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Author SHA1 Message Date
Leo Famulari 1ae44b802b
gnu: Add python-pythondialog. 
* gnu/packages/python.scm (python-pythondialog): New variable.
(python2-pythondialog): Inherit from PYTHON-PYTHONDIALOG.

Co-authored-by: Vincent Legoll <vincent.legoll@idgrilles.fr>
 2016-08-06 22:55:36 -04:00
Alex Griffin e87c7ec2de
gnu: Add bs1770gain. 
* gnu/packages/video.scm (bs1770gain): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-08-06 22:50:15 -04:00
Ben Woodcroft 1817d30ad3
gnu: ruby-cucumber-core: Update to 1.5.0. 
* gnu/packages/ruby.scm (ruby-cucumber-core): Update to 1.5.0.
 2016-08-06 21:37:37 +10:00
Ben Woodcroft 9e12eba866
gnu: Add python-biom-format. 
* gnu/packages/bioinformatics.scm (python-biom-format,
python2-biom-format): New variables.
 2016-08-06 09:44:28 +10:00
Ben Woodcroft da4ac1aaa4
gnu: Add python-future. 
* gnu/packages/python.scm (python-future, python2-future): New
variables.
 2016-08-06 09:44:28 +10:00
Leo Famulari fd34d4f449
gnu: icedtea-8: Update to 3.1.0. 
Fixes CVE-2016-{3458,3485,3500,3508,3550,3587,3606,3598,3610}.

* gnu/packages/java.scm (icedtea-8): Update to 3.1.0.
[native-inputs]: Add SHENANDOAH-DROP.
 2016-08-05 18:43:19 -04:00
Leo Famulari 2b836df375
gnu: icedtea-7: Update to 2.6.7. 
Fixes CVE-2016-{3458,3485,3500,3508,3550,3598,3606,3610}.

* gnu/packages/java.scm (icedtea-7):  Update to 2.6.7.
 2016-08-05 18:43:19 -04:00
David Craven 00f4690568
services: Add spice vdagent service. 
* gnu/services/spice.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* doc/guix.texi (Various Services): New subheading.
 2016-08-05 21:48:43 +02:00
David Craven e02cd2b8fe
gnu: spice-vdagent: Set Exec path in spice-vdagent.desktop. 
* gnu/packages/spice.scm (spice-vdagent): Set Exec path in
spice-vdagent.desktop.
 2016-08-05 21:48:43 +02:00
David Craven 38b9ce44db
gnu: qemu: Enable spice support. 
* gnu/packages/qemu.scm (qemu)[inputs]: Add SPICE and VIRGLRENDERER.
  (qemu-minimal)[inputs]: Remove SPICE and VIRGLRENDERER.
 2016-08-05 21:48:43 +02:00
David Craven 2f04282297
gnu: qemu: Reorder inputs alphabetically. 
* gnu/packages/qemu.scm (qemu): Reorder inputs alphabetically.
 2016-08-05 21:48:43 +02:00
ng0 4cc4d363f2
gnu: tor: Update to 0.2.8.6. 
* gnu/packages/tor.scm (tor): Update to 0.2.8.6.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-08-05 21:18:34 +02:00
Andreas Enge a1e0652dd8
gnu: qjson: Remove package. 
* gnu/packages/qt.scm (qjson): Delete variable.
 2016-08-05 21:16:36 +02:00
ng0 c744f5c0ad
gnu: Add ircii. 
* gnu/packages/irc.scm (ircii): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-08-05 15:10:04 -04:00
Erik Edrosa e28e74a518
gnu: Add guile-commonmark 
* gnu/packages/guile.scm (guile-commonmark): New variable.
 2016-08-05 09:25:41 +02:00
Ricardo Wurmus f467c35261
gnu: tuxguitar: Update to 1.3.2. 
* gnu/packages/music.scm (tuxguitar): Update to 1.3.2.
[arguments]: Use ant-build-system and rearrange build phases.
[native-inputs]: Remove field.
 2016-08-04 21:32:13 +02:00
Ludovic Courtès d77a0bd6f1
ui: Remove dependency on (gnu system file-systems). 
* guix/ui.scm (specification->file-system-mapping): Move to...
* gnu/system/file-systems.scm (specification->file-system-mapping):
... here.
 2016-08-04 19:38:33 +02:00
Ludovic Courtès 7912677c1e
gnu: gcc: Reintroduce dependency on Texinfo. 
This partly reverts 868c13c53a, which
introduced a regression whereby gcc@5 and gcc@6 would no longer contain
their Info manual.

