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Author SHA1 Message Date
Ricardo Wurmus 3acb8c857c gnu: deeptools: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
 2016-03-03 13:47:12 +01:00
Ricardo Wurmus 14bda1ff49 gnu: deeptools: Change "propagated-inputs" to "inputs". 
* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
 2016-03-03 13:47:02 +01:00
Ricardo Wurmus 69e0e03c36 gnu: Add python-pybigwig. 
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
  New variables.
 2016-03-03 13:46:52 +01:00
Ricardo Wurmus d454640c38 gnu: python-pysam: Update to 0.8.4. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
 2016-03-03 13:46:39 +01:00
Ricardo Wurmus 55a9a8c2b9 gnu: python-pysam, python2-pysam: Move to bioinformatics.scm. 
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
  ...here.
 2016-03-03 13:46:26 +01:00
Lukas Gradl e90819c40a gnu: Add procmail. 
* gnu/packages/patches/procmail-ambiguous-getline-debian.patch: New file.
 * gnu-system.am (dist_patch_DATA): Add it.
 * gnu/packages/mail.scm (procmail): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-03-02 20:44:18 -05:00
Mathieu Lirzin 1b846da8c3 utils: Use '@' for separating package names and version numbers. 
This provides the ability to use numbers in package names.

Fixes <http://bugs.gnu.org/19219>.

* guix/utils.scm (package-name->name+version): New procedure.
* gnu/packages.scm (%find-package): Add a FALLBACK? keyword argument.
Use the previous method when no package is found.
(specification->package+output, specification->package): Adapt
documentation to new syntax.
* doc/guix.texi (Invoking guix package, Invoking guix import): Likewise.
* guix/ui.scm (package-specification->name+version+output): Likewise.
* guix/scripts/import/hackage.scm (show-help): Likewise.
* tests/guix-build.sh: Adapt to new syntax.
* tests/guix-lint.sh: Likewise.
* tests/guix-package.sh: Likewise.
* tests/ui.scm ("package-specification->name+version+output"): Likewise.
* tests/utils.scm ("package-name->name+version"): Likewise.
* NEWS: Mention new syntax.
 2016-03-02 21:41:41 +01:00
Mathieu Lirzin fad155d47e packages: Factorize package specification search. 
* gnu/packages.scm (%find-package): New procedure.
(specification->package, specification->package+output): Use it.
 2016-03-02 21:41:41 +01:00
Mark H Weaver b134a80c36 gnu: icecat: Update bundled graphite2 to 1.3.6 [unspecified security fixes]. 
* gnu/packages/patches/icecat-update-graphite2-pt2.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add patch.
 2016-03-02 15:13:15 -05:00
Mark H Weaver bd009cd95d gnu: nss: Update to 3.21.1. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.21.1.
 2016-03-02 15:13:14 -05:00
Mark H Weaver d47ad0890c gnu: graphite2: Replace with 1.3.6 [unspecified security fixes]. 
See <https://bodhi.fedoraproject.org/updates/FEDORA-2016-dec1faadc5>

* gnu/packages/fontutils.scm (graphite2)[replacement]: New field.
(graphite2-1.3.6): New variable.
 2016-03-02 15:12:18 -05:00
Jessica Tallon c285a400a2 gnu: Add password-store. 
* gnu/packages/password-utils.scm (password-store): New variable.

Co-authored-by: Andreas Enge <andreas@enge.fr>
Co-authored-by: Leo Famulari <leo@famulari.name>
 2016-03-02 14:18:51 -05:00
Roel Janssen dd6e70f920 gnu: Add cppcheck. 
* gnu/packages/check.scm (cppcheck): New variable.
 2016-03-02 15:17:56 +01:00
Mark H Weaver ed742bc4b4 gnu: openssl: Enable ssl2 at build time to ensure ABI compatible graft. 
Fixes <https://debbugs.gnu.org/22876>
Reported by Christopher Allan Webber <cwebber@dustycloud.org>.

