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* gnu: Add r-ape.•••* gnu/packages/bioinformatics.scm (r-ape): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+22
* gnu: Add r-fpc.•••* gnu/packages/statistics.scm (r-fpc): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+31
* gnu: Add r-trimcluster.•••* gnu/packages/statistics.scm (r-trimcluster): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+20
* gnu: Add r-robustbase.•••* gnu/packages/statistics.scm (r-robustbase): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+23
* gnu: Add r-deoptimr.•••* gnu/packages/statistics.scm (r-deoptimr): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+23
* gnu: Add r-prabclus.•••* gnu/packages/statistics.scm (r-prabclus): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+22
* gnu: Add r-mclust.•••* gnu/packages/statistics.scm (r-mclust): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+24
* gnu: Add r-flexmix.•••* gnu/packages/statistics.scm (r-flexmix): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+24
* gnu: Add r-modeltools.•••* gnu/packages/statistics.scm (r-modeltools): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+20
* gnu: Add r-diptest.•••* gnu/packages/statistics.scm (r-diptest): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Jean Pierre Bonnal2017-03-111-0/+20
* gnu: Add obnam.•••* gnu/packages/backup.scm (obnam): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac2017-03-101-0/+33
* gnu: icestorm: Replace reference in icebox_vlog.•••* gnu/packages/fpga.scm (icestorm)[arguments]: Add phase "fix-usr-local" to replace reference to /usr/local/share. Theodoros Foradis2017-03-101-0/+5
* gnu: dub: Update to 1.2.2.•••* gnu/packages/ldc.scm (dub): Update to 1.2.2. Danny Milosavljevic2017-03-101-2/+2
* services: openssh: Fix 'PrintLastLog' default behaviour.•••* gnu/services/ssh.scm (openssh-config-file): Add 'print-last-log?' option. (<openssh-configuration>)[print-last-log?]: Add it. (openssh-activation): Touch /var/log/lastlog. * doc/guix.texi (Networking Services): Document 'print-last-log?'. Before that, the service did not work as expected because /var/log/lastlog did not exist. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Clément Lassieur2017-03-101-0/+13
* services: openssh: Remove deprecated options.•••* gnu/services/ssh.scm (openssh-config-file): Remove them. (<openssh-configuration>)[rsa-authentication?]: Remove it. (<openssh-configuration>)[protocol-number]: Remove it. * doc/guix.texi (Networking Services): Remove them. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Clément Lassieur2017-03-101-10/+0
* services: openssh: Enable PAM.•••* gnu/services/ssh.scm: (openssh-pam-services): New procedure. (openssh-service-type): Use it to extend PAM-ROOT-SERVICE-TYPE. (<openssh-configuration>)[challenge-response-authentication?]: New field. (<openssh-configuration>)[use-pam?]: New field. (openssh-config-file): Add them. * doc/guix.texi (Networking Services): Document them. Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org> Clément Lassieur2017-03-101-1/+20
* system: Avoid '_' as a pattern variable in 'match'.•••* gnu/system.scm (operating-system-root-file-system): Don't use '_' as a wildcard in 'match', to cope with literal semantics in 2.2. Ludovic Courtès2017-03-101-2/+2
* services: Create /var/log upon activation.•••When launching a container created with guix system container, the attempt to create /var/log/wtmp would fail, as /var/log did not exist. * gnu/services.scm (activation-script): Create /var/log Co-authored-by: Ludovic Courtès <ludo@gnu.org> Christopher Baines2017-03-101-2/+5
* services: Add exim-service-type.•••* gnu/services/mail.scm (<exim-configuration>): New record type. (exim-computed-config-file, exim-shepherd-service, exim-activation, exim-etc, exim-profile): New procedures. (exim-service-type, %exim-accounts): New variables. * doc/guix.text (Mail Services): Document it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Carlo Zancanaro2017-03-101-1/+101
* gnu: hmmer: Build reproducibly.•••* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file. * gnu/packages/bioinformatics.scm (hmmer): Use it. Ben J. Woodcroft2017-03-102-9/+33
* gnu: Add sambamba.•••* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New variables. Ricardo Wurmus2017-03-101-0/+97
* gnu: pidgin: Update to 2.12.0 [fixes CVE-2017-2640].•••* gnu/packages/messaging.scm (pidgin): Update to 2.12.0. Leo Famulari2017-03-101-2/+2
* gnu: neomutt: Configure with 'lmdb' and 'kyotocabinet'.•••* gnu/packages/mail.scm (neomutt)[configure]: Add '--with-kyotocabinet' and '--with-lmdb'. [inputs]: Add 'lmdb' and 'kyotocabinet'. Signed-off-by: Kei Kebreau <kei@openmailbox.org> ng02017-03-091-1/+5
* gnu: neomutt: Update to 20170306.•••* gnu/packages/mail.scm (neomutt): Update to 20170306. Signed-off-by: Kei Kebreau <kei@openmailbox.org> ng02017-03-091-2/+2
