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2508 Commits

Author SHA1 Message Date
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
Ludovic Courtès 7f5c2a9cc1 services: static-networking-service: Switch to (guix build syscalls). 
* gnu/services/networking.scm (static-networking-service): Remove
  #:inetutils parameter.  Rewrite using 'configure-network-interface'
  and 'set-network-interface-flags'.
 2014-12-19 17:15:53 +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
Ludovic Courtès 61ff0a3a18 install: Use a low-memory nscd caching policy. 
* gnu/system/install.scm (%nscd-minimal-caches): New variable.
  (installation-services): Use as 'nscd-service' argument.
 2014-12-14 17:26:03 +01:00
Ludovic Courtès 6454b33345 services: Make 'nscd-service' configurable; cache hosts/services by default. 
Before that, as it was given an empty configuration file, nscd would
actually have all its caches disabled.

* gnu/services/base.scm (<nscd-configuration>, <nscd-cache>): New record
  types.
  (%nscd-default-caches, %nscd-default-configuration): New variables.
  (nscd.conf-file): New procedure.
  (nscd-service): Add 'config' parameter.  Use 'nscd.conf-file', and
  pass its result as the '-f' parameter of nscd.
* doc/guix.texi (Base Services): Update 'nscd-service' documentation
  accordingly.  Document 'nscd-configuration', 'nscd-cache',
  '%nscd-default-configuration', and '%nscd-default-caches'.
 2014-12-14 16:29:24 +01:00
Ludovic Courtès 45c5b47b96 activation: Copy the account skeletons when creating the 'root' account. 
* gnu/build/activation.scm (%skeleton-directory): New variable.
  (dot-or-dot-dot?, copy-account-skeletons): New procedure.
  (add-user): Use 'copy-account-skeletons'.
  (activate-etc): Use 'dot-or-dot-dot?'.
 2014-12-13 22:31:08 +01:00
Ludovic Courtès ccc2678b0d system: grub: Make sure the font and background image are always found. 
* gnu/system/grub.scm (eye-candy): Add 'search --file --set'.
 2014-12-13 22:15:01 +01:00
Ludovic Courtès 6c777cf88c system: Adjust 'grub.cfg' to work on systems with a separate /boot. 
Fixes <http://bugs.gnu.org/19220>.
Reported by Nikita Karetnikov <nikita@karetnikov.org>.

* gnu/system/grub.scm (grub-configuration-file)[entry->gexp]: Add
  'search --file --set'.
  (grub-configuration-file)[builder]: Remove 'search.file'.
 2014-12-13 22:13:57 +01:00
Ludovic Courtès 5c5e7bdafd vm: Use QEMU's standard VGA emulation by default. 
* gnu/system/vm.scm (common-qemu-options): Add "-vga std".
 2014-12-13 17:18:05 +01:00
Ludovic Courtès b2bd7c253a services: xorg: Run the window manager from a login shell. 
This is a followup to 1d18d87, which fixes <http://bugs.gnu.org/19119>.

* gnu/services/xorg.scm (xinitrc)[builder]: Add 'exec-from-login-shell'
  procedure.  Use it instead of 'execl' when launching XSESSION, WMAKER,
  or RATPOISON.
 2014-12-13 16:22:34 +01:00
Ludovic Courtès a8a086e392 system: Add sudo to '%base-packages'. 
* gnu/system.scm (%base-packages): Add SUDO.
 2014-12-13 16:22:34 +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
Ludovic Courtès 97ab2c0fb6 system: /etc/profile defines 'MANPATH', which includes the global profile. 
* gnu/system.scm (etc-directory)[profile]: Set 'MANPATH'.
 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