41bc22a7de
gnu: r-backports: Update to 1.0.4.
...
* gnu/packages/statistics.scm (r-backports): Update to 1.0.4.
2016-10-26 16:23:30 +02:00
72263db73d
gnu: r-foreign: Update to 0.8-67.
...
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-67.
2016-10-26 16:23:30 +02:00
130410d941
gnu: r-cluster: Update to 2.0.5.
...
* gnu/packages/statistics.scm (r-cluster): Update to 2.0.5.
2016-10-26 16:23:29 +02:00
e7622804aa
gnu: r-acepack: Update to 1.4.0.
...
* gnu/packages/statistics.scm (r-acepack): Update to 1.4.0.
2016-10-26 16:23:29 +02:00
bff4dc6324
gnu: r-r6: Update to 2.2.0.
...
* gnu/packages/statistics.scm (r-r6): Update to 2.2.0.
2016-10-26 16:23:29 +02:00
e0a9093139
gnu: r-evaluate: Update to 0.10.
...
* gnu/packages/statistics.scm (r-evaluate): Update to 0.10.
2016-10-26 16:23:28 +02:00
2d9da70bbe
gnu: r-reshape2: Update to 1.4.2.
...
* gnu/packages/statistics.scm (r-reshape2): Update to 1.4.2.
2016-10-26 16:23:28 +02:00
c2a9e99134
gnu: r-stringi: Update to 1.1.2.
...
* gnu/packages/statistics.scm (r-stringi): Update to 1.1.2.
2016-10-26 16:23:28 +02:00
03f72a1e1f
gnu: r-matrix: Update to 1.2-7.1.
...
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-7.1.
2016-10-26 16:23:27 +02:00
9e087a1fde
gnu: r-colorspace: Update to 1.2-7.
...
* gnu/packages/statistics.scm (r-colorspace): Update to 1.2-7.
2016-10-26 16:23:27 +02:00
e1c2b7e2e1
gnu: r-jsonlite: Update to 1.1.
...
* gnu/packages/web.scm (r-jsonlite): Update to 1.1.
2016-10-26 16:23:27 +02:00
2ffcd6607b
gnu: r-curl: Update to 2.2.
...
* gnu/packages/web.scm (r-curl): Update to 2.2.
2016-10-26 16:23:26 +02:00
a46cc723ff
gnu: r-seqinr: Update to 3.3-3.
...
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
2016-10-26 16:23:26 +02:00
062737a178
gnu: r-rcpparmadillo: Update to 0.7.500.0.0.
...
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to
7.500.0.
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.500.0.0.
2016-10-26 16:23:25 +02:00
7397cd9e3f
gnu: armadillo: Update to 7.500.0.
...
* gnu/packages/maths.scm (armadillo): Update to 7.500.0.
2016-10-26 16:23:25 +02:00
8e1369f19a
gnu: r-rmarkdown: Update to 1.1.
...
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.1.
[propagated-inputs]: Add r-evaluate, r-tibble.
2016-10-26 16:23:25 +02:00
c70271ec48
gnu: bioperl-minimal: Update to 1.7.0.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
2016-10-26 16:23:24 +02:00
39df253e2b
gnu: mupdf: Modify CVE-2016-8674 patch to apply to 1.9a.
...
The fix from upstream did not apply cleanly due to many context changes.
This was adapted by cloning mupdf 1.9a from git and fixing conflicts
after applying our patches and cherry-picking upstream commit 1e03c06.
This is a follow-up to 47a04fca99
2016-10-26 15:03:42 +01:00
b2a2232c33
gnu: python-certifi: Update to 2016.8.31.
...
* gnu/packages/python.scm (python-certifi): Update to 2016.8.31.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-10-26 14:31:16 +03:00
07b1fb8675
gnu: security-token: Use 'license:' prefix.
...
* gnu/packages/security-token.scm (libyubikey)[license]: Add prefix.
(ykclient)[license]: Add prefix.
2016-10-26 11:00:58 +01:00
f9c339603d
gnu: yubico.scm: Rename to security-token.scm.
...
* gnu/packages/yubico.scm: Delete file.
* gnu/packages/security-token.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
2016-10-26 10:45:49 +01:00
7a6213cbd7
gnu: offlineimap: Install documentation.
...
* gnu/packages/mail.scm (offlineimap)[native-inputs]: Add asciidoc and
libxslt.
[arguments]: Add phases 'build-documentation' and
'install-documentation' to build and install manpages. Also remove
unneeded key 'inputs' from 'wrap-binary' phase.
2016-10-26 10:45:49 +01:00
d2a9b531fb
gnu: notmuch: Update to 0.23.1.
...
* gnu/packages/patches/notmuch-emacs-25-compatibility-fix.patch: Delete
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/mail.scm (notmuch): Update to 0.23.1. Remove patch.
