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Author SHA1 Message Date
Rutger Helling
8420c7a356
gnu: linux-libre: Change URL to HTTPS. 
* gnu/packages/linux.scm (linux-libre): Change URL to HTTPS.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-11-12 15:46:44 -05:00
Efraim Flashner
1650cf9284
gnu: mupdf: Unbundle mujs. 
* gnu/packages/pdf.scm (mupdf)[source]: Remove bundled mujs.
[inputs]: Add mujs.
 2017-11-12 19:39:21 +02:00
Efraim Flashner
89ba894eb3
gnu: Add mujs. 
* gnu/packages/javascript.scm (mujs): New variable.
 2017-11-12 19:39:20 +02:00
Efraim Flashner
76379dcace
gnu: mupdf: Use https. 
* gnu/packages/pdf.scm (mupdf)[source]: Use https.
[home-page]: Same.
 2017-11-12 19:39:20 +02:00
Efraim Flashner
31f248fa2c
gnu: pdf.scm: Arrange modules alphabetically. 
* gnu/packages/pdf.scm: Arrange modules alphabetically.
 2017-11-12 19:39:17 +02:00
Efraim Flashner
b07bfd06ee
gnu: lash: Don't build static libraries. 
* gnu/packages/audio.scm (lash)[arguments]: Add configure-flag to
disable static libraries.
 2017-11-12 12:04:49 +02:00
Efraim Flashner
44df780768
gnu: lash: Don't build lashd. 
This fixes bug#28174.

* gnu/packages/audio.scm (lash)[arguments]: Add phase to skip building lashd.
 2017-11-12 12:04:46 +02:00
Kei Kebreau
c7b433de47
gnu: glib-networking: Update to 2.54.1. 
* gnu/packages/gnome.scm (glib-networking): Update to 2.54.1.
 2017-11-12 01:17:10 -05:00
Efraim Flashner
1e2a36e1b0
gnu: ffmpeg: Reduce the size of the closure. 
* gnu/packages/video.scm (ffmpeg)[arguments]: Add new configure flags to
disable the html man pages and the static libraries.
 2017-11-12 07:11:29 +02:00
Efraim Flashner
7e0d513fb9
gnu: mupdf: Use Texinfo for the description. 
* gnu/packages/pdf.scm (mupdf)[description]: Use Texinfo to mark up the
description.
 2017-11-12 07:11:25 +02:00
Leo Famulari
b7ca42aa99
gnu: w3m: Find an editor in the environment. 
* gnu/packages/w3m.scm (w3m)[arguments]: Pass an empty value for --with-editor
in #:configure-flags.
[source]: Use git-file-name.
 2017-11-11 23:04:39 -05:00
Leo Famulari
882d921344
gnu: mupdf: Actually fix CVE-2017-15587. 
The original fix could be removed by an optimizing compiler.

