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15154 Commits

Author SHA1 Message Date
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
Tobias Geerinckx-Rice 70fc93cb28
gnu: python-ptyprocess: Update to 0.5.1. 
* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1.
 2017-03-16 05:44:01 +01:00
Kei Kebreau 26a657f06a
gnu: Add prboom-plus. 
* gnu/packages/games.scm (prboom-plus): New variable.
 2017-03-15 23:14:42 -04:00
Gábor Boskovits 5b5cf3c765
gnu: Add tftp-hpa. 
* gnu/packages/networking.scm (tftp-hpa): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 18:24:30 -04:00
Andy Wingo 80a725726d
gnu: guile-next: Update to 2.2.0. 
* gnu/packages/guile.scm (guile-next): Update to 2.2.0.
 2017-03-15 22:59:40 +01:00
Leo Famulari dce8ac54b4
gnu: profanity: Make the source URL version-agnostic. 
* gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source
URL.
 2017-03-15 17:20:27 -04:00
Tobias Geerinckx-Rice cf8d068775
gnu: units: Update to 2.14. 
* gnu/packages/maths.scm (units): Update to 2.14.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice 3d602acb13
gnu: no-more-secrets: Update to 0.3.2. 
* gnu/packages/games.scm (no-more-secrets): Update to 0.3.2.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice 7ea523853c
gnu: mailutils: Update to 3.2. 
* gnu/packages/mail.scm (mailutils): Update to 3.2.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice f38607536e
gnu: Use INSTALL-FILE where appropriate. 
* gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler
INSTALL-FILE for COPY-FILE when invoked with redundant arguments.
* gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity,
edirect, fasttree, rsem, samtools-0.1): Likewise.
* gnu/packages/code.scm (withershins): Likewise.
* gnu/packages/conky.scm (conky): Likewise.
* gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise.
* gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise.
* gnu/packages/engineering.scm (librecad): Likewise.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice 618e4bfbad
gnu: cryptsetup: Update to 1.7.4. 
* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.4.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice 4e128dd582
gnu: man-pages: Update to 4.10. 
* gnu/packages/man.scm (man-pages): Update to 4.10.
[home-page]: Use HTTPS.
 2017-03-15 22:19:38 +01:00
Mekeor Melire a829c6501b
gnu: Add profanity. 
* gnu/packages/messaging.scm (profanity): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00
Mekeor Melire 781d3b070c
gnu: Add libstrophe. 
* gnu/packages/messaging.scm (libstrophe): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00
Mekeor Melire 13292ee570
gnu: Add libmesode. 
* gnu/packages/messaging.scm (libmesode): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00
Leo Famulari 9e61d1534a
gnu: bitcoin-core: Update to 0.14.0. 
* gnu/packages/finance.scm (bitcoin-core): Update to 0.14.0.
 2017-03-15 15:48:43 -04:00
Marius Bakke bd102157a1
gnu: mariadb: Update to 10.1.22 [fixes CVE-2017-3302 and CVE-2017-3313]. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.22.
 2017-03-15 15:08:31 +01:00
Efraim Flashner 27bf00e691
gnu: python-waf: Update to 1.9.8. 
* gnu/packages/python.scm (python-waf, python2-waf): Update to 1.9.8.
[home-page]: Use https.
 2017-03-15 13:08:56 +02:00
Tobias Geerinckx-Rice 283234a309
gnu: direnv: Update to 2.11.3. 
* gnu/packages/shellutils.scm (direnv): Update to 2.11.3.
 2017-03-15 03:45:57 +01:00
Tobias Geerinckx-Rice 68c10f31f9
gnu: conky: Update to 1.10.6. 
* gnu/packages/conky.scm (conky): Update to 1.10.6.
 2017-03-15 03:45:56 +01:00
Tobias Geerinckx-Rice 708e76287c
gnu: obs: Update to 18.0.1. 
* gnu/packages/video.scm (obs): Update to 18.0.1.
