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Author SHA1 Message Date
Efraim Flashner 0e7c3ba1c0
gnu: perl-mojolicious: Update to 7.29. 
* gnu/packages/perl-web.scm (perl-mojolicious): Update to 7.29.
 2017-03-22 12:56:23 +02:00
Efraim Flashner c70b50efb9
gnu: perl-io-compress: Update to 2.074. 
* gnu/packages/compression.scm (perl-io-compress): Update to 2.074.
[propagated-inputs]: Update minimum versions to 2.074.
 2017-03-22 12:50:36 +02:00
Efraim Flashner c0b7b797a2
gnu: perl-compress-raw-bzip2: Update to 2.074. 
* gnu/packages/compression.scm (perl-compress-raw-bzip2): Update to 2.074.
 2017-03-22 12:45:55 +02:00
Efraim Flashner 02b067d782
gnu: perl-compress-raw-zlib: Update to 2.074. 
* gnu/packages/compression.scm (perl-compress-raw-zlib): Update to 2.074.
 2017-03-22 12:40:05 +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
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
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
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
Tobias Geerinckx-Rice 6809d9377b
gnu: ngircd: Use HTTPS. 
* gnu/packages/messaging.scm (ngircd)[source, home-page]: Use HTTPS.
 2017-03-20 22:44:06 +01:00
Tobias Geerinckx-Rice 07b7a66526
gnu: ngircd: Use the phrase ‘IRC’ in its description. 
* gnu/packages/messaging.scm (ngircd)[description]: Use ‘IRC’ with @dfn.
 2017-03-20 22:44:06 +01:00
Tobias Geerinckx-Rice 341ed63f47
gnu: ngircd: Use ‘modify-phases’ syntax. 
* gnu/packages/messaging.scm (ngircd)[arguments]: Use ‘modify-phases’.
 2017-03-20 22:44:06 +01:00
Tobias Geerinckx-Rice 4fd95d9170
gnu: ngircd: Update to 24. 
* gnu/packages/messaging.scm (ngircd): Update to 24.
[source]: Remove upstreamed DNS lookup patch.
* gnu/packages/patches/ngircd-no-dns-in-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-03-20 22:44:06 +01:00
Tobias Geerinckx-Rice 500fc65b5b
gnu: znc: Run test suite. 
* gnu/packages/messaging.scm (znc)[arguments]: Enable tests.  Add an
‘unpack-googletest’ phase and add ‘--with-gtest=’ to #:configure-flags.
[native-inputs]: Add googletest source.
 2017-03-20 22:44:05 +01:00
Tobias Geerinckx-Rice f0bce02664
gnu: simple-scan: Update to 3.24.0. 
* gnu/packages/gnome.scm (simple-scan): Update to 3.24.0.
 2017-03-20 22:44:05 +01:00
Ricardo Wurmus e2c4fe7c62
gnu: Add r-cairo. 
* gnu/packages/statistics.scm (r-cairo): New variable.
 2017-03-20 21:16:11 +01:00
Hartmut Goebel 94e24d8124
gnu: Add comments on why setting QT_QPA_PLATFORM for tests. 
* gnu/packages/astronomy.scm (stellarium): Add comment.
* gnu/packages/display-managers.scm (greenisland): dito.
* gnu/packages/kde-frameworks.scm (kguiaddons, kwidgetsaddons,
  kcompletion, baloo, kbookmarks, kconfigwidgtes, kdesignerplugin,
  kemoticons, kglobalaccel, kiconthemes, kio, knewstuff, kparts,
  kpeople, krunner, kservice, ktexteditor, ktextwidgets, kxmlgui,
  plasma-framework): dito.
* gnu/packages/qt.scm (qtsvg): dito.
 2017-03-20 20:56:49 +01:00
Kei Kebreau 0b5d078f8b
gnu: Add freedoom. 
* gnu/packages/games.scm (freedoom): New variable.
 2017-03-20 14:29:44 -04:00
Efraim Flashner 6f9ba4c91c
gnu: Remove wxwidgets@2.8. 
* gnu/packages/wxwidgets.scm (wxwidgets@2.8): Remove variable.
 2017-03-20 18:33:30 +02:00
Efraim Flashner 36e17ab417
gnu: audacity: Use gtk+@3. 
