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Author SHA1 Message Date
David Craven bfa96eba56
gnu: bluez-qt: Update to 5.27.0. 
* gnu/packages/kde-frameworks.scm (bluez-qt): Update to 5.27.0 and
  fix indentation.
 2016-10-29 23:51:43 +02:00
David Craven 5eb1b33b6b
gnu: attica: Update to 5.27.0. 
* gnu/packages/kde-frameworks.scm (attica): Update to 5.27.0.
 2016-10-29 23:51:43 +02:00
David Craven 84dee85291
gnu: phonon: Fix indentation. 
* gnu/packages/kde-frameworks.scm (phonon): Fix indentation.
 2016-10-29 23:51:43 +02:00
David Craven bd0fc238f8
gnu: kpmcore: Fix indentation. 
* gnu/packages/kde-frameworks.scm (kpmcore): Fix indentation.
 2016-10-29 23:51:43 +02:00
David Craven 443a60aaae
gnu: gpgmepp: Update to 16.08.2. 
* gnu/packages/kde-frameworks (gpgmepp): Update to 16.08.2.
 2016-10-29 23:51:43 +02:00
David Craven 1c484e980f
gnu: extra-cmake-modules: Update to 5.27.0. 
* gnu/packages/kde-frameworks.scm (extra-cmake-modules): Update to
  5.27.0.
 2016-10-29 23:51:43 +02:00
David Craven b68bf48af9
gnu: Add flex-2.6.1. 
* gnu/packages/flex.scm (flex-2.6.1): New variable.
 2016-10-29 23:51:43 +02:00
Alex Vong ee5fb7ee50
gnu: Add python2-rpython. 
* gnu/packages/python.scm (python2-rpython): New variable.
 2016-10-29 23:49:05 +02:00
Efraim Flashner 8f210c0e0e
gnu: ccache: Update to 3.3.3. 
* gnu/packages/ccache.scm (ccache): Update to 3.3.3.
 2016-10-30 00:05:26 +03:00
Efraim Flashner 7dd55dfeca
gnu: python-waf: Update to 1.9.5. 
* gnu/packages/python.scm (python-waf): Update to 1.9.5.
[arguments]: Shorten custom build phase.
[source]: Use http.
[home-page]: Use http.
 2016-10-30 00:05:13 +03:00
Efraim Flashner 603d55de4a
gnu: ffmpeg: Update to 3.2. 
* gnu/packages/video.scm (ffmpeg): Update to 3.2.
 2016-10-29 22:16:44 +03:00
Efraim Flashner 0b37c4cda7
gnu: vapoursynth: Update to 35. 
* gnu/packages/video.scm (vapoursynth): Update to 35.
 2016-10-29 22:16:44 +03:00
Efraim Flashner 812de5bf1e
gnu: offlineimap: Update to 7.0.9. 
* gnu/packages/mail.scm (offlineimap): Update to 7.0.9.
 2016-10-29 22:16:43 +03:00
Efraim Flashner 4d73cb5441
gnu: chess: Update to 6.2.4. 
* gnu/packages/games.scm (chess): Update to 6.2.4.
[home-page]: Use https.
 2016-10-29 22:16:42 +03:00
Marius Bakke a7e75125c8
gnu: vim: Update to 8.0.0054. 
* gnu/packages/vim.scm (vim): Update to 8.0.0054.
 2016-10-29 20:04:57 +01:00
Tobias Geerinckx-Rice dadf6622e9
gnu: borg: Update to 1.0.8. 
* gnu/packages/backup.scm (borg): Update to 1.0.8.
 2016-10-29 14:24:51 +02:00
Tobias Geerinckx-Rice 58c4f11e43
gnu: Add radeontop. 
* gnu/packages/linux.scm (radeontop): New variable.
 2016-10-29 14:19:01 +02:00
Mark H Weaver b8df914f37
gnu: linux-libre: Update to 4.8.5. 
* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.8.5.
 2016-10-28 20:11:20 -04:00
Mark H Weaver a56b3229f4
gnu: linux-libre@4.4: Update to 4.4.28. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.28.
