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* Merge branch 'master' into core-updatesLeo Famulari2017-07-23
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| * gnu: getmail: Update to 5.1.ng02017-07-22
| | | | | | | | | | | | * gnu/packages/mail.scm (getmail): Update to 5.1. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: metabat: Update to 2.11.1.Ben Woodcroft2017-07-23
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
| * gnu: python-plastid: Update to 0.4.8.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
| * gnu: bcftools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.5. [origin]: Remove fix-makefile patch. [arguments]: Add configure flags, add LIBS make flag. Do not delete configure phase. * gnu/packages/patches/bcftools-fix-makefile.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * gnu: samtools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
| * gnu: htslib: Update to 1.5.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
| * gnu: python-pysam: Update to 0.11.2.2.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
| * gnu: bamm: Use htslib-1.3.Ben Woodcroft2017-07-23
| | | | | | | | | | * gnu/packages/bioinformatics (htslib-1.3): New variable. (bamm)[inputs]: Replace htslib with htslib-1.3.
| * gnu: bcftools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1. [arguments]: Move Makefile modifications from here ... [source]: ... to added patch. Adjust patch for update to 1.4. * gnu/packages/patches/bcftools-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
| * gnu: samtools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1. [arguments]: Add '--with-htslib=system' configure flag. [inputs]: Add htslib.
| * gnu: htslib: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1. [inputs]: Add curl, openssl.
| * gnu: samtools: Use "modify-phases" syntax.Ben Woodcroft2017-07-23
| | | | | | | | | | * gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases" syntax.
| * gnu: bspwm: Update to 0.9.3.ng02017-07-22
| | | | | | | | | | | | * gnu/packages/wm.scm (bspwm): Update to 0.9.3. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: Add oksh.ng02017-07-22
| | | | | | | | | | | | * gnu/packages/shells.scm (oksh): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: quassel: Enable TLS.Ryan Moe2017-07-22
| | | | | | | | | | | | | | | | * gnu/packages/patches/quassel-fix-tls-check.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/irc.scm (quassel)[source]: Use it. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: youtube-dl: Update to 2017.07.23.Tobias Geerinckx-Rice2017-07-23
| | | | | | | | * gnu/packages/video.scm (youtube-dl): Update to 2017.07.23.
| * gnu: mosh: Update to 1.3.2.Tobias Geerinckx-Rice2017-07-23
| | | | | | | | * gnu/packages/ssh.scm (mosh): Update to 1.3.2.
| * gnu: Add openmolar.Ricardo Wurmus2017-07-22
| | | | | | | | | | | | | | * gnu/packages/medical.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. Co-authored-by: Quiliro <quiliro@fsfla.org>
| * gnu: Add python-pyqt+qscintilla.Ricardo Wurmus2017-07-22
| | | | | | | | * gnu/packages/qt.scm (python-pyqt+qscintilla): New variable.
| * gnu: Add python-qscintilla.Ricardo Wurmus2017-07-22
| | | | | | | | | | | | * gnu/packages/qt.scm (python-qscintilla): New variable. Co-authored-by: Quiliro <quiliro@fsfla.org>
| * gnu: Add qscintilla.Ricardo Wurmus2017-07-22
| | | | | | | | | | | | * gnu/packages/qt.scm (qscintilla): New variable. Co-authored-by: Quiliro <quiliro@fsfla.org>
| * gnu: Add cran module.Ricardo Wurmus2017-07-22
| | | | | | | | | | | | * gnu/packages/cran.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/statistics.scm (r-colorspace): Move to cran.scm.
| * gnu: linux-libre: Update to 4.12.3.Mark H Weaver2017-07-22
| | | | | | | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.3. (%linux-libre-hash): Update hash.
| * gnu: linux-libre@4.9: Update to 4.9.39.Mark H Weaver2017-07-22
| | | | | | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.39.
| * gnu: linux-libre@4.4: Update to 4.4.78.Mark H Weaver2017-07-22
| | | | | | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.78.
| * gnu: r-s4vectors: Update to 0.14.3.Ricardo Wurmus2017-07-22
| | | | | | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
| * gnu: r-genomicranges: Update to 1.28.4.Ricardo Wurmus2017-07-22
| | | | | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
| * gnu: Remove python-fake-factory leftovers.Marius Bakke2017-07-22
| | | | | | | | | | | | | | This is a followup to c799eb2eb8b1a820147af96988eddaa9f752994b. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
| * gnu: Remove python-fake-factory.Marius Bakke2017-07-22
| | | | | | | | | | | | | | Superseded by python-faker since ce7911ddae5d30ba73c8c9552b7d4e71268e5db3. * gnu/packages/python.scm (python-fake-factory, python2-fake-factory): Remove variables.