* gnu/packages/gcc.scm (gcc-5)[native-inputs]: Remove.
 2016-08-04 19:38:33 +02:00
Leo Famulari e686e633ad
gnu: curl: Replace with 7.50.1 [fixes CVE-2016-{3739,4802,5419,5420,5421]. 
* gnu/packages/curl.scm (curl)[replacement]: New field.
(curl-7.50.1): New variable.
 2016-08-04 12:57:36 -04:00
Tobias Geerinckx-Rice 7ccb874a29
gnu: zsh: Move to shells.scm. 
* gnu/packages/zsh.scm (zsh): Move from here ...
* gnu/packages/shells.scm (zsh): ... to here.
* gnu/packages/zsh.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Remove zsh.scm.
 2016-08-04 08:17:39 -04:00
Mark H Weaver 536fc5f8cd
Merge branch 'core-updates' 2016-08-04 08:17:05 -04:00
Mark H Weaver 0832787e5c
Revert "Merge branch 'core-updates'" 
This reverts commit 455859a50f.
 2016-08-04 08:16:38 -04:00
Mark H Weaver 5b098cc4b9
Revert "gnu: zsh: Move to shells.scm." 
This reverts commit 12b63ab505.
 2016-08-04 08:16:27 -04:00
Ricardo Wurmus 8b52167e77
gnu: python-statsmodels: Fix tests. 
* gnu/packages/statistics.scm (python-statsmodels): Add patch to fix tests.
(python2-statsmodels)[propagated-inputs]: Add python2-pytz.
* gnu/packages/patches/python-statsmodels-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-08-04 13:40:13 +02:00
Andreas Enge 6ad08117d9
gnu: gtk-doc: Disable parallel tests. 
* gnu/packages/gtk.scm (gtk-doc)[arguments]: Disable parallel tests.
 2016-08-04 12:46:28 +02:00
Andreas Enge 9d19e18d24
gnu: gtk-doc: Update to 1.25. 
* gnu/packages/gtk.scm (gtk-doc): Update to 1.25.
 2016-08-04 12:46:28 +02:00
Ben Woodcroft 752bb44794
gnu: python2-bz2file: Use python-2. 
This is a followup to 124df723a0.
Problem reported by Andreas Enge <andreas@enge.fr>.

* gnu/packages/python.scm (python2-bz2file)[arguments]: Use python-2.
 2016-08-04 20:09:40 +10:00
Andreas Enge 2470d779c9
gnu: qt: Update to 5.6.1-1. 
* gnu/packages/qt.scm (qt): Update to 5.6.1-1.

Co-authored-by: David Craven <david@craven.ch>
 2016-08-04 09:56:03 +02:00
Andreas Enge cce28b0c3a
gnu: qt: Use modify-phases syntax. 
* gnu/packages/qt.scm (qt): Use modify-phases syntax.
 2016-08-04 09:56:03 +02:00
Andreas Enge 7972d8a2e9
gnu: qtbase: Modify .cmake files to enable modules in different packages. 
* gnu/packages/qt.scm (qtbase)[arguments]: In the configure phase, modify
.cmake and .cmake.in files so that find_package honors CMAKE_PREFIX_PATH.
 2016-08-04 01:19:12 +02:00
Ricardo Wurmus 0ea179fd92
gnu: Add GCompris. 
* gnu/packages/education.scm (gcompris): New variable.
 2016-08-03 18:50:26 +02:00
Ludovic Courtès 134f657318
Merge branch 'version-0.11.0' 2016-08-03 18:37:18 +02:00
Ricardo Wurmus 97b9da6897
gnu: Add discrover. 
* gnu/packages/bioinformatics.scm (discrover): New variable.
 2016-08-03 17:20:26 +02:00
ng0 b7194849ad
Rename references to (gnu packages tcsh). 
* gnu/packages/algebra.scm, gnu/packages/boost.scm,
gnu/packages/maths.scm, gnu/packages/tex.scm, gnu/packages/vim.scm:
Change broken references to module (gnu packages tcsh) to (gnu packages
shells).
 2016-08-03 16:22:31 +02:00
Ben Woodcroft afde1a264b
gnu: fxtract: Restrict to x86_64-linux. 
* gnu/packages/bioinformatics.scm (fxtract)[supported-systems]: Restrict to
  x86_64-linux.
 2016-08-03 21:22:02 +10:00
Ben Woodcroft 124df723a0
gnu: python-bz2file: Disable tests. 
* gnu/packages/python.scm (python-bz2file)[arguments]: Disable
tests.
(python2-bz2file)[arguments]: New field.
 2016-08-03 21:08:39 +10:00
Ludovic Courtès d76f44e84c
gnu: mdadm: Build without '-Werror' 
* gnu/packages/linux.scm (mdadm)[arguments]: Add 'remove-W-error'
phase.
 2016-08-03 12:10:00 +02:00
Ludovic Courtès 8aceca50cd
gnu: guix: Update development snapshot. 
* gnu/packages/package-management.scm (guix-devel): Update to 4420940.
(guix): Set to GUIX-DEVEL.
 2016-08-03 10:56:45 +02:00
Tobias Geerinckx-Rice 12b63ab505
gnu: zsh: Move to shells.scm. 
* gnu/packages/zsh.scm (zsh): Move from here ...
* gnu/packages/shells.scm (zsh): ... to here.
* gnu/packages/zsh.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Remove zsh.scm.
 2016-08-03 04:54:34 +02:00
Tobias Geerinckx-Rice d754347cb4
gnu: tcsh: Move to shells.scm. 
* gnu/packages/tcsh.scm (tcsh): Move from here ...
* gnu/packages/shells.scm (tcsh): ... to here.
* gnu/packages/tcsh.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Remove tcsh.scm.
 2016-08-03 04:54:29 +02:00
Tobias Geerinckx-Rice 9a57d3e6a1
gnu: rc: Move to shells.scm. 
* gnu/packages/rc.scm (rc): Move from here ...
* gnu/packages/shells.scm (rc): ... to here.
* gnu/packages/rc.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Remove rc.scm.
 2016-08-03 04:54:24 +02:00
Tobias Geerinckx-Rice 618977ae38
gnu: fish: Move to shells.scm. 
* gnu/packages/fish.scm (fish): Move from here ...
* gnu/packages/shells.scm (fish): ... to here.
* gnu/packages/fish.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Remove fish.scm.
 2016-08-03 04:54:18 +02:00
Tobias Geerinckx-Rice c356339d62
gnu: Add dash. 
* gnu/packages/shells.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register it.
 2016-08-03 04:54:11 +02:00
Ludovic Courtès 4420940f20
gnu: guix: Update to 0.11.0. 
* gnu/packages/package-management.scm (guix-0.10.0): Rename to...
(guix-0.11.0): ... this.  Adjust users.
(guix): Set to GUIX-0.11.0.
 2016-08-03 01:19:46 +02:00
Ludovic Courtès 10618627bf
mapped-devices: raid-device-mapping: Avoid non-top-level 'use-modules'. 
Fixes <http://bugs.gnu.org/24135>.
Reported by myglc2 <myglc2@gmail.com>.

