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2016-03-03gnu: python-pysam: Move cython and setuptools to native inputs....* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move "python-cython" and "python-setuptools" from here... [native-inputs]: ... to here. Ricardo Wurmus
2016-03-03gnu: deeptools: Update to 2.1.1....* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1. [inputs]: Add "python2-numpydoc" and "python2-pybigwig". Ricardo Wurmus
2016-03-03gnu: deeptools: Change "propagated-inputs" to "inputs"....* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move all inputs from here... [inputs]: ...to here. Ricardo Wurmus
2016-03-03gnu: Add python-pybigwig....* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig): New variables. Ricardo Wurmus
2016-03-03gnu: python-pysam: Update to 0.8.4....* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4. Ricardo Wurmus
2016-03-03gnu: 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. Ricardo Wurmus
2016-03-02gnu: 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> Lukas Gradl
2016-03-02gnu: 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. Mark H Weaver
2016-03-02gnu: nss: Update to 3.21.1....* gnu/packages/gnuzilla.scm (nss): Update to 3.21.1. Mark H Weaver
2016-03-02gnu: 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. Mark H Weaver
2016-03-02gnu: 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> Jessica Tallon
2016-03-02gnu: Add cppcheck....* gnu/packages/check.scm (cppcheck): New variable. Roel Janssen
2016-03-02gnu: 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. Mark H Weaver
2016-03-02gnu: 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. 宋文武
2016-03-01gnu: 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. Leo Famulari
2016-03-01gnu: openssh: Update to 7.2p1....* gnu/packages/ssh.scm (openssh): Update to 7.2p1. Leo Famulari
2016-03-01gnu: libressl: Update to 2.2.6....* gnu/packages/tls.scm (libressl): Update to 2.2.6. Leo Famulari
2016-03-01gnu: parallel: Update to 20160222....* gnu/packages/parallel.scm (parallel): Update to 20160222. Leo Famulari
2016-03-01gnu: r-go-db: Bioconductor changed URL for data downloads....* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL. Pjotr Prins
2016-03-01gnu: r-iranges: Update to 2.4.8....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8. Pjotr Prins
2016-03-01gnu: r-s4vectors: Update to 0.8.11....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11. Pjotr Prins
2016-03-01gnu: r-ggplot2: Update to 2.0.0....* gnu/packages/statistics.scm (r-ggplot2): Update to 2.0.0. Pjotr Prins
2016-03-01gnu: openssl: Replace with 1.0.2g [fixes CVE-2016-{0800,0705,0798,0797,0799,0......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. Ludovic Courtès
2016-03-01gnu: tiled: Use 'modify-phases'....* gnu/packages/game-development.scm (tiled)[arguments]: Use 'modify-phases'. Efraim Flashner
2016-03-01gnu: tiled: Update to 0.15.1....* gnu/packages/game-development.scm (tiled): Update to 0.15.1. Efraim Flashner
2016-03-01gnu: Add PePr....* gnu/packages/bioinformatics.scm (pepr): New variable. Ricardo Wurmus
2016-03-01gnu: Add bwa-pssm....* gnu/packages/bioinformatics.scm (bwa-pssm): New variable. Ricardo Wurmus
2016-03-01gnu: Add gdsl....* gnu/packages/datastructures.scm (gdsl): New variable. Ricardo Wurmus
2016-03-01gnu: 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. Efraim Flashner
2016-03-01gnu: irssi: Use 'modify-phases'....* gnu/packages/irc.scm (irssi)[arguments]: Use 'modify-phases'. Efraim Flashner
2016-03-01gnu: 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. Efraim Flashner
2016-03-01gnu: Add quassel....* gnu/packages/irc.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Register it. Efraim Flashner
2016-03-01gnu: Add snorenotify....* gnu/packages/kde.scm (snorenotify): New variable. Efraim Flashner
2016-03-01gnu: Add qca....* gnu/packages/kde.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Register it. Efraim Flashner
2016-03-01gnu: Add oxygen-icons....* gnu/packages/kde-frameworks.scm (oxygen-icons): New variable. Efraim Flashner
2016-02-29gnu: Add desmume....* gnu/packages/games.scm (desmume): New variable. Manolis Ragkousis
2016-02-29gnu: 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. Mark H Weaver
2016-02-29gnu: 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. Christopher Allan Webber
2016-02-29gnu: 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. Ricardo Wurmus
2016-02-28gnu: msmtp: Install msmtpq....* gnu/packages/mail.scm (msmtp)[arguments]: Install msmtpq scripts. Leo Famulari
2016-02-28gnu: 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. Ludovic Courtès
2016-02-28gnu: 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. Andreas Enge
2016-02-28gnu: xrandr: Update to 1.5.0....* gnu/packages/xorg.scm (xrandr): Update to 1.5.0. Efraim Flashner
2016-02-28gnu: libqmi: Update to 1.12.8....* gnu/packages/freedesktop.scm (libqmi): Update to 1.12.8. Efraim Flashner
2016-02-28gnu: wayland: Update to 1.10.0....* gnu/packages/freedesktop.scm (wayland): Update to 1.10.0. [arguments]: Disable parallel tests. Efraim Flashner
2016-02-28gnu: libinput: Update to 1.2.0....* gnu/packages/freedesktop.scm (libinput): Update to 1.2.0. Efraim Flashner
2016-02-28gnu: 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. Efraim Flashner
2016-02-28gnu: Add python-backports-abc....* gnu/packages/python.scm (python-backports-abc): New variable. Efraim Flashner
2016-02-27gnu: 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. Mark H Weaver
2016-02-27gnu: 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> Tobias Geerinckx-Rice
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