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Author SHA1 Message Date
Efraim Flashner
7a5b944eb5 gnu: Add python-futures. 
* gnu/packages/python.scm (python-futures, python2-futures): New variables.
 2016-01-17 22:37:04 +02:00
Efraim Flashner
c9e330d001 gnu: Add python-keystoneclient. 
* gnu/packages/openstack.scm (python-keystoneclient)
(python2-keystoneclient): New variables.
 2016-01-17 22:37:04 +02:00
Ricardo Wurmus
fb492b9a64 gnu: vmpk: Update to 0.6.2a. 
* gnu/packages/music.scm (vmpk): Update to 0.6.2a.
 2016-01-17 19:57:07 +01:00
Ricardo Wurmus
cfac12723a gnu: drumstick: Update to 1.0.2. 
* gnu/packages/music.scm (drumstick): Update to 1.0.2.
 2016-01-17 19:57:00 +01:00
Efraim Flashner
81c29cccaa gnu: mpv: Add features. 
* gnu/packages/video.scm (mpv)[inputs]: Add libvdpau.
[arguments]: Add gpl3 and zsh completion flags.
 2016-01-17 20:43:51 +02:00
Efraim Flashner
3161d32d37 gnu: Add vdpauinfo. 
* gnu/packages/video.scm (vdpauinfo): New variable.
 2016-01-17 20:43:51 +02:00
Efraim Flashner
d5650f86a7 gnu: Add libvdpau. 
* gnu/packages/video.scm (libvdpau): New variable.
 2016-01-17 20:43:51 +02:00
Eric Bavier
2328b47c64 gnu: Add autojump. 
* gnu/packages/admin.scm (autojump): New variable.
 2016-01-17 01:44:15 -06:00
Eric Bavier
f5a8491b69 gnu: hevea: Update to 2.28. 
* gnu/packages/ocaml.scm (hevea): Update to 2.28.
  [arguments]: Add 'patch-/bin/sh phase.
 2016-01-17 01:04:43 -06:00
Eric Bavier
90907a22bc gnu: unison: Add "doc" output. 
* gnu/packages/ocaml.scm (unison)[source]: Use svn-fetch with snippet.
  [outputs]: New field.
  [native-inputs]: Add ghostscript, texlive, hevea, and lynx.
  [arguments]: Add 'install-doc phase.
 2016-01-17 01:04:43 -06:00
Ricardo Wurmus
2309ed6862 gnu: samtools-0.1: Adapt to changes in "samtools" variable. 
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
  "LIBCURSES" make flag; delete "configure" phase; disable tests outside
  of "substitute-keyword-arguments".
 2016-01-16 15:50:51 +01:00
Ludovic Courtès
7ba903b6db linux-modules: Support 'modprobe.blacklist' on the command line. 
* gnu/build/linux-modules.scm (file-name->module-name)
(module-black-list): New procedure.
* gnu/build/linux-modules.scm (load-linux-module*): Add #:black-list
parameter.
[black-listed?, load-dependencies]: New procedures.
Use them.
 2016-01-16 14:45:47 +01:00
Alex Kost
b8300494c0 Move <boot-parameters> to (gnu system). 
* guix/scripts/system.scm (previous-grub-entries)
  (display-system-generation): Use accessors instead of matching
  <boot-parameters>.
  (boot-parameters, boot-parameters?, boot-parameters-label)
  (boot-parameters-root-device, boot-parameters-kernel)
  (boot-parameters-kernel-arguments, read-boot-parameters): Move to...
* gnu/system.scm: ... here. Export them.
 2016-01-16 13:02:21 +03:00
宋文武
c3e919d7a0 gnu: Add python-hy. 
* gnu/packages/python.scm (python-hy, python2-hy): New variables.
 2016-01-16 08:18:37 +08:00
宋文武
e224b7d0bd gnu: Add python-rply. 
* gnu/packages/python.scm (python-rply, python2-rply): New variables.
