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6971 commits

Author SHA1 Message Date
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