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2016-03-03gnu: python-pysam: Update to 0.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
2016-03-03gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.Ricardo Wurmus
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to... * gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): ...here.
2016-03-02gnu: Add procmail.Lukas Gradl
* 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>
2016-03-02gnu: icecat: Update bundled graphite2 to 1.3.6 [unspecified security fixes].Mark H Weaver
* 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.
2016-03-02gnu: nss: Update to 3.21.1.Mark H Weaver
* gnu/packages/gnuzilla.scm (nss): Update to 3.21.1.
2016-03-02gnu: graphite2: Replace with 1.3.6 [unspecified security fixes].Mark H Weaver
See <https://bodhi.fedoraproject.org/updates/FEDORA-2016-dec1faadc5> * gnu/packages/fontutils.scm (graphite2)[replacement]: New field. (graphite2-1.3.6): New variable.
2016-03-02gnu: Add password-store.Jessica Tallon
* 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>
2016-03-02gnu: Add cppcheck.Roel Janssen
* gnu/packages/check.scm (cppcheck): New variable.
2016-03-02gnu: openssl: Enable ssl2 at build time to ensure ABI compatible graft.Mark H Weaver
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.
2016-03-02gnu: xfce: Don't wrap 'startxfce4'.宋文武
The necessary environment variables are set by 'etc/profile' now. * gnu/packages/xfce.scm (xfce)[build-system]: Use 'trivial-build-system'. [arguments]: Simplify.
2016-03-01gnu: ilmbase: Add patch to fix build on i686.Leo Famulari
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.
2016-03-01gnu: openssh: Update to 7.2p1.Leo Famulari
* gnu/packages/ssh.scm (openssh): Update to 7.2p1.
2016-03-01gnu: libressl: Update to 2.2.6.Leo Famulari
* gnu/packages/tls.scm (libressl): Update to 2.2.6.
2016-03-01gnu: parallel: Update to 20160222.Leo Famulari
* gnu/packages/parallel.scm (parallel): Update to 20160222.
2016-03-01gnu: r-go-db: Bioconductor changed URL for data downloads.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
2016-03-01gnu: r-iranges: Update to 2.4.8.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
2016-03-01gnu: r-s4vectors: Update to 0.8.11.Pjotr Prins
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
2016-03-01gnu: r-ggplot2: Update to 2.0.0.Pjotr Prins
* gnu/packages/statistics.scm (r-ggplot2): Update to 2.0.0.
2016-03-01gnu: openssl: Replace with 1.0.2g [fixes ↵Ludovic Courtès
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.
2016-03-01gnu: tiled: Use 'modify-phases'.Efraim Flashner
* gnu/packages/game-development.scm (tiled)[arguments]: Use 'modify-phases'.
2016-03-01gnu: tiled: Update to 0.15.1.Efraim Flashner
* gnu/packages/game-development.scm (tiled): Update to 0.15.1.
2016-03-01gnu: Add PePr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pepr): New variable.
2016-03-01gnu: Add bwa-pssm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
2016-03-01gnu: Add gdsl.Ricardo Wurmus
* gnu/packages/datastructures.scm (gdsl): New variable.
2016-03-01gnu: weechat: Move to irc.scm.Efraim Flashner
* 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.
2016-03-01gnu: irssi: Use 'modify-phases'.Efraim Flashner
* gnu/packages/irc.scm (irssi)[arguments]: Use 'modify-phases'.
2016-03-01gnu: irssi: Move to irc.scm.Efraim Flashner
* 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.
2016-03-01gnu: Add quassel.Efraim Flashner
* gnu/packages/irc.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Register it.
2016-03-01gnu: Add snorenotify.Efraim Flashner
* gnu/packages/kde.scm (snorenotify): New variable.
2016-03-01gnu: Add qca.Efraim Flashner
* gnu/packages/kde.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Register it.
2016-03-01gnu: Add oxygen-icons.Efraim Flashner
* gnu/packages/kde-frameworks.scm (oxygen-icons): New variable.
2016-02-29gnu: Add desmume.Manolis Ragkousis
* gnu/packages/games.scm (desmume): New variable.
2016-02-29gnu: curl: Use updated libssh2 [fixes CVE-2016-7087].Mark H Weaver
* gnu/packages/curl.scm (curl)[inputs]: Use libssh2. * gnu/packages/ssh.scm (libssh2-1.4): Remove variable.
2016-02-29gnu: Remove python2-pil.Christopher Allan Webber
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.
2016-02-29gnu: guile-for-guile-emacs: Use guile-2.0 search paths.Ricardo Wurmus
* gnu/packages/guile.scm (guile-for-guile-emacs)[native-search-paths]: Use the same search paths as guile-2.0.
2016-02-28gnu: msmtp: Install msmtpq.Leo Famulari
* gnu/packages/mail.scm (msmtp)[arguments]: Install msmtpq scripts.
2016-02-28gnu: git: Install symlinks instead of hard links.Ludovic Courtès
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.
2016-02-28gnu: libwnck: Rename variable for GTK+ 2 variant.Andreas Enge
* 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.
2016-02-28gnu: xrandr: Update to 1.5.0.Efraim Flashner
* gnu/packages/xorg.scm (xrandr): Update to 1.5.0.
2016-02-28gnu: libqmi: Update to 1.12.8.Efraim Flashner
* gnu/packages/freedesktop.scm (libqmi): Update to 1.12.8.
2016-02-28gnu: wayland: Update to 1.10.0.Efraim Flashner
* gnu/packages/freedesktop.scm (wayland): Update to 1.10.0. [arguments]: Disable parallel tests.
2016-02-28gnu: libinput: Update to 1.2.0.Efraim Flashner
* gnu/packages/freedesktop.scm (libinput): Update to 1.2.0.
2016-02-28gnu: python-tornado: Update to 4.3.Efraim Flashner
* gnu/packages/python.scm (python-tornado): Update to 4.3. [native-inputs]: Add python-backports-abc. (python2-tornado)[inputs]: Add python2-singledispatch.
2016-02-28gnu: Add python-backports-abc.Efraim Flashner
* gnu/packages/python.scm (python-backports-abc): New variable.
2016-02-27gnu: bitlbee: Update to 3.4.1.Mark H Weaver
* 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.
2016-02-27gnu: btrfs-progs: Update to 4.4.1.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (btrfs-progs): Update to 4.4.1. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-02-27gnu: scribus: Update to 1.5.1.Ricardo Wurmus
* 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.
2016-02-27gnu: arandr: Add "xrandr" to inputs.Ricardo Wurmus
* gnu/packages/xdisorg.scm (arandr)[inputs]: Add "xrandr". [arguments]: Add build phase "make-xrandr-available" to ensure "xrandr" executable is found at runtime.
2016-02-27gnu: Fix misplaced commas (unquote).Mark H Weaver
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).
2016-02-27gnu: Add emacs-god-mode.Ricardo Wurmus
* gnu/packages/emacs.scm (emacs-god-mode): New variable.
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