 2016-01-16 08:18:37 +08:00
宋文武
4ecdeef8ae gnu: Add python-astor. 
* gnu/packages/python.scm (python-astor, python2-astor): New variables.
 2016-01-16 08:18:37 +08:00
宋文武
c06a3de93a gnu: Add python-clint. 
* gnu/packages/python.scm (python-clint, python2-clint): New variables.
 2016-01-16 08:17:04 +08:00
宋文武
2216e15cc3 gnu: Add python-args. 
* gnu/packages.scm (python-args, python2-args): New variables.
 2016-01-16 08:16:51 +08:00
Leo Famulari
78e6c4a862 gnu: Add khal. 
* gnu/packages/calendar.scm (khal): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
b97c1bfd56 gnu: python-urwid: Disable failing test test_remove_watch_file. 
* gnu/packages/python.scm (python-urwid)[arguments]: Add
'disable-failing-test' phase.
[source]: Use pypi-uri.
 2016-01-15 16:45:24 -05:00
Leo Famulari
226d333103 gnu: Update python-tzlocal to 1.2. 
* gnu/packages/python.scm (python-tzlocal): Update to 1.2.
[source]: Use pypi-uri.
[arguments]: Remove the custom 'unpack phase.
[native-inputs]: Remove unzip, python-setuptools.
[propagated-inputs]: Add python-pytz.
 2016-01-15 16:45:24 -05:00
Leo Famulari
6bbbb53eeb gnu: Add python-sphinxcontrib-newsfeed. 
* gnu/packages/python.scm (python-sphinxcontrib-newsfeed): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
5c299bf016 gnu: Add python-icalendar. 
* gnu/packages/python.scm (python-icalendar): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
a2f6a3d502 gnu: Add vdirsyncer. 
* gnu/packages/dav.scm (vdirsyncer): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
f75bbb028a gnu: Add radicale. 
* gnu/packages/dav.scm (radicale): New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
 2016-01-15 16:45:24 -05:00
Leo Famulari
89b8a5516f gnu: Add python-pytest-xprocess. 
* gnu/packages/python.scm (python-pytest-xprocess): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
28cecbb7cc gnu: Add python-wsgi-intercept. 
* gnu/packages/python.scm (python-wsgi-intercept): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
d7e729fe08 gnu: Add python-pytest-localserver. 
* gnu/packages/python.scm (python-pytest-localserver): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
6720dbb49f gnu: Add python-pytest-cache. 
* gnu/packages/python.scm (python-pytest-cache): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
848964fe11 gnu: Add python-execnet. 
* gnu/packages/python.scm (python-execnet): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
7b3a4ee4c3 gnu: Add python-apipkg. 
* gnu/packages/python.scm (python-apipkg): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
7b17cab902 gnu: Add python-click-log. 
* gnu/packages/python.scm (python-click-log): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
d1deb90b3f gnu: Add python-click-threading. 
* gnu/packages/python.scm (python-click-threading): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
561bb3cb1a gnu: Add python-requests-toolbelt. 
* gnu/packages/python.scm (python-requests-toolbelt): New variable.
 2016-01-15 16:45:24 -05:00
Leo Famulari
5c6eea2ad1 gnu: Add python-atomicwrites. 
* gnu/packages/python.scm (python-atomicwrites): New variable.
 2016-01-15 16:45:24 -05:00
Ricardo Wurmus
f5ca44b86e gnu: glade: Update to 3.18.5. 
* gnu/packages/gnome.scm (glade): Update to 3.18.5.
[arguments]: Disable tests; add "fix-docbook" phase.
[inputs]: Replace "gtk+-2" with "gtk+".
[native-inputs]: Add "itstool", "libxslt", "docbook-xml", "docbook-xsl";
replace "python" with "python-2".
 2016-01-15 22:29:37 +01:00
Mark H Weaver
45f2ffb48c gnu: openssh: Update to 7.1p2. 
