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* Merge branch 'master' into core-updatesLeo Famulari2017-07-23
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| * gnu: isc-dhcp: Update bundled bind to 9.9.10-P3.Leo Famulari2017-07-23
| | | | | | | | | | | | | | | | | | This fixes a regression introduced in the fix for CVE-2017-3142, in BIND 9.9.10-P2, commit ecb232bdfcb2718de5944bcf4d9c4e288ec41519. See 'CHANGELOG' in the source distribution for more information. * gnu/packages/admin.scm (isc-dhcp): Update bundled bind to 9.9.10-P3.
| * gnu: bind: Update to 9.11.1-P3.Leo Famulari2017-07-23
| | | | | | | | | | | | | | | | | | This fixes a regression introduced in the fix for CVE-2017-3142, in BIND 9.11.1-P2, commit faa1369e3cb72bda4ba8b63029d0ad780df9cf78. See 'CHANGELOG' in the source distribution for more information. * gnu/packages/dns.scm (isc-bind): Update to 9.11.1-P3.
| * gnu: ncurses/gpm: Move to (gnu packages ncurses).Mark H Weaver2017-07-23
| | | | | | | | | | | | | | | | | | This is needed to avoid compilation problems caused by the cyclic dependency between (gnu packages ncurses) and (gnu packages linux). * gnu/packages/linux.scm (ncurses/gpm): Move to ... * gnu/packages/ncurses.scm (ncurses/gpm): ... here. Fix misleading indentation. Add (gnu packages linux) to the module imports.
| * gnu: Add support for aarch64's compiled kernel.Efraim Flashner2017-07-23
| | | | | | | | | | | | * gnu/packages/linux.scm (linux-libre)[arguments]: Add to the regex to find and install the aarch64-linux kernel. * gnu/system.scm (system-linux-image-file-name): Add entry for aarch64.
| * gnu: Add xf86-video-freedreno.Efraim Flashner2017-07-23
| | | | | | | | * gnu/packages/xorg.scm (xf86-video-freedreno): New variable.
| * gnu: Add u-boot-odroid-c2.Efraim Flashner2017-07-23
| | | | | | | | * gnu/packages/bootloaders.scm (u-boot-odroid-c2): New variable.
| * gnu: u-boot: Update to 2017.07.Efraim Flashner2017-07-23
| | | | | | | | * gnu/packages/bootloaders.scm (u-boot): Update to 2017.07.
| * gnu: tevent: Update to 0.9.33.Marius Bakke2017-07-23
| | | | | | | | * gnu/packages/samba.scm (tevent): Update to 0.9.33.
| * gnu: talloc: Update to 2.1.10.Marius Bakke2017-07-23
| | | | | | | | * gnu/packages/samba.scm (talloc): Update to 2.1.10.
| * 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: metabat: Fix boost-related compilation issue.Ben Woodcroft2017-07-23
| | | | | | | | | | | | | | | | Reported by Leo Famulari. * gnu/packages/patches/metabat-fix-boost-issue.patch: New file. * gnu/packages/bioinformatics.scm (metabat): Use it. * gnu/local.mk (dist_patch_DATA): Add it.
* | 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.
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