* gnu/system/mapped-devices.scm (open-raid-device): Avoid non-top-level
'use-modules' form.
 2016-08-03 00:07:06 +02:00
Ludovic Courtès 35c4aec88d
build: Add missing procps patch to the distribution. 
The patch was added to gnu/local.mk in
d46123aade and inadvertently removed in a
subsequent merge.

* gnu/local.mk (dist_patch_DATA): Add procps-non-linux.patch.
 2016-08-02 23:43:29 +02:00
Leo Famulari 4e92d76a40
gnu: python-atomicwrites: Update to 1.1.0. 
* gnu/packages/python.scm (python-atomicwrites, python2-atomicwrites):
Update to 1.1.0.
 2016-08-02 16:24:11 -04:00
Francesco Frassinelli 319ac02b5a
gnu: Add Seren. 
* gnu/packages/telephony.scm (seren): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-08-02 22:12:45 +03:00
Pjotr Prins 0a4ebe0148
gnu: Add Elixir. 
* gnu/packages/elixir.scm: New file.
* gnu/packages/patches/elixir-disable-failing-tests.patch: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add module.
(dist_patch_DATA): Add patch.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2016-08-02 18:31:29 +02:00
Leo Famulari deb6482ec6
gnu: libressl: Update to 2.4.2. 
* gnu/packages/tls.scm (libressl): Update to 2.4.2.
 2016-08-02 12:22:59 -04:00
Ludovic Courtès ab3a64507a
system: Define 'GUIX_LOCPATH' to work around 'glibc' package defect. 
Our 'glibc' package currently ignores /run/current-system/locale,
although the intent is to look for locales in that directory.

* gnu/packages/base.scm (glibc/linux): Add comment about
/run/current-system/locale being ignored.
* gnu/system.scm (operating-system-environment-variables): Add
'GUIX_LOCPATH'.
* gnu/tests/base.scm (run-basic-test): Add "locale" test.
 2016-08-02 18:07:19 +02:00
Alex Sassmannshausen e2b12a55c1
gnu: Add perl-log-any-adapter-log4perl. 
* gnu/packages/perl.scm (perl-log-any-adapter-log4perl): New variable.
 2016-08-02 16:39:08 +02:00
Alex Sassmannshausen 9ec9e49466
gnu: Add perl-log-log4perl. 
* gnu/packages/perl.scm (perl-log-log4perl): New variable.
 2016-08-02 16:39:08 +02:00
Alex Sassmannshausen cf5e49cdc5
gnu: Add perl-log-any. 
* gnu/packages/perl.scm (perl-log-any): New variable.
 2016-08-02 16:39:08 +02:00
Ricardo Wurmus fede3a903e
gnu: Add emacs-visual-fill-column. 
* gnu/packages/emacs.scm (emacs-visual-fill-column): New variable.
 2016-08-02 15:20:43 +02:00
Christopher W. Carpenter 3701f014b1
gnu: ccl: Update to 1.11. 
* gnu/packages/lisp.scm (ccl): Update to 1.11.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-08-02 21:04:56 +08:00
Ricardo Wurmus dda3627141
gnu: r-variantannotation: Update to 1.18.6. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.6.
 2016-08-02 14:47:46 +02:00
Ricardo Wurmus 005ca42396
gnu: r-genomationdata: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.4.2.
 2016-08-02 14:47:46 +02:00
Ludovic Courtès 7b5fc3a320
gnu: kde-frameworks: Fix version numbers. 
Fixes a regression introduced in
d26e2b9f30.

* gnu/packages/kde-frameworks.scm (kwindowsystem, oxygen-icons): Set to
"5.21.0".
 2016-08-02 14:40:17 +02:00
Ludovic Courtès 47e2fe3cdf
gnu: extra-cmake-modules: Add proper 'version'. 
Fixes a regression introduced in
d26e2b9f30.

* gnu/packages/kde-frameworks.scm (extra-cmake-modules)[version]: Set to
"5.21.0".
 2016-08-02 14:28:47 +02:00
Ludovic Courtès 873b51b340
mapped-devices: Bail out when RAID sources don't show up. 
* gnu/system/mapped-devices.scm (open-raid-device): Bail out after 20
loop iterations.
 2016-08-02 13:53:25 +02:00
Ludovic Courtès 7f8ad82bf2
mapped-devices: Make RAID device opening message clearer. 
* gnu/system/mapped-devices.scm (open-raid-device): Rename 'source' to
'sources'.  Make 'waiting' message more informative.
(close-raid-device): Rename 'source' to 'sources'.
 2016-08-02 13:53:25 +02:00
Ludovic Courtès dfe06f6e7f
mapped-devices: Do not always use (gnu build file-systems). 
Fixes <http://bugs.gnu.org/24129>.
Reported by myglc2 <myglc2@gmail.com>.