* gnu/packages/tls.scm (openssl-1.0.2g)[arguments]: Override the inherited
  'configure' phase to add "enable-ssl2" as an argument to ./config.
 2016-03-02 01:58:42 -05:00
宋文武 6150b5c780 gnu: xfce: Don't wrap 'startxfce4'. 
The necessary environment variables are set by 'etc/profile' now.

* gnu/packages/xfce.scm (xfce)[build-system]: Use 'trivial-build-system'.
[arguments]: Simplify.
 2016-03-02 08:32:47 +08:00
Leo Famulari 5e8276dcf4 gnu: ilmbase: Add patch to fix build on i686. 
Fixes <http://bugs.gnu.org/22049>.

* gnu/packages/patches/ilmbase-fix-tests.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/graphics.scm (ilmbase)[source]: Add patch.
 2016-03-01 19:08:31 -05:00
Leo Famulari 88ccca45f6 gnu: openssh: Update to 7.2p1. 
* gnu/packages/ssh.scm (openssh): Update to 7.2p1.
 2016-03-01 16:32:41 -05:00
Leo Famulari 599860d2b9 gnu: libressl: Update to 2.2.6. 
* gnu/packages/tls.scm (libressl): Update to 2.2.6.
 2016-03-01 16:30:13 -05:00
Leo Famulari 043c3f0bed gnu: parallel: Update to 20160222. 
* gnu/packages/parallel.scm (parallel): Update to 20160222.
 2016-03-01 15:15:38 -05:00
Pjotr Prins f82c8c3cba gnu: r-go-db: Bioconductor changed URL for data downloads. 
* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
 2016-03-01 19:47:26 +02:00
Pjotr Prins 27acfaea4c gnu: r-iranges: Update to 2.4.8. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
 2016-03-01 19:47:26 +02:00
Pjotr Prins 8921841da8 gnu: r-s4vectors: Update to 0.8.11. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
 2016-03-01 19:47:25 +02:00
Pjotr Prins b70fa3c7f7 gnu: r-ggplot2: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-ggplot2): Update to 2.0.0.
 2016-03-01 19:47:24 +02:00
Ludovic Courtès caeadfddb0 gnu: openssl: Replace with 1.0.2g [fixes CVE-2016-{0800,0705,0798,0797,0799,0702,0703,0704}]. 
See <http://openssl.org/news/secadv/20160301.txt>.
Also fixes <http://bugs.gnu.org/22831>.