 2017-03-15 03:45:56 +01:00
Tobias Geerinckx-Rice 17753e6edb
gnu: youtube-dl: Update to 2017.03.15. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.15.
 2017-03-15 03:45:55 +01:00
Tobias Geerinckx-Rice a988cbb766
gnu: stress-make: Fix description. 
* gnu/packages/debug.scm (stress-make)[description]: Fix typo.
Avoid ambiguous use of ‘in order’.
 2017-03-15 03:45:55 +01:00
Tobias Geerinckx-Rice d540156c69
gnu: znc: Update to 1.6.5. 
* gnu/packages/messaging.scm (znc): Update to 1.6.5.
 2017-03-15 03:43:21 +01:00
Tobias Geerinckx-Rice 6d57723ac8
gnu: grue-hunter: Correctly install documentation. 
* gnu/packages/games.scm (grue-hunter)[arguments]: Install and populate
‘/share/doc/grue-hunter’ as a directory, not a plain file.
 2017-03-15 01:10:31 +01:00
Tobias Geerinckx-Rice b2d748edff
gnu: samtools: End installation phases with truth. 
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]:
Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
 2017-03-15 01:10:30 +01:00
Leo Famulari 35dcfed370
gnu: w3m: Update to 0.5.3+git20170102 [security fixes]. 
See 'NEWS' and 'ChangeLog' in the source distribution for more
information about the security-related bug fixes.

* gnu/packages/w3m.scm (w3m): Update to 0.5.3+git20170102.
 2017-03-14 18:26:28 -04:00
Leo Famulari 2eab5db300
Revert "gnu: gitolite: Fix shebangs in hooks." 
This change embedded store references in the shebangs of scripts that
were meant to be copied out of the store. Those scripts would break when
the interpreters expected by the shebangs were garbage collected.

<https://debbugs.gnu.org/cgi/bugreport.cgi?bug=25966#28>

This reverts commit d0c16adb19.
 2017-03-14 18:26:28 -04:00
Marius Bakke 796d2f2d0b
Revert "gnu: nss: Use 'modify-phases' syntax." 
This reverts commit 87f1c7efc1.
 2017-03-14 22:29:18 +01:00
Marius Bakke 031349075a
Revert "gnu: nss, nss-certs: Update to 3.29.3." 
Hydra failed to build this version. See discussion at
https://lists.gnu.org/archive/html/guix-devel/2017-03/msg00408.html.

This reverts commit 4f3dcdd99b.
 2017-03-14 22:26:18 +01:00
Julien Lepiller edda7ebec1
gnu: Add ocaml-ppx-typerep-conv. 
* gnu/packages/ocaml.scm (ocaml-ppx-typerep-conv): New variable.
 2017-03-14 22:09:56 +01:00
Julien Lepiller d2203187fe
gnu: Add ocaml-ppx-let. 
* gnu/packages/ocaml.scm (ocaml-ppx-let): New variable.
 2017-03-14 22:09:50 +01:00
Julien Lepiller 250ac438e7
gnu: Add ocaml-ppx-enumerate. 
* gnu/packages/ocaml.scm (ocaml-ppx-enumerate): New variable.
 2017-03-14 22:09:48 +01:00
Julien Lepiller a43160ee6f
gnu: Add ocaml-ppx-assert. 
* gnu/packages/ocaml.scm (ocaml-ppx-assert): New variable.
 2017-03-14 22:09:46 +01:00
Julien Lepiller 651563bd71
gnu: Add ocaml-ppx-here. 
* gnu/packages/ocaml.scm (ocaml-ppx-here): New variable.
 2017-03-14 22:09:44 +01:00
Julien Lepiller 14af90cfbd
gnu: Add ocaml-ppx-variants-conv. 
* gnu/packages/ocaml.scm (ocaml-ppx-variants-conv): New variable.
 2017-03-14 22:09:41 +01:00
Julien Lepiller 334436f051
gnu: Add ocaml-ppx-sexp-conv. 