2016-10-26 10:45:49 +01:00
8f5f6c922f
gnu: vlc: Add x265 support.
...
* gnu/packages/video.scm (vlc)[inputs]: Add x265.
2016-10-26 12:19:19 +03:00
e3cb00d210
gnu: gst-plugins-bad: Add x265 support.
...
* gnu/packages/gstreamer.scm (gst-plugins-bad)[inputs]: Add x265.
2016-10-26 12:19:18 +03:00
d505801a06
gnu: ffmpeg: Add x265 support.
...
* gnu/packages/video.scm (ffmpeg)[inputs]: Add x265.
[arguments]: Add '--enable-libx265' flag.
2016-10-26 12:19:18 +03:00
7bc7ffc243
gnu: Add x265.
...
* gnu/packages/video.scm (x265): New variable.
2016-10-26 12:19:18 +03:00
1df790d50d
gnu: Add psyclpc.
...
* gnu/packages/psyc.scm (psyclpc): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-10-26 11:29:35 +03:00
19262a718e
gnu: opensmtpd: Fix 'license' field.
...
* gnu/packages/mail.scm (opensmtpd)[license]: Use LICENSE:OPENSSL, not
OPENSSL.
(opensmtpd-extras)[license]: Likewise.
2016-10-26 10:19:18 +02:00
59198f8fff
gnu: r-genomationdata: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
2016-10-26 09:28:23 +02:00
e357bec836
gnu: r-bamsignals: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
2016-10-26 09:28:23 +02:00
53ca52f013
gnu: r-rhtslib: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0.
[native-inputs]: Add autoconf.
2016-10-26 09:28:23 +02:00
da22da862b
gnu: r-zlibbioc: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
2016-10-26 09:28:22 +02:00
809251e164
gnu: r-motifrg: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
2016-10-26 09:28:22 +02:00
21d6c7a3e1
gnu: r-seqlogo: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
2016-10-26 09:28:22 +02:00
51c3c4900f
gnu: r-genomation: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0.
[propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors.
[inputs]: Add zlib.
2016-10-26 09:28:21 +02:00
e92dd6f5e0
gnu: r-seqpattern: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0.
[propagated-inputs]: Add r-kernsmooth.
2016-10-26 09:28:21 +02:00
acf6f7e0c3
gnu: r-impute: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
2016-10-26 09:28:21 +02:00
3d74c04451
gnu: r-bsgenome: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
2016-10-26 09:28:20 +02:00
30ec4de738
gnu: r-topgo: Update to 2.26.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0.
[propagated-inputs]: Add r-dbi.
2016-10-26 09:28:20 +02:00
3587b464fc
gnu: r-graph: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
2016-10-26 09:28:19 +02:00
d1b1587cad
gnu: r-go-db: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
2016-10-26 09:28:19 +02:00
b17aac083e
gnu: r-genomicfeatures: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
2016-10-26 09:28:18 +02:00
6a45fd9aea
gnu: r-rtracklayer: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
2016-10-26 09:28:18 +02:00
4ab32f0cd6
gnu: r-genomicalignments: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.10.0.
2016-10-26 09:28:18 +02:00
08da08d296
gnu: r-summarizedexperiment: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.4.0.
2016-10-26 09:28:17 +02:00
c0ccef41ae
gnu: r-rsamtools: Update to 1.26.1.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
2016-10-26 09:28:17 +02:00
47d39b6e7a
gnu: r-biostrings: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
2016-10-26 09:28:17 +02:00
89559a124e
gnu: r-biocparallel: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
2016-10-26 09:28:16 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
557a4b8e61
gnu: Add r-kernsmooth.
...
* gnu/packages/statistics.scm (r-kernsmooth): New variable.
2016-10-26 09:28:07 +02:00
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
6c18c4f603
gnu: elfutils: Update to 0.167.
...
* gnu/packages/elf.scm (elfutils): Update to 0.167.
2016-10-25 22:11:59 -04:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2dfa90721d
gnu: weechat: Update to 1.6.
...
* gnu/packages/irc.scm (weechat): Update to 1.6.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-10-23 17:10:22 -04:00
903276d066
gnu: Add python-flask-sqlalchemy.
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* gnu/packages/python.scm (python-flask-sqlalchemy): New variable.
2016-10-23 19:41:11 +02:00
31288222d4
gnu: Add python-flask-basicauth.
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* gnu/packages/python.scm (python-flask-basicauth): New variable.
2016-10-23 19:41:10 +02:00
999d964d64
gnu: Add python-flask-restful.
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* gnu/packages/python.scm (python-flask-restful): New variable.
2016-10-23 19:31:39 +02:00
Ricardo Wurmus