variable.
* gnu: Add BSgenome.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
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