* gnu/packages/ocaml.scm (ocaml-ppx-sexp-conv): New variable.
 2017-03-14 22:09:39 +01:00
Julien Lepiller d1d90df63b
gnu: Add ocaml-variantslib. 
* gnu/packages/ocaml.scm (ocaml-variantslib): New variable.
 2017-03-14 22:09:37 +01:00
Julien Lepiller ef0051b2c5
gnu: Add ocaml-typerep. 
* gnu/packages/ocaml.scm (ocaml-typerep): New variable.
 2017-03-14 22:09:33 +01:00
Julien Lepiller d19c1b4105
gnu: Add ocaml-sexplib. 
* gnu/packages/ocaml.scm (ocaml-sexplib): New variable.
 2017-03-14 22:09:14 +01:00
Kei Kebreau 9099a45792
gnu: asciidoc: Add XML and XSLT support. 
* gnu/packages/documentation.scm (asciidoc)[arguments]: Add
set-xml-binary-paths phase.
[inputs]: Add libxml2 and libxslt.
 2017-03-14 15:57:54 -04:00
Ludovic Courtès 5895ec8aa2
pack: Add '--symlink'. 
* guix/scripts/pack.scm (self-contained-tarball): Add #:symlinks
parameter.
[build](symlink->directives): New procedure
(directives): New variable.
Add call to 'evaluate-populate-directive'.  Pass the directories among
DIRECTIVES to 'tar'.
(%default-options): Add 'symlinks'.
(%options, show-help): Add '--symlink'.
(guix-pack): Honor it.
* gnu/build/install.scm (evaluate-populate-directive): Export.
* doc/guix.texi (Invoking guix pack): Document it.
 2017-03-14 17:57:27 +01:00
Ludovic Courtès 6b63c43e06
pack: Add '--localstatedir' option. 
* guix/scripts/pack.scm (self-contained-tarball): Add #:localstatedir?
parameter and honor it.
(%options, show-help): Add '--localstatedir'.
(guix-pack): Honor it.
* gnu/build/install.scm (populate-single-profile-directory): Add
 #:register? parameter and honor it.
* doc/guix.texi (Binary Installation): Use '--localstatedir' in
example.
(Invoking guix pack): Document it.
 2017-03-14 17:57:27 +01:00
Leo Famulari 9b05ccfedd
gnu: linux-libre@4.1: Update to 4.1.39. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.39.
 2017-03-14 12:55:20 -04:00
Leo Famulari 962cbb24c5
gnu: windowmaker: Use modify-phases syntax. 
* gnu/packages/gnustep.scm (windowmaker)[arguments]: Use modify-phases.
 2017-03-14 12:10:16 -04:00
Leo Famulari 8cac5bca12
gnu: windowmaker: Update to 0.95.8. 
* gnu/packages/gnustep.scm (windowmaker): Update to 0.95.8.
 2017-03-14 12:10:12 -04:00
Efraim Flashner d779305db0
gnu: aria2: Update to 1.31.0. 
* gnu/packages/bittorrent.scm (aria2): Update to 1.31.0.
 2017-03-14 15:05:27 +02:00
Ludovic Courtès 28958b646f
gnu: python-parsedatetime: Update to 2.3. 
Version 2.1 was apparently time-sensitive and started failing like this:

  ======================================================================
  FAIL: testFloat (tests.TestDelta.test)
  ----------------------------------------------------------------------
  Traceback (most recent call last):
    File "/tmp/guix-build-python2-parsedatetime-2.1.drv-0/parsedatetime-2.1/tests/TestDelta.py", line 64, in testFloat
      self.cal.parse('1.4 months ago', self.source), months=-1.4)
    File "/tmp/guix-build-python2-parsedatetime-2.1.drv-0/parsedatetime-2.1/tests/TestDelta.py", line 37, in assertDelta
      self.assertTrue(diff < 0.05, '%s is not less than 0.05' % diff)
  AssertionError: 0.0666666666667 is not less than 0.05

  ----------------------------------------------------------------------

* gnu/packages/python.scm (python-parsedatetime): Update to 2.3.