 2016-10-28 20:09:02 -04:00
Eric Bavier fba78d18c2
gnu: mumps: Upgrade to 5.0.2. 
* gnu/packages/maths.scm (mumps): Upgrade to 5.0.2.
[arguments]: Properly return boolean from install phase.
 2016-10-28 15:53:32 -05:00
Marius Bakke a9afb956b3
gnu: vim: Update to 8.0.0051. 
* gnu/packages/vim.scm (vim): Update to 8.0.0051.
[source]: Change to github release archive.
 2016-10-28 20:55:09 +01:00
Leo Famulari 0df955401f
Merge branch 'master' into core-updates 2016-10-28 13:59:32 -04:00
Leo Famulari 044ac8d294
gnu: python-twobitreader: Update to 3.1.4. 
* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader):
Update to 3.1.4.
 2016-10-28 13:59:11 -04:00
Leo Famulari 900fb8d005
gnu: python-twobitreader: Disable the test suite. 
The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-twobitreader to fail.

* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader)[arguments]: Disable the tests.
 2016-10-28 13:59:11 -04:00
Roel Janssen ed8bc028f7
gnu: Add emacs-org-trello. 
* gnu/packages/emacs.scm (emacs-org-trello): New variable.
 2016-10-28 19:50:32 +02:00
Leo Famulari a6447e7fb6
Merge branch 'master' into core-updates 2016-10-28 13:40:17 -04:00
Leo Famulari e359b31a60
gnu: python-wsgiproxy2: Disable the test suite. 
* gnu/packages/python.scm (python-wsgiproxy2, python2-wsgiproxy2)[arguments]:
Disable the tests.
 2016-10-28 13:39:38 -04:00
Leo Famulari 67fd4a12cb
gnu: python-beautifulsoup4: Update to 4.5.1. 
* gnu/packages/python.scm (python-beautifulsoup4, python2-beautifulsoup4):
Update to 4.5.1.
 2016-10-28 13:39:38 -04:00
Leo Famulari 5f37f0b66e
gnu: python-beautifulsoup4: Run the test suite. 
* gnu/packages/python.scm (python-beautifulsoup4)[arguments]: Add field
run python-2 -> python-3 conversion script and test suite.
(python2-beautifulsoup4)[arguments]: Specify use of python-2.
 2016-10-28 13:39:37 -04:00
Leo Famulari 92c3ef2cf3
gnu: python-feedparser: Disable the test suite. 
The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-feedparser to fail.

* gnu/packages/python.scm (python-feedparser, python2-feedparser)[arguments]:
Disable the tests.
 2016-10-28 13:39:37 -04:00
Leo Famulari 95bff4f697
gnu: libwebp: Fix CVE-2016-9085. 
* gnu/packages/patches/libwebp-CVE-2016-9085.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/image.scm (libwebp)[source]: Use it.
 2016-10-28 13:39:37 -04:00
Leo Famulari b2ed5ca7aa
gnu: libwebp: Update to 0.5.1. 
* gnu/packages/image.scm (libwebp): Update to 0.5.1.
 2016-10-28 13:39:33 -04:00
Roel Janssen 36e5d10387
gnu: Add emacs-request. 
* gnu/packages/emacs.scm (emacs-request): New variable.
 2016-10-28 19:29:35 +02:00
Thomas Danckaert fc381a3325
gnu: Add qwt. 
* gnu/packages/qt.scm (qwt): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2016-10-28 14:47:36 +01:00
宋文武 aa98b3b273
gnu: gxmessage: Don't install 'icon-theme.cache'. 
* gnu/packages/gxmessage.scm (gxmessage)[arguments]: Add
'skip-gtk-update-icon-cache' phase.
[native-inputs]: Remove gtk+:bin.
 2016-10-28 21:04:11 +08:00
Mark H Weaver 3b6f8b579b
gnu: python-parse: Fix patch file name in gnu/local.mk. 
This is a followup to commit aa6c09ed71.

* gnu/local.mk (dist_patch_DATA):
"python-python-parse-too-many-fields.patch" =>
"python-parse-too-many-fields.patch".
