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15238 Commits

Author SHA1 Message Date
Ricardo Wurmus d553cd6015
gnu: python-pysam: Run tests in parallel. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in
parallel.
 2017-03-22 12:21:39 +01:00
Ricardo Wurmus 611154efc8
gnu: python-pysam: Run tests before installation. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
 2017-03-22 12:21:39 +01:00
Ricardo Wurmus 9488776a18
gnu: python-pysam: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
 2017-03-22 12:21:38 +01:00
Efraim Flashner 378de69c59
Merge remote-tracking branch 'origin/master' into core-updates 2017-03-22 12:57:37 +02:00
Leo Famulari d8be338f16
gnu: openssh: Update to 7.5p1. 
* gnu/packages/ssh.scm (openssh): Update to 7.5p1.
 2017-03-22 02:37:31 -04:00
Leo Famulari 22f25392cf
gnu: ntp: Update to 4.2.8p10 [security fixes]. 
Fixes CVE-2016-9042 and CVE-2017-{6451,6452,6455,6458,6459,6460,6462,6463,6464}
and others. See 'NEWS' in the source code for more information.

* gnu/packages/ntp.scm (ntp): Update to 4.2.8p10.
 2017-03-22 01:41:41 -04:00
Tobias Geerinckx-Rice 8e71896340
gnu: python-psycopg2: Update to 2.6.2. 
* gnu/packages/python.scm (python-psycopg2): Update to 2.6.2.
 2017-03-22 02:03:35 +01:00
Tobias Geerinckx-Rice 35e1a0f1a7
gnu: python-zope-component: Update to 4.3.0. 
* gnu/packages/python.scm (python-zope-component): Update to 4.3.0.
[source]: Use pypi-uri.
 2017-03-22 02:03:35 +01:00
Tobias Geerinckx-Rice c56ad5e291
gnu: python-atomicwrites: Update to 1.1.5. 
* gnu/packages/python.scm (python-atomicwrites): Update to 1.1.5.
 2017-03-22 02:03:34 +01:00
Tobias Geerinckx-Rice 4c4d4df393
gnu: python-texttable: Update to 0.8.7. 
* gnu/packages/python.scm (python-texttable): Update to 0.8.7.
 2017-03-22 02:03:34 +01:00
Tobias Geerinckx-Rice d5c183d134
gnu: python-feedgenerator: Update to 1.9. 
* gnu/packages/python.scm (python-feedgenerator): Update to 1.9.
 2017-03-22 02:03:34 +01:00
Tobias Geerinckx-Rice d25bee2600
gnu: python-wrapt: Update to 1.10.8. 
* gnu/packages/python.scm (python-wrapt): Update to 1.10.8.
[source]: Use pypi-uri.
 2017-03-22 02:03:33 +01:00
Tobias Geerinckx-Rice b9463fdba2
gnu: python-py: Update to 1.4.32. 
* gnu/packages/python.scm (python-py): Update to 1.4.32.
 2017-03-22 02:03:33 +01:00
Tobias Geerinckx-Rice 5095bc7d71
gnu: python-sphinx-cloud-sptheme: Update to 1.8.0. 
* gnu/packages/python.scm (python-sphinx-cloud-sptheme): Update to 1.8.0.
 2017-03-22 02:03:33 +01:00
Tobias Geerinckx-Rice 9e59478f8d
gnu: python-wcwidth: Update to 0.1.7. 
* gnu/packages/python.scm (python-wcwidth): Update to 0.1.7.
[source]: Use pypi-uri.
 2017-03-22 02:03:32 +01:00
Tobias Geerinckx-Rice 4ffbe8c6d7
gnu: python-markdown: Update to 2.6.8. 
* gnu/packages/python.scm (python-markdown): Update to 2.6.8.
 2017-03-22 02:03:32 +01:00
Tobias Geerinckx-Rice 2d431b0130
gnu: dns: Return #t instead of something undefined. 
* gnu/packages/dns.scm (yadifa, knot)[arguments]: Return #t after calling
‘substitute*’.
(knot)[source]: Return #t after calling ‘delete-file-recursively’.
 2017-03-22 02:03:31 +01:00
Ludovic Courtès 7dbd75b3cf
file-systems: Add missing docstring. 
* gnu/system/file-systems.scm (file-system-type-predicate): Add
docstring.
 2017-03-21 22:33:07 +01:00
Ludovic Courtès 278d486b0c
file-systems: Do not use (gnu packages …). 
Fixes a regression introduced in
7208995426 whereby (gnu system
file-systems) would pull in (gnu packages …) module, which in turn
breaks when importing things like (gnu build shepherd).

* gnu/system/file-systems.scm (file-system-type-predicate): Export.
(file-system-packages): Move to...
* gnu/system/linux-initrd.scm (file-system-packages): ... here.  Add
docstring.
* gnu/services/base.scm: Use it.
* tests/file-systems.scm ("does not pull (gnu packages …)"): New test.