* gnu/packages/audacity.scm (audacity)[inputs]: Remove wxwidgets-gtk2,
gtk+@2, add wxwidgets and gtk+.
 2017-03-20 18:04:01 +02:00
Efraim Flashner 2314474b01
gnu: wxwidgets: Build with webkitgtk. 
* gnu/packages/wxwidgets.scm (wxwidgets)[inputs]: Remove webkitgtk@2.4,
add webkitgtk.
 2017-03-20 18:02:41 +02:00
Ricardo Wurmus 4f9998c66f
gnu: snakemake: Add runtime dependencies. 
* gnu/packages/python.scm (snakemake)[propagated-inputs]: Add python-wrapt and
python-requests.
 2017-03-20 15:13:19 +01:00
Leo Famulari 0420e89682
gnu: mpd: Update to 0.20.6. 
* gnu/packages/mpd.scm (mpd): Update to 0.20.6.
 2017-03-19 21:55:09 -04:00
Kei Kebreau 1a0c4437ab
gnu: Add deutex. 
gnu/packages/game-development.scm (deutex): New variable.
 2017-03-19 21:43:05 -04:00
Arun Isaac f75b1400ee
gnu: obnam: Enable tests. 
* gnu/packages/backup.scm (obnam)[arguments]: Replace 'check' phase with
  custom function.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-20 00:40:32 +01:00
Arun Isaac 315944a393
gnu: Add python-pylint. 
* gnu/packages/python.scm (python-pylint, python2-pylint): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-20 00:40:31 +01:00
Arun Isaac 61550dedf3
gnu: Add python2-coverage-test-runner. 
* gnu/packages/python.scm (python2-coverage-test-runner): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-20 00:40:31 +01:00
Arun Isaac 23db3fc67d
gnu: Add python-configparser. 
* gnu/packages/python.scm (python-configparser, python2-configparser): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-20 00:40:30 +01:00
Arun Isaac 965a083ed2
gnu: Add python2-backports-functools-lru-cache. 
* gnu/packages/python.scm (python2-backports-functools-lru-cache): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-20 00:40:30 +01:00
Arun Isaac 6ba0af7960
gnu: Add python-isort. 
* gnu/packages/python.scm (python-isort, python2-isort): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-20 00:40:30 +01:00
Arun Isaac d5ef113c05
gnu: Add python-astroid. 
* gnu/packages/python.scm (python-astroid, python2-astroid): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-20 00:40:30 +01:00
Arun Isaac 6fdbd86d0f
gnu: Add libircclient. 
* gnu/packages/messaging.scm (libircclient): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-19 19:18:06 -04:00
rennes e05fc441cd
gnu: Add pdfgrep. 
* guix/gnu/packages/pdf.scm (pdfgrep): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-19 18:30:10 -04:00
Mark H Weaver 8299c697af
gnu: linux-libre: Update to 4.10.4. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.4.
(%linux-libre-hash): Update hash.
 2017-03-19 17:18:15 -04:00
Mark H Weaver 92c42164a2
gnu: linux-libre@4.9: Update to 4.9.16. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.16.
 2017-03-19 17:16:38 -04:00
Mark H Weaver 9baf0171a4
gnu: linux-libre@4.4: Update to 4.4.55. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.55.
 2017-03-19 17:14:56 -04:00
Danny Milosavljevic 9970ef6134
services: Remove Tab character from source code whitespace. 
* gnu/services/base.scm (file-system-shepherd-service): Remove Tab character
from source code whitespace.
 2017-03-19 21:36:55 +01:00
Danny Milosavljevic fc1bfca253
gnu: u-boot: Update to 2017.03. 
* gnu/packages/bootloaders.scm (u-boot): Update to 2017.03.
 2017-03-19 21:35:17 +01:00
Mark H Weaver 6191fef4e0
gnu: icecat: Add selected fixes from upstream mozilla-esr45. 
* gnu/packages/gnuzilla.scm (icecat)[source][patches]: Add selected fixes from
the upstream mozilla-esr45 repository.
 2017-03-19 15:55:06 -04:00
Mark H Weaver 512fc6db7b
gnu: libevent@2.0: Add fix from upstream. 
This fix was cherry-picked by Mozilla from upstream libevent-2.1 to its
bundled copy of libevent-2.0.21 in mozilla-esr45.