 2016-10-27 20:31:19 -04:00
Mark H Weaver 3d82676919
Merge branch 'master' into core-updates 2016-10-27 20:21:26 -04:00
Efraim Flashner f9a65318dd
gnu: python-parse: Use 'modify-phases' syntax. 
* gnu/packages/python.scm (python-parse)[arguments]: Use 'modify-phases'
syntax.
 2016-10-27 23:29:56 +03:00
Efraim Flashner aa6c09ed71
gnu: python-parse: Fix failing test. 
* gnu/packages/python.scm (python-parse)[origin]: Add patch.
* gnu/packages/patches/python-parse-too-many-fields.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-10-27 23:28:07 +03:00
Efraim Flashner d18c69aa2a
gnu: python-pytest-django: Add missing test input. 
* gnu/packages/django.scm (python-pytest-django)[native-inputs]: Add
python-django.
 2016-10-27 22:27:31 +03:00
Efraim Flashner fa7cd33378
gnu: python-django-filter: Add inputs for tests. 
* gnu/packages/django.scm (python-django-filter)[native-inputs]: Add
python-django, python-mock.
 2016-10-27 22:18:30 +03:00
Efraim Flashner 13c4d8746b
gnu: python-wtforms: Skip optional tests. 
* gnu/packages/python.scm (python-wtforms)[arguments]: Add a phase
preventing tests from failing when optional tests aren't run.
 2016-10-27 22:13:22 +03:00
Efraim Flashner b6e0804953
gnu: lightning: Add missing input. 
* gnu/packages/assembly.scm (lightning)[native-inputs]: Add zlib.
 2016-10-27 21:13:05 +03:00
Roel Janssen 7500e42b3e
gnu: Add r-mutationalpatterns. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
 2016-10-27 20:07:05 +02:00
Efraim Flashner 377bfbc1f8
gnu: gxmessage: Add missing input. 
* gnu/packages/gxmessage.scm (gxmessage)[native-inputs]: Add gtk+3-bin.
 2016-10-27 21:03:08 +03:00
Efraim Flashner 327be74720
gnu: jasper: Updat eto 1.900.16. 
* gnu/packages/image.scm (japer): Update to 1.900.16.
 2016-10-27 20:14:17 +03:00
Kei Kebreau 233fbb6102
gnu: windowmaker: Add support for more image formats. 
* gnu/packages/gnustep.scm (windowmaker)[inputs]: Add giflib, libpng,
and libtiff.
 2016-10-27 10:51:05 -04:00
Roel Janssen b5ce25cc0e
gnu: r: Use uname from Guix 
* gnu/packages/statistics.scm (r): Use uname from Guix.
 2016-10-27 16:37:24 +02:00
Marius Bakke 6178274d19
gnu: python-urllib3: Update to 1.18.1. 
* gnu/packages/python.scm (python-urllib3): Update to 1.18.1.
[home-page]: Use https URL.
 2016-10-27 14:03:07 +01:00
Ludovic Courtès 245cc5f5d5
tests: Test installation with a RAID root partition. 
* gnu/tests/install.scm (%raid-root-os, %raid-root-os-source)
(%raid-root-installation-script, %test-raid-root-os): New variables.
 2016-10-27 13:48:52 +02:00
Ludovic Courtès 49baaff4d2
file-systems: 'disk-partitions' detected partitions from mapped devices. 
Previously, partitions of mdadm- or cryptsetup-produced block devices
would not be returned by 'disk-partitions'.

* gnu/build/file-systems.scm (disk-partitions)[last-character]: New
procedure.
[partition?]: Add 'name' parameter and rewrite.  Adjust caller.
* gnu/build/file-systems.scm (ENOENT-safe): Silently ignore ENOMEDIUM.
 2016-10-27 13:48:52 +02:00
Ludovic Courtès b800b8da21
tests: Add #:memory-size parameter for the command to run the installed OS. 
* gnu/tests/install.scm (qemu-command/writable-image): Add #:memory-size
parameter and honor it.
 2016-10-27 13:48:52 +02:00
Ludovic Courtès 4ed2f515d6
mapped-devices: Use 'mdadm-static' in 'raid-device-mapping'. 