* gnu/packages/patches/mupdf-CVE-2017-15587.patch: Revise patch.
 2017-11-11 22:34:24 -05:00
Tobias Geerinckx-Rice
07cc9245e6
gnu: libusb-compat: Use the same home page as libusb. 
* gnu/packages/libusb.scm (libusb-compat)[home-page]: Update.
 2017-11-12 03:25:49 +01:00
Tobias Geerinckx-Rice
5ade9bc769
gnu: fcgi: Fix typo in description. 
* gnu/packages/web.scm (fcgi)[description]: Fix typo.
 2017-11-12 03:25:48 +01:00
Tobias Geerinckx-Rice
d1b5043947
gnu: fcgi: Use archived home page fork. 
* gnu/packages/web.scm (fcgi)[home-page]: Use archived version.
 2017-11-12 03:25:48 +01:00
Tobias Geerinckx-Rice
9c2917f9e7
gnu: lynx: Use new home page. 
* gnu/packages/web-browsers.scm (lynx)[home-page]: Update.
 2017-11-12 03:25:47 +01:00
Tobias Geerinckx-Rice
6862e4bfe7
gnu: perl-mime-types: Update to 2.14. 
* gnu/packages/perl.scm (perl-mime-types): Update to 2.14.
 2017-11-12 03:25:47 +01:00
Ludovic Courtès
f9035ef213
gnu: mailutils: Update to 3.4. 
* gnu/packages/mail.scm (mailutils): Update to 3.4.
 2017-11-11 23:21:54 +01:00
Ludovic Courtès
cda2e2c719
gnu: emacs-emms: Update to 4.4. 
* gnu/packages/emacs.scm (emms): Update to 4.4.
 2017-11-11 23:21:54 +01:00
Jan Nieuwenhuizen
327df26fbf
gnu: nyacc: Update to 0.82.4. 
* gnu/packages/mes.scm (nyacc): Update to 0.82.4.
 2017-11-11 23:11:04 +01:00
Leo Famulari
4564782c3d
gnu: nvi: Build with support for Unicode text. 
* gnu/packages/nvi.scm (nvi)[arguments]: Pass '--enable-widechar'
to #:configure-flags.
 2017-11-11 12:00:37 -05:00
Marius Bakke
56f35d92f5
gnu: lvm2: Update to 2.02.176. 
* gnu/packages/linux.scm (lvm2): Update to 2.02.176.
 2017-11-11 07:40:55 +01:00
Marius Bakke
ec03062171
gnu: libstaroffice: Update to 0.0.5. 
* gnu/packages/libreoffice.scm (libstaroffice): Update to 0.0.5.
 2017-11-11 07:18:34 +01:00
Marius Bakke
45d5c80253
gnu: libvisio: Update to 0.1.6. 
* gnu/packages/libreoffice.scm (libvisio): Update to 0.1.6.
[source](patches): Remove.
* gnu/packages/patches/libvisio-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-11-11 07:15:39 +01:00
Marius Bakke
7a9283a619
gnu: libetonyek: Update to 0.1.7. 
* gnu/packages/libreoffice.scm (libetonyek): Update to 0.1.7.
[source](patches): Remove.
[arguments]<#:phases>: Remove.
[native-inputs]: Remove AUTOCONF and AUTOMAKE.
* gnu/packages/patches/libetonyek-build-with-mdds-1.2.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-11-11 07:13:01 +01:00
Rutger Helling
074ff555ab
gnu: libreoffice: Update to 5.3.7.2 and enable GTK3. 
* gnu/packages/libreoffice.scm (libreoffice): Update to 5.3.7.2
[source]: Change URL to HTTPS.
[inputs]: Add gtk+.
[configure-flags]: Remove "--disable-gtk3".

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-11 07:03:06 +01:00
Alex Vong
ce1ac8eea6
gnu: python2-rpython: Update to 0.2.1. 
* gnu/packages/python.scm (python2-rpython): Update to 0.2.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-11 07:00:22 +01:00
Alex Vong
e65acb3124
gnu: python-sympy: Update to 1.1.1. 
* gnu/packages/python.scm (python-sympy, python2-sympy): Update to 1.1.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-11 06:57:00 +01:00
Marius Bakke
e077e7da7f
gnu: python-sqlparse: Fix syntax error. 
This is a follow-up to commit 8d688cd27f.