[native-inputs]: Add PYTHON-PYTEST and PYTHON-PYTEST-RUNNER.
[propagated-inputs]: New field.
 2017-03-14 11:18:16 +01:00
ng0 a4651f6411
gnu: Add dovecot-libsodium-plugin. 
* gnu/packages/mail.scm (dovecot-libsodium-plugin): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-14 10:28:57 +01:00
ng0 944a5cdd0d
gnu: Add dovecot-trees. 
* gnu/packages/mail.scm (dovecot-trees): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-14 10:28:57 +01:00
Leo Famulari a70782d37b
gnu: wireless-regdb: Update to 2017.03.07. 
* gnu/packages/linux.scm (wireless-regdb): Update to 2017.03.07.
 2017-03-14 01:58:35 -04:00
Ludovic Courtès 0f11f64022
gnu: guile-cairo: Honor the Guile effective version. 
* gnu/packages/gtk.scm (guile-cairo)[arguments]: Add #:modules.
Get the effective version of Guile and use that in installation
directory names.
 2017-03-13 22:26:54 +01:00
Ludovic Courtès b97438650d
gnu: guile-cairo: Use 'modify-phases'. 
* gnu/packages/gtk.scm (guile-cairo)[arguments]: Use 'modify-phases'.
 2017-03-13 22:18:13 +01:00
Ludovic Courtès 12773de3e7
gnu: Add guile2.2-lib. 
* gnu/packages/guile.scm (guile2.2-lib): New variable.
 2017-03-13 21:52:38 +01:00
humanitiesNerd a71c863834
gnu: Add python-flask-login. 
* gnu/packages/python.scm (python-flask-login, python2-flask-login): New
variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-13 19:36:56 +01:00
humanitiesNerd 78c5566365
gnu: Add python-flask-htmlmin. 
* gnu/packages/python.scm (python-flask-htmlmin, python2-flask-htmlmin): New
variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-13 19:36:55 +01:00
humanitiesNerd 35db2d3cb7
gnu: Add python-htmlmin. 
* gnu/packages/python.scm (python-htmlmin, python2-htmlmin): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-03-13 19:36:54 +01:00
Marius Bakke 1bbbb0b4af
gnu: diffoscope: Update to 78. 
* gnu/packages/package-management.scm (diffoscope): Update to 78.
 2017-03-13 19:16:19 +01:00
Marius Bakke 8298df96ac
gnu: Add minizip. 
* gnu/packages/compression.scm (minizip): New variable.
 2017-03-13 19:16:19 +01:00
Marius Bakke dd8ecb386c
gnu: notmuch: Update to 0.24. 
* gnu/packages/mail.scm (notmuch, python-notmuch, python2-notmuch): Update to
0.24.
 2017-03-13 18:21:23 +01:00
Marius Bakke 17fb6fb105
gnu: xf86-video-intel: Update to 2.99.917-4-7e9e92c. 
* gnu/packages/xorg.scm (xf86-video-intel): Update to 2.99.917-4-7e9e92c.
 2017-03-13 18:21:23 +01:00
Marius Bakke ca453df7c8
gnu: xf86-video-nouveau: Update to 1.0.14. 
* gnu/packages/xorg.scm (xf86-video-nouveau): Update to 1.0.14.
 2017-03-13 18:21:22 +01:00
Marius Bakke 4f3dcdd99b
gnu: nss, nss-certs: Update to 3.29.3. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.29.3.
* gnu/packages/certs.scm (nss-certs): Update to 3.29.3.
 2017-03-13 18:21:22 +01:00
Marius Bakke 87f1c7efc1
gnu: nss: Use 'modify-phases' syntax. 
* gnu/packages/gnuzilla.scm (nss)[arguments]: Use 'modify-phases'.
 2017-03-13 18:21:22 +01:00
Alex Kost 7a4dea524b
gnu: manaplus: Update to 1.7.3.4. 