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
 2016-01-15 02:46:12 -05:00
Mark H Weaver
1beec63ac8 Revert "gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]." 
This reverts commit 6d139e53b5.
 2016-01-15 02:45:58 -05:00
Mark H Weaver
6d139e53b5 gnu: openssh: Update to 7.1p2 [fixes CVE-0216-0778]. 
* gnu/packages/ssh.scm (openssh): Update to 7.1p2.
 2016-01-14 10:39:00 -05:00
David Thompson
df1f1d6936 gnu: Add docker-compose. 
* gnu/packages/docker.scm (docker-compose): New variable.
 2016-01-14 09:17:12 -05:00
David Thompson
b42c9c8124 gnu: Add python-dockerpty. 
* gnu/packages/docker.scm (python-dockerpty): New variable.
 2016-01-14 09:16:22 -05:00
David Thompson
d020bfc2df gnu: Add python-docker-py. 
* gnu/packages/docker.scm: New file.
* Makefile.am (GNU_SYSTEM_MODULES): Add it.
 2016-01-14 09:16:22 -05:00
David Thompson
67c52bb3e7 gnu: Add python-websocket-client. 
* gnu/packages/python.scm (python-websocket-client): New variable.
 2016-01-14 09:12:23 -05:00
David Thompson
210bf49754 gnu: Add python-texttable. 
* gnu/packages/python.scm (python-texttable, python2-texttable): New
variables.
 2016-01-14 09:12:23 -05:00
David Thompson
b3667afbd2 gnu: Update python-jsonschema to 2.5.1. 
* gnu/packages/python.scm (python-jsonschema): Update to 2.5.1.
[inputs]: Add python-vcversioner.
 2016-01-14 09:12:06 -05:00
David Thompson
ea521b42c2 gnu: Add python-vcversioner. 
* gnu/packages/python.scm (python-vcversioner, python2-vcversioner): New
variables.
 2016-01-14 09:05:19 -05:00
David Thompson
e90051808b gnu: Add version 2.7 variant of python-requests. 
* gnu/packages/python.scm (python-requests-2.7): New variable.
 2016-01-14 09:05:19 -05:00
Ricardo Wurmus
3141b83d4d gnu: r-go-db: Add missing input. 
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
  "r-annotationdbi".
 2016-01-14 14:43:59 +01:00
Ricardo Wurmus
d7786ce9b0 gnu: r-sparsem: Add missing "gfortran" input. 
* gnu/packages/statistics.scm (r-sparsem)[inputs]: Add "gfortran".
 2016-01-14 14:43:59 +01:00
Ricardo Wurmus
0047d26a22 gnu: bowtie: Update to 2.2.6. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
 2016-01-14 14:43:25 +01:00
Efraim Flashner
2d12284d38 gnu: gnupg: Add TOFU support. 
* gnu/packages/gnupg.scm (gnupg)[inputs]: Add sqlite.
 2016-01-14 15:05:36 +02:00
Ben Woodcroft
6b6f7d6a0e gnu: orfm: Update to 0.5.3. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
 2016-01-14 08:00:10 +10:00
Ben Woodcroft
3d84a99e73 gnu: Add ruby-bio-commandeer. 
* gnu/packages/ruby.scm (ruby-bio-commandeer): New variable.
 2016-01-14 08:00:02 +10:00
Ben Woodcroft
7c033c4627 gnu: Add ruby-systemu. 
* gnu/packages/ruby.scm (ruby-systemu): New variable.
 2016-01-14 07:51:44 +10:00
Ricardo Wurmus
e5a19fed19 gnu: julia: Update to 0.4.3. 
* gnu/packages/julia.scm (julia): Update to 0.4.3.
(libuv-julia): Update to 07730c4bd595.
 2016-01-13 17:05:38 +01:00
Mark H Weaver
75418ae0fd gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605]. 
* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1.