* gnu/system/mapped-devices.scm (device-mapping-service-type): Remove
'modules' field from 'shepherd-service' form.
(open-luks-device): Add 'use-modules' form.
 2016-08-02 13:53:25 +02:00
David Craven d26e2b9f30
gnu: kde-frameworks: Remove kde-frameworks-version. 
* gnu/packages/kde-frameworks (kde-frameworks-version): Delete variable.
  (kwindowsystem)[version]: Replace kde-frameworks-version with version string.
  (oxygen-icons)[version]: Replace kde-frameworks-version with version string.
 2016-08-02 13:29:47 +02:00
David Craven b93502d6ba
gnu: network-manager: Propagate GLIB. 
* gnu/packages/gnome.scm (network-manager)[propagated-inputs]: Add glib.
 2016-08-02 13:28:21 +02:00
Andreas Enge cc30a47273
gnu: powwow: Use HTTPS download. 
* gnu/packages/games.scm (powwow)[source]: Use HTTPS URL.
 2016-08-02 11:21:00 +02:00
Leo Famulari 5f518cadc3
gnu: vdirsyncer: Update to 0.11.3. 
* gnu/packages/dav.scm (vdirsyncer): Update to 0.11.3.
 2016-08-01 21:06:42 -04:00
nee 826a3ca22c
gnu: Add supertux. 
* gnu/packages/games.scm (supertux): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-08-01 20:40:20 -04:00
Leo Famulari 621954ba4e
gnu: htop: Update to 2.0.2. 
* gnu/packages/admin.scm (htop): Update to 2.0.2.
 2016-08-01 19:06:18 -04:00
Ludovic Courtès 455859a50f
Merge branch 'core-updates' 2016-08-01 23:30:52 +02:00
Ludovic Courtès a8cb87abe9
install: Add nvi to the image. 
* gnu/system/install.scm (installation-os)[packages]: Add NVI.
* doc/guix.texi (Proceeding with the Installation): Mention it.
 2016-08-01 23:08:48 +02:00
Mark H Weaver 742effef56
gnu: openssh: Update to 7.3p1. 
* gnu/packages/ssh.scm (openssh): Update to 7.3p1.
[source]: Remove patches.
* gnu/packages/patches/openssh-CVE-2015-8325.patch,
gnu/packages/patches/openssh-CVE-2016-6210-1.patch,
gnu/packages/patches/openssh-CVE-2016-6210-2.patch,
gnu/packages/patches/openssh-CVE-2016-6210-3.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
 2016-08-01 14:27:08 -04:00
Kei Kebreau 660e005c21
gnu: red-eclipse: Replace string with version number variable. 
* gnu/packages/games.scm (red-eclipse)[phases]: Replace it.
 2016-08-01 13:42:29 -04:00
Ludovic Courtès a348af403d
gnu: texlive-texmf: Mark as non-substitutable. 
* gnu/packages/tex.scm (texlive-texmf)[arguments]: Add #:substitutable?.
 2016-08-01 19:00:43 +02:00
Kei Kebreau 66c65aafa7
gnu: red-eclipse: Add example server configuration file to config 
directory.

* gnu/packages/games.scm (red-eclipse)[phases]: Add server configuration
file.
 2016-08-01 11:48:39 -04:00
Kei Kebreau 14b865dc3e
gnu: red-eclipse: Update to 1.5.5. 
* gnu/packages/games.scm (red-eclipse): Update to 1.5.5.
[arguments]: Adjust phases.
[inputs]: Use sdl2.
 2016-08-01 11:47:18 -04:00
Kei Kebreau 06438b07b9
gnu: dmidecode: Update to 3.0. 
* gnu/packages/admin.scm (dmidecode): Update to 3.0.
[arguments]: Use ’modify-phases’ instead of ‘alist-delete’.
 2016-08-01 08:55:28 -04:00
Ricardo Wurmus a4e6356e11
gnu: Add trio. 
* gnu/packages/code.scm (trio): New variable.
 2016-08-01 14:06:03 +02:00
Ben Woodcroft 26af1c8d13
gnu: ruby-ffi: Update to 1.9.14. 
* gnu/packages/ruby.scm (ruby-ffi): Update to 1.9.14.
 2016-08-01 21:30:49 +10:00
Ben J Woodcroft 7b01f250e4
gnu: ruby-nokogiri: Update to 1.6.8. 
* gnu/packages/ruby.scm (ruby-nokogiri): Update to 1.6.8.
[arguments]: Remove 'update-dependency' phase.  Add 'patch-extconf' phase.
[native-inputs]: Remove ruby-rake-compiler.
[propagated-inputs]: Add ruby-pkg-config.
 2016-08-01 21:30:49 +10:00
Ben J Woodcroft 2de61e340c
gnu: Add ruby-pkg-config. 
* gnu/packages/ruby.scm (ruby-pkg-config): New variable.
 2016-08-01 21:30:49 +10:00
Ludovic Courtès 683a4a34cd
gnu: openssh: Add dependency on xauth. 
Partly fixes <http://bugs.gnu.org/23317>.
Reported by Danny Milosavljevic <dannym@scratchpost.org>.

* gnu/packages/ssh.scm (openssh)[inputs]: Add XAUTH.
 2016-08-01 11:26:33 +02:00
Andreas Enge 2be896dec1
gnu: unison: Add input ghostscript. 
* gnu/packages/ocaml.scm (unison)[native-inputs]: Add ghostscript.