* gnu/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/libevent.scm (libevent-2.0)[source][patches]: Add it.
 2017-03-19 15:54:58 -04:00
Danny Milosavljevic 26e34e1e12
services: file-system-shepherd-service: Make it find the fsck programs. 
Fixes <https://bugs.gnu.org/25917>.

* gnu/services/base.scm (file-system-shepherd-service): Use
file-system-packages.
 2017-03-19 18:49:30 +01:00
Ludovic Courtès 7c86c03109
gnu: guile-commonmark: Default to Guile 2.2. 
* gnu/packages/guile.scm (guile-commonmark)[inputs]: Replace GUILE-2.0
with GUILE-2.2.
(guile2.0-commonmark): New variable.
(guile2.2-commonmark): Mark as deprecated.
(haunt)[propagated-inputs]: Use GUILE-COMMONMARK.
 2017-03-19 18:14:22 +01:00
Ludovic Courtès bdf1022dec
gnu: guile-reader: Default to Guile 2.2. 
* gnu/packages/guile.scm (guile-reader)[inputs]: Change GUILE-2.0 to
GUILE-2.2.
(guile2.0-reader): New variable.
(guile2.2-reader): Mark as deprecated.
(haunt)[propagated-inputs]: Use GUILE-READER instead of
GUILE2.2-READER.
 2017-03-19 18:14:22 +01:00
Ludovic Courtès bd19f65a85
gnu: haunt: Default to Guile 2.2. 
* gnu/packages/guile.scm (haunt)[inputs]: Replace GUILE-2.0 with
GUILE-2.2.
[propagated-inputs]: Replace GUILE-READER and GUILE-COMMONMARK with
their 2.2 variant.
(guile2.0-haunt): New variable.
(guile2.2-haunt): Mark as deprecated.
 2017-03-19 18:14:22 +01:00
Ludovic Courtès 8f4acad71b
gnu: Add 'package-for-guile-2.0'. 
* gnu/packages/guile.scm (guile-2.2-package-name): Rename to...
(guile-variant-package-name): ... this.  Change to return a lambda.
(package-for-guile-2.2): Adjust accordingly.
(package-for-guile-2.0): New procedure.
 2017-03-19 18:14:22 +01:00
Ludovic Courtès f6396d862f
gnu: Rename "guile-next" to "guile". 
* gnu/packages/guile.scm (guile-next): Rename to...
(guile-2.2): ... this.  Update users.
[name]: Change to "guile".
[synopsis]: Remove.
[properties]: Remove 'upstream-name', 'ftp-server', and
'ftp-directory'.
* gnu/packages/bioinformatics.scm (rcas-web): Update accordingly.
* gnu/packages/tls.scm (gnutls/guile-2.2): Likewise.
* tests/guix-build.sh: Use 'guile@2.2' instead of 'guile-next'.
* doc/guix.texi (Package Transformation Options): Update examples that
referred to "guile-next".
 2017-03-19 18:14:22 +01:00
Manolis Ragkousis 8df672aad5
gnu: Add GNU Mach. 
* gnu/packages/hurd.scm (gnumach): New variable.

Co-authored-by: Rene Saavedra <rennes@openmailbox.org>
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-19 18:14:22 +01:00
Ricardo Wurmus f729a4d8b2
gnu: niftilib: Simplify build phases. 
* gnu/packages/image.scm (niftilib)[arguments]: Use make-flags instead of
replacing "configure" phase; simplify "install" phase.
 2017-03-19 14:26:33 +01:00
Efraim Flashner eba72e1716
gnu: apl: Update to 1.7. 
* gnu/packages/apl.scm (apl): Update to 1.7.
[home-page]: Use https.
 2017-03-18 21:28:20 +02:00
Christopher Allan Webber 525acb6e82
gnu: guile-8sync: Update to 0.4.2. 
* gnu/packages/guile.scm (guile-8sync): Update to 0.4.2.
 2017-03-18 12:22:13 -05:00
Taylan Ulrich Bayırlı/Kammer 57d0bdf8c6
gnu: guix: Don't ignore user's GUILE_LOAD_COMPILED_PATH. 
* gnu/packages/package-management.scm (guix-0.12.0): Guile skips invalid .go
  files since 2.0.12 so we don't need to override GUILE_LOAD_COMPILED_PATH to
  prevent problems anymore.