 2016-01-13 09:38:57 -05:00
Ricardo Wurmus
c44734115a gnu: samtools: Update to 1.3. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
 2016-01-13 15:12:22 +01:00
Ludovic Courtès
98f2339189 gnu: skribilo: Update to 0.9.3. 
* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3.
[native-inputs]: New field.
 2016-01-13 11:13:34 +01:00
Eric Bavier
c91d3fb7f4 gnu: boost: Update to 1.60.0. 
* gnu/packages/boost.scm (boost): Update to 1.60.0.
  [source]: Remove patch.
* gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch
* gnu-system.am (dist_patch_DATA): Remove patch.

Also fix dependent packages:

* gnu/packages/patches/csound-header-ordering.patch: New patch.
* gnu/packages/audio.scm (csound)[source]: Use it.
  [arguments]: Add 'set-flags phase.
* gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch.
* gnu/packages/libreoffice.scm (libcmis)[source]: Use it.
  (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags.
  (librevenge)[inputs]: Move boost from here...
  [propogated-inputs]: to here.
  [arguments]: Add LDFLAGS to #:configure-flags.
* gnu/packages/patches/openimageio-boost-1.60.patch: New patch.
* gnu/packages/graphics.scm (openimageio): Use it.
* gnu-system.am (dist_patch_DATA): Add patches.
 2016-01-12 21:07:53 +01:00
Eric Bavier
3abe8136fd gnu: boost: Use modify-phases. 
* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
 2016-01-12 20:53:14 +01:00
Mark H Weaver
16aa649117 gnu: sudo: Add fix for CVE-2015-5602. 
* gnu/packages/patches/sudo-CVE-2015-5602.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/admin.scm (sudo)[source]: Add patch.
 2016-01-12 11:23:06 -05:00
Efraim Flashner
9d9951d6a6 gnu: global: Use modify-phases syntax. 
* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
 2016-01-12 14:47:10 +02:00
Efraim Flashner
94c3a6f1a6 gnu: global: Update to 6.5.2. 
* gnu/packages/code.scm (global): Update to 6.5.2.
 2016-01-12 14:39:15 +02:00
Ricardo Wurmus
9f40b1171b gnu: icedtea-6: Fix directory name in "unpack" phase. 
* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory
  prefix in the "unpack" phase to "icedtea6-".
 2016-01-12 11:39:21 +01:00
Mark H Weaver
6b0d24b17c gnu: linux-libre: Update to 4.4. 
* gnu/packages/linux.scm (linux-libre): Update to 4.4.
* gnu/packages/linux-libre-i686.conf,
  gnu/packages/linux-libre-x86_64.conf: Update from
  <https://jxself.org/git/kernel-configs.git>.
 2016-01-11 19:13:37 -05:00
Ben Woodcroft
81f3e0c1f3 gnu: Add fxtract. 
* gnu/packages/bioinformatics.scm (fxtract): New variable.
 2016-01-12 07:49:19 +10:00
Efraim Flashner
ec70fec559 gnu: youtube-dl: Update to 2016.01.09. 
* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
 2016-01-11 13:30:50 +02:00
Andreas Enge
4879d2ff66 gnu: gp2c: Update to 0.0.9pl5. 
* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
 2016-01-11 11:24:52 +01:00
Andreas Enge
4a6635f353 gnu: texlive: Use modify-phases syntax. 
* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases
  syntax.
 2016-01-11 10:59:29 +01:00
Efraim Flashner
a916c82649 gnu: man-pages: Update to 4.04. 
* gnu/packages/man.scm (man-pages): Update to 4.04.
[source]: Add alternate location.
 2016-01-11 09:37:50 +02:00
Ben Woodcroft
9b9b7ffd8e gnu: bedtools: Update to 2.25.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'.  Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
 2016-01-11 00:36:13 +10:00
Ben Woodcroft
6573ac82ad gnu: bedtools: Use modify-phases. 
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
 2016-01-11 00:36:13 +10:00
Andreas Enge
695bea9803 gnu: r: Update to 3.2.3. 