This is a follow-up to commit e83a13faa2.
 2016-08-01 10:24:07 +02:00
Mark H Weaver 3d337bbc39
Merge branch 'master' into core-updates 2016-07-31 23:27:03 -04:00
Mark H Weaver 4e8efc15fb
gnu: linux-libre@4.1: Update to 4.1.29. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.29.
 2016-07-31 23:24:54 -04:00
ng0 3920868c0c
gnu: Add libgnomekbd. 
* gnu/packages/gnome.scm (libgnomekbd): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-08-01 01:11:57 +02:00
Eric Le Bihan cf04df0701
gnu: Add s6-linux-utils. 
* gnu/packages/skarnet.scm (s6-linux-utils): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-08-01 01:11:57 +02:00
Eric Le Bihan 915db95f67
gnu: Add s6-portable-utils. 
* gnu/packages/skarnet.scm (s6-portable-utils): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-08-01 01:11:57 +02:00
Eric Le Bihan 35977a8897
gnu: Add s6-rc. 
* gnu/packages/skarnet.scm (s6-rc): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-08-01 01:11:57 +02:00
Ludovic Courtès 5e74529271
gnu: units: Update to 2.13. 
* gnu/packages/maths.scm (units): Update to 2.13.
 2016-08-01 01:11:57 +02:00
Matthew Jordan ec91bcb500
gnu: Add Go 1.6. 
* gnu/packages/golang.scm (go-1.6): New variable.

Co-authored-by: Efraim Flashner <efraim@flashner.co.il>
Co-authored-by: Andy Wingo <wingo@igalia.com>
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-08-01 01:11:57 +02:00
Leo Famulari f92d99a5a3
gnu: imagemagick: Update to 6.9.5-4 [fixes CVE-2016-6491]. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-4.
 2016-07-31 18:58:19 -04:00
Albin Söderqvist eb3bd6762a
gnu: openttd: Update to 1.6.1. 
* gnu/packages/games.scm (openttd): Update to 1.6.1 and expand the
package description.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-07-31 22:52:12 +02:00
Andy Patterson 932b2ea206
gnu: ecl: Use "kernel-headers" instead of "linux-headers" to designate input. 
* gnu/packages/lisp.scm (ecl)[arguments]: Use "kernel-headers" as the
identifier for an input.

This is a follow-up to commit 55de892b43.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-07-31 20:13:16 +02:00
Andreas Enge 42bf34298e
gnu: rapicorn: Add patch to handle isnan. 
* gnu/packages/patches/rapicorn-isnan.patch: New file.
* gnu/packages/graphics.scm (rapicorn)[source]: Add patch.
* gnu/local.mk (dist_patch_DATA): Register patch.
 2016-07-31 18:16:25 +02:00
Andreas Enge acac969fa2
gnu: fastcap: Add input ghostscript. 
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Add ghostscript.

This is a follow-up to commit e83a13faa2.
 2016-07-31 17:11:15 +02:00
Andreas Enge dceba1c19b
gnu: zsh: Update to 5.2. 
* gnu/packages/zsh.scm (zsh): Update to 5.2.
 2016-07-31 17:05:36 +02:00
Andreas Enge ce430bd637
gnu: tcc: Use "kernel-headers" instead of "linux-headers" to designate input. 
* gnu/packages/c.scm (tcc)[arguments]: Use "kernel-headers" as identifier
for an input.

This is a follow-up to commit 55de892b43.
 2016-07-31 16:50:12 +02:00
Andreas Enge 70a967209c
gnu: dealii: Unregister deleted patch. 
* gnu/local.mk (dist_patch_DATA): Drop deleted patch.

This is a follow-up to commit 101e847294.
 2016-07-31 16:37:39 +02:00
Andreas Enge 101e847294
gnu: dealii: Update to 8.4.1. 
* gnu/packages/maths.scm (dealii): Update to 8.4.1.
* gnu/packages/patches/dealii-p4est-interface.patch: Remove file.
 2016-07-31 15:22:41 +02:00
Andreas Enge 7b995c7bcb
gnu: wine: Update to 1.9.15. 
* gnu/packages/wine.scm (wine): Update to 1.9.15.
 2016-07-31 12:11:05 +02:00
Andreas Enge bb484529cc
gnu: python-alembic: Update to 0.8.7. 
* gnu/packages/python.scm (python-alembic): Update to 0.8.7.
 2016-07-31 11:18:53 +02:00
Andreas Enge 33906d54c1
gnu: perl-xml-libxml: Update to 2.0128. 
* gnu/packages/xml.scm (perl-xml-libxml): Update to 2.0128.
 2016-07-31 09:55:14 +02:00
宋文武 85860fdf82
gnu: glibc-locales: Fix build. 
* gnu/packages/patches/glibc-locales.patch: Adjust to glibc-2.23.
* gnu/packages/base.scm (glibc-locales)[arguments]:
Pass 'lib_cv_complocaledir'.
 2016-07-31 10:42:47 +08:00
Tomáš Čech 2fa66f451a
gnu: mutt: Update to 1.6.2. 
* gnu/packages/mail.scm(mutt): Update to 1.6.2.
 2016-07-30 22:37:56 +02:00
Kei Kebreau 4bc37bf0c3
gnu: Add python-pygame. 
* gnu/packages/game-development.scm (python-pygame): New variable.
 2016-07-30 14:32:49 -04:00
Kei Kebreau d8841cc52e
gnu: Add libsmpeg. 
* gnu/packages/video.scm (libsmpeg): New variable.
 2016-07-30 14:31:58 -04:00
Leo Famulari 6661db4e97
gnu: stellarium: Improve description. 
Suggested by Danny Milosavljevic <dannym@scratchpost.org>.

* gnu/packages/education.scm (stellarium)[description]: Mention telescope
tracking.
 2016-07-30 10:05:44 -04:00
Ludovic Courtès c2c54ebd91
gnu: Add glibc 2.22. 
* gnu/packages/base.scm (glibc-2.22): New variable.
(glibc-2.21): Inherit from it; remove 'arguments' field.
 2016-07-30 15:47:28 +02:00
Ludovic Courtès 716753cb97
tests: base: Correct invalid merge. 
Fixes a regression introduced by merge commit
7575655212.