 2017-03-18 18:26:11 +01:00
Danny Milosavljevic 7601b9f7ce
gnu: wine: Update to 2.4. 
* gnu/packages/wine.scm (wine): Update to 2.4.
 2017-03-18 17:26:02 +01:00
John Darrington 21122bd79e
gnu: Add niftilib. 
* gnu/packages/image.scm (niftilib): New variable.
 2017-03-18 15:25:59 +01:00
ng0 d54db52e7f
bug#26152: [PATCH] gnu: limnoria: Update to 20170110. 
* gnu/packages/irc.scm (limnoria): Update to 20170110.

Signed-off-by: Danny Milosavljevic <dannym@scratchpost.org>
 2017-03-18 11:51:21 +01:00
Danny Milosavljevic 7208995426
file-systems: Factorize file-system-packages. 
* gnu/system/linux-initrd.scm (base-initrd): Move helper-packages body to ...
* gnu/system/file-systems.scm (file-system-packages): ... here.  New variable.
Also export it.
 2017-03-18 10:38:51 +01:00
Danny Milosavljevic 84aac61c81
gnu: rustc: Fix process test. 
* gnu/packages/rust.scm (rustc)[arguments]: Rename 'patch-lockfile-test
to 'patch-tests.  Add another substitution.
 2017-03-18 10:37:02 +01:00
John Darrington 6d5f63b690
gnu: Add maxflow. 
* gnu/packages/maths.scm (maxflow): New variable.
 2017-03-18 10:31:54 +01:00
John Darrington a53d6719bc
gnu: Add itpp. 
* gnu/packages/maths.scm (itpp): New variable.
 2017-03-18 10:31:50 +01:00
Tobias Geerinckx-Rice b6bd9a79d4
gnu: emacs-slime: Update to 2.19. 
* gnu/packages/emacs.scm (emacs-slime): Update to 2.19.
 2017-03-18 01:49:38 +01:00
Ben Woodcroft 55f7a27cee
gnu: ocaml-qtest: Update to 2.5. 
* gnu/packages/ocaml.scm (ocaml-qtest): Update to 2.5.
 2017-03-18 09:52:29 +10:00
Marius Bakke 7c78beb33c
gnu: libbluray: Update to 1.0.0. 
* gnu/packages/video.scm (libbluray): Update to 1.0.0.
 2017-03-17 20:41:16 +01:00
Marius Bakke 715dd13d8e
gnu: libx264: Update to 20170316-2245. 
* gnu/packages/video.scm (libx264): Update to 20170316-2245.
 2017-03-17 20:41:15 +01:00
Marius Bakke 2a047d59e0
gnu: libwebp: Update to 0.6.0. 
* gnu/packages/image.scm (libwebp): Update to 0.6.0.
[source]: Remove patch.
* gnu/packages/patches/libwebp-CVE-2016-9085.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-03-17 20:41:15 +01:00
Marius Bakke cbef2796ed
gnu: ninja: Update to 1.7.2. 
* gnu/packages/ninja.scm (ninja): Update to 1.7.2.
[source]: Remove patch.
* gnu/packages/patches/ninja-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-03-17 20:41:15 +01:00
Tobias Geerinckx-Rice 039601e097
gnu: btrfs-progs: Use @dfn in description. 
* gnu/packages/linux.scm (btrfs-progs)[description]: Use @dfn.
 2017-03-17 20:39:58 +01:00
Tobias Geerinckx-Rice 0d3ddd490b
gnu: btrfs-progs: Update to 4.10.1. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.10.1.
 2017-03-17 20:39:58 +01:00
Danny Milosavljevic 893bc3f402
gnu: cargo: Use upstream cargo. 
* gnu/packages/rust.scm (cargo): Use upstream cargo.
 2017-03-17 16:48:08 +01:00
Danny Milosavljevic b0dcb529af
gnu: rust: Update to 1.15.0. 
* gnu/packages/rust.scm (%rust-bootstrap-binaries-version): Update to 1.14.0.
(%rust-bootstrap-binaries): Update to 1.14.0.
(rustc): Update to 1.15.0.
[arguments]: Pass "--disable-rustbuild" to configure.