* gnu/packages/python.scm (python-sqlparse)[arguments]: Add missing lambda.
 2017-11-11 06:40:50 +01:00
Tobias Geerinckx-Rice
8d688cd27f
gnu: python-sqlparse: Update to 0.2.4. 
* gnu/packages/python.scm (python-sqlparse, python2-sqlparse): Update to
0.2.4.
[arguments]: Don't invoke ‘2to3’.
 2017-11-11 05:17:59 +01:00
Tobias Geerinckx-Rice
795ec760e4
install: Fix typo. 
* gnu/system/install.scm (installation-os): Fix typo in comment.
 2017-11-11 05:17:59 +01:00
Tobias Geerinckx-Rice
9629c6b4b2
gnu: cyrus-sasl: Use new home page. 
* gnu/packages/cyrus-sasl.scm (cyrus-sasl)[home-page]: Update.
 2017-11-11 05:17:58 +01:00
Tobias Geerinckx-Rice
11ed4108fb
gnu: methylkit: Use new home page. 
* gnu/packages/bioinformatics.scm (methylkit)[home-page]: Update.
 2017-11-11 05:17:58 +01:00
Ben Woodcroft
7c087150ec
gnu: vsearch: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.0.
 2017-11-11 09:33:16 +10:00
Leo Famulari
74c0aeb027
gnu: webkitgtk: Update to 2.18.3 [fixes CVE-2017-{13788,13798,13803}]. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.18.3.
 2017-11-10 12:48:15 -05:00
Leo Famulari
adf7e69cab
gnu: qemu: Fix CVE-2017-{15038,15268,15289}. 
* gnu/packages/patches/qemu-CVE-2017-15038.patch,
gnu/packages/patches/qemu-CVE-2017-15268.patch,
gnu/packages/patches/qemu-CVE-2017-15289.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/virtualization.scm (qemu)[source]: Use them.
 2017-11-10 12:16:31 -05:00
Kei Kebreau
d4d7d70912
gnu: Fix hunspell-dict-en-* dictionary installation. 
* gnu/packages/aspell.scm (aspell-word-list)[arguments]: Install the .dic file
for all hunspell dictionaries.
 2017-11-10 11:59:09 -05:00
Ricardo Wurmus
0af4df7e61
gnu: cutadapt: Update to 1.14. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.14.
 2017-11-10 15:32:42 +01:00
Ricardo Wurmus
ae451b9dc2
gnu: synergy: Fix minor problems with the package definitions. 
* gnu/packages/synergy.scm (synergy)[source]: Return #t in the snippet.
[arguments]: Let build phases return #t; fix typo in comment.
[home-page]: Change to redirection target.
[description]: Fix typo.
 2017-11-10 15:19:06 +01:00
Jelle Licht
177475cfb5
gnu: password-store: Install passmenu script. 
* gnu/packages/password-utils (password-store)
  [inputs]: Add dmenu and xdotool.
  [arguments]<#:phases>['patch-passmenu-path']: New phase.
  [arguments]<#:phases>['install-passmenu']: New phase.
 2017-11-10 14:22:28 +01:00
Diego Nicola Barbato
011f57695a
gnu: Add Epson escpr printer driver. 
* gnu/packages/cups.scm (escpr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-10 13:07:54 +01:00
Efraim Flashner
179b7ac66d
gnu: postgresql@9.6: Update to 9.6.6 [security fixes]. 
This fixes CVE-2017-12172, CVE-2017-15098, CVE-2017-15099.

* gnu/packages/databases.scm (postgresql@9.6): Update to 9.6.6.
 2017-11-10 10:24:13 +02:00
Mark H Weaver
74bea6a036
gnu: linux-libre: Update to 4.13.12. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.13.12.
(%linux-libre-hash): Update hash.
 2017-11-09 21:11:00 -05:00
Mark H Weaver
4cacbf33a6
gnu: linux-libre@4.9: Update to 4.9.61. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.61.
 2017-11-09 21:10:14 -05:00
Mark H Weaver
3a79bd03ff
gnu: linux-libre@4.4: Update to 4.4.97. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.97.
 2017-11-09 21:09:34 -05:00
Mark H Weaver
f8071bea91
gnu: linux-libre@4.1: Update to 4.1.46. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.46.
 2017-11-09 21:08:51 -05:00
Tobias Geerinckx-Rice
3c3d20c8f3
gnu: libpsl: Update to 0.19.1. 
* gnu/packages/web.scm (libpsl): Update to 0.19.1.
 2017-11-10 02:37:15 +01:00
Rutger Helling
1d8e73ba67
gnu: postgresql: Update to 10.1 [security fixes]. 
Fixes CVE-2017-12172, CVE-2017-15098 and CVE-2017-15099.

* gnu/packages/databases.scm (postgresql): Update to 10.1.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-10 01:22:53 +01:00
Kyle Meyer
e99f045cc8
gnu: Add r-directlabels. 
* gnu/packages/statistics.scm (r-directlabels): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-09 23:54:48 +01:00
Alex Vong
d3150731a8
gnu: emacs-ahungry-theme: Update to 1.8.0. 
* gnu/packages/emacs.scm (emacs-ahungry-theme): Update to 1.8.0.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-09 23:54:48 +01:00
Marek Benc
f021382be4
gnu: Add nxbelld. 
* gnu/packages/xdisorg.scm (nxbelld): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-09 23:54:48 +01:00
Efraim Flashner
d8f075c3a3
gnu: %intel-compatible-systems: Re-add variable. 
This is a follow-up to cfbe7b7f4c.

* gnu/packages/linux.scm (%intel-compatible-systems): New variable.
 2017-11-09 22:25:48 +02:00
Mathieu Othacehe
cfbe7b7f4c
gnu: linux: Add linux-libre arm kernel. 
* Makefile.am (AUX_FILES): Add arm config file.
* gnu/packages/aux-files/linux-libre/4.13-arm.conf: New file.
* gnu/packages/linux.scm (%intel-compatible-systems): Rename to
  %linux-compatible-systems and add "armhf-linux".
  (linux-libre): Adapt consequently.