* Revert "gnu: neomutt: Configure with 'lmdb' and 'tokyocabinet'."•••'kyotocabinet' is more current than tokyocabinet in development and supported in neomutt aswell. This reverts commit ef91e2b964ec0952698dd1bf7daf76624fed2145. Signed-off-by: Kei Kebreau <kei@openmailbox.org> ng02017-03-091-5/+2
* gnu: hiawatha: Adjust description.•••* gnu/packages/web.scm (hiawatha)[description]: Adjust it. Signed-off-by: Kei Kebreau <kei@openmailbox.org> ng02017-03-091-4/+3
* gnu: Add font-tamzen.•••* gnu/packages/fonts.scm (font-tamzen): New variable. Signed-off-by: Kei Kebreau <kei@openmailbox.org> ng02017-03-091-0/+64
* gnu: btrfs-progs/static: Correct description.•••* gnu/packages/linux.scm (btrfs-progs/static)[description]: Use the correct name of the btrfs-progs package and @command{} mark-up. Tobias Geerinckx-Rice2017-03-091-3/+3
* gnu: btrfs-progs: Update to 4.10.•••* gnu/packages/linux.scm (btrfs-progs): Update to 4.10. Tobias Geerinckx-Rice2017-03-091-2/+2
* gnu: ibus-anthy: Update to 1.5.9.•••* gnu/packages/ibus.scm (ibus-anthy): Update to 1.5.9. Tobias Geerinckx-Rice2017-03-091-2/+2
* gnu: ibus: Update to 1.5.15.•••* gnu/packages/ibus.scm (ibus): Update to 1.5.15. Tobias Geerinckx-Rice2017-03-091-2/+2
* gnu: pius: Update to 2.2.4.•••* gnu/packages/gnupg.scm (pius): Update to 2.2.4. Tobias Geerinckx-Rice2017-03-091-2/+2
* gnu: youtube-dl: Update to 2017.03.07.•••* gnu/packages/video.scm (youtube-dl): Update to 2017.03.07. Tobias Geerinckx-Rice2017-03-091-2/+2
* gnu: graphicsmagick: Build with 16 bit quantum depth.•••Octave requires graphicsmagick to be built with 16 bit quantum depth. * gnu/packages/imagemagick.scm (graphicsmagick)[arguments]: Add "--with-quantum-depth=16" and "--enable-quantum-library-names" to #:configure-flags. Signed-off-by: Leo Famulari <leo@famulari.name> Arun Isaac2017-03-091-0/+2
* gnu: octave: Build with curl and graphicsmagick.•••* gnu/packages/maths.scm (octave)[inputs]: Add curl and graphicsmagick. Signed-off-by: Leo Famulari <leo@famulari.name> Arun Isaac2017-03-091-1/+4
* gnu: xf86-input-libinput: Update to 0.25.0.•••* gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.25.0. Marius Bakke2017-03-091-2/+2
* gnu: Add python2-larch.•••* gnu/packages/python.scm (python2-larch): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac2017-03-091-0/+31
* gnu: Add python2-tracing.•••* gnu/packages/python.scm (python2-tracing): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac2017-03-091-0/+26
* gnu: Add python2-ttystatus.•••* gnu/packages/python.scm (python2-ttystatus): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac2017-03-091-0/+25
* gnu: Add python2-cliapp.•••* gnu/packages/python.scm (python2-cliapp): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com> Arun Isaac2017-03-091-1/+28
* gnu: python-numpy-documentation: Use full git commit hash in submodule.•••* gnu/packages/python.scm (python-numpy-documentation, python2-numpy-documentation)[native-inputs]: Update hash of SCIPY-SPHINX-THEME. Fix indentation of a line. Marius Bakke2017-03-091-2/+2
* gnu: Remove obsolete numpy comment.•••* gnu/packages/python.scm: Remove comment. Marius Bakke2017-03-091-2/+0
* gnu: inetutils: Disable parallel tests.•••* gnu/packages/admin.scm (inetutils)[arguments]: Add #:parallel-tests? #f. Marius Bakke2017-03-091-1/+4
* gnu: python-pandas: Really fix build on 32bit.•••* gnu/packages/patches/python-pandas-skip-failing-tests.patch: Fix confusion with same-named test. Marius Bakke2017-03-091-27/+17
* gnu: Add rsnapshot.•••* gnu/packages/backup.scm (rsnapshot): New variable. Thomas Danckaert2017-03-091-0/+38
* gnu: python-fake-factory: Add back missing patch file.•••This reverts the removal of "python-fake-factory-fix-build-32bit.patch" by commit ce7911ddae5d30ba73c8c9552b7d4e71268e5db3. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Mark H Weaver2017-03-092-0/+37
* gnu: inetutils: Set the $localstatedir.•••This is a followup to commit 6f5d28f9d05aaa9743b3aac6bceb2c6323122d2d. * gnu/packages/admin.scm (inetutils)[arguments]: Pass '--localstatedir=/var' to #:configure-flags. Leo Famulari2017-03-091-0/+2
* gnu: icecat: Add fixes from upstream Firefox ESR 45.8.0.•••Includes fixes for CVE-2017-5398, CVE-2017-5400, CVE-2017-5401, CVE-2017-5402, CVE-2017-5404, CVE-2017-5405, CVE-2017-5407, CVE-2017-5408, CVE-2017-5409, and CVE-2017-5410. * gnu/packages/gnuzilla.scm (icecat)[source]: Add selected fixes from the upstream mozilla-esr45 repository. Mark H Weaver2017-03-091-1/+33
* gnu: icecat: Update to 45.7.0-gnu1.•••* gnu/packages/gnuzilla.scm (icecat): Update to 45.7.0-gnu1. Remove patches included in 45.7.0. Mark H Weaver2017-03-091-60/+3
* gnu: r: Remove obsolete configure flags.•••* gnu/packages/statistics.scm (r)[arguments]: Remove obsolete configure flags. Ricardo Wurmus2017-03-091-5/+1
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