* gnu/packages/patches/openssl-c-rehash-in.patch: New file.
* gnu/packages/tls.scm (openssl)[replacement]: New field.
(openssl-1.0.2g): New variable.
 2016-03-01 16:00:46 +01:00
Efraim Flashner d06fc008bd gnu: tiled: Use 'modify-phases'. 
* gnu/packages/game-development.scm (tiled)[arguments]: Use 'modify-phases'.
 2016-03-01 14:55:55 +02:00
Efraim Flashner e8ea01d902 gnu: tiled: Update to 0.15.1. 
* gnu/packages/game-development.scm (tiled): Update to 0.15.1.
 2016-03-01 14:55:55 +02:00
Ricardo Wurmus d1e32822b4 gnu: Add PePr. 
* gnu/packages/bioinformatics.scm (pepr): New variable.
 2016-03-01 11:51:24 +01:00
Ricardo Wurmus d29150b55d gnu: Add bwa-pssm. 
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
 2016-03-01 10:31:04 +01:00
Ricardo Wurmus b4464d384c gnu: Add gdsl. 
* gnu/packages/datastructures.scm (gdsl): New variable.
 2016-03-01 10:30:04 +01:00
Efraim Flashner e288f0075c gnu: weechat: Move to irc.scm. 
* gnu/packages/weechat.scm (weechat): Move from here ...
* gnu/packages/irc.scm (weechat): ... to here.
* gnu/packages/weechat.scm: Delete file.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove weechat.scm.
 2016-03-01 11:09:32 +02:00
Efraim Flashner a61bd6a5e3 gnu: irssi: Use 'modify-phases'. 
* gnu/packages/irc.scm (irssi)[arguments]: Use 'modify-phases'.
 2016-03-01 11:09:32 +02:00
Efraim Flashner 27930f853d gnu: irssi: Move to irc.scm. 
* gnu/packages/irssi.scm (irssi): Move from here ...
* gnu/packages/irc.scm (irssi): ... to here.
* gnu/packages/irssi.scm: Delete file.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove irssi.scm.
 2016-03-01 11:09:32 +02:00
Efraim Flashner 980f058d92 gnu: Add quassel. 
* gnu/packages/irc.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Register it.
 2016-03-01 11:09:32 +02:00
Efraim Flashner 550791b8f1 gnu: Add snorenotify. 
* gnu/packages/kde.scm (snorenotify): New variable.
 2016-03-01 11:09:32 +02:00
Efraim Flashner d34c594aeb gnu: Add qca. 
* gnu/packages/kde.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Register it.
 2016-03-01 11:09:32 +02:00
Efraim Flashner d8ea278204 gnu: Add oxygen-icons. 
* gnu/packages/kde-frameworks.scm (oxygen-icons): New variable.
 2016-03-01 11:09:32 +02:00
Manolis Ragkousis fea1f275bc gnu: Add desmume. 
* gnu/packages/games.scm (desmume): New variable.
 2016-02-29 22:04:53 -05:00
Mark H Weaver 8d5ceb120d gnu: curl: Use updated libssh2 [fixes CVE-2016-7087]. 
* gnu/packages/curl.scm (curl)[inputs]: Use libssh2.
* gnu/packages/ssh.scm (libssh2-1.4): Remove variable.
 2016-02-29 20:09:29 -05:00
Christopher Allan Webber aa5946edb2 gnu: Remove python2-pil. 
python2-pil is vulnerable to several security issues (CVE-2016-0740,
CVE-2016-0775, and CVE-2016-2533).  Fortunately, python2-pillow provides
equivalent functionality, so this package can be cleanly removed.

* gnu/packages/python.scm (python2-pil): Remove variable.
 2016-02-29 15:01:20 -08:00
Ricardo Wurmus daeb61f7a9 gnu: guile-for-guile-emacs: Use guile-2.0 search paths. 
* gnu/packages/guile.scm (guile-for-guile-emacs)[native-search-paths]:
  Use the same search paths as guile-2.0.
 2016-02-29 07:10:40 +01:00
Leo Famulari 823e2ed4b3 gnu: msmtp: Install msmtpq. 
* gnu/packages/mail.scm (msmtp)[arguments]: Install msmtpq scripts.
 2016-02-28 22:06:24 -05:00
Ludovic Courtès 1a59b6d014 gnu: git: Install symlinks instead of hard links. 
This reduces nar size by a factor of 10.
Fixes <http://bugs.gnu.org/21949>.