* gnu/tests/base.scm (run-basic-test)[test]: Fix list of 'use-modules'
and 'test-begin' call.
 2016-07-30 15:47:28 +02:00
Ben Woodcroft c4382cd18f
gnu: diamond: Update to 0.8.17. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.
 2016-07-30 23:02:57 +10:00
ng0 9b12bc7032
gnu: gnunet-gtk: Configure with gnunet path. 
* gnun/packages/gnunet.scm (gnunet-gtk)[arguments]: Add '--with-gnunet'
to #:configure-flags.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-07-30 15:33:57 +08:00
Eric Bavier d25639731a
gnu: Add tuxpaint-config. 
* gnu/packages/games.scm (tuxpaint-config): New variable.
 2016-07-29 23:17:44 -05:00
Eric Bavier c3d850f232
gnu: Add tuxpaint-stamps. 
* gnu/packages/games.scm (tuxpaint-stamps): New variable.
 2016-07-29 21:50:15 -05:00
Eric Bavier 9b1ada4e81
gnu: Add Tux Paint. 
* gnu/packages/games.scm (tuxpaint): New variable.
* gnu/packages/patches/tuxpaint-stamps-path.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-07-29 21:50:15 -05:00
Alex Griffin 23319ed674
gnu: beets: Update to 1.3.19. 
* gnu/packages/music.scm (beets): Update to 1.3.19.
[source]: Remove patch to skip failing tests.
* gnu/packages/patches/beets-image-test-failure.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-29 19:19:49 -04:00
Leo Famulari d1c9d3bb42
gnu: python-protobuf: Update to 3.0.0. 
* gnu/packages/protobuf.scm (python-protobuf, python2-protobuf):
Update to 3.0.0.
 2016-07-29 19:04:31 -04:00
Leo Famulari 48b7e4a6c1
gnu: btrfs-progs: Update to 4.6.1 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.6.1.
[native-inputs]: Add WHICH.
 2016-07-29 18:58:48 -04:00
Mark H Weaver 359aba76b6
Merge branch 'master' into core-updates 2016-07-29 18:29:58 -04:00
Mark H Weaver 9bdf56dc13
gnu: gd: Add fix for gd2_read test. 
* gnu/packages/patches/gd-fix-gd2-read-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Add patch.
 2016-07-29 18:28:40 -04:00
Leo Famulari de30a6e0f0
gnu: protobuf: Update to 2.6.1. 
* gnu/packages/protobuf.scm (protobuf): Update to 2.6.1.
[source]: Update to new upstream URL.
 2016-07-29 16:41:06 -04:00
Mark H Weaver 31c995f8af
Revert "gnu: gd: Add fix for gd2_read test." 
This reverts commit ce290354ec.
 2016-07-29 16:17:35 -04:00
Mark H Weaver ce290354ec
gnu: gd: Add fix for gd2_read test. 
* gnu/packages/patches/gd-fix-gd2-read-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Add patch.
 2016-07-29 16:06:43 -04:00
Leo Famulari 814572aff5
gnu: wireshark: Update to 2.0.5. 
* gnu/packages/networking.scm (wireshark): Update to 2.0.5.
 2016-07-29 15:08:55 -04:00
Leo Famulari d260015062
gnu: perl-dbd-mysql: Update to 4.035 [fixes CVE-2015-8949]. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.035.
 2016-07-29 14:49:30 -04:00
Mark H Weaver 0bab3af078
Merge branch 'master' into core-updates 2016-07-29 14:18:07 -04:00
Mark H Weaver 682a7d2338
gnu: linux-libre@4.4: Update to 4.4.16. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.16.
 2016-07-29 14:14:25 -04:00
Mark H Weaver a81445737d
gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]. 
* gnu/packages/patches/gd-CVE-2016-5766.patch,
gnu/packages/patches/gd-CVE-2016-6128.patch,
gnu/packages/patches/gd-CVE-2016-6132.patch,
gnu/packages/patches/gd-CVE-2016-6214.patch,
gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files.
* gnu/packages/patches/gd-fix-tests-on-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gd.scm (gd): Update to 2.2.3.
[source]: Update patches field accordingly.
 2016-07-29 13:56:39 -04:00
Leo Famulari f54510d29b
gnu: virt-viewer: Remove SPICE-PROTOCOL from inputs. 
This is a followup to ba9e2ee64a.

* gnu/packages/spice.scm (virt-viewer)[inputs]: Remove SPICE-PROTOCOL.
 2016-07-29 12:50:29 -04:00
Leo Famulari 3c4a8f03a2
gnu: spice-gtk: Remove LIBUSB from inputs. 
This is a followup to 0d05a739d2.

