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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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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
c4a667bfa5
gnu: Add missing module import to (gnu packages gl).
...
This is a followup to commit f1267c872f
2016-10-24 22:45:38 -04:00
f1267c872f
gnu: mesa: Fix 'wayland-egl-symbols-check' on MIPS.
...
* gnu/packages/patches/mesa-wayland-egl-symbols-check-mips.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gl.scm (mesa)[source]: Add patch when building on MIPS.
2016-10-24 22:28:32 -04:00
ffde82c9ec
system: grub: Use Guile-{RSVG,Cairo} instead of Inkscape + ImageMagick.
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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
19a65e7c8c
gnu: perl-eval-closure: Update to 0.14.
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* gnu/packages/perl.scm (perl-eval-closure): Update to 0.14.
2016-10-24 17:29:25 -04:00
d91025e3d0
gnu: Add coda.
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* 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.
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* 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
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* 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.
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* 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
4691428059
gnu: twolame: Make the test suite compatible with Perl 5.24.
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* gnu/packages/audio.scm (twolame)[source]: Add snippet to fix test.
2016-10-24 16:19:25 -04:00
405be8dceb
gnu: efl: Update to 1.18.2.
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* 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.
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* 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.
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* 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'.
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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.
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* 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.
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* 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.
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* 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".
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* 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.
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* 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
ef73acd30d
gnu: diffoscope: Disable failing test.
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* gnu/packages/package-management.scm (diffoscope)[arguments]: Add
'disable-failing-test' phase.
2016-10-23 17:05:09 -04:00
1bafad5661
gnu: audit: Use GnuTLS instead of OpenSSL.
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* gnu/packages/admin.scm (audit)[inputs]: Replace openssl with gnutls.
2016-10-23 16:38:21 -04:00
93cb98d481
gnu: icu4c: On MIPS, pass --with-data-packaging=archive to configure.
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* gnu/packages/icu4c.scm (icu4c)[arguments]: On MIPS, pass
"--with-data-packaging=archive" to configure.
2016-10-23 14:18:26 -04:00
ca0635b4ba
Merge branch 'master' into core-updates
2016-10-23 14:16:39 -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
0990edfecb
gnu: Add python-aniso8601.
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* gnu/packages/python.scm (python-aniso8601): New variable.
2016-10-23 19:31:39 +02:00
04ce840a82
gnu: Add bluefish.
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* gnu/packages/gnome.scm (bluefish): New variable.
2016-10-23 19:26:30 +02:00
373e765ec3
gnu: openconnect: Update to 7.07.
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* gnu/packages/vpn.scm (openconnect): Update to 7.07.
2016-10-23 16:33:04 +02:00
bdc74f07c3
gnu: weex: Use ‘modify-phases’.
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* gnu/packages/ftp.scm (weex): Use the ‘modify-phases’ syntax.
2016-10-23 16:33:04 +02:00
5f5b57681c
gnu: Add guitarix-lv2.
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* gnu/packages/audio.scm (guitarix-lv2): New variable.
2016-10-23 15:47:35 +02:00
84d53724ba
gnu: Add mod-utilities.
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* gnu/packages/music.scm (mod-utilities): New variable.
2016-10-23 15:47:35 +02:00
3d4b1bb9a1
gnu: Add jalv-select.
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* gnu/packages/music.scm (jalv-select): New variable.
2016-10-23 15:47:35 +02:00
c2c9e74891
gnu: Add mod-host.
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* gnu/packages/music.scm (mod-host): New variable.
2016-10-23 15:47:35 +02:00
875dc49b00
gnu: jasper: Update to 1.900.13.
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* gnu/packages/image.scm (jasper): Update to 1.900.13.
[arguments]: Build with -std=c99 support.
2016-10-23 16:32:04 +03:00
5cb7974109
gnu: Add libpsyc.
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* gnu/packages/psyc.scm (libpsyc): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-10-23 16:32:03 +03:00
3a14b2bcf6
gnu: Add perl-net-psyc.
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* gnu/packages/psyc.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-10-23 16:32:03 +03:00
860eda621b
gnu: vmpk: Remove package.