* gnu/packages/version-control.scm (git)[arguments]: Pass
NO_INSTALL_HARDLINKS as #:make-flags.
 2016-02-28 16:41:53 +01:00
Andreas Enge dbb7a08175 gnu: libwnck: Rename variable for GTK+ 2 variant. 
* gnu/packages/gnome.scm (libwnck-1): Rename this...
  (libwnck-2): ...to this.
* gnu/packages/xfce.scm (xfce4-panel, xfce4-xkb-plugin, xfce4-session,
  xfwm4, xfdesktop)[inputs]: Adapt.
 2016-02-28 15:59:56 +01:00
Efraim Flashner 2236da6e97 gnu: xrandr: Update to 1.5.0. 
* gnu/packages/xorg.scm (xrandr): Update to 1.5.0.
 2016-02-28 14:13:30 +02:00
Efraim Flashner 97a0859593 gnu: libqmi: Update to 1.12.8. 
* gnu/packages/freedesktop.scm (libqmi): Update to 1.12.8.
 2016-02-28 13:42:34 +02:00
Efraim Flashner 9012e118ff gnu: wayland: Update to 1.10.0. 
* gnu/packages/freedesktop.scm (wayland): Update to 1.10.0.
[arguments]: Disable parallel tests.
 2016-02-28 13:32:52 +02:00
Efraim Flashner d3e3d7f02a gnu: libinput: Update to 1.2.0. 
* gnu/packages/freedesktop.scm (libinput): Update to 1.2.0.
 2016-02-28 13:08:08 +02:00
Efraim Flashner a724924beb gnu: python-tornado: Update to 4.3. 
* gnu/packages/python.scm (python-tornado): Update to 4.3.
[native-inputs]: Add python-backports-abc.
(python2-tornado)[inputs]: Add python2-singledispatch.
 2016-02-28 10:53:42 +02:00
Efraim Flashner 6b59fc1020 gnu: Add python-backports-abc. 
* gnu/packages/python.scm (python-backports-abc): New variable.
 2016-02-28 10:53:35 +02:00
Mark H Weaver 9579118922 gnu: bitlbee: Update to 3.4.1. 
* gnu/packages/patches/bitlbee-configure-doc-fix.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/messaging.scm (bitlbee): Update to 3.4.1.
[source]: Remove patch.
 2016-02-27 21:10:56 -05:00
Tobias Geerinckx-Rice 9c7f7e2da9 gnu: btrfs-progs: Update to 4.4.1. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.4.1.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-02-27 22:39:51 +02:00
Ricardo Wurmus a003b5b650 gnu: scribus: Update to 1.5.1. 
* gnu/packages/scribus.scm (scribus): Update to 1.5.1.
[source]: Remove patch.
* gnu/packages/patches/scribus-qobject.patch: Delete file.
* gnu-system.am (dist_patch_DATA): Remove it.
 2016-02-27 16:34:20 +01:00
Ricardo Wurmus b951e26fe5 gnu: arandr: Add "xrandr" to inputs. 
* gnu/packages/xdisorg.scm (arandr)[inputs]: Add "xrandr".
[arguments]: Add build phase "make-xrandr-available" to ensure "xrandr"
executable is found at runtime.
 2016-02-27 16:25:26 +01:00
Mark H Weaver b35461748b gnu: Fix misplaced commas (unquote). 
Fix many occurrences of comma (unquote) being placed immediately after the
previous list item, e.g. ("ncurses", ncurses) in the inputs.