* gnu/system/mapped-devices.scm (open-raid-device, close-raid-device):
Use MDADM-STATIC instead of MDADM.  Use 'file-append'.
 2016-10-27 13:48:52 +02:00
Ludovic Courtès 631fda7e90
gnu: Add mdadm-static. 
* gnu/packages/linux.scm (mdadm-static): New variable.
 2016-10-27 13:48:52 +02:00
Efraim Flashner 7d876afdd8
gnu: libmikmod: Update to 3.3.10. 
* gnu/packages/sdl.scm (libmikmod): Update to 3.3.10.
 2016-10-27 12:23:04 +03:00
Efraim Flashner 355d8e873b
gnu: sdl2: Update to 2.0.5. 
* gnu/packages/sdl.scm (sdl2): Update to 2.0.5.
 2016-10-27 12:23:04 +03:00
Efraim Flashner 5d5790ce44
gnu: Use 'https' for libsdl urls. 
* gnu/packages/sdl.scm (sdl, sdl2, sdl-image, sdl-mixer, sdl-net)
(sdl-ttf, sdl2-image, sdl2-ttf)[source]: Use https.
[home-page]: Use https.
 2016-10-27 12:23:03 +03:00
Tobias Geerinckx-Rice 483b7ce7ae
gnu: mcelog: Update to 144. 
* gnu/packages/linux.scm (mcelog): Update to 144.
 2016-10-27 11:03:34 +02:00
Tobias Geerinckx-Rice 6270769dc2
gnu: btrfs-progs: Update to 4.8.2. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.8.2.
 2016-10-27 11:03:34 +02:00
Mike Gerwitz cd9ed6c1cb
gnu: gnupg: Add support for pcsc-lite. 
* gnu/packages/gnupg.scm (gnupg)[inputs]: Add pcsc-lite.
[arguments]: Rename phase 'patch-config-files' to 'patch-paths'.  Patch
`scd/scdaemon.c' with absolute path of libpcsclite.so.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2016-10-27 09:56:54 +01:00
Mike Gerwitz a6b256affc
gnu: Add pcsc-lite. 
* gnu/packages/security-token.scm (pcsc-lite): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2016-10-27 09:56:52 +01:00
ng0 8888fe826c
gnu: Add dbacl. 
* gnu/packages/textutils.scm (dbacl): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-10-27 11:42:39 +03:00
Efraim Flashner 5fd84e288c
gnu: valgrind: Use 'modify-phases' syntax. 
* gnu/packages/valgrind.scm (valgrind)[arguments]: Use 'modify-phases'
syntax.
 2016-10-27 11:42:38 +03:00
Efraim Flashner e68168eb87
gnu: valgrind: Update to 3.12.0. 
* gnu/packages/valgrind.scm (valgrind): Update to 3.12.0.
 2016-10-27 11:42:29 +03:00
Hartmut Goebel 49a531f545
gnu: python-pathlib2: Add comment. 
As suggested by Efraim Flashner.

* gnu/packages/python.scm (python-pathlib2): Add comment.
 2016-10-27 10:09:10 +02:00
Leo Famulari f02fb6dd6b
gnu: btrfs-progs: Update to 4.8.2. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.8.2.
 2016-10-27 00:43:37 -04:00
Leo Famulari 9045c086df
gnu: blender: Update to 2.78a. 
* gnu/packages/graphics.scm (blender): Update to 2.78a.
 2016-10-27 00:30:47 -04:00
Leo Famulari fad8bf977d
gnu: python-s3transfer: Run the tests. 
* gnu/packages/python.scm (python-s3transfer, python2-s3transfer)[arguments]:
Use python-nose to run the tests.
[native-inputs]: Add python-mock and python-nose.
 2016-10-26 21:41:28 -04:00
Leo Famulari 522fc32ebd
gnu: shotwell: Update to 0.25.0. 
* gnu/packages/gnome.scm (shotwell): Update to 0.25.0.
[inputs]: Add gcr.
 2016-10-26 20:10:05 -04:00
Leo Famulari 30b1267830
gnu: vdirsyncer: Update to 0.14.0. 