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The vmpk package has been broken for a while and attempts to fix it have
failed. The package "jack-keyboard" offers similar features.
* gnu/packages/music.scm (vmpk): Remove variable.
2016-10-23 15:06:36 +02:00
1a0633e79b
gnu: Add supertuxkart.
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* gnu/packages/games.scm (supertuxkart): New variable.
2016-10-23 15:05:19 +02:00
9ba88890f7
gnu: gambit-c: Update to 4.8.5.
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* gnu/packages/scheme.scm (gambit-c): Update to 4.8.5.
[source]: Update source tarball name.
2016-10-23 14:37:36 +03:00
27668c79de
gnu: gambit-c: Use 'modify-phases' syntax.
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* gnu/packages/scheme.scm (gambit-c)[arguments]: Use 'modify-phases'
syntax.
2016-10-23 14:37:36 +03:00
71dcdaf31f
gnu: gambit-c: Update to 4.7.9.
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* gnu/packages/scheme.scm (gambit-c): Update to 4.7.9.
2016-10-23 14:37:36 +03:00
fb685df8f8
gnu: bigloo: Use 'modify-phases' syntax.
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* gnu/packages/scheme.scm (bigloo)[arguments]: Use 'modify-phases' syntax.
2016-10-23 14:37:36 +03:00
04014de6f5
gnu: hop: Use 'modify-phases' syntax.
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* gnu/packages/scheme.scm (hop)[arguments]: Use 'modify-phases' syntax.
2016-10-23 14:37:35 +03:00
eccd1d24c9
gnu: hop: Update to 2.5.1.
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* gnu/packages/scheme.scm (hop): Update to 2.5.1.
[source]: Remove patch.
* gnu/packages/patches/hop-bigloo-4.0b.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2016-10-23 14:37:28 +03:00
5ed7f28da5
gnu: mpg321: Update to 0.3.2.
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* gnu/packages/mp3.scm (mpg321): Update to 0.3.2.
2016-10-23 05:01:02 -04:00
d78b652c16
gnu: mpg123: Update to 1.23.8.
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* gnu/packages/mp3.scm (mpg123): Update to 1.23.8.
2016-10-23 04:55:26 -04:00
844f4f6e62
gnu: beast: Disable parallel-build.
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* gnu/packages/music.scm (beast)[arguments]: Disable parallel builds to
prevent a race condition.
2016-10-23 07:47:03 +03:00
d661894159
gnu: infamous-plugins: Remove compiler optimizations.
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* gnu/packages/audio.scm (infamous-plugins)[arguments]: Add phase
removing built-in compiler optimizations in the source code.
2016-10-23 07:47:03 +03:00
7ca6830482
gnu: python2-validictory: Add missing input.
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* gnu/packages/python.scm (python2-validictory)[native-inputs]: Add
python2-setuptools.
(python-validictory)[properties]: New field.
2016-10-23 07:47:03 +03:00
ff1e2b59bf
gnu: ffmpeg: Update to 3.1.5.
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* gnu/packages/video.scm (ffmpeg): Update to 3.1.5.
2016-10-23 07:47:03 +03:00
04ed5444fe
gnu: mutt: Update to 1.7.1.
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* gnu/packages/mail.scm (mutt): Update to 1.7.1.
2016-10-23 07:47:03 +03:00
ad6198a5f9
gnu: Add vim-full.
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* gnu/packages/vim.scm (vim-full): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2016-10-23 07:47:02 +03:00
84a79b8c42
gnu: aria2: Update to 1.28.0.
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* gnu/packages/bittorrent.scm (aria2): Update to 1.28.0.
2016-10-23 07:46:49 +03:00
35680748a6
gnu: linux-libre: Update to 4.8.4.
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* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.8.4.
2016-10-23 00:21:20 -04:00
62cf3ae09b
gnu: linux-libre@4.4: Update to 4.4.27.
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* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.27.
2016-10-23 00:18:42 -04:00
0881b616f4
gnu: guile-ncurses: Update to version 2.0.
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* gnu/packages/guile.scm (guile-ncurses): Update version to 2.0.
2016-10-22 17:24:39 +02:00
Ricardo Wurmus