* gnu/packages/base.scm (patch, gnu-make),
  gnu/packages/bioinformatics.scm (hmmer),
  gnu/packages/bittorrent.scm (aria2),
  gnu/packages/compression.scm (pbzip2),
  gnu/packages/databases.scm (recutils),
  gnu/packages/fonts.scm (font-terminus),
  gnu/packages/freedesktop.scm (xdg-utils, elogind),
  gnu/packages/games.scm (gnujump),
  gnu/packages/gnome.scm (libidl, gnumeric, eog, gedit),
  gnu/packages/gnunet.scm (gnunet),
  gnu/packages/gnuzilla.scm (mozjs, nspr),
  gnu/packages/gtk.scm (gtksourceview, gdk-pixbuf),
  gnu/packages/lua.scm (lua),
  gnu/packages/openstack.scm (python-swiftclient),
  gnu/packages/perl.scm (perl-json-any),
  gnu/packages/polkit.scm (polkit-qt),
  gnu/packages/python.scm (wrap-python3, python-oauthlib)
  (python-mccabe-0.2.1, python-contextlib2, python2-rauth),
  gnu/packages/qt.scm (qtkeychain),
  gnu/packages/ruby.scm (ruby-nokogiri),
  gnu/packages/screen.scm (screen),
  gnu/packages/ssh.scm (libssh),
  gnu/packages/video.scm (ffmpeg, mplayer),
  gnu/packages/vim.scm (vim),
  gnu/packages/xdisorg.scm (redshift),
  gnu/packages/xfce.scm (xfce4-panel, xfce4-settings),
  gnu/packages/xnee.scm (xnee),
  gnu/packages/xorg.scm (font-adobe100dpi, font-adobe75dpi),
  gnu/packages/zsh.scm (zsh): Fix misplaced commas (unquote).
 2016-02-27 08:49:26 -05:00
Ricardo Wurmus 48766ea85f gnu: Add emacs-god-mode. 
* gnu/packages/emacs.scm (emacs-god-mode): New variable.
 2016-02-27 13:50:18 +01:00
Ricardo Wurmus 048bfba163 gnu: Add gtklick. 
* gnu/packages/music.scm (gtklick): New variable.
 2016-02-27 12:27:21 +01:00
Ricardo Wurmus 6ab4712d6e gnu: python2-pygtk: Add libglade to inputs. 
* gnu/packages/gtk.scm (python2-pygtk)[inputs]: Add "libglade".
 2016-02-27 12:27:21 +01:00
Ricardo Wurmus a91d72e23a gnu: Add pyliblo. 
* gnu/packages/audio.scm (python-pyliblo, python2-pyliblo): New
  variables.
 2016-02-27 12:27:21 +01:00
Mark H Weaver b460a99890 gnu: linux-libre-4.1: Update to 4.1.18. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.18.
 2016-02-27 02:36:16 -05:00
Mark H Weaver 3dad786b64 gnu: linux-libre: Update to 4.4.3. 
* gnu/packages/linux.scm (linux-libre): Update to 4.4.3.
 2016-02-27 02:36:10 -05:00
Mark H Weaver 4ed737b2ab gnu: gtk-doc: Improve fix-docbook phase. 
* gnu/packages/gtk.scm (gtk-doc)[arguments]: In the 'fix-docbook' phase,
avoid hard-coding the docbook-xsl version number, and return #t.
 2016-02-25 22:24:32 -05:00
Danny Milosavljevic b31fbea566 gnu: Add python-psycopg2. 
* gnu/packages/python.scm (python-psycopg2, python2-psycopg2): New variables.
 2016-02-25 14:35:28 -08:00
Leo Famulari 7dd21101a3 gnu: diffoscope: Update to 49. 
* gnu/packages/package-management.scm (diffoscope): Update to 49.
[source]: Use pypi-uri.
[arguments]: Use python-3. Enable tests. Add 'dependency-on-python-magic' phase
and remove 'dependency-on-rpm' phase.
[native-inputs]: Remove python2-setuptools.
[inputs]: Replace python2-file, python2-debian, python2-libarchive-c,
python2-tlsh, python2-pytest, python2-chardet with python-3 variants.
 2016-02-25 17:06:25 -05:00
Rene Saavedra 66d59111e3 gnu: Add dconf-editor. 
* gnu/packages/gnome.scm (dconf-editor): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-25 16:36:10 -05:00
Andy Wingo 735e84c7bd gnu: libx264: Change source URL to HTTP. 
* gnu/packages/video.scm (libx264): Download via HTTP.  The videolan ftp
  server does not work with IPv6.
 2016-02-25 22:33:40 +01:00
Andy Wingo b4787e71ac gnu: gtk-doc: Fix build. 
* gnu/packages/gtk.scm (gtk-doc): Fix build.
