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2154 Commits

Author SHA1 Message Date
Ricardo Wurmus
be7134bf75 gnu: Add pysam. 
* gnu/packages/python.scm (python-pysam, python2-pysam): New variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-26 23:28:13 +01:00
Ricardo Wurmus
ee97be9fb4 gnu: Add fastjar. 
* gnu/packages/compression.scm (fastjar): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-26 23:28:13 +01:00
Mark H Weaver
fb916f4dd6 gnu: qemu: Update to 2.2.0. 
* gnu/packages/qemu.scm (qemu): Update to 2.2.0.
 2014-12-26 09:01:15 -05:00
Mark H Weaver
53a427cf20 gnu: ntp: Update to 4.2.8. 
* gnu/packages/ntp.scm (ntp): Update to 4.2.8.  Add openssl to inputs.
  Add pkg-config to native-inputs.  Change source URI to archive.ntp.org.
 2014-12-25 00:19:36 -05:00
Ludovic Courtès
764c077b30 Revert "gnu: matplotlib: Comment out python2-matplotlib." 
This reverts commit afc720d34c.
 2014-12-23 19:17:17 +01:00
Federico Beffa
afc720d34c gnu: matplotlib: Comment out python2-matplotlib. 
* gnu/packages/python.scm (python2-matplotlib, python2-scipy, python2-numpy):
  Comment out python2-matplotlib and the packages making use of it as the
  generation of the derivation of these packages takes very long.
 2014-12-23 17:56:48 +01:00
宋文武
eea3e54c59 gnu: Add xfce4-terminal. 
* gnu/packages/xfce.scm (xfce4-terminal): New variable.
 2014-12-20 13:06:01 +08:00
宋文武
ea57378f24 gnu: Add vte. 
* gnu/packages/gnome.scm (vte, vte/gtk+-2): New variables.
 2014-12-20 13:01:47 +08:00
Ricardo Wurmus
2c7ee16720 gnu: Add bowtie 
* gnu/packages/bioinformatics.scm (bowtie): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-19 18:50:28 +01:00
Ricardo Wurmus
cdae969ae5 gnu: Add Clone. 
* gnu/packages/perl.scm (perl-clone): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-19 17:15:53 +01:00
Federico Beffa
9e0997230c gnu: cairocffi: Move to python module. 
* gnu/packages/gtk.scm, gnu/packages/python.scm (python-cairocffi,
  python2-cairocffi): Move variables from gtk to python module to avoid
  circular dependency.

Reported by Mark H Weaver <mhw@netris.org>
 2014-12-18 22:00:19 +01:00
Federico Beffa
25f9a068f2 gnu: matplotlib: Add gtk3 backends and optional dependency. Adjust inputs. 
* gnu/packages/python.scm (python-matplotlib, python2-matplotlib): Add gtk3
  backends with the necessary inputs and a 'configure-environment' phase.  Add
  the optional 'python-pillow' dependency.  Move 'python-pyparsing' from
  'inputs' to 'propagated-inputs' as it is required at run time.
 2014-12-18 17:58:10 +01:00
Federico Beffa
63cd6e5a95 gnu: Add cairocffi. 
* gnu/packages/gtk.scm (python-cairocffi, python2-cairocffi): New variables.
 2014-12-18 17:58:10 +01:00
Federico Beffa
6fa144692c gnu: Add xcffib 
* gnu/packages/python.scm (python-xcffib, python2-xcffib): New variables.
 2014-12-18 17:58:10 +01:00
Ludovic Courtès
46a3e00b5b gnu: icecat: Build with PulseAudio support. 
* gnu/packages/gnuzilla.scm (icecat)[arguments]: Add
  --enable-pulseaudio.
 2014-12-17 14:06:59 +01:00
Jason Self
80db9915a0 gnu: linux-libre: Update to 3.18.1 
* gnu/packages/linux.scm (linux-libre): Update to version 3.18.1.
 2014-12-17 04:30:52 -08:00
Ricardo Wurmus
7576cbd6da gnu: Add Test::Simple. 
* gnu/packages/perl.scm (perl-test-simple): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:28 +01:00
Ricardo Wurmus
0ad3969fcd gnu: Add Test::Deep. 
* gnu/packages/perl.scm (perl-test-deep): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:28 +01:00
Ricardo Wurmus
9dc8a1577f gnu: Add Test::NoWarnings. 
* gnu/packages/perl.scm (perl-test-nowarnings): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:28 +01:00
Ricardo Wurmus
ea0a52d7d6 gnu: Add Test::Tester. 
* gnu/packages/perl.scm (perl-test-tester): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-17 00:11:27 +01:00
Federico Beffa
6a84316848 Revert "gnu: python-numpy-bootstrap: Reduce matrix size in failing test." 
This reverts commit 31557440c2 as it did not
provide the desired effect.  The test is still failing.
 2014-12-16 18:37:13 +01:00
Ricardo Wurmus
81de56479a gnu: Add bedtools 
* gnu/packages/bioinformatics.scm (bedtools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-16 18:17:15 +01:00
Tomáš Čech
b336da21e9 gnu: tmux: Update to 1.9a. 
* gnu/packages/tmux.scm (tmux): Update to 1.9a