The config file for arm is taken from debian armmp kernel. It's a generic
firmware for ARMv7 multiplatform compatible SoCs.
 2017-11-09 20:35:11 +01:00
Leo Famulari
3694a9b33b
gnu: chromaprint: Update to 1.4.2. 
* gnu/packages/mp3.scm (chromaprint): Update to 1.4.2.
 2017-11-09 13:23:39 -05:00
Kei Kebreau
ad9b8987f3
gnu: libwnck: Update to 3.24.1. 
* gnu/packages/gnome.scm (libwnck): Update to 3.24.1.
 2017-11-09 12:17:37 -05:00
Ludovic Courtès
5475749960
system: Do not set 'TZ'. 
Fixes <https://bugs.gnu.org/29212>.
Reported by Diego Nicola Barbato <dnbarbato@posteo.de>.

* gnu/system.scm (operating-system-environment-variables): Remove "TZ".
 2017-11-09 09:59:21 +01:00
Ben Woodcroft
da4a707c88
gnu: roary: Update to 3.11.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.11.0.
[inputs]: Add perl-digest-md5-file.
 2017-11-09 18:12:32 +10:00
Kei Kebreau
e5f748a6c0
gnu: totem: Enable parallel build. 
* gnu/packages/gnome.scm (totem)[arguments]: Set #:parallel-build? to #t
implicitly.
 2017-11-08 20:43:40 -05:00
Leo Famulari
8f220b7b41
gnu: tremc: Update to 0.9.0-1.9755b50. 
* gnu/packages/bittorrent.scm (tremc): Update to 0.9.0-1.9755b50.
[version]: Use git-version.
[source]: Use git-file-name.
 2017-11-08 19:32:32 -05:00
Leo Famulari
ea1f073d73
gnu: slurm: Update to 16.05.11 [fixes CVE-2017-15566]. 
* gnu/packages/parallel.scm (slurm): Update to 16.05.11.
[source]: Use the recommended download URL.
 2017-11-08 19:32:31 -05:00
Leo Famulari
a3dd13ae0e
gnu: rpm: Update to 4.13.0.2 [fixes CVE-2017-{7500,7501}]. 
* gnu/packages/package-management.scm (rpm): Update to 4.13.0.2.
 2017-11-08 19:00:07 -05:00
Leo Famulari
7df4194b16
gnu: python-icalendar: Update to 4.0.0. 
* gnu/packages/python.scm (python-icalendar): Update to 4.0.0.
 2017-11-08 18:36:29 -05:00
Leo Famulari
03b154f800
gnu: syncthing: Update to 0.14.40. 
* gnu/packages/syncthing.scm (syncthing): Update to 0.14.40.
[inputs]: Add go-github-com-zillode-notify.
 2017-11-08 17:24:02 -05:00
Leo Famulari
52ff28e4aa
gnu: Add go-github-com-zillode-notify. 
* gnu/packages/syncthing.scm (go-github-com-zillode-notify): New variable.
 2017-11-08 17:24:01 -05:00
Leo Famulari
4cf6827de3
gnu: go-github-com-audriusbutkevicius-kcp-go: Update to 0.0.0-1.8ae5f52. 
* gnu/packages/syncthing.scm (go-github-com-audriusbutkevicius-kcp-go):
Update to 0.0.0-1.8ae5f52.
[propagated-inputs]: Add go-github-com-tjfoc-gmsm-sm4.
 2017-11-08 17:24:01 -05:00
Leo Famulari
f44169c2a7
gnu: Add go-github-com-tjfoc-gmsm-sm4. 
* gnu/packages/syncthing.scm (go-github-com-tjfoc-gmsm-sm4): New variable.
 2017-11-08 17:24:01 -05:00
Ludovic Courtès
49483f7138
services: Add 'lookup-service-types'. 
* gnu/services.scm (lookup-service-types): New procedure.
* tests/services.scm ("lookup-service-types"): New test.
 2017-11-08 22:31:58 +01:00
Ludovic Courtès
3943913fac
services: 'fold-service-types' includes (gnu services). 
* gnu/services.scm (all-service-modules): New procedure.
(fold-service-types): Use it for the default MODULES value.
 2017-11-08 22:31:58 +01:00
Ludovic Courtès
a3d37f3ae5
services: 'fold-service-types' honors its seed. 
* gnu/services.scm (fold-service-types): Use SEED instead of '().
 2017-11-08 22:31:58 +01:00
Hartmut Goebel
0af94ad52f
gnu: service: Update comment. 
* gnu/services/base.scm (guix-activation): Update comment.
 2017-11-08 18:23:06 +01:00
Hartmut Goebel
d9565f7d87
install: Use overlayfs instead of unionfs. 
I dediced to keep adding /tmp as tmpfs since I was not able to trigger bug
while still using unionfs, so I could not verify whether this mount is still
needed with overlayfs.  Mapping /tmp to tmpfs does not harm, so we are on the
save side.