 2016-02-25 22:33:20 +01:00
Efraim Flashner 2865c81c71 gnu: youtube-dl: Update to 2016.02.22. 
* gnu/packages/video.scm (youtube-dl): Update to 2016.02.22.
 2016-02-25 22:54:03 +02:00
Efraim Flashner eb6e2e812a gnu: python-decorator: Update to 4.0.9. 
* gnu/packages/python.scm (python-decorator): Update to 4.0.9.
 2016-02-25 21:05:37 +02:00
Efraim Flashner cc0c4fdedd gnu: python-traitlets: Update to 4.1.0. 
* gnu/packages/python.scm (python-traitlets): Update to 4.1.0.
[native-inputs]: Add python-mock.
 2016-02-25 21:05:37 +02:00
Efraim Flashner c6ebd40da1 gnu: python-mccabe: Update to 0.4.0. 
* gnu/packages/python.scm (python-mccabe): Update to 0.4.0.
[inputs]: Add python-pytest, python-pytest-runner.
(python-mccabe-0.2.1)[inputs]: Only use python-setuptools.
 2016-02-25 21:05:37 +02:00
Efraim Flashner 43789136d2 gnu: python-flake8: Update to 2.5.4. 
* gnu/packages/python.scm (python-flake8): Update to 2.5.4.
[inputs]: Use recent python-pep8, python-pyflakes.
 2016-02-25 21:05:37 +02:00
Efraim Flashner db251311cf gnu: python-pep8: Update to 1.7.0. 
* gnu/packages/python.scm (python-pep8): Update to 1.7.0.
 2016-02-25 21:05:37 +02:00
Efraim Flashner a4d9609c98 gnu: python-networkx: Update to 1.11. 
* gnu/packages/python.scm (python-networkx): Update to 1.11.
 2016-02-25 21:05:37 +02:00
Efraim Flashner 6f068e081b gnu: python-hypothesis: Update to 3.0.4. 
* gnu/packages/python.scm (python-hypothesis): Update to 3.0.4.
[native-inputs]: Remove python-setuptools.
(python2-hypothesis): Use 'strip-python2-variant'.
[native-inputs]: Add python2-enum34, python2-setuptools.
 2016-02-25 21:05:37 +02:00
Efraim Flashner fee04c198c gnu: python-html5lib: Update to 1.0b8. 
* gnu/packages/python.scm (python-html5lib): Update to 1.0b8.
 2016-02-25 21:05:37 +02:00
Efraim Flashner b6785c2e3a gnu: python-isodate: Update to 0.5.4. 
* gnu/packages/python.scm (python-isodate): Update to 0.5.4.
 2016-02-25 21:05:37 +02:00
Efraim Flashner 9d813ec147 gnu: python-wsgi-intercept: Update to 1.1.2. 
* gnu/packages/python.scm (python-wsgi-intercept): Update to 1.1.2.
[native-inputs]: Add python-six.
 2016-02-25 21:05:37 +02:00
Efraim Flashner 29f20168cf gnu: python-pytest-localserver: Update to 0.3.5. 
* gnu/packages/python.scm (python-pytest-localserver): Update to 0.3.5.
 2016-02-25 21:05:37 +02:00
Efraim Flashner da8b011d2a gnu: python-requests-toolbelt: Update to 0.6.0. 
* gnu/packages/python.scm (python-requests-toolbelt): Update to 0.6.0.
 2016-02-25 21:05:37 +02:00
Efraim Flashner 74a066f9a0 gnu: python-requests: Update to 2.9.1. 
* gnu/packages/python.scm (python-requests): Update to 2.9.1.
 2016-02-25 21:05:37 +02:00
Efraim Flashner 40981b5c18 gnu: python-wheel: Update to 0.29.0. 
* gnu/packages/python.scm (python-wheel): Update to 0.29.0.
 2016-02-25 21:05:37 +02:00
Christopher Allan Webber a8f20f63dc gnu: Add python-pastescript. 
* gnu/packages/python.scm (python-pastescript, python2-pastescript):
  New variables.
 2016-02-25 11:01:56 -08:00
Christopher Allan Webber c4a7904c21 gnu: Add python-paste. 
* gnu/packages/python.scm (python-paste, python2-paste): New variables.
* gnu/packages/patches/python-paste-remove-timing-test.patch: New file.
* gnu/packages/patches/python-paste-remove-website-test.patch: New file.
* gnu-system.am (dist_patch_DATA): Add them.
 2016-02-25 11:01:45 -08:00
Mark H Weaver e62b5c6903 Merge branch 'media-updates' 2016-02-25 13:50:19 -05:00
Ludovic Courtès 736f9ffce2 gnu: Add missing import in bioinformatics.scm. 
This is a followup to 1baee94.

