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15516 Commits

Author SHA1 Message Date
Ricardo Wurmus 9405333186
gnu: r-biomart: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus e45dc05781
gnu: r-annotationdbi: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 464870caf7
gnu: r-biobase: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 92a740afac
gnu: r-genomicranges: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1.
[propagated-inputs]: Add r-iranges, r-s4vectors.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 1d048589ca
gnu: r-xvector: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 753bc32b8e
gnu: r-limma: Update to 3.30.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 37d96f1dde
gnu: r-variantannotation: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.20.0.
[propagated-inputs]: Add r-biobase, r-biostrings, r-iranges,
r-rtracklayer, r-s4vectors, r-xvector.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 5e48005fa9
gnu: r-edger: Update to 3.16.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0.
[propagated-inputs]: Add r-locfit.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus dece310a25
gnu: r-genomeinfodb: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 7f354dafb1
gnu: r-iranges: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus b120c5f3a2
gnu: r-s4vectors: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 22c5d736af
gnu: r-dnacopy: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus 5c7b04e0c3
gnu: r-biocinstaller: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus f0b297e17b
gnu: r-biocgenerics: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus c9b5046a18
gnu: r-grohmm: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus 1265d3877b
gnu: r-systempiper: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus b87b41a74d
gnu: r-shortread: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus ae6899b683
gnu: r-gostats: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus 816599c1e7
gnu: r-category: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus 558d02c361
gnu: r-gseabase: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus 700c780dcf
gnu: r-rbgl: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus 55cd914c3d
gnu: r-annotationforge: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0.
[propagated-inputs]: Add r-rcurl.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus e1db8dd813
gnu: r-deseq2: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus 1e66e71921
gnu: r-genefilter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus 6faa2a48f0
gnu: r-geneplotter: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus 9beba74f66
gnu: r-annotate: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0.
 2016-10-26 09:28:07 +02:00
Ricardo Wurmus 557a4b8e61
gnu: Add r-kernsmooth. 
* gnu/packages/statistics.scm (r-kernsmooth): New variable.
 2016-10-26 09:28:07 +02:00
Ricardo Wurmus f9875807e8
gnu: emacs-emms-player-mpv: Update to 0.0.10. 
* gnu/packages/emacs.scm (emacs-emms-player-mpv): Update to 0.0.10.
 2016-10-26 09:28:07 +02:00
Ricardo Wurmus a98470b5be
import cran: Use URL for Bioconductor 3.4. 
* guix/import/cran.scm (%bioconductor-svn-url): Update to release URL
for version 3.4.
 2016-10-26 09:28:06 +02:00
Leo Famulari 6c18c4f603
gnu: elfutils: Update to 0.167. 
* gnu/packages/elf.scm (elfutils): Update to 0.167.
 2016-10-25 22:11:59 -04:00
Leo Famulari 3de764f7a7
gnu: gtk+-2: Update to 2.24.31 [fixes CVE-2013-7447]. 
* gnu/packages/gtk.scm (gtk+-2): Update to 2.24.31.
 2016-10-25 16:33:13 -04:00
Kei Kebreau 47a04fca99
gnu: mupdf: Fix CVE-2016-8674. 
* gnu/packages/patches/mupdf-CVE-2016-8674.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pdf.scm (mupdf): Use it.
 2016-10-25 12:50:50 -04:00
Thomas Danckaert 4b12fe5cab
gnu: coda: Remove bundled libraries. 
* gnu/packages/maths.scm (coda): Remove bundled libraries.
[source]: Add patch and snippet to remove bundled zlib, pcre and expat.
[inputs]: Add system zlib, pcre and expat.
* gnu/packages/patches/coda-use-system-libs.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-25 14:56:37 +02:00
Ludovic Courtès 301d73f68c
build: 'guilemoduledir' honors $GUILE_EFFECTIVE_VERSION. 
* configure.ac: Define 'guilemoduledir' as a function of
$GUILE_EFFECTIVE_VERSION.
 2016-10-25 14:00:33 +02:00
Ludovic Courtès 8ce84bf1f5
svg: Autoload Guile-RSVG and Guile-Cairo. 
Fixes compilation by 'guix pull' where Guile-{RSVG,Cairo} are missing.
Reported by Efraim Flashner.