* gnu/packages/spice.scm (spice-gtk)[inputs]: Remove LIBUSB.
 2016-07-29 12:50:29 -04:00
David Craven efcada41e7
gnu: Order module imports in (gnu packages qemu) alphabetically. 
* gnu/packages/qemu.scm: Order module imports alphabetically.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:43:55 +02:00
David Craven 6799ed7614
gnu: Add xf86-video-qxl. 
* gnu/packages/xorg.scm (xf86-video-qxl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:41:30 +02:00
David Craven c38fb02e9b
gnu: Add libinput-minimal. 
* gnu/packages/freedesktop.scm (libinput-minimal): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:40:24 +02:00
David Craven 66e076642c
gnu: Remove trailing periods from synopsis. 
* gnu/packages/emacs.scm (emacs-smart-mode-line): Update synopsis.
* gnu/packages/gnustep.scm (wmfire): Update synopsis.
* gnu/packages/haskell.scm (ghc-socks): Update synopsis.
* gnu/packages/kde-frameworks.scm (oxygen-icons): Update synopsis.
* gnu/packages/openstack.scm (python-bandit): Update synopsis.
* gnu/packages/perl.scm (perl-test-trap): Update synopsis.
* gnu/packages/python.scm (python-backports-abc): Update synopsis.
* gnu/packages/ruby.scm (python-cryptography-vectors): Update synopsis.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:37:22 +02:00
David Craven 0160458bf8
gnu: Use define-public to export packages. 
* gnu/packages/bison.scm (bison): Define public.
* gnu/packages/flex.scm (flex): Define public.
* gnu/packages/pulseaudio.scm (libsndfile, libsamplerate, pulseaudio): Define
public.
* gnu/packages/sdl.scm (sdl, sdl2, libmikmod, sdl-gfx, sdl-image, sdl-mixer,
sdl-net, sdl-ttf): Define public.
* gnu/packages/search.scm (xapian): Remove unnecessary #:export.
* gnu/packages/swig.scm (swig): Define public.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:35:20 +02:00
Ludovic Courtès 35e4b3d546
gnu: iptables: Mention "firewall". 
Suggested by ng0 <ng0@we.make.ritual.n0.is>.

* gnu/packages/linux.scm (iptables)[description]: Mention "firewall".
 2016-07-29 17:32:03 +02:00
Eric Le Bihan 7c6bdeec23
gnu: Add s6-networking. 
* gnu/packages/skarnet.scm (s6-networking): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan 798b776deb
gnu: Add s6-dns. 
* gnu/packages/skarnet.scm (s6-dns): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan 918cee467d
gnu: Add s6. 
* gnu/packages/skarnet.scm (s6): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan 2f016ac150
gnu: execline: Update to 2.1.5.0. 
* gnu/packages/skarnet.scm (execline): Update to 2.1.5.0.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan 892aa89477
gnu: skalibs: Update to 2.3.10.0. 
* gnu/packages/skarnet.scm (skalibs): Update to 2.3.10.0.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Danny Milosavljevic 2614de3c5a
gnu: Add stellarium. 
* gnu/local.mk: Include gnu/packages/education.scm .
* gnu/packages/education.scm: Add new file.
* gnu/packages/education.scm (stellarium): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Leo Famulari ba9e2ee64a
gnu: spice-gtk: Propagate SPICE-PROTOCOL. 
* gnu/packages/spice.scm (spice-gtk)[inputs]: Move SPICE-PROTOCOL to...
[propagated-inputs]: ... here.
 2016-07-29 11:16:23 -04:00
Leo Famulari 0d05a739d2
gnu: usbredir: Propagate LIBUSB. 
* gnu/packages/spice.scm (usbredir)[inputs]: Replace field with ...
[propagated-inputs]: ... new field.
 2016-07-29 11:16:23 -04:00
Ludovic Courtès 6e6ddebf48
gnu: guix: Add dependency on zlib. 
* gnu/packages/package-management.scm (guix-0.10.0)[inputs]: Add ZLIB.
 2016-07-29 11:39:30 +02:00
Alex Griffin 61201e46a7
gnu: password-store: Wrap PATH. 
* gnu/packages/password-utils.scm (password-store)
[arguments]: Wrap PATH more thoroughly.
[native-inputs]: Move getopt to inputs.
[inputs]: Add sed.

Signed-off-by: Mathieu Lirzin <mthl@gnu.org>
 2016-07-29 11:00:31 +02:00
Ludovic Courtès f33e71fca2
gnu: perl-dbd-pg: Add description. 
* gnu/packages/databases.scm (perl-dbd-pg)[description]: Add non-empty
description.
 2016-07-29 10:22:31 +02:00
Ludovic Courtès a3947cb1b8
gnu: Sync GNU descriptions with upstream. 
From 'guix lint -c gnu-description'.

* gnu/packages/gnunet.scm (gnunet): Adjust description.
* gnu/packages/marst.scm (marst): Likewise.
* gnu/packages/maths.scm (c-graph): Likewise.
* gnu/packages/networking.scm (macchanger): Likewise.
 2016-07-29 10:13:12 +02:00
Nicolas Goaziou c777570b57
gnu: Add sshpass. 
* gnu/packages/ssh.scm (sshpass): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 00:04:39 +02:00
Leo Famulari cfbb3b0d00
gnu: python-beautifulsoup4: Update to 4.5.0. 
* gnu/packages/python.scm (python-beautifulsoup4, python2-beautifulsoup4):
Update to 4.5.0.
 2016-07-28 17:50:52 -04:00
ng0 adca268e97
gnu: perl-devel-symdump: Update to 2.17. 
* gnu/packages/perl.scm (perl-devel-symdump): Update to 2.17.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:41:06 -04:00
David Craven 6144dff516
gnu: Add virt-viewer. 
* gnu/packages/spice.scm (virt-viewer): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven 33b0f4a4b2
gnu: Add spice-vdagent. 
* gnu/packages/spice.scm (spice-vdagent): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven 3cbd37e440
gnu: Add spice. 
* gnu/packages/spice.scm (spice): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven bb28cf90e9
gnu: Add spice-gtk. 
* gnu/packages/spice.scm (spice-gtk): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven 289e472f56
gnu: Add spice-protocol. 
* gnu/packages/spice.scm (spice-protocol): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
David Craven 2ef2654de4
gnu: Add virglrenderer. 
* gnu/packages/spice.scm (virglrenderer): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
David Craven 1d2c67c11e
gnu: Add usbredir. 
* gnu/packages/spice.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
Leo Famulari 49d725a108
Merge branch 'master' into core-updates 2016-07-28 16:46:27 -04:00
Leo Famulari a1dfa02233
Revert "gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]." 
This reverts commit ae46cd0e4c.
 2016-07-28 16:45:02 -04:00
Mark H Weaver 622c22ccb4
Merge branch 'master' into core-updates 2016-07-28 14:13:26 -04:00
Mark H Weaver ae46cd0e4c
gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]. 
* gnu/packages/patches/gd-CVE-2016-5766.patch,
gnu/packages/patches/gd-CVE-2016-6128.patch,
gnu/packages/patches/gd-CVE-2016-6132.patch,
gnu/packages/patches/gd-CVE-2016-6214.patch,
gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files.
* gnu/packages/patches/gd-fix-tests-on-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gd.scm (gd): Update to 2.2.3.
[source]: Update patches field accordingly.
 2016-07-28 14:06:12 -04:00
Ludovic Courtès 386b71d1b9
gnu: commencement: 'guile-final' is now "hidden". 
This way, we no longer have this annoying warning:

  $ guix build guile -n
  guix build: warning: ambiguous package specification `guile'
  guix build: warning: choosing guile-2.0.11 from gnu/packages/guile.scm:128:2

* gnu/packages/commencement.scm (guile-final): Use 'hidden-package'.
* tests/packages.scm ("fold-packages, hidden package"): New test.
 2016-07-28 18:53:13 +02:00
Ludovic Courtès 6980511b73
packages: Add 'hidden-package'. 
* guix/packages.scm (hidden-package, hidden-package?): New procedures.
* gnu/packages.scm (fold-packages): Filter out 'hidden-package?'.
* tests/packages.scm ("hidden-package"): New test.
 2016-07-28 18:50:43 +02:00
Alex Griffin cb55f9c652
gnu: Add asciinema. 
* gnu/packages/terminals.scm (asciinema): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-28 15:43:40 +02:00
Alex Griffin 71d9b98078
gnu: gnome: Propagate file-roller. 
* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-28 15:42:30 +02:00
Ludovic Courtès 212163f8d5
gnu: dico: Patch 'idxgcide' bug. 
* gnu/packages/patches/dico-idxgcide-bug.patch: New file.
* gnu/packages/dico.scm (dico)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-07-28 14:18:59 +02:00
Ludovic Courtès c6b3dc69bd
gnu: vlc: Drop -ffast-math from the compilation flags. 
* gnu/packages/video.scm (vlc)[arguments]: Add "ac_cv_c_fast_math=no" to
  #:configure-flags.
 2016-07-28 13:56:05 +02:00
Ben Woodcroft 6547708f71
gnu: r-genomicfeatures: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
 2016-07-28 21:54:44 +10:00
Ben Woodcroft 2c9f6251fc
gnu: r-bsgenome: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft b0f0778a7c
gnu: r-iranges: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft f403941f81
gnu: r-limma: Update to 3.28.17. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft 2b2ff0bd91
gnu: r-xvector: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft a463055862
gnu: r-genomicranges: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft bab15ccec4
gnu: r-annotationdbi: Update to 1.34.4. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft a22999f245
gnu: r-biocparallel: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft d104fc607d
gnu: r-biostrings: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 1864e051c9
gnu: r-summarizedexperiment: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 29b0cc8ad5
gnu: r-genomicalignments: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 5131e21064
gnu: r-rtracklayer: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 2a3e325f5e
gnu: r-genomeinfodb: Update to 1.8.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft ae32c58e28
gnu: r-bsgenome: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft e426cd7421
gnu: r-iranges: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 1c4ad6076c
gnu: r-limma: Update to 3.28.17. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft bd0cc37834
gnu: r-xvector: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 362f39d667
gnu: r-genomicranges: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft ae60f3801a
gnu: r-annotationdbi: Update to 1.34.4. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 7a0594fb5d
gnu: r-biocparallel: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 658f36e569
gnu: r-biostrings: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 0d159d84e2
gnu: r-summarizedexperiment: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 722b4c919d
gnu: r-genomicalignments: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 380d3f8657
gnu: r-rtracklayer: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 303163c7b9
gnu: r-genomeinfodb: Update to 1.8.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft 2d88825183
gnu: r-genomicfeatures: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft d6dfc39f68
gnu: r-s4vectors: Update to 0.10.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
 2016-07-28 12:31:22 +02:00
Ben Woodcroft f2e791750b
gnu: r-s4vectors: Update to 0.10.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
 2016-07-28 20:13:42 +10:00
Andreas Enge 4320c1c39f
gnu: asymptote: Add native input gs. 
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Add gs.

This is a follow-up to commit d8eb912132.
 2016-07-28 11:34:57 +02:00
Andreas Enge e309c75610
Merge remote-tracking branch 'origin/master' into core-updates 2016-07-28 11:08:55 +02:00
Leo Famulari e335b82c4e
gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}]. 
* gnu/packages/patches/mysql-fix-failing-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/databases.scm (mysql): Update to 5.7.13.
 2016-07-28 02:08:49 -04:00
Tomáš Čech 46e4e84ffc
gnu: the-silver-searcher: Update to 0.32.0. 
* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
 2016-07-28 08:05:04 +02:00