* gnu/packages/games.scm (manaplus): Update to 1.7.3.4.
 2017-03-13 18:21:10 +03:00
Alex Kost 846344d053
gnu: git-modes: Update to 1.2.4. 
* gnu/packages/emacs.scm (git-modes): Update to 1.2.4.
 2017-03-13 18:21:10 +03:00
Alex Kost 2617050b3b
gnu: magit: Update to 2.10.3. 
* gnu/packages/emacs.scm (magit): Update to 2.10.3.
 2017-03-13 18:21:10 +03:00
Andy Wingo 0216137237
gnu: guile-next: Update to 2.1.8. 
* gnu/packages/guile.scm (guile-next): Update to 2.1.8.
 2017-03-13 12:22:38 +01:00
pjotrp 3288e647e3
gnu: r-hexbin: Update to 1.27.1-1. 
The package tarball was updated in place, resulting in a change in the hash
value.  We decided to bump the version to 1.27.1-1 instead of keeping the
version at upstream's 1.27.1.

* gnu/packages/statistics.scm (r-hexbin): Update to 1.27.1-1.
 2017-03-13 10:34:00 +01:00
Ludovic Courtès 8f7ea70913
gnu: guile-next: Increase max-silent-time. 
* gnu/packages/guile.scm (guile-next)[properties]: Add 'max-silent-time'.
 2017-03-13 10:30:33 +01:00
Leo Famulari 59bb178cce
gnu: linux-libre@4.4: Update to 4.4.53. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.53.
 2017-03-13 00:56:58 -04:00
Leo Famulari 7bc57e760c
gnu: linux-libre@4.9: Update to 4.9.14. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.14.
 2017-03-13 00:56:58 -04:00
Leo Famulari 49a8c92cbe
gnu: linux-libre: Update to 4.10.2. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.2.
(%linux-libre-hash): Update hash.
 2017-03-13 00:56:58 -04:00
Andy Patterson 108f69c448
gnu: ecl: Update to 16.1.3. 
* gnu/packages/lisp.scm (ecl): Update to 16.1.3.
[arguments]: Use a different method to set the binary used for tests.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-12 23:47:40 -04:00
Marius Bakke 3f06f43058
gnu: irssi: Update to 1.0.2. 
* gnu/packages/irc.scm (irssi): Update to 1.0.2.
 2017-03-12 19:58:52 +01:00
Clément Lassieur 720cb10c15
services: Move configuration functions that shouldn't be factorized. 
* gnu/services/configuration.scm (serialize-field, serialize-string)
(serialize-space-separated-string-list, space-separated-string-list?)
(serialize-file-name, file-name?, serialize-boolean): Move these functions...
* gnu/services/cups.scm: ...to this file.
* gnu/services/kerberos.scm: ...to this file.

Configuration syntaxes are very specific to services.  Some services may have
the same configuration syntax, but none of them is common enough to be
abstracted in configuration.scm.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
 2017-03-12 19:09:32 +01:00
Clément Lassieur 56aef188a2
services: dovecot: Reimplement proper configuration functions. 
* gnu/services/mail.scm (uglify-field-name, serialize-field, serialize-string)
(space-separated-string-list?, serialize-space-separated-string-list)
(file-name?, serialize-file-name, serialize-boolean): Add them.

These functions were inadvertently changed while being factorized in
gnu/service/configuration.scm.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
 2017-03-12 19:08:50 +01:00
Ludovic Courtès 239c22663a
Add 'guix pack'. 
* gnu/system/install.scm (self-contained-tarball): Move to...
* guix/scripts/pack.scm: ... here.  New file.
* doc/guix.texi (Binary Installation): Mention 'guix pack'.
(Invoking guix pack): New node.
* build-aux/make-binary-tarball.scm: Remove.
* Makefile.am (MODULES): Add guix/scripts/pack.scm.
(EXTRA_DIST): Remove build-aux/make-binary-tarball.scm.
