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9388 Commits

Author SHA1 Message Date
Ricardo Wurmus c6a24d6e92 gnu: Add smithlab-cpp. 
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
 2015-11-20 15:22:06 +01:00
Ricardo Wurmus 3d51ec919e gnu: edirect: Update home page. 
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
  slash to home page.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus c52a382c4a gnu: sra-tools: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 9e5ef614aa gnu: ncbi-vdb: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 614a8977cb gnu: ngs-java: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus d6a1cd7cae gnu: ngs-sdk: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 2c84ba7e11 gnu: Add ruby-net-ssh. 
* gnu/packages/ruby.scm (ruby-net-ssh): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 4f2a52aeb5 gnu: Add ruby-mocha. 
* gnu/packages/ruby.scm (ruby-mocha): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus d93062fd5c gnu: Add ruby-redcarpet. 
* gnu/packages/ruby.scm (ruby-redcarpet): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 97aee8d3eb gnu: Add ruby-introspection. 
* gnu/packages/ruby.scm (ruby-introspection): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 4016ba3fd0 gnu: Add ruby-instantiator. 
* gnu/packages/ruby.scm (ruby-instantiator): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 21f7b7bd80 gnu: Add ruby-blankslate. 
* gnu/packages/ruby.scm (ruby-blankslate): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 25d6d49b3e gnu: Add ruby-metaclass. 
* gnu/packages/ruby.scm (ruby-metaclass): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 3383f5bdab gnu: Add ruby-test-unit. 
* gnu/packages/ruby.scm (ruby-test-unit): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus cc5aeb8c7d gnu: Add ruby-packnga. 
* gnu/packages/ruby.scm (ruby-packnga): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus c1f52261e2 gnu: Add ruby-gettext. 
* gnu/packages/ruby.scm (ruby-gettext): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus e2333ea391 gnu: Add ruby-text. 
* gnu/packages/ruby.scm (ruby-text): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 347eb21e1d gnu: Add ruby-locale. 
* gnu/packages/ruby.scm (ruby-locale): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus f88bacaf6f gnu: Add ruby-power-assert. 
* gnu/packages/ruby.scm (ruby-power-assert): New variable.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 9641a89957 gnu: bless: Build only for x86_64. 
* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
 2015-11-20 11:32:32 +01:00
Ricardo Wurmus 0536727efe gnu: htseq: Propagate numpy. 
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
  from here ...
[propagated-inputs]: ... to here.
 2015-11-20 11:32:32 +01:00
Ricardo Wurmus dffdef0f0f gnu: ant: Update to 1.9.6. 
* gnu/packages/java.scm (ant): Update to 1.9.6.
 2015-11-20 11:32:32 +01:00
Ludovic Courtès b2a72238b9 gnu: guix: Update development snapshot to 5c36edc. 
* gnu/packages/package-management.scm (guix-devel): Update to 5c36edc.
 2015-11-19 22:33:01 +01:00
Ludovic Courtès 5c36edc818 doc: Mention fonts for Asian languages. 
Suggested by Alex Vong <alexvong1995@gmail.com>.

* doc/guix.texi (Application Setup): Explain how to install X11 fonts
  for Asian languages.
 2015-11-19 17:39:48 +01:00
Ludovic Courtès 28d939af0e doc: Update documentation of the 'services' field. 
* doc/guix.texi (operating-system Reference): The 'services' field now
  contains a list of service objects.
 2015-11-19 17:39:48 +01:00
Ricardo Wurmus bc8bf605fc gnu: jack-2: Fix jack_control script. 
* gnu/packages/audio.scm (jack-2)[inputs]: Add python2-dbus.
[arguments]: Use python-2 and add build phase to wrap jack_control
Python script.
 2015-11-19 16:10:52 +01:00
Ricardo Wurmus 80e6f37e30 services: Add udev-rule procedure. 
* gnu/services/base.scm (udev-rule): New procedure.