* gnu/packages/statistics.scm (r): Update to 3.2.3.
 2016-01-09 23:18:28 +01:00
Andreas Enge
13035f5a03 gnu: icecat: Update to 38.5.2-gnu1. 
* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
 2016-01-09 22:51:28 +01:00
Ben Woodcroft
4c40fa0229 gnu: ruby-2.1: Update to 2.1.8. 
* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.
 2016-01-09 14:53:58 +10:00
Leo Famulari
f32274a71e gnu: i2c-tools: Update source and home-page URLs. 
* gnu/packages/linux.scm (i2c-tools)[source]: Update URL.
[home-page]: Update URL.
 2016-01-08 16:42:27 -05:00
Leo Famulari
3a04d5d4e4 gnu: lm-sensors: Update source and home-page URLs. 
* gnu/packages/linux.scm (lm-sensors)[source]: Update URL.
[home-page]: Update URL.
 2016-01-08 16:42:27 -05:00
Mark H Weaver
bea25ae83c gnu: nss: Update to 3.21 [fixes CVE-2015-7575]. 
* gnu/packages/gnuzilla.scm (nss): Update to 3.21.
  [arguments]: In configure phase, setenv CC=gcc.
* gnu/packages/patches/nss-pkgconfig.patch: Adapt to NSS 3.21.
 2016-01-08 15:29:50 -05:00
Mathieu Lirzin
2409f37f28 gnu: Add missing (gnu packages gcc) import. 
* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
 2016-01-08 14:18:46 +01:00
Mathieu Lirzin
9ef824c10e gnu: xterm: Update to 322. 
* gnu/packages/xorg.scm (xterm): Update to 322.
 2016-01-08 14:12:29 +01:00
宋文武
a65e26f091 gnu: epiphany: Update to 3.18.2. 
* gnu/packages/gnome.scm (epiphany): Update to 3.18.2.
 2016-01-08 17:34:08 +08:00
宋文武
19e5258d84 gnu: webkitgtk: Update to 2.10.4. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.10.4.
 2016-01-08 17:34:08 +08:00
Pjotr Prins
c8d969b58f gnu: Add Pfff. 
* gnu/packages/textutils.scm (pfff): New variable.
 2016-01-07 21:13:35 +01:00
Alex Kost
fbbaa4dde8 gnu: mpv: Remove 'samba' input. 
This is a heavy-weight and uncommon feature.  See
<http://lists.gnu.org/archive/html/guix-devel/2015-12/msg00701.html>.

* gnu/packages/video.scm (mpv)[inputs]: Remove 'samba'.
 2016-01-07 22:30:18 +03:00
Ricardo Wurmus
cb933df6da gnu: Add genomation. 
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
03ea5a357e gnu: Add seqPattern. 
* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
c43a011de3 gnu: Add impute. 
* gnu/packages/bioinformatics.scm (r-impute): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
c63cef6699 gnu: Add BSgenome. 
* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
fbf6045e33 gnu: Add plotly. 
* gnu/packages/statistics.scm (r-plotly): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
a28d646b63 gnu: Add viridis. 
* gnu/packages/statistics.scm (r-viridis): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
d547ce5e70 gnu: Add topGO. 
* gnu/packages/bioinformatics.scm (r-topgo): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
e05c37da4a gnu: Add matrixStats. 
* gnu/packages/statistics.scm (r-matrixstats): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
3703ffb41f gnu: Add R.rsp. 
* gnu/packages/statistics.scm (r-r-rsp): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
a63efbb453 gnu: Add R.cache. 
* gnu/packages/statistics.scm (r-r-cache): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
9c94b53b5b gnu: Add R.utils. 
* gnu/packages/statistics.scm (r-r-utils): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
c8c75a8d88 gnu: Add R.oo. 
* gnu/packages/statistics.scm (r-r-oo): New variable.
 2016-01-07 17:18:17 +01:00
Ricardo Wurmus
8bfe007c9c gnu: Add R.methodsS3. 