| * gnu: python-pyopenssl: Update to 17.2.0.Marius Bakke2017-07-22
| | | | | | | | | | | | | | | | * gnu/packages/patches/python-pyopenssl-17.1.0-test-overflow.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. * gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl): Update to 17.2.0. [native-inputs]: Add PYTHON-FLAKY. [source](patches): Remove.
| * gnu: Add python-flaky.Marius Bakke2017-07-22
| | | | | | | | * gnu/packages/python.scm (python-flaky, python2-flaky): New variables.
| * gnu: maim: Update to 5.4.64.Marius Bakke2017-07-22
| | | | | | | | * gnu/packages/xdisorg.scm (maim): Update to 5.4.64.
| * gnu: slop: Update to 6.3.47.Marius Bakke2017-07-22
| | | | | | | | | | * gnu/packages/xdisorg.scm (slop): Update to 6.3.47. [inputs]: Add GLEW.
| * gnu: parallel: Update to 20170722.Tobias Geerinckx-Rice2017-07-22
| | | | | | | | * gnu/packages/parallel.scm (parallel): Update to 20170722.
| * gnu: font-gnu-unifont: Update to 10.0.05.Tobias Geerinckx-Rice2017-07-22
| | | | | | | | * gnu/packages/fonts.scm (font-gnu-unifont): Update to 10.0.05.
| * gnu: nano: Update to 2.8.6.Tobias Geerinckx-Rice2017-07-22
| | | | | | | | * gnu/packages/nano.scm (nano): Update to 2.8.6.
| * gnu: acct: Update to 6.6.4.Tobias Geerinckx-Rice2017-07-22
| | | | | | | | * gnu/packages/acct.scm (acct): Update to 6.6.4.
| * gnu: Add conda.Muriithi Frederick Muriuki2017-07-22
| | | | | | | | | | | | * gnu/packages/package-management.scm (conda): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| * gnu: Add python-conda.Muriithi Frederick Muriuki2017-07-22
| | | | | | | | | | | | | | * gnu/packages/package-management.scm (python-conda, python2-conda): New variables. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| * gnu: Add python-anaconda-client.Muriithi Frederick Muriuki2017-07-22
| | | | | | | | | | | | | | * gnu/packages/package-management.scm (python-anaconda-client, python2-anaconda-client): New variables. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| * gnu: Add python-clyent.Muriithi Frederick Muriuki2017-07-22
| | | | | | | | * gnu/packages/python.scm (python-clyent, python2-clyent): New variables.
| * gnu: Update python-pytz to 2017.2.Muriithi Frederick Muriuki2017-07-22
| | | | | | | | | | | | * gnu/packages/python.scm (python-pytz, python2-pytz): Update to 2017.2. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| * gnu: man-pages: Update to 4.12.Tobias Geerinckx-Rice2017-07-22
| | | | | | | | * gnu/packages/man.scm (man-pages): Update to 4.12.
| * gnu: tint2: Update to 0.14.6.Eric Bavier2017-07-21
| | | | | | | | * gnu/packages/xdisorg.scm (tint2): Update to 0.14.6.
| * gnu: icedtea@3: Update to 3.5.0 [security fixes].Leo Famulari2017-07-21
| | | | | | | | | | | | | | | | Fixes CVE-2017-{10053,10067,10074,10074,10078,10081,10087,10089,10090,10096, 10101,10102,10107,10108,10109,10110,10111,10115,10116,10118,10135,10176,10193, 10198}. * gnu/packages/java.scm (icedtea-8): Update to 3.5.0.
| * services: cuirass: Add fallback parameter.Mathieu Othacehe2017-07-21
| | | | | | | | | | | | * gnu/services/cuirass.scm (<cuirass-configuration>)[fallback?]: New field. (cuirass-shepherd-service): Take it into account. * doc/guix.texi (Continuous Integration): Document it.
| * gnu: vim: Update to 8.0.0727 [fixes CVE-2017-11109].Leo Famulari2017-07-21
| | | | | | | | | | * gnu/packages/vim.scm (vim): Update to 8.0.0727. (vim-full)[source]: Add field and hold back at version 8.0.0600.
| * gnu: mysql: Update to 5.7.19.Leo Famulari2017-07-21
| | | | | | | | * gnu/packages/databases.scm (mysql): Update to 5.7.19.
| * gnu: libpsl: Update to 0.18.0.Tobias Geerinckx-Rice2017-07-21
| | | | | | | | | | | | * gnu/packages/web.scm (libpsl): Update to 0.18.0. [native-inputs]: Add pkg-config. [inputs]: Replace icu4c with libidn2; add libunistring.
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