(kvm-udev-rule): Rewrite as variable in terms of udev-rule.
 2015-11-19 16:10:52 +01:00
Eric Bavier c3c61a781c gnu: ghc-unordered-containers: Enable tests. 
* gnu/packages/haskell.scm (ghc-unordered-containers)
  [arguments]: Remove.
  [inputs]: Add ghc-chasingbottoms, ghc-test-framework,
  ghc-test-framework-hunit, and ghc-test-framework-quickcheck2.
 2015-11-19 03:13:20 -06:00
Eric Bavier 4eca62be49 gnu: Add ghc-chasingbottoms. 
* gnu/packages/haskell.scm (ghc-chasingbottoms): New variable.
 2015-11-19 03:13:20 -06:00
Eric Bavier 19206f5eb8 gnu: ghc-attoparsec: Enable tests. 
* gnu/packages/haskell.scm (ghc-attoparsec)[arguments]: Remove.
  [inputs]: Add ghc-quickcheck, ghc-quickcheck-unicode,
  ghc-test-framework, and ghc-test-framework-quickcheck2.
 2015-11-19 03:13:19 -06:00
Eric Bavier ab715ec9ae gnu: Add ghc-test-framework-quickcheck2. 
* gnu/packages/haskell.scm (ghc-test-framework-quickcheck2): New
  variable.
 2015-11-19 03:13:19 -06:00
Eric Bavier e1c1b71c38 gnu: ghc-async: Enable tests. 
* gnu/packages/haskell.scm (ghc-async)[arguments]: Remove.
  [inputs]: Add ghc-hunit, ghc-test-framework, and
  ghc-test-framework-hunit.
 2015-11-19 03:13:19 -06:00
Eric Bavier 0eeaa169a0 gnu: ghc-regex-posix: Propagate inputs. 
* gnu/packages/haskell.scm (ghc-regex-posix): Propagate ghc-regex-base
  input.
 2015-11-19 03:13:19 -06:00
Eric Bavier 1fe25c573a gnu: Add ghc-test-framework-hunit. 
* gnu/packages/haskell.scm (ghc-test-framework-hunit): New variable.
 2015-11-19 03:13:19 -06:00
Eric Bavier 09655c676b gnu: Add ghc-test-framework. 
* gnu/packages/haskell.scm (ghc-test-framework): New variable.
 2015-11-19 03:13:19 -06:00
Eric Bavier 1472ba2546 gnu: Add ghc-libxml. 
* gnu/packages/haskell.scm (ghc-libxml): New variable.
 2015-11-19 03:13:19 -06:00
Eric Bavier ccd7b30872 gnu: Add ghc-hostname. 
* gnu/packages/haskell.scm (ghc-hostname): New variable.
 2015-11-19 03:13:19 -06:00
Efraim Flashner d2a5210844 gnu: tilda: Update to 1.3.0. 
* gnu/packages/terminals.scm (tilda): Update to 1.3.0.
[inputs]: Switch vte from 0.36 to 0.40, remove zip.
 2015-11-19 14:45:45 +02:00
Efraim Flashner e30be98653 gnu: youtube-dl: Update to 2015.11.18. 
* gnu/packages/video.scm (youtube-dl): Update to 2015.11.18.
 2015-11-19 09:48:41 +02:00
Mark H Weaver 3470fe002c gnu: libsndfile: Add fixes for CVE-2014-9496 and CVE-2015-7805. 
* gnu/packages/patches/libsndfile-CVE-2014-9496.patch,
  gnu/packages/patches/libsndfile-CVE-2015-7805.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/pulseaudio.scm (libsndfile)[source]: Add patches.
 2015-11-18 17:47:40 -05:00
Mark H Weaver b4a88dc25f gnu: libxslt: Add fix for CVE-2015-7995. 
* gnu/packages/patches/libxslt-CVE-2015-7995.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/xml.scm (libxslt)[source]: Add patch.