* gnu/packages/dav.scm (vdirsyncer): Update to 0.14.0.
 2016-10-26 19:56:15 -04:00
Ludovic Courtès 5479aa2b7c
tests: Test installation with store on a separate partition. 
This is a followup to 0f65f54ebd.

* gnu/tests/install.scm (%separate-store-os, %separate-store-os-source)
(%separate-store-installation-script, %test-separate-store-os): New
variables.
 2016-10-27 01:00:42 +02:00
Leo Famulari 02c73adcdf
Merge branch 'master' into core-updates 2016-10-26 19:00:06 -04:00
Leo Famulari a19da40630
gnu: perl-www-curl: Fix build failure. 
* gnu/packages/patches/perl-www-curl-remove-symbol.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/web.scm (perl-www-curl)[source]: Use it.
 2016-10-26 18:44:16 -04:00
ng0 5d73e30000
gnu: Add lci. 
* gnu/packages/lolcode.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-10-26 20:39:27 +03:00
Christopher Allan Webber 8caeb11772
gnu: Add autossh. 
* gnu/packages/ssh.scm (autossh): New variable.
 2016-10-26 11:22:17 -05:00
Ricardo Wurmus aba6463975
gnu: r: Update to 3.3.1. 
* gnu/packages/statistics.scm (r): Update to 3.3.1.
 2016-10-26 18:14:17 +02:00
Ricardo Wurmus a8e893b0b8
gnu: r-matrixstats: Update to 0.51.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.51.0.
 2016-10-26 16:23:32 +02:00
Ricardo Wurmus fd54f65e72
gnu: r-r-utils: Update to 2.4.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.4.0.
 2016-10-26 16:23:32 +02:00
Ricardo Wurmus 89242ea47f
gnu: r-irlba: Update to 2.1.2. 
* gnu/packages/statistics.scm (r-irlba): Update to 2.1.2.
 2016-10-26 16:23:31 +02:00
Ricardo Wurmus 4f2ebc16ce
gnu: r-codetools: Update to 0.2-15. 
* gnu/packages/statistics.scm (r-codetools): Update to 0.2-15.
 2016-10-26 16:23:31 +02:00
Ricardo Wurmus cf738e961e
gnu: r-snow: Update to 0.4-2. 
* gnu/packages/statistics.scm (r-snow): Update to 0.4-2.
 2016-10-26 16:23:31 +02:00
Ricardo Wurmus 41bc22a7de
gnu: r-backports: Update to 1.0.4. 
* gnu/packages/statistics.scm (r-backports): Update to 1.0.4.
 2016-10-26 16:23:30 +02:00
Ricardo Wurmus 72263db73d
gnu: r-foreign: Update to 0.8-67. 
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-67.
 2016-10-26 16:23:30 +02:00
Ricardo Wurmus 130410d941
gnu: r-cluster: Update to 2.0.5. 
* gnu/packages/statistics.scm (r-cluster): Update to 2.0.5.
 2016-10-26 16:23:29 +02:00
Ricardo Wurmus e7622804aa
gnu: r-acepack: Update to 1.4.0. 
* gnu/packages/statistics.scm (r-acepack): Update to 1.4.0.
 2016-10-26 16:23:29 +02:00
Ricardo Wurmus bff4dc6324
gnu: r-r6: Update to 2.2.0. 
* gnu/packages/statistics.scm (r-r6): Update to 2.2.0.
 2016-10-26 16:23:29 +02:00
Ricardo Wurmus e0a9093139
gnu: r-evaluate: Update to 0.10. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.10.
 2016-10-26 16:23:28 +02:00
Ricardo Wurmus 2d9da70bbe
gnu: r-reshape2: Update to 1.4.2. 
* gnu/packages/statistics.scm (r-reshape2): Update to 1.4.2.
 2016-10-26 16:23:28 +02:00
Ricardo Wurmus c2a9e99134
gnu: r-stringi: Update to 1.1.2. 
* gnu/packages/statistics.scm (r-stringi): Update to 1.1.2.
