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2016-01-15gnu: Add python-pytest-xprocess.Leo Famulari
* gnu/packages/python.scm (python-pytest-xprocess): New variable.
2016-01-15gnu: Add python-wsgi-intercept.Leo Famulari
* gnu/packages/python.scm (python-wsgi-intercept): New variable.
2016-01-15gnu: Add python-pytest-localserver.Leo Famulari
* gnu/packages/python.scm (python-pytest-localserver): New variable.
2016-01-15gnu: Add python-pytest-cache.Leo Famulari
* gnu/packages/python.scm (python-pytest-cache): New variable.
2016-01-15gnu: Add python-execnet.Leo Famulari
* gnu/packages/python.scm (python-execnet): New variable.
2016-01-15gnu: Add python-apipkg.Leo Famulari
* gnu/packages/python.scm (python-apipkg): New variable.
2016-01-15gnu: Add python-click-log.Leo Famulari
* gnu/packages/python.scm (python-click-log): New variable.
2016-01-15gnu: Add python-click-threading.Leo Famulari
* gnu/packages/python.scm (python-click-threading): New variable.
2016-01-15gnu: Add python-requests-toolbelt.Leo Famulari
* gnu/packages/python.scm (python-requests-toolbelt): New variable.
2016-01-15gnu: Add python-atomicwrites.Leo Famulari
* gnu/packages/python.scm (python-atomicwrites): New variable.
2016-01-15gnu: glade: Update to 3.18.5.Ricardo Wurmus
* gnu/packages/gnome.scm (glade): Update to 3.18.5. [arguments]: Disable tests; add "fix-docbook" phase. [inputs]: Replace "gtk+-2" with "gtk+". [native-inputs]: Add "itstool", "libxslt", "docbook-xml", "docbook-xsl"; replace "python" with "python-2".
2016-01-15gnu: openssh: Update to 7.1p2.Mark H Weaver
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
2016-01-15Revert "gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]."Mark H Weaver
This reverts commit 6d139e53b596ca154800d154b37fcd22741c629c.
2016-01-14gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778].Mark H Weaver
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
2016-01-14gnu: Add docker-compose.David Thompson
* gnu/packages/docker.scm (docker-compose): New variable.
2016-01-14gnu: Add python-dockerpty.David Thompson
* gnu/packages/docker.scm (python-dockerpty): New variable.
2016-01-14gnu: Add python-docker-py.David Thompson
* gnu/packages/docker.scm: New file. * Makefile.am (GNU_SYSTEM_MODULES): Add it.
2016-01-14gnu: Add python-websocket-client.David Thompson
* gnu/packages/python.scm (python-websocket-client): New variable.
2016-01-14gnu: Add python-texttable.David Thompson
* gnu/packages/python.scm (python-texttable, python2-texttable): New variables.
2016-01-14gnu: Update python-jsonschema to 2.5.1.David Thompson
* gnu/packages/python.scm (python-jsonschema): Update to 2.5.1. [inputs]: Add python-vcversioner.
2016-01-14gnu: Add python-vcversioner.David Thompson
* gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New variables.
2016-01-14gnu: Add version 2.7 variant of python-requests.David Thompson
* gnu/packages/python.scm (python-requests-2.7): New variable.
2016-01-14gnu: r-go-db: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi".
2016-01-14gnu: r-sparsem: Add missing "gfortran" input.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
2016-01-14gnu: bowtie: Update to 2.2.6.Ricardo Wurmus
* 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.
2016-01-14gnu: gnupg: Add TOFU support.Efraim Flashner
* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.
2016-01-14gnu: orfm: Update to 0.5.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas.
2016-01-14gnu: Add ruby-bio-commandeer.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
2016-01-14gnu: Add ruby-systemu.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-systemu): New variable.
2016-01-13gnu: julia: Update to 0.4.3.Ricardo Wurmus
* gnu/packages/julia.scm (julia): Update to 0.4.3. (libuv-julia): Update to 07730c4bd595.
2016-01-13gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].Mark H Weaver
* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.
2016-01-13gnu: samtools: Update to 1.3.Ricardo Wurmus
* 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.
2016-01-13gnu: skribilo: Update to 0.9.3.Ludovic Courtès
* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3. [native-inputs]: New field.
2016-01-12gnu: boost: Update to 1.60.0.Eric Bavier
* 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.
2016-01-12gnu: boost: Use modify-phases.Eric Bavier
* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
2016-01-12gnu: sudo: Add fix for CVE-2015-5602.Mark H Weaver
* 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.
2016-01-12gnu: global: Use modify-phases syntax.Efraim Flashner
* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
2016-01-12gnu: global: Update to 6.5.2.Efraim Flashner
* gnu/packages/code.scm (global): Update to 6.5.2.
2016-01-12gnu: icedtea-6: Fix directory name in "unpack" phase.Ricardo Wurmus
* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-".
2016-01-11gnu: linux-libre: Update to 4.4.Mark H Weaver
* 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>.
2016-01-12gnu: Add fxtract.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fxtract): New variable.
2016-01-11gnu: youtube-dl: Update to 2016.01.09.Efraim Flashner
* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
2016-01-11gnu: gp2c: Update to 0.0.9pl5.Andreas Enge
* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
2016-01-11gnu: texlive: Use modify-phases syntax.Andreas Enge
* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax.
2016-01-11gnu: man-pages: Update to 4.04.Efraim Flashner
* gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location.
2016-01-11gnu: bedtools: Update to 2.25.0.Ben Woodcroft
* 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.
2016-01-11gnu: bedtools: Use modify-phases.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2016-01-09gnu: r: Update to 3.2.3.Andreas Enge
* gnu/packages/statistics.scm (r): Update to 3.2.3.
2016-01-09gnu: icecat: Update to 38.5.2-gnu1.Andreas Enge
* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
2016-01-09gnu: ruby-2.1: Update to 2.1.8.Ben Woodcroft
* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.
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