(guix-binary.%.tar.xz): Rewrite using 'guix pack'.
* build-aux/hydra/gnu-system.scm (tarball-jobs): Adjust accordingly.
 2017-03-12 17:47:25 +01:00
Ludovic Courtès 998ac26a1e
gnu: tintin++: Use a mirror:// URI. 
* gnu/packages/games.scm (tintin++)[source]: Use mirror://sourceforge.
 2017-03-12 17:47:25 +01:00
Tobias Geerinckx-Rice 301f12ec92
gnu: offlineimap: Update to 7.0.14. 
* gnu/packages/mail.scm (offlineimap): Update to 7.0.14.
 2017-03-12 15:44:37 +01:00
Leo Famulari 0a6bd107e5
gnu: Add le-certs. 
* gnu/packages/certs.scm (le-certs): New variable.
 2017-03-12 03:23:16 -04:00
Clément Lassieur eba560765a
services: dovecot: Fix unix_listeners and fifo_listeners path types. 
* gnu/services/mail.scm (unix-listener-configuration)[path]
(fifo-listener-configuration)[path]: Change type from 'file-name' to 'string'.
* doc/guix.texi (Mail Services): Document it.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
 2017-03-12 01:30:23 +01:00
Raoul Jean Pierre Bonnal a5935d1946
gnu: Add r-tsne. 
* gnu/packages/bioinformatics.scm (r-tsne): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:07 +10:00
Raoul Jean Pierre Bonnal 02eec38ee1
gnu: Add r-ranger. 
* gnu/packages/statistics.scm (r-ranger): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:07 +10:00
Raoul Jean Pierre Bonnal d1906e3147
gnu: Add r-tclust. 
* gnu/packages/statistics.scm (r-tclust): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:07 +10:00
Raoul Jean Pierre Bonnal 5a200a24eb
gnu: Add r-sn. 
* gnu/packages/statistics.scm (r-sn): New variable.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal 06085b5bc5
gnu: Add r-numderiv. 
* gnu/packages/statistics.scm (r-numderiv): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal fe68c8a990
gnu: Add r-mnormt. 
* gnu/packages/statistics.scm (r-mnormt): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal 362ea0dc29
gnu: Add r-rcppprogress. 
* gnu/packages/statistics.scm (r-rcppprogress): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal aa890f6185
gnu: Add r-caret. 
* gnu/packages/statistics.scm (r-caret): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal ab2ec643c3
gnu: Add r-car. 
* gnu/packages/statistics.scm (r-car): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal a3eb8c8191
gnu: Add r-pbkrtest. 
* gnu/packages/statistics.scm (r-pbkrtest): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal 51fc7d8c31
gnu: Add r-lme4. 
* gnu/packages/statistics.scm (r-lme4): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal c549864d90
gnu: Add r-nloptr. 
* gnu/packages/statistics.scm (r-nloptr): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal 49dc1fa5cb
gnu: Add r-quantreg. 
* gnu/packages/statistics.scm (r-quantreg): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal 545d0789fc
gnu: Add r-matrixmodels. 
* gnu/packages/statistics.scm (r-matrixmodels): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal aa84100011
gnu: Add r-modelmetrics. 
* gnu/packages/statistics.scm (r-modelmetrics): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal 21cfad44c1
gnu: Add r-rcppeigen. 
* gnu/packages/statistics.scm (r-rcppeigen): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:06 +10:00
Raoul Jean Pierre Bonnal 0392f82fd5
gnu: Add r-minqa. 
* gnu/packages/statistics.scm (r-minqa): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-12 10:28:05 +10:00
Danny Milosavljevic 5a717a95b3
gnu: wine: Update to 2.3. 
* gnu/packages/wine.scm (wine): Update to 2.3.
 2017-03-12 00:00:25 +01:00
Thomas Danckaert 4bff300b53
gnu: Add phonon-backend-gstreamer. 