 2016-10-26 16:23:28 +02:00
Ricardo Wurmus 03f72a1e1f
gnu: r-matrix: Update to 1.2-7.1. 
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-7.1.
 2016-10-26 16:23:27 +02:00
Ricardo Wurmus 9e087a1fde
gnu: r-colorspace: Update to 1.2-7. 
* gnu/packages/statistics.scm (r-colorspace): Update to 1.2-7.
 2016-10-26 16:23:27 +02:00
Ricardo Wurmus e1c2b7e2e1
gnu: r-jsonlite: Update to 1.1. 
* gnu/packages/web.scm (r-jsonlite): Update to 1.1.
 2016-10-26 16:23:27 +02:00
Ricardo Wurmus 2ffcd6607b
gnu: r-curl: Update to 2.2. 
* gnu/packages/web.scm (r-curl): Update to 2.2.
 2016-10-26 16:23:26 +02:00
Ricardo Wurmus a46cc723ff
gnu: r-seqinr: Update to 3.3-3. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
 2016-10-26 16:23:26 +02:00
Ricardo Wurmus 062737a178
gnu: r-rcpparmadillo: Update to 0.7.500.0.0. 
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to
7.500.0.
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.500.0.0.
 2016-10-26 16:23:25 +02:00
Ricardo Wurmus 7397cd9e3f
gnu: armadillo: Update to 7.500.0. 
* gnu/packages/maths.scm (armadillo): Update to 7.500.0.
 2016-10-26 16:23:25 +02:00
Ricardo Wurmus 8e1369f19a
gnu: r-rmarkdown: Update to 1.1. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.1.
[propagated-inputs]: Add r-evaluate, r-tibble.
 2016-10-26 16:23:25 +02:00
Ricardo Wurmus c70271ec48
gnu: bioperl-minimal: Update to 1.7.0. 
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
 2016-10-26 16:23:24 +02:00
Marius Bakke 39df253e2b
gnu: mupdf: Modify CVE-2016-8674 patch to apply to 1.9a. 
The fix from upstream did not apply cleanly due to many context changes.
This was adapted by cloning mupdf 1.9a from git and fixing conflicts
after applying our patches and cherry-picking upstream commit 1e03c06.

This is a follow-up to 47a04fca99.

* gnu/packages/patches/mupdf-CVE-2016-8674.patch: Adapt to 1.9a.
 2016-10-26 15:03:42 +01:00
ng0 b2a2232c33
gnu: python-certifi: Update to 2016.8.31. 
* gnu/packages/python.scm (python-certifi): Update to 2016.8.31.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-10-26 14:31:16 +03:00
Marius Bakke 07b1fb8675
gnu: security-token: Use 'license:' prefix. 
* gnu/packages/security-token.scm (libyubikey)[license]: Add prefix.
(ykclient)[license]: Add prefix.
 2016-10-26 11:00:58 +01:00
Marius Bakke f9c339603d
gnu: yubico.scm: Rename to security-token.scm. 
* gnu/packages/yubico.scm: Delete file.
* gnu/packages/security-token.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
 2016-10-26 10:45:49 +01:00
Marius Bakke 7a6213cbd7
gnu: offlineimap: Install documentation. 
* gnu/packages/mail.scm (offlineimap)[native-inputs]: Add asciidoc and
libxslt.
[arguments]: Add phases 'build-documentation' and
'install-documentation' to build and install manpages. Also remove
unneeded key 'inputs' from 'wrap-binary' phase.
 2016-10-26 10:45:49 +01:00
Marius Bakke d2a9b531fb
gnu: notmuch: Update to 0.23.1. 
* gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch: Delete
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/mail.scm (notmuch): Update to 0.23.1. Remove patch.
 2016-10-26 10:45:49 +01:00
Efraim Flashner 8f5f6c922f
gnu: vlc: Add x265 support. 
* gnu/packages/video.scm (vlc)[inputs]: Add x265.
 2016-10-26 12:19:19 +03:00
Efraim Flashner e3cb00d210
gnu: gst-plugins-bad: Add x265 support. 