* gnu/packages/statistics.scm (r-r-methodss3): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
a69a593595 gnu: Add base64enc. 
* gnu/packages/statistics.scm (r-base64enc): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
a8227e4ae9 gnu: Add DT. 
* gnu/packages/statistics.scm (r-dt): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
d706257b5b gnu: Add SparseM. 
* gnu/packages/statistics.scm (r-sparsem): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
fb25d8803f gnu: Add GO.db. 
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
2fd7c04984 gnu: Add GenomicFeatures. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
317755ff0f gnu: Add rtracklayer. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
d8a828af78 gnu: Add GenomicAlignments. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
6e76dda2d0 gnu: Add SummarizedExperiment. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
f8d74f7018 gnu: Add Rsamtools. 
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
bf15935337 gnu: Add Biostrings. 
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
e91d362e48 gnu: Add BiocParallel. 
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
c465fa72ed gnu: Add biomaRt. 
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
8b7bce740d gnu: Add AnnotationDbi. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
555e3399dc gnu: Add Biobase. 
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
bc899123e7 gnu: Add snow. 
* gnu/packages/statistics.scm (r-snow): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
6b82f56cf9 gnu: Add futile.logger. 
* gnu/packages/statistics.scm (r-futile-logger): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
b9ff33b50e gnu: Add futile.options. 
* gnu/packages/statistics.scm (r-futile-options): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
ca65d387fd gnu: Add lambda.r. 
* gnu/packages/statistics.scm (r-lambda-r): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
543ded3619 gnu: Add r-xml. 
* gnu/packages/statistics.scm (r-xml): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
cefaa79c9e gnu: Add RCurl. 
* gnu/packages/statistics.scm (r-rcurl): New variable.
 2016-01-07 17:18:16 +01:00
Ricardo Wurmus
21e4d6a9cf gnu: Add RSQLite. 
* gnu/packages/statistics.scm (r-rsqlite): New variable.
 2016-01-07 17:18:15 +01:00
Raimon Grau
fe9451c50a gnu: Add xmlstarlet. 
* gnu/packages/xml.scm (xmlstarlet): New variable.
 2016-01-07 16:00:00 +01:00
宋文武
29e255ca83 gnu: zita-convolver: Drop the '-march=native' optimization. 
* gnu/packages/audio.scm (zita-convolver)[source]: Add snippet.
 2016-01-07 22:47:32 +08:00
宋文武
6dff495580 gnu: zita-resampler: Drop the '-march=native' optimization. 
* gnu/packages/audio.scm (zita-resampler)[source]: Add snippet.
 2016-01-07 22:47:32 +08:00
Ben Woodcroft
7d3a1a2dd2 gnu: Add ruby-ansi. 
* gnu/packages/ruby.scm (ruby-ansi): New variable.
 2016-01-07 15:36:05 +01:00
Ricardo Wurmus
5dfd276602 gnu: edirect: Update to 3.50. 
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
 2016-01-07 11:25:24 +01:00
Leo Famulari
62339e2d49 gnu: w3m: Enable SSL, disable broken protocols and ciphers. 
Fixes <http://bugs.gnu.org/16791>.

* gnu/packages/patches/w3m-force-ssl_verify_server-on.patch: New file.
* gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch: New file.
* gnu/packages/patches/w3m-disable-weak-ciphers.patch: New file.
* gnu/packages/w3m.scm (w3m)[source]: Add patches.
* gnu-system.am (dist_patch_DATA): Add the new files.
 2016-01-07 02:35:38 -05:00
Leo Famulari
e6352001c4 gnu: w3m: Update patch to use '-p1'. 
* gnu/packages/patches/w3m-fix-compile.patch: Rename this file...
* gnu/packages/patches/w3m-libgc.patch: ...to this, and adjust patch
prefix level to '-p1'.
* gnu-system.am (dist_patch_DATA): Update patch name.
