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2016-03-04gnu: libgit2: Update to 0.23.4.Ludovic Courtès
* gnu/packages/version-control.scm (libgit2): Update to 0.23.4.
2016-03-04gnu: findnewest: Update to 0.3.Ludovic Courtès
* gnu/packages/version-control.scm (findnewest): Update to 0.3.
2016-03-03gnu: exim: Update to 4.86.2 [fixes CVE-2016-1531].Leo Famulari
* gnu/packages/mail.scm (exim): Update to 4.86.2.
2016-03-03gnu: Add byzanz.David Thompson
* gnu/packages/gnome.scm (byzanz): New variable.
2016-03-03gnu: youtube-dl: Update to 2016.03.01.Efraim Flashner
* gnu/packages/video.scm (youtube-dl): Update to 2016.03.01.
2016-03-03gnu: mpv: Update to 0.16.0.Efraim Flashner
* gnu/packages/video.scm (mpv): Update to 0.16.0.
2016-03-03gnu: perl: Replace with patched version [fixes CVE-2016-2381].Leo Famulari
* gnu/packages/patches/perl-CVE-2016-2381.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/perl.scm (perl)[replacement]: New field. (perl-fixed): New variable. * gnu/packages/commencement.scm (perl-boot0)[replacement]: New field.
2016-03-03gnu: irssi: Support proxy, socks, bot.Efraim Flashner
* gnu/packages/irc.scm (irssi)[arguments]: Add configure flags to support proxy, socks and bot.
2016-03-03gnu: irssi: Update to 0.8.18.Efraim Flashner
* gnu/packages/irc.scm (irssi): Update to 0.8.18. [source]: Update uri.
2016-03-03gnu: python-pysam: Move cython and setuptools to native inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move "python-cython" and "python-setuptools" from here... [native-inputs]: ... to here.
2016-03-03gnu: deeptools: Update to 2.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1. [inputs]: Add "python2-numpydoc" and "python2-pybigwig".
2016-03-03gnu: deeptools: Change "propagated-inputs" to "inputs".Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move all inputs from here... [inputs]: ...to here.
2016-03-03gnu: Add python-pybigwig.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig): New variables.
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.
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