* gnu/system/install.scm (make-cow-store): Mount /gnu/store without additional
  read-only bind-mount, since in overlayfs the "lower" level is always
  read-only. Add work-dir required by overlayfs. No need to sleep anymore
  since now using the mount syscall. [unionfs]: Remove now unused function.
  (%installation-services): Update comment.
  (installation-os)[file-systems]: Update comment.
 2017-11-08 18:23:06 +01:00
Hartmut Goebel
c828969036
build: Use overlayfs instead of unionfs. 
Overlayfs is part of the kernel, while unionfs needs FUSE.  This also reduces
the size of the initrd by ca. 4.3% (487K).

* gnu/build/linux-boot.scm (mount-root-file-system): Remove optional parameter
  "unionfs"; mount using overlayfs instead of unionfs; new directory layout
  requied by overlayfs; update documentation.
  [mark-as-not-killable]: Remove now unused function

* gnu/system/linux-initrd.scm (file-system-packages): Remove now unused
  packages "unionfs-fuse/static" and thus unused related 'if'.
  (linux-modules): Replace "fuse" by "overlay".
 2017-11-08 18:23:05 +01:00
Ricardo Wurmus
34260a10d7
gnu: miso: Use pypi-uri. 
* gnu/packages/bioinformatics.scm (miso)[source]: Use pypi-uri.
 2017-11-08 17:41:08 +01:00
Ricardo Wurmus
e5c17b8d9d
gnu: Add r-vcd. 
* gnu/packages/cran.scm (r-vcd): New variable.
 2017-11-08 17:34:35 +01:00
Ricardo Wurmus
018cf270a3
gnu: Add r-laeken. 
* gnu/packages/cran.scm (r-laeken): New variable.
 2017-11-08 17:34:11 +01:00
Ricardo Wurmus
697e341e74
gnu: fastcap: Use texlive-tiny. 
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Replace texlive with
texlive-tiny.
[arguments]: Fix indentation; set HOME in "make-pdf" phase to avoid font
errors with texlive-tiny.
 2017-11-08 17:15:24 +01:00
Ricardo Wurmus
7e3aca2b78
gnu: librecad: Fix build. 
* gnu/packages/engineering.scm (librecad)[arguments]: Add phase
"patch-boost-error".
 2017-11-08 16:21:54 +01:00
Ricardo Wurmus
b72b42cf02
gnu: Add r-performanceanalytics. 
* gnu/packages/cran.scm (r-performanceanalytics): New variable.
 2017-11-08 16:21:54 +01:00
Ricardo Wurmus
3699383e6f
gnu: Add r-xts. 
* gnu/packages/cran.scm (r-xts): New variable.
 2017-11-08 16:21:53 +01:00
Ricardo Wurmus
5a80c15c14
gnu: Remove "open source" from descriptions. 
All software in Guix is Free Software.

* gnu/packages/aidc.scm (libdmtx)[description]: Remove "open source" string.
* gnu/packages/firmware.scm (seabios)[description]: Likewise.
* gnu/packages/libupnp.scm (libupnp)[description]: Likewise.
* gnu/packages/maths.scm (cubicle)[description]: Likewise.
* gnu/packages/mingw.scm (mingw-w64)[description]: Likewise.
* gnu/packages/game-development.scm (openmw)[description]: Likewise.
[synopsis]: Remove "Free software".
 2017-11-08 16:21:53 +01:00
Ricardo Wurmus
88fb156288
gnu: pcb: Update to 4.0.2. 
* gnu/packages/engineering.scm (pcb): Update to 4.0.2.
[arguments