* gnu/packages/w3m.scm (w3m)[source]: Update patch name.
[source]: Drop patch flag -p0.
 2016-01-07 02:35:38 -05:00
Ludovic Courtès
d4aaf95401 build-system/gnu: Make 'package-with-explicit-inputs' idempotent. 
* guix/build-system/gnu.scm (package-with-explicit-inputs): Use
  'ensure-keyword-arguments' instead of appending to ARGS.
* gnu/packages/commencement.scm (static-bash-for-glibc): Add missing
  #:guile argument.
 2016-01-06 23:08:22 +01:00
Ludovic Courtès
dff9141c5e gnu: guix: Update development snapshot to f888c0b. 
* gnu/packages/package-management.scm (guix-devel): Update to f888c0b.
 2016-01-06 23:08:22 +01:00
Eric Bavier
c7b08410de gnu: gmsh: Update to 2.11.0. 
* gnu/packages/maths.scm (gmsh): Update to 2.11.0.
  [arguments]: Replace 'check phase.
 2016-01-06 10:49:23 -06:00
Ludovic Courtès
7b78f359d1 gnu: sudo: Use /var/run/sudo instead of /run/sudo. 
* gnu/packages/admin.scm (sudo)[arguments]: Pass
--with-rundir=/var/run/sudo since /var/run is cleaned up at boot time on
GuixSD whereas /run is not.
 2016-01-06 15:51:31 +01:00
Ludovic Courtès
3c4c8c3e06 services: cleanup-service: Catch 'system-error' instead of everything. 
This makes sure that critical errors such as unbound-variable do not go
undetected.

* gnu/services.scm (cleanup-gexp): Introduce local 'fail-safe' macro and
use it.  Remove uses of 'false-if-exception'.
 2016-01-06 14:49:48 +01:00
Ludovic Courtès
341ae58213 gnu: ldc: Fix license. 
* gnu/packages/ldc.scm (ldc)[license]: Replace invalid use of
'license:x11-style' by LICENSE:BOOST1.0.
 2016-01-06 14:21:53 +01:00
Ricardo Wurmus
a243e12aba gnu: icedtea7: Rename to icedtea-7. 
* gnu/packages/java.scm (icedtea7): Rename variable to...
(icedtea-7): ...this.
(icedtea): Refer to "icedtea-7".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus
d028740622 gnu: icedtea6: Rename to icedtea-6. 
* gnu/packages/java.scm (icedtea6): Rename variable to...
(icedtea-6): ...this.
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus
5452588c1a gnu: icedtea6, icedtea7: Rename package to "icedtea". 
* gnu/packages/java.scm (icedtea6): Change package name to "icedtea".
(icedtea7): Inherit package name.
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus
d2540f80c2 gnu: Add and use default IcedTea. 
* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus
d91488908b gnu: icedtea6, icedtea7: Unpack to "openjdk.src". 
* gnu/packages/java.scm (icedtea6)[arguments]: Unpack OpenJDK sources to
"openjdk.src".
(icedtea7)[arguments]: Inherit "--with-openjdk-src-dir" flag; refer to
"openjdk.src" in build phases; simplify "unpack" phase.
[native-inputs]: Rename "openjdk-drop" to "openjdk-src".
 2016-01-06 11:38:50 +01:00
Ricardo Wurmus
43c565d2e7 gnu: Add Jellyfish. 
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
 2016-01-06 11:10:46 +01:00
Andreas Enge
7d1f8d4f52 gnu: calibre: Update to 2.48.0. 
* gnu/packages/ebook.scm (calibre): Update to 2.48.0.
 2016-01-05 22:46:54 +01:00
Roel Janssen
a7ec569c98 gnu: Add LDC. 
* gnu/packages/ldc.scm: New file.
* gnu/packages/patches/ldc-disable-tests.patch: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add ldc.scm.
  (dist_patch_DATA): Add patch file.