* gnu/packages/gstreamer.scm (gst-plugins-bad)[inputs]: Add x265.
 2016-10-26 12:19:18 +03:00
Efraim Flashner d505801a06
gnu: ffmpeg: Add x265 support. 
* gnu/packages/video.scm (ffmpeg)[inputs]: Add x265.
[arguments]: Add '--enable-libx265' flag.
 2016-10-26 12:19:18 +03:00
Efraim Flashner 7bc7ffc243
gnu: Add x265. 
* gnu/packages/video.scm (x265): New variable.
 2016-10-26 12:19:18 +03:00
ng0 1df790d50d
gnu: Add psyclpc. 
* gnu/packages/psyc.scm (psyclpc): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-10-26 11:29:35 +03:00
Ludovic Courtès 19262a718e
gnu: opensmtpd: Fix 'license' field. 
* gnu/packages/mail.scm (opensmtpd)[license]: Use LICENSE:OPENSSL, not
OPENSSL.
(opensmtpd-extras)[license]: Likewise.
 2016-10-26 10:19:18 +02:00
Ricardo Wurmus 59198f8fff
gnu: r-genomationdata: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus e357bec836
gnu: r-bamsignals: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus 53ca52f013
gnu: r-rhtslib: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0.
[native-inputs]: Add autoconf.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus da22da862b
gnu: r-zlibbioc: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 809251e164
gnu: r-motifrg: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 21d6c7a3e1
gnu: r-seqlogo: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 51c3c4900f
gnu: r-genomation: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0.
[propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors.
[inputs]: Add zlib.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus e92dd6f5e0
gnu: r-seqpattern: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0.
[propagated-inputs]: Add r-kernsmooth.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus acf6f7e0c3
gnu: r-impute: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus 3d74c04451
gnu: r-bsgenome: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
 2016-10-26 09:28:20 +02:00
Ricardo Wurmus 30ec4de738
gnu: r-topgo: Update to 2.26.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0.
[propagated-inputs]: Add r-dbi.
 2016-10-26 09:28:20 +02:00
Ricardo Wurmus 3587b464fc
gnu: r-graph: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
 2016-10-26 09:28:19 +02:00
Ricardo Wurmus d1b1587cad
gnu: r-go-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
 2016-10-26 09:28:19 +02:00
Ricardo Wurmus b17aac083e
gnu: r-genomicfeatures: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 6a45fd9aea
gnu: r-rtracklayer: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 4ab32f0cd6
gnu: r-genomicalignments: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.10.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 08da08d296
gnu: r-summarizedexperiment: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.4.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus c0ccef41ae
gnu: r-rsamtools: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 47d39b6e7a
gnu: r-biostrings: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 89559a124e
gnu: r-biocparallel: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 9405333186
gnu: r-biomart: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus e45dc05781
gnu: r-annotationdbi: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 464870caf7
gnu: r-biobase: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 92a740afac
gnu: r-genomicranges: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1.
[propagated-inputs]: Add r-iranges, r-s4vectors.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 1d048589ca
gnu: r-xvector: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 753bc32b8e
gnu: r-limma: Update to 3.30.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 37d96f1dde
gnu: r-variantannotation: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.20.0.
[propagated-inputs]: Add r-biobase, r-biostrings, r-iranges,
r-rtracklayer, r-s4vectors, r-xvector.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 5e48005fa9
gnu: r-edger: Update to 3.16.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0.
[propagated-inputs]: Add r-locfit.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus dece310a25
gnu: r-genomeinfodb: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 7f354dafb1
gnu: r-iranges: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus b120c5f3a2
gnu: r-s4vectors: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 22c5d736af
gnu: r-dnacopy: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus 5c7b04e0c3
gnu: r-biocinstaller: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus f0b297e17b
gnu: r-biocgenerics: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus c9b5046a18
gnu: r-grohmm: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus 1265d3877b
gnu: r-systempiper: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus b87b41a74d
gnu: r-shortread: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus ae6899b683
gnu: r-gostats: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus 816599c1e7
gnu: r-category: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus 558d02c361
gnu: r-gseabase: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0.
 2016-10-26 09:28:09 +02:00