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| * gnu: Add python-execnet.•••* gnu/packages/python.scm (python-execnet): New variable. Leo Famulari2016-01-151-0/+28
| * gnu: Add python-apipkg.•••* gnu/packages/python.scm (python-apipkg): New variable. Leo Famulari2016-01-151-0/+22
| * gnu: Add python-click-log.•••* gnu/packages/python.scm (python-click-log): New variable. Leo Famulari2016-01-151-0/+19
| * gnu: Add python-click-threading.•••* gnu/packages/python.scm (python-click-threading): New variable. Leo Famulari2016-01-151-0/+19
| * gnu: Add python-requests-toolbelt.•••* gnu/packages/python.scm (python-requests-toolbelt): New variable. Leo Famulari2016-01-151-0/+19
| * gnu: Add python-atomicwrites.•••* gnu/packages/python.scm (python-atomicwrites): New variable. Leo Famulari2016-01-151-0/+17
| * gnu: glade: Update to 3.18.5.•••* 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". Ricardo Wurmus2016-01-151-5/+22
| * gnu: openssh: Update to 7.1p2.•••* gnu/packages/ssh.scm (openssh): Update to 7.1p2. Mark H Weaver2016-01-151-3/+3
| * Revert "gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]."•••This reverts commit 6d139e53b596ca154800d154b37fcd22741c629c. Mark H Weaver2016-01-151-3/+3
| * gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778].•••* gnu/packages/ssh.scm (openssh): Update to 7.1p2. Mark H Weaver2016-01-141-3/+3
| * gnu: Add docker-compose.•••* gnu/packages/docker.scm (docker-compose): New variable. David Thompson2016-01-141-0/+34
| * gnu: Add python-dockerpty.•••* gnu/packages/docker.scm (python-dockerpty): New variable. David Thompson2016-01-141-0/+21
| * gnu: Add python-docker-py.•••* gnu/packages/docker.scm: New file. * Makefile.am (GNU_SYSTEM_MODULES): Add it. David Thompson2016-01-141-0/+52
| * gnu: Add python-websocket-client.•••* gnu/packages/python.scm (python-websocket-client): New variable. David Thompson2016-01-141-0/+27
| * gnu: Add python-texttable.•••* gnu/packages/python.scm (python-texttable, python2-texttable): New variables. David Thompson2016-01-141-0/+22
| * gnu: Update python-jsonschema to 2.5.1.•••* gnu/packages/python.scm (python-jsonschema): Update to 2.5.1. [inputs]: Add python-vcversioner. David Thompson2016-01-141-3/+4
| * gnu: Add python-vcversioner.•••* gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New variables. David Thompson2016-01-141-0/+24
| * gnu: Add version 2.7 variant of python-requests.•••* gnu/packages/python.scm (python-requests-2.7): New variable. David Thompson2016-01-141-0/+12
| * gnu: r-go-db: Add missing input.•••* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add "r-annotationdbi". Ricardo Wurmus2016-01-141-0/+2
| * gnu: r-sparsem: Add missing "gfortran" input.•••* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran". Ricardo Wurmus2016-01-141-1/+3
| * gnu: bowtie: Update to 2.2.6.•••* 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. Ricardo Wurmus2016-01-142-53/+16
| * gnu: gnupg: Add TOFU support.•••* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite. Efraim Flashner2016-01-141-3/+5
| * gnu: orfm: Update to 0.5.3.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3. [native-inputs]: Add inputs required for tests. [description]: Add commas. Ben Woodcroft2016-01-141-3/+7
| * gnu: Add ruby-bio-commandeer.•••* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable. Ben Woodcroft2016-01-141-0/+36
| * gnu: Add ruby-systemu.•••* gnu/packages/ruby.scm (ruby-systemu): New variable. Ben Woodcroft2016-01-141-0/+28
* | gnu: Add dependency on Perl's 'Module::Build' as needed.•••'Module::Build' was deprecated in Perl 5.20 and removed in 5.22. Some packages need to explicitly depend on it now. * gnu/packages/perl.scm (perl-class-factory-util): (perl-date-manip, perl-devel-checkbin): Add 'native-inputs' field. (perl-module-build)[description]: Mention that it used to be in Perl. * gnu/packages/web.scm (perl-cgi-simple)[native-inputs]: Add PERL-MODULE-BUILD. Ludovic Courtès2016-01-172-8/+13