 2017-03-21 22:33:07 +01:00
Efraim Flashner 4f7a9e0bff
gnu: vapoursynth: Update to 37. 
* gnu/packages/video.scm (vapoursynth): Update to 37.
 2017-03-21 22:36:33 +02:00
Efraim Flashner 60092c181c
gnu: zimg: Update to 2.5. 
* gnu/packages/image.scm (zimg): Update to 2.5.
 2017-03-21 22:35:32 +02:00
Leo Famulari 049e02eaa2
gnu: libesmtp: Add alternate source URL. 
* gnu/packages/mail.scm (libesmtp)[source]: Add alternate URL.
 2017-03-21 16:33:08 -04:00
Leo Famulari a9681c74ca
gnu: python-pillow: Fix test failures with freetype-2.7. 
* gnu/packages/patches/python-pillow-freetype-2.7-test-failure.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python-pillow, python2-pillow)[source]: Use it.
 2017-03-21 16:20:10 -04:00
Efraim Flashner 83a3464793
gnu: openblas: Add support for aarch64. 
* gnu/packages/maths.scm (openblas)[arguments]: Mark aarch64 as
substitutable, build for target ARMv8.
 2017-03-21 22:03:05 +02:00
Clément Lassieur 36f666c63d
tests: ssh: Add a test for SFTP. 
* gnu/tests/ssh.scm (run-ssh-test): Introduce "SFTP file writing and reading".
Make 'sftp?' a keyword parameter.
(%test-openssh): Pass #:sftp? #t to 'run-ssh-test'.
 2017-03-21 20:49:26 +01:00
Clément Lassieur cfaf4d1165
tests: ssh: Abstract session connection and authentication. 
* gnu/tests/ssh.scm (run-ssh-test): Introduce make-session-for-test,
call-with-connected-session and call-with-connected-session/auth.
(run-ssh-test)["connect"]: Rename to "shell command".  Abstract its session
connection and authentication work into the above three functions.
 2017-03-21 20:49:26 +01:00
Clément Lassieur 12723370e5
services: openssh: Add 'subsystems' option. 
* gnu/services/ssh.scm (openssh-config-file): Add it.
(<openssh-configuration>)[subsystems]: Add it.
* doc/guix.texi (Networking Services): Document it.
 2017-03-21 20:49:26 +01:00
Clément Lassieur 4ca3e9b7b6
services: openssh: Cosmetic changes. 
* gnu/services/ssh.scm (<openssh-configuration>): Reformat to fit in 80
columns.
 2017-03-21 20:49:26 +01:00
Rodger Fox a42619e5e2
gnu: Add lmms. 
* gnu/packages/music.scm (lmms): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-21 15:37:29 -04:00
Arun Isaac 0b608ec4ce
gnu: Add megaglest. 
* gnu/packages/games.scm (megaglest): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-21 15:15:35 -04:00
Arun Isaac fb731c9232
gnu: Add megaglest-data. 
* gnu/packages/games.scm (megaglest-data): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-21 15:15:35 -04:00
Efraim Flashner 8ea71f2005
gnu: ots: Use 'modify-phases' syntax. 
* gnu/packages/ots.scm (ots)[arguments]: Use 'modify-phases' syntax.
 2017-03-21 20:58:52 +02:00
Efraim Flashner b1d3e0a93b
gnu: ots: Add download mirror. 
* gnu/packages/ots.scm (ots)[source]: Add Debian mirror.
 2017-03-21 20:58:51 +02:00
rennes 8e4b7b7514
gnu: xf86-video-vmware: Fix build failure due to missing LLVM. 
* gnu/packages/xorg.scm (xf86-video-vmware)[inputs]: Add llvm.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-21 14:24:37 -04:00
Leo Famulari 7fc72c7731
gnu: libcmis: Update to 0.5.1. 
* gnu/packages/libreoffice.scm (libcmis): Update to 0.5.1.
[source]: Use new source URL. Remove obsolete patch
'libcmis-fix-test-onedrive.patch'.
[home-page]: Update URL.
* gnu/packages/patches/libcmis-fix-test-onedrive.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-03-21 13:38:13 -04:00
Efraim Flashner a160778cba
gnu: x265: Fix build on aarch64. 
* gnu/packages/video.scm (x265)[arguments]: On aarch64 add a
configure-flag to enable PIC.
 2017-03-21 18:01:05 +02:00
Kei Kebreau 4b0e636701
gnu: Adjust asciidoc-related build options. 
Commits 9099a45792 and
3078821d13 make many package inputs and
build configurations related to asciidoc obsolete.

* gnu/packages/compton.scm (compton)[inputs]: Remove docbook-xml,
libxml2 and libxslt.
* gnu/packages/mail.scm (offlinemap)[native-inputs]: Remove libxslt.
* gnu/packages/linux.scm (btrfs-progs)[native-inputs]: Remove docbook-xml.
(perf)[inputs]: Remove docbook-xml and libxslt.
* gnu/packages/text-editors.scm (kakoune)[native-inputs]: Remove libxslt.
* gnu/packages/version-control.scm (cgit)[native-inputs]: Remove
docbook-xml, docbook-xsl, libxml2 and libxslt.
(cvs-fast-export)[native-inputs]: Remove docbook-xml, docbook-xsl,
libxml2 and libxslt.
* gnu/packages/web.scm (qutebrowser)[native-inputs]: Remove docbook-xml,
docbook-xsl, libxml2, and libxslt.
(tinyproxy)[native-inputs]: Remove docbook-xml, docbook-xsl, libxml2 and
libxslt.
* gnu/packages/wm.scm (awesome)[make-flags]: Remove XML_CATALOG_FILES flag.
(i3-wm)[inputs]: Remove docbook-xml.
[native-inputs]: Add libxml2.
 2017-03-21 11:15:08 -04:00
Arun Isaac ed428a58ec
gnu: Add swaks. 
* gnu/packages/mail.scm (swaks): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-21 15:42:44 +01:00
Marius Bakke 3411937b15
gnu: git: Update to 2.12.1. 
* gnu/packages/version-control.scm (git): Update to 2.12.1.
 2017-03-21 13:45:57 +01:00
humanitiesNerd 6330ece9e3
gnu: Add perl-ole-storage-lite. 
* gnu/packages/perl.scm (perl-ole-storage-lite): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-21 12:55:47 +01:00
humanitiesNerd 2b9d2df799
gnu: Add perl-crypt-rc4. 
* gnu/pakages/perl.scm (perl-crypt-rc4): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-21 12:55:43 +01:00
Marius Bakke 4b9a5bd990
gnu: kodi: Wrap executable so it finds libcurl. 
* gnu/packages/kodi.scm (kodi)[arguments]: Add 'wrap' phase.
 2017-03-21 12:37:41 +01:00
Leo Famulari f826c8c7ee
gnu: go@1.4, go@1.7: Skip test that fails with tzdata-2017a. 
* gnu/packages/golang.scm (go-1.4, go-1.7)[arguments]: Disable the test
TestParseInLocation in 'prebuild' phase.
 2017-03-21 01:30:39 -04:00
Marius Bakke 3b4efb1f45
gnu: dtc: Update to 1.4.4. 
* gnu/packages/bootloaders.scm (dtc): Update to 1.4.4.
[source]: Use mirror://kernel.org.
 2017-03-21 01:13:06 +01:00
Marius Bakke d3d92ec2ba
gnu: greenisland: Update to 0.9.0.1. 
* gnu/packages/display-managers.scm (greenisland): Update to 0.9.0.1.
 2017-03-21 01:13:06 +01:00
Marius Bakke 38190ea5ef
gnu: vim: Update to 8.0.0494. 
* gnu/packages/patches/vim-CVE-2017-5953.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/vim.scm (vim, vim-full): Update to 8.0.0494.
[source]: Remove patch.
(vim-full)[arguments]: Add two phases to drop tests and start xorg.
[native-inputs]: Add XORG-SERVER.
 2017-03-20 23:35:39 +01:00
Marius Bakke f69e20341f
gnu: kodi: Update to 18.0_alpha-0-b35147e. 
* gnu/packages/kodi.scm (libdvdnav/kodi, libdvdread/kodi, libdvdcss/kodi): New
variables.
(kodi): Update to 18.0_alpha-0-b35147e.
[source]: Download from git. Unbundle more stuff.
[build-system]: Change to CMAKE-BUILD-SYSTEM.
[arguments]: Add #:configure-flag to disable nonfree components. Rework phases
to patch bundled software and bootstrap more libraries.
[native-inputs]: Remove CMAKE, DOXYGEN, GAWK and WHICH. Add LIBDVDCSS/KODI,
LIBDVDNAV/KODI and LIBDVDREAD/KODI.
[inputs]: Remove BOOST, BZIP2, ENCA, GPERF, JASPER, LIBMODPLUG, LIBSAMPLERATE,
LIBXMU, LIBXT, MESA-UTILS, SDL2 and UNZIP. Add FMT, GIFLIB, LCMS and LIBDRM.
[license]: Update for remaining software bundles.
 2017-03-20 23:35:39 +01:00
Marius Bakke 0a15ee7b63
gnu: Add fmt. 
* gnu/packages/pretty-print.scm (fmt): New variable.
 2017-03-20 23:35:39 +01:00
Leo Famulari deee8a9dfc
gnu: Remove leftover patch. 
* gnu/packages/patches/openjpeg-use-after-free-fix.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-03-20 18:25:02 -04:00
Leo Famulari 957699ee92
gnu: openjpeg: Remove obsolete patches. 
* gnu/packages/patches/openjpeg-CVE-2016-5157.patch,
gnu/packages/patches/openjpeg-CVE-2016-7163.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/image.scm (openjpeg)[source]: Remove them.
 2017-03-20 18:24:58 -04:00