* gnu/packages/bioinformatics.scm: Add missing import.
 2016-02-25 12:48:08 +01:00
Nils Gillmann a65e2a02fc gnu: Add kyotocabinet. 
* gnu/packages/databases.scm (kyotocabinet): New variable.
 2016-02-25 11:56:00 +01:00
Ricardo Wurmus 1baee943ca gnu: Add libBigWig. 
* gnu/packages/bioinformatics.scm (libbigwig): New variable.
 2016-02-25 11:43:44 +01:00
Jan Nieuwenhuizen 1644f0cd87 gnu: guile-json: Update to 0.5.0. 
* gnu/packages/guile.scm (guile-json): Update to 0.5.0.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-02-25 09:19:30 +01:00
Ricardo Wurmus b16043a361 gnu: ardour: Update to 4.7. 
* gnu/packages/audio.scm (ardour): Update to 4.7.
 2016-02-25 09:17:35 +01:00
宋文武 f072e9adf5 gnu: xdg-utils: Propagate xprop and xset. 
Fixes <http://bugs.gnu.org/22755>.

* gnu/packages/freedesktop.scm (xdg-utils): Propagate xprop and xset.
 2016-02-25 08:54:42 +08:00
Leo Famulari 85267efb2a gnu: libssh: Update to 0.7.3 [fixes CVE-2016-0739]. 
* gnu/packages/patches/libssh-CVE-2014-0017.patch: Delete file.
* gnu/packages/patches/libssh-0.6.5-CVE-2016-0739.patch: New file.
* gnu-system.am (dist_patch_DATA): Adjust accordingly.
* gnu/packages/ssh.scm (libssh): Update to 0.7.3.
  (libssh-0.5): Rename to...
  (libssh-0.6): ... this.  Update to 0.6.5.
  [source]: Add patch for CVE-2016-0739.
  (guile-ssh)[inputs]: Use libssh-0.6.

Modified-By: Mark H Weaver <mhw@netris.org>
 2016-02-24 16:32:09 -05:00
Leo Famulari 78d80c5c6a gnu: libssh2: Update to 1.7.0 [fixes CVE-2016-0787]. 
* gnu/packages/ssh.scm (libssh2): Update to 1.7.0.
  (libssh2-1.4): New variable.
* gnu/packages/curl.scm (curl)[inputs]: Use libssh4-1.4.

Modified-By: Mark H Weaver <mhw@netris.org>
 2016-02-24 16:32:08 -05:00
Mark H Weaver bf6996c9cf gnu: xf86-video-intel: Update to 2.99.917-1-d167280. 
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-1-d167280.
 2016-02-24 13:56:57 -05:00
Efraim Flashner a49332a0c0 gnu: gdb: Update to 7.11. 
* gnu/packages/gdb.scm (gdb): Update to 7.11.
 2016-02-24 20:52:12 +02:00
Efraim Flashner c73210d7a9 gnu: kde-frameworks: Update to 5.19.0. 
* gnu/packages/kde-frameworks.scm (kwindowsystem): Update to 5.19.0.
(extra-cmake-modules): Update to 5.19.0.
 2016-02-24 20:25:25 +02:00
Andy Wingo 79fd74facd gnu: services: Start X with -configdir. 
* gnu/services/xorg.scm (%default-xorg-modules): New public variable.
(xorg-configuration-directory): New function.
(xorg-start-command): Add #:modules keyword argument, defaulting to
%default-xorg-modules.  Build an xorg.conf.d directory from those
modules, and pass it to X via the -configdir parameter.
 2016-02-24 11:49:57 -05:00
Andy Wingo d0a6437f7d gnu: libxaw: Update to 1.0.13. 
* gnu/packages/xorg.scm (libxaw): Update to 1.0.13.
 2016-02-24 11:49:57 -05:00
Andy Wingo ea9763dae0 gnu: libxt: Update to 1.1.5. 
* gnu/packages/xorg.scm (libxt): Update to 1.1.5.
 2016-02-24 11:49:57 -05:00
Andy Wingo f1aeae762d gnu: libx11: Update to 1.6.3. 
* gnu/packages/xorg.scm (libx11): Update to 1.6.3.
 2016-02-24 11:49:57 -05:00
Andy Wingo 0eae6b2d91 gnu: xorg-server: Update to 1.18.1. 
* gnu/packages/xorg.scm (xorg-server): Update to 1.18.1.
 2016-02-24 11:49:57 -05:00