* | gnu: ffmpeg: Update to 2.8.5.•••* gnu/packages/video.scm (ffmpeg): Update to 2.8.5. Mark H Weaver2016-01-151-3/+3
* | gnu: librsvg: Update to 2.40.13 [fixes CVE-2015-7558].•••* gnu/packages/patches/librsvg-tests.patch: Delete file. * gnu-system.am (dist_patch_DATA): Remove it. * gnu/packages/gnome.scm (librsvg): Update to 2.40.13. [source]: Remove patch. Mark H Weaver2016-01-152-32/+3
* | gnu: automake: Adjust to deal with Perl 5.22.•••Fixes <http://bugs.gnu.org/22375>. * gnu/packages/patches/automake-regexp-syntax.patch: New file. * gnu/packages/autotools.scm (automake)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it. Ludovic Courtès2016-01-152-2/+38
* | gnu: gawk: Protect against random failures of the 'fts' test.•••* gnu/packages/patches/gawk-fts-test.patch: New file. * gnu/packages/gawk.scm (gawk)[source]: Use it. * gnu-system.am (dist_patch_DATA): Add it. Ludovic Courtès2016-01-142-2/+55
* | gnu: cross-gcc-arguments: Enable C++, disable building of libstdc++-v3.•••* gnu/packages/cross-base.scm (cross-gcc-arguments)[arguments]: Disable building libstdc++-v3 and enable building C++ compiler. Ricardo Wurmus2016-01-131-4/+5
* | Merge branch 'master' into core-updatesLudovic Courtès2016-01-1358-738/+2981
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| * gnu: julia: Update to 0.4.3.•••* gnu/packages/julia.scm (julia): Update to 0.4.3. (libuv-julia): Update to 07730c4bd595. Ricardo Wurmus2016-01-131-6/+6
| * gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].•••* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1. Mark H Weaver2016-01-131-3/+3
| * gnu: samtools: Update to 1.3.•••* 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. Ricardo Wurmus2016-01-131-27/+12
| * gnu: skribilo: Update to 0.9.3.•••* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3. [native-inputs]: New field. Ludovic Courtès2016-01-131-3/+6
| * gnu: boost: Update to 1.60.0.•••* 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. Eric Bavier2016-01-128-26/+132
| * gnu: boost: Use modify-phases.•••* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases. Eric Bavier2016-01-121-24/+23
| * gnu: sudo: Add fix for CVE-2015-5602.•••* 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. Mark H Weaver2016-01-122-1/+374
| * gnu: global: Use modify-phases syntax.•••* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax. Efraim Flashner2016-01-121-12/+11
| * gnu: global: Update to 6.5.2.•••* gnu/packages/code.scm (global): Update to 6.5.2. Efraim Flashner2016-01-121-2/+3
| * gnu: icedtea-6: Fix directory name in "unpack" phase.•••* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-". Ricardo Wurmus2016-01-121-1/+1
| * gnu: linux-libre: Update to 4.4.•••* 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>. Mark H Weaver2016-01-113-132/+344
| * gnu: Add fxtract.•••* gnu/packages/bioinformatics.scm (fxtract): New variable. Ben Woodcroft2016-01-121-0/+66
| * gnu: youtube-dl: Update to 2016.01.09.•••* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09. Efraim Flashner2016-01-111-2/+2
| * gnu: gp2c: Update to 0.0.9pl5.•••* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5. Andreas Enge2016-01-111-3/+3
| * gnu: texlive: Use modify-phases syntax.•••* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax. Andreas Enge2016-01-111-61/+58
| * gnu: man-pages: Update to 4.04.•••* gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location. Efraim Flashner2016-01-111-5/+10
| * gnu: bedtools: Update to 2.25.0.•••* 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. Ben Woodcroft2016-01-112-185/+3
| * gnu: bedtools: Use modify-phases.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases. Ben Woodcroft2016-01-111-19/+19
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