 2016-01-05 16:24:57 +01:00
Dmitry Bogatov
1075b43737 gnu: Add emacs-undo-tree. 
* gnu/packages/emacs.scm (emacs-undo-tree): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-01-05 00:28:42 +01:00
Ludovic Courtès
fe542b9762 gnu: emacs: Remove 'info.info'. 
* gnu/packages/emacs.scm (emacs)[arguments]: Use 'modify-phases'.  Add
'remove-info.info' phase.
 2016-01-05 00:28:42 +01:00
Ludovic Courtès
fb74174958 linux-boot: Remove verbose output for module loads. 
* gnu/build/linux-boot.scm (boot-system): Leave
'current-module-debugging-port' unchanged.
* gnu/build/linux-modules.scm (load-linux-module*): Update comment about
'mmap'.
 2016-01-05 00:28:42 +01:00
Ludovic Courtès
be7be9e8dd services: Move /tmp cleanup to a separate service. 
* gnu/services.scm (compute-boot-script): Remove /tmp and /var/run
deletion code from here.
(cleanup-gexp): New procedure with /tmp and /var/run deletion code
formerly in 'compute-boot-script'.
(cleanup-service-type): New variable.
* gnu/system.scm (essential-services): Add an instance of
CLEANUP-SERVICE-TYPE.
 2016-01-05 00:28:42 +01:00
Ludovic Courtès
94af9daa73 services: boot: Reinstate /tmp and /var/run deletion. 
For some time /tmp and /var/run were not being deleted because
'delete-file-recursively' was unbound.

* gnu/services.scm (compute-boot-script)[%modules, modules, compiled]:
New variables.  Use them to augment the module search path.
 2016-01-05 00:28:42 +01:00
Ricardo Wurmus
4828ff91ff gnu: gtk+: Add patch to support GUIX_GTK3_PATH. 
* gnu/packages/patches/gtk3-respect-GUIX_GTK3_PATH: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gtk.scm (gtk+) [source]: Add patch.
[native-search-paths]: Add search path for GUIX_GTK3_PATH.
 2016-01-04 16:11:10 -05:00
Ricardo Wurmus
2a6afac905 gnu: gtk+-2: Add patch to support GUIX_GTK2_PATH. 
* gnu/packages/patches/gtk2-respect-GUIX_GTK2_PATH: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gtk.scm (gtk+-2) [source]: Add patch.
[native-search-paths]: Add search path for GUIX_GTK2_PATH.
 2016-01-04 16:11:10 -05:00
Ricardo Wurmus
c2e87caaa6 gnu: julia: Update to 0.4.2. 
* gnu/packages/patches/julia-0.3.10-fix-empty-array.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
* gnu/packages/julia.scm (julia): Update to 0.4.2.
[arguments]: Remove phase "fix-building-with-mcjit-llvm"; replace phase
"patch-include-path" with "fix-include-and-link-paths"; add phase
"hardcode-paths"; add missing make-flags.
[inputs]: Replace "pcre" with "pcre2"; replace "git" with "libgit2"; add
"coreutils"; add "libuv-julia"; add "wget"; add "which".
[native-inputs]: Remove "which".
 2016-01-04 11:35:57 +01:00
Ricardo Wurmus
50b40d0709 gnu: Add libuv-julia. 
* gnu/packages/julia.scm (libuv-julia): New variable.
 2016-01-04 11:35:57 +01:00
Ricardo Wurmus
f1e3a8aed2 gnu: utf8proc: Update to 1.3.1. 
* gnu/packages/textutils.scm (utf8proc): Update to 1.3.1.
[arguments]: Remove custom "install" phase.
 2016-01-04 11:35:57 +01:00
Leo Famulari
77553dff86 gnu: samba: Update to 4.3.3. 
Fixes CVE-2015-{3223,5252,5299,5296,8467,5330}.

* gnu/packages/samba.scm (samba): Update to 4.3.3.
 2016-01-03 14:59:49 -05:00