* gnu/packages/kde-frameworks.scm (phonon-backend-gstreamer): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-11 22:23:28 +01:00
Thomas Danckaert 5578c2987e
gnu: phonon: Install Qt extensions. 
* gnu/packages/kde-frameworks.scm (phonon)[arguments]: Add
-DPHONON-INSTALL_QT_EXTENSIONS_INTO_SYSTEM_QT configure flag, and patch the
installation directory.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-11 22:23:28 +01:00
Sergei Trofimovich 612af7ff66
gnu: re2: Set CXX for cross-compilation. 
* gnu/packages/regex.scm (re2)[arguments]: Specify CXX in #:make-flags.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-11 22:23:28 +01:00
Mathieu Othacehe e7b9dac7b1
gnu: cuirass: Update to 0.0.1 revision 5. 
* gnu/packages/ci.scm (cuirass): Update to 0.0.1 revision 5.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-11 22:23:28 +01:00
Leo Famulari c4b15cb54f
gnu: imagemagick: Update to 6.9.7-10. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.7-10.
 2017-03-11 12:35:57 -05:00
rsiddharth a15638034e
gnu: Add ghc-unexceptionalio. 
* gnu/packages/haskell.scm (ghc-unexceptionalio): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-11 12:43:36 +01:00
Arun Isaac 55fa53491b
gnu: Add emacs-memoize. 
* gnu/packages/emacs.scm (emacs-memoize): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-11 12:43:36 +01:00
Mathieu Othacehe 47bdc5a173
linux-initrd: Add a raw-initrd and use it to define base-initrd. 
* gnu/system/linux-initrd.scm (raw-initrd): New exported variable.
(base-initrd): Use raw-initrd to build the initrd.
* doc/guix.texi (Initial RAM Disk): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-03-11 12:43:36 +01:00
Leo Famulari c84c8f66f5
gnu: wget: Fix CVE-2017-6508. 
* gnu/packages/patches/wget-CVE-2017-6508.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/wget.scm (wget)[source]: Use it.
 2017-03-10 22:36:58 -05:00
Raoul Jean Pierre Bonnal e08ad76658
gnu: Add r-fnn. 
* gnu/packages/statistics.scm (r-fnn): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 11:55:28 +10:00
Raoul Jean Pierre Bonnal 7711f61450
gnu: Add r-pbapply. 
* gnu/packages/statistics.scm (r-pbapply): New variable.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 11:51:50 +10:00
Raoul Jean Pierre Bonnal d4cebae286
gnu: Add r-vgam. 
* gnu/packages/statistics.scm (r-vgam): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 11:47:02 +10:00
Ben Woodcroft fbf45d6ea7
gnu: vsearch: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
 2017-03-11 11:37:15 +10:00
Raoul Jean Pierre Bonnal 036cd0cb8b
gnu: Add r-ape. 
* gnu/packages/bioinformatics.scm (r-ape): New variable.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Raoul Jean Pierre Bonnal a409e8b52f
gnu: Add r-fpc. 
* gnu/packages/statistics.scm (r-fpc): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Raoul Jean Pierre Bonnal 5da4f84f1f
gnu: Add r-trimcluster. 
* gnu/packages/statistics.scm (r-trimcluster): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Raoul Jean Pierre Bonnal c0cab38e03
gnu: Add r-robustbase. 
* gnu/packages/statistics.scm (r-robustbase): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Raoul Jean Pierre Bonnal cda0720805
gnu: Add r-deoptimr. 
* gnu/packages/statistics.scm (r-deoptimr): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Raoul Jean Pierre Bonnal c962816dc4
gnu: Add r-prabclus. 
* gnu/packages/statistics.scm (r-prabclus): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Raoul Jean Pierre Bonnal 5638e15475
gnu: Add r-mclust. 
* gnu/packages/statistics.scm (r-mclust): New variable.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:25 +10:00
Raoul Jean Pierre Bonnal a1f2668e6c
gnu: Add r-flexmix. 
* gnu/packages/statistics.scm (r-flexmix): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:25 +10:00