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-16 18:17:15 +01:00
Ricardo Wurmus
f3cd952b45 gnu: samtools: disable tests for non-64-bit systems 
* gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
  systems because of an upstream bug in the test data.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-16 18:17:15 +01:00
Mark H Weaver
a142e38e9d gnu: groff: Disable parallel builds. 
* gnu/packages/groff.scm (groff): Disable parallel builds.
 2014-12-16 11:16:54 -05:00
Mark H Weaver
dec7ab5953 gnu: groff: Update to 1.22.3. 
* gnu/packages/groff.scm (groff): Update to 1.22.3.
 2014-12-16 03:28:06 -05:00
Mark H Weaver
a6e818586b gnu: ghostscript: Update to 9.14.0. 
* gnu/packages/ghostscript.scm (ghostscript): Update to 9.14.0.
  Change license to agpl3+.
 2014-12-16 03:08:00 -05:00
Mark H Weaver
6b282cc9fb gnu: lcms: Update to 2.6. 
* gnu/packages/ghostscript.scm (lcms): Update to 2.6.
 2014-12-16 03:07:57 -05:00
Mark H Weaver
9f8552fab5 gnu: icecat: Apply security updates for CVE-2014-{1587,1590,1592,1593,1594}. 
* gnu/packages/patches/icecat-CVE-2014-1587-bug-1042567.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1072847.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1079729.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1080312.patch,
  gnu/packages/patches/icecat-CVE-2014-1587-bug-1089207.patch,
  gnu/packages/patches/icecat-CVE-2014-1590.patch,
  gnu/packages/patches/icecat-CVE-2014-1592.patch,
  gnu/packages/patches/icecat-CVE-2014-1593.patch,
  gnu/packages/patches/icecat-CVE-2014-1594.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat): Add them.
 2014-12-15 20:42:53 -05:00
Tomáš Čech
6cb89466ba gnu: Add bullet. 
* gnu/packages/game-development.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2014-12-15 08:09:04 -05:00
宋文武
5a659a489e gnu: Add vala. 
* gnu/packages/gnome.scm (vala): New variable.
 2014-12-15 18:51:30 +08:00
Mark H Weaver
5afbfb9924 gnu: youtube-dl: Update to 2014.12.15. 
* gnu/packages/video.scm (youtube-dl): Update to 2014.12.15.
 2014-12-15 03:36:54 -05:00
Mark H Weaver
bfb8486929 gnu: Add xfce4-battery-plugin. 
* gnu/packages/xfce.scm (xfce4-battery-plugin): New variable.
 2014-12-14 19:46:12 -05:00
Mark H Weaver
d814f921f1 gnu: xfce4-panel: Support panel plugins from other packages. 
* gnu/packages/patches/xfce4-panel-plugins.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/xfce.scm (xfce4-panel): Add the patch, and a
  native search path specification for X_XFCE4_LIB_DIRS.
 2014-12-14 19:45:59 -05:00
Federico Beffa
31557440c2 gnu: python-numpy-bootstrap: Reduce matrix size in failing test. 
* gnu/packages/python.scm (python-numpy-bootstrap): Add phase
  'fix-failing-tests.
 2014-12-14 20:01:22 +01:00
John Darrington
de51bf58b9 gnu: Add xdotool. 
* gnu/packages/xdisorg.scm (xdotool): New variable.
 2014-12-14 18:43:22 +01:00
Federico Beffa
c1125a04bb gnu: python-numpy-bootstrap: Make tests verbose. 
* gnu/packages/python.scm (python-numpy-bootstrap): Make tests verbose to
  allow test failure debugging on hydra.
 2014-12-13 09:44:26 +01:00
宋文武
aba42c98b3 gnu: xfconf: Disable parallel tests. 
* gnu/packages/xfce.scm (xfconf): Add 'arguments' field.
 2014-12-13 11:15:03 +08:00
Ricardo Wurmus
4e10a22168 gnu: Add samtools 
* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-13 00:01:06 +01:00
Mark H Weaver
c9d512faac gnu: Add nginx. 
* gnu/packages/web.scm (nginx): New variable.
 2014-12-12 08:57:21 -05:00
Mark H Weaver
90dcf9c8c5 gnu: pcre: Update to 8.36 and enable JIT support. 
* gnu/packages/pcre.scm (pcre): Update to 8.36.  Enable JIT support.
 2014-12-12 08:56:56 -05:00
宋文武
8a3c54e0a1 gnu: Add xfdesktop. 
* gnu/packages/xfce.scm (xfdesktop): New variable.
 2014-12-12 20:50:12 +08:00
宋文武
3a4bfddee7 gnu: Add xfwm4. 
* gnu/packages/xfce.scm (xfwm4): New variable.
 2014-12-12 20:49:07 +08:00
宋文武
aac0380040 gnu: Add thunar-volman. 
* gnu/packages/xfce.scm (thunar-volman): New variable.
 2014-12-12 20:45:50 +08:00
宋文武
5c776d2706 gnu: Add thunar. 
* gnu/packages/xfce.scm (thunar): New variable.
 2014-12-12 20:44:04 +08:00
宋文武
55613927ea gnu: Add xfce4-settings. 
* gnu/packages/xfce.scm (xfce4-settings): New variable.
 2014-12-12 20:41:51 +08:00
宋文武
9a8a040dfe gnu: Add xfce4-session. 
* gnu/packages/xfce.scm (xfce4-session): New variable.
 2014-12-12 20:39:12 +08:00
宋文武
c5c2f9bbb0 gnu: Add xfce4-appfinder. 
* gnu/packages/xfce.scm (xfce4-appfinder): New variable.
 2014-12-12 20:36:44 +08:00
宋文武
3b3a7fe78c gnu: Add xfce4-panel. 
* gnu/packages/xfce.scm (xfce4-panel): New variable.
 2014-12-12 20:35:25 +08:00
宋文武
305bc4cca8 gnu: Add tumbler. 
* gnu/packages/xfce.scm (tumbler): New variable.
 2014-12-12 20:27:04 +08:00