* gnu/build/svg.scm: Use 'module-autoload!' rather than 'module-use!'.
 2016-10-25 13:57:28 +02:00
Mark H Weaver e9a19bde40
gnu: linux-libre@4.1: Update to 4.1.35. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.35.  Remove
patch.
* gnu/packages/patches/linux-libre-4.1-CVE-2016-5195.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2016-10-24 22:53:18 -04:00
Ludovic Courtès ffde82c9ec
system: grub: Use Guile-{RSVG,Cairo} instead of Inkscape + ImageMagick. 
Based on a suggestion by Andy Wingo at
<https://lists.gnu.org/archive/html/guix-devel/2015-08/msg00753.html>.

* gnu/build/svg.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/system/grub.scm (svg->png): Add #:width and #:height.  Rewrite to
use (gnu build svg).
(resize-image): Remove.
(grub-background-image): Adjust accordingly.
 2016-10-25 01:21:28 +02:00
Thomas Danckaert d91025e3d0
gnu: Add coda. 
* gnu/packages/maths.scm (coda): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-24 23:14:52 +02:00
Thomas Danckaert d3c4f3bb00
gnu: Add hdf-eos2. 
* gnu/packages/maths.scm (hdf-eos2): New variable.
* gnu/packages/patches/hdf-eos2-build-shared.patch: New file.
* gnu/packages/patches/hdf-eos2-remove-gctp.patch: New file.
* gnu/packages/patches/hdf-eos2-fortrantests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patches.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-24 23:05:20 +02:00
Amirouche 3b5783fcd9
gnu: Add guile-bytestructures 
* gnu/packages/guile.scm (guile-bytestructures): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-24 22:51:52 +02:00
Julien Lepiller 8c00b83818
services: nginx: Virtual hosts are first-class configuration items. 
* gnu/services/web.scm (<nginx-vhost-configuration>): New record type.
(config-domain-strings): New procedure.
(config-index-strings): New procedure.
(default-nginx-vhost-config): New procedure.
(default-nginx-config): Add vhost support and temporary directories
(nginx-activation): Create temporary directories
(nginx-service): Add vhost-list key.
* doc/guix.texi (Web Services): Document 'nginx-vhost-configuration'.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-10-24 22:50:40 +02:00
Efraim Flashner 405be8dceb
gnu: efl: Update to 1.18.2. 
* gnu/packages/enlightenment.scm (efl): Update to 1.18.2.
 2016-10-24 22:01:00 +03:00
Kei Kebreau c201b28bfa
gnu: red-eclipse: Update to 1.5.6. 
* gnu/packages/games.scm (red-eclipse): Update to 1.5.6.
[arguments]: Adjust phases.
 2016-10-24 13:25:39 -04:00
ng0 9c798f9036
gnu: Add whois. 
* gnu/packages/networking.scm (whois): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2016-10-24 17:40:53 +01:00
宋文武 bd1b1e0517
gnu: gnumeric: Use 'glib-or-gtk-build-system'. 
Reported by Pjotr Prins <pjotr.public12@thebird.nl>.

* gnu/packages/gnome.scm (gnumeric)[build-systems]: Switch to
GLIB-OR-GTK-BUILD-SYSTEM.
 2016-10-24 19:19:34 +08:00
Leo Famulari 02cfea6627
gnu: musl: Fix CVE-2016-8859. 
* gnu/packages/patches/musl-CVE-2016-8859.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/musl.scm (musl)[source]: Use it.
 2016-10-23 18:08:17 -04:00
Kei Kebreau 8e3017cc65
gnu: windowmaker: Update to 0.95.7. 
* gnu/packages/gnustep.scm (windowmaker): Update to 0.95.7.
 2016-10-23 17:52:28 -04:00
Arun Isaac 0f6b6cb996
gnu: gajim: Update to 0.16.6. 
* gnu/packages/messaging.scm (gajim): Update to 0.16.6.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-10-23 17:40:50 -04:00
Arun Isaac d6465efaa9
gnu: gajim: License is "version 3 only". 
* gnu/packages/messaging.scm (gajim)[license]: Change to GPL3.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-10-23 17:40:50 -04:00
Leo Famulari 41e94ad50a
nls: Update 'fr' translation. 2016-10-23 17:22:18 -04:00