 2017-03-17 16:48:06 +01:00
Kei Kebreau 8f98581613
gnu: libpng-apng: Remove unnecessary call to libtool. 
* gnu/packages/image.scm (libpng-apng)[phases]: Remove it.
 2017-03-17 11:36:27 -04:00
ng0 114a325e8f
gnu: Add libpng-apng. 
* gnu/packages/image.scm (libpng-apng): New variable.

Co-authored-by: Kei Kebreau <kei@openmailbox.org>
 2017-03-17 11:25:15 -04:00
Ben Woodcroft 0a3063d640
gnu: Add ocaml-mcl. 
* gnu/packages/machine-learning.scm (ocaml-mcl): New variable.
 2017-03-17 21:43:27 +10:00
Ben Woodcroft ba1be533ad
gnu: Add ocaml-gsl. 
* gnu/packages/maths.scm (ocaml-gsl): New variable.
 2017-03-17 21:43:25 +10:00
Ben Woodcroft 91df9eaefa
gnu: Add ocaml-csv. 
* gnu/packages/ocaml.scm (ocaml-csv): New variable.
 2017-03-17 21:43:13 +10:00
Ben Woodcroft 0c4dbdc23e
gnu: Add ocaml-sqlite3. 
* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
 2017-03-17 21:19:23 +10:00
Ricardo Wurmus ef71ed8ffa
gnu: snakemake: Update to 3.11.2. 
* gnu/packages/python.scm (snakemake): Update to 3.11.2.
 2017-03-17 10:14:03 +01:00
Ricardo Wurmus 60c9190e21
gnu: r-minimal: Fix remaining reproducibility problems. 
Fixes <https://bugs.gnu.org/25598>.

* gnu/packages/statistics.scm (r-minimal)[arguments]: Add remaining
reproducibility fixes to "build-reproducibly" phase.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus 2d7c4ae3ee
gnu: r: Rename to r-minimal. 
* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus f1fe5283c9
gnu: Add r-with-recommended-packages. 
* gnu/packages/statistics.scm (r-with-recommended-packages): New variable.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus aeb64f3cb2
gnu: r: Do not build recommended packages. 
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus 6eaa9bfba6
gnu: r-survival: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-survival): Move up to set of recommended R
packages.
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus 4b005c7a75
gnu: Add r-spatial. 
* gnu/packages/statistics.scm (r-spatial): New variable.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus 567b154fb0
gnu: r-rpart: Move to the set of recommended packages. 
* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus a5a343656b
gnu: r-nnet: Move to set of recommended R packages. 
* gnu/packages/machine-learning.scm (r-nnet): Move from here...
* gnu/packages/statistics.scm (r-nnet): ...to here because the other
recommended R packages are here.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus ac8d738b97
gnu: r-mgcv: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus 248f65269a
gnu: Add r-nlme. 
* gnu/packages/statistics.scm (r-nlme): New variable.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus 69e14f9ec7
gnu: r-matrix: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus 060c12868b
gnu: r-lattice: Move to other recommended R packages. 
* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus e88bad6ddb
gnu: Add r-kernsmooth. 
* gnu/packages/statistics.scm (r-kernsmooth): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus 69fddd2d6e
gnu: Add r-foreign. 
* gnu/packages/statistics.scm (r-foreign): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus c1999c5910
gnu: Add r-codetools. 
* gnu/packages/statistics.scm (r-codetools): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus a27bfb8484
gnu: Add r-cluster. 
* gnu/packages/statistics.scm (r-cluster): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus 7489258751
gnu: Add r-class. 
* gnu/packages/statistics.scm (r-class): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus c7e80a7e0d
gnu: Add r-mass. 
* gnu/packages/statistics.scm (r-mass): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus 8f0069170c
gnu: Add r-boot. 
* gnu/packages/statistics.scm (r-boot): New variable.
 2017-03-17 10:14:00 +01:00
Tobias Geerinckx-Rice 54d556bdd7
gnu: youtube-dl: Update to 2017.03.16. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
 2017-03-17 03:11:35 +01:00
Kei Kebreau 3078821d13
gnu: asciidoc: Use local docbook-xml package. 
* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml.
[arguments]: Add 'make-local-docbook-xml' phase.