 2015-11-18 17:47:40 -05:00
Mark H Weaver ee6bb0cc76 gnu: libxml2: Add fixes for CVE-2015-{1819,7941,7942,8035} and other bugs. 
* gnu/packages/patches/libxml2-CVE-2015-1819.patch,
  gnu/packages/patches/libxml2-CVE-2015-7941-pt1.patch,
  gnu/packages/patches/libxml2-CVE-2015-7941-pt2.patch,
  gnu/packages/patches/libxml2-CVE-2015-7942-pt1.patch,
  gnu/packages/patches/libxml2-CVE-2015-7942-pt2.patch,
  gnu/packages/patches/libxml2-CVE-2015-8035.patch,
  gnu/packages/patches/libxml2-bug-737840.patch,
  gnu/packages/patches/libxml2-bug-738805.patch,
  gnu/packages/patches/libxml2-bug-746048.patch,
  gnu/packages/patches/libxml2-bug-747437.patch,
  gnu/packages/patches/libxml2-bug-751603.patch,
  gnu/packages/patches/libxml2-bug-751631.patch,
  gnu/packages/patches/libxml2-bug-754946.patch,
  gnu/packages/patches/libxml2-bug-754947.patch,
  gnu/packages/patches/libxml2-bug-755857.patch,
  gnu/packages/patches/libxml2-fix-catalog-corruption.patch,
  gnu/packages/patches/libxml2-id-attrs-in-xmlSetTreeDoc.patch,
  gnu/packages/patches/libxml2-node-sort-order-pt1.patch,
  gnu/packages/patches/libxml2-node-sort-order-pt2.patch: New files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/xml.scm (libxml2)[source]: Add patches.
 2015-11-18 17:47:40 -05:00
Mark H Weaver 328a14e869 gnu: libpng: Update to 1.5.24 [fixes CVE-2015-8126]. 
* gnu/packages/image.scm (libpng): Update to 1.5.24.
 2015-11-18 17:47:40 -05:00
Mark H Weaver 21ef9843e4 Revert "gnu: libpng: Use 1.5.24 as a replacement [fixes CVE-2015-8126]." 
This reverts commit 1b076e630f.
 2015-11-18 17:47:17 -05:00
Ricardo Wurmus c797fabe79 services: Export udev-configuration procedures. 
* gnu/services/base.scm (udev-configuration, udev-configuration?,
  udev-configuration-rules): Export.
 2015-11-18 22:04:48 +01:00
Ludovic Courtès 7be4a4b0ae gnu: weechat: Fix patching of assignments to 'python2_bin'. 
Fixes a regression introduced in a9346fa.

* gnu/packages/weechat.scm (weechat)[arguments]: Make sure PYTHON2_BIN
  can be freed with 'free'.
 2015-11-18 18:01:50 +01:00
Ludovic Courtès b567abcf1a gnu: weechat: Encode as UTF-8. 
* gnu/packages/weechat.scm: Reencode as UTF-8.
 2015-11-18 18:01:30 +01:00
Ludovic Courtès a9346faee6 gnu: weechat: Record the absolute file name of 'python'. 
Fixes <http://bugs.gnu.org/21879>.
Reported by Luis Felipe López Acevedo <felipe.lopez@openmailbox.org>.

* gnu/packages/weechat.scm (weechat)[arguments]: Add
  'set-python-file-name' phase.
 2015-11-18 17:47:09 +01:00
Ludovic Courtès e33cf9a69a gnu: weechat: Use 'modify-phases'. 
* gnu/packages/weechat.scm (weechat)[arguments]: Use 'modify-phases'.
  Remove 'fix-file' phase.
 2015-11-18 17:47:09 +01:00
Mark H Weaver f4a4a71885 gnu: python-tornado: Use the preferred home-page. 
* gnu/packages/python.scm (python-tornado)[home-page]: Use the preferred
  one.
 2015-11-18 09:45:47 -05:00