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* gnu: ldb: Update to 1.1.31.Marius Bakke2017-07-23
| | | | | * gnu/packages/samba.scm (ldb): Update to 1.1.31. [native-inputs]: Add CMOCKA.
* gnu: cmocka: Update to 1.1.1.Marius Bakke2017-07-23
| | | | * gnu/packages/check.scm (cmocka): Update to 1.1.1.
* gnu: tdb: Update to 1.3.14.Marius Bakke2017-07-23
| | | | * gnu/packages/databases.scm (tdb): Update to 1.3.14.
* gnu: python-scipy: Update to 0.19.1.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-scipy): Update to 0.19.1. [source]: Use 'pypi-uri'.
* gnu: python-matplotlib: Update to 2.0.2.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-matplotlib): Update to 2.0.2. [source]: Use 'pypi-uri'.
* gnu: python-pyparsing: Update to 2.2.0.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-pyparsing, python2-pyparsing): Update to 2.2.0.
* gnu: python-pyparsing: Use 'modify-phases' syntax.Marius Bakke2017-07-23
| | | | | * gnu/packages/python.scm (python-pyparsing)[arguments]<#:phases>: Use 'modify-phases'.
* gnu: Add xmobar.Oleg Pykhalov2017-07-23
| | | | | | gnu/packages/wm.scm (xmobar): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: bash-completion: Update to 2.7.Efraim Flashner2017-07-23
| | | | * gnu/packages/bash.scm (bash-completion): Update to 2.7.
* 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.
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