 2017-03-16 21:35:50 -04:00
Tobias Geerinckx-Rice f9cdf1c15b
gnu: Add knot. 
* gnu/packages/dns.scm (knot): New variable.
 2017-03-17 02:32:01 +01:00
Tobias Geerinckx-Rice 754667f0eb
gnu: Add liburcu. 
* gnu/packages/datastructures.scm (liburcu): New variable.
 2017-03-17 02:32:00 +01:00
Tobias Geerinckx-Rice 366efcb2fb
gnu: dns: Fix typo and use @dfn in descriptions. 
* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms.
(yadifa)[description]: Likewise, and fix a typo.
 2017-03-17 02:32:00 +01:00
Leo Famulari 2ec5ba859f
gnu: linux-libre: Update to 4.10.3. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3.
(%linux-libre-hash): Update hash.
 2017-03-16 19:40:40 -04:00
Leo Famulari 2044306f05
gnu: linux-libre@4.4: Update to 4.4.54. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
 2017-03-16 19:40:39 -04:00
Leo Famulari bcc5b74173
gnu: linux-libre@4.9: Update to 4.9.15. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
 2017-03-16 19:40:39 -04:00
Leo Famulari 49ac6dbb0a
gnu: qemu: Fix CVE-2017-{2620,2630}. 
* gnu/packages/patches/qemu-CVE-2017-2620.patch,
gnu/packages/patches/qemu-CVE-2017-2630.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/qemu.scm (qemu)[source]: Use them.
 2017-03-16 19:40:08 -04:00
Leo Famulari 1e5b8beeff
gnu: virglrenderer: Fix CVE-2017-6386. 
* gnu/packages/patches/virglrenderer-CVE-2017-6386.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/spice.scm (virglrenderer)[source]: Use it.
 2017-03-16 19:39:55 -04:00
Mathieu Othacehe 34d60c49cb
services: connman: Rework service. 
* gnu/services/networking.scm (connman-service): Remove.
(<connman-configuration>): New record specifying the package
to be used (connman) and whether vpn plugin shall be
disabled (disable-vpn?).
(connman-configuration): New exported variable.
(connman-configuration?): New exported variable.
(connman-service-type): Export it.

* doc/guix.texi (Networking Services): Adjust accordingly.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-16 22:50:14 +01:00
Clément Lassieur 2c715a9223
gnu: password-store: Fix compatibility with GnuPG 2.1.19. 
* gnu/packages/patches/password-store-gnupg-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/password-utils.scm (password-store)[source]: Use it.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
 2017-03-16 19:58:43 +01:00
Raoul Jean Pierre Bonnal 2441c28414
gnu: Add r-seurat. 
* gnu/packages/bioinformatics.scm (r-seurat): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-03-16 14:54:58 +01:00
Ricardo Wurmus 79849358f8
gnu: sra-tools: Update to 2.8.2-1. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
 2017-03-16 13:40:36 +01:00
Ricardo Wurmus d5e1716239
gnu: ncbi-vdb: Install configuration files. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
 2017-03-16 13:39:53 +01:00
Ricardo Wurmus 558e23074e
gnu: ncbi-vdb: Override search path for java-ngs. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
 2017-03-16 13:38:39 +01:00
Ricardo Wurmus 701111989e
gnu: ncbi-vdb: Use modify-phases syntax. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
 2017-03-16 10:20:56 +01:00
Ricardo Wurmus 5021f54787
gnu: ncbi-vdb: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
 2017-03-16 10:19:25 +01:00
Ricardo Wurmus 6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
 2017-03-16 10:18:48 +01:00
Tobias Geerinckx-Rice 0f03c53168
gnu: Add pzstd. 
* gnu/packages/compression.scm (pzstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice f6ac3101ff
gnu: Add zstd. 
* gnu/packages/compression.scm (zstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice 9186216268
gnu: python-publicsuffix2: Update to 2.20160818. 
* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice 192b887a03
gnu: awscli: Update to 1.11.63. 
* gnu/packages/python.scm (awscli): Update to 1.11.63.
 2017-03-16 05:44:01 +01:00
Tobias Geerinckx-Rice d93985fe22
gnu: python-botocore: Update to 1.5.26. 
* gnu/packages/python.scm (python-botocore): Update to 1.5.26.
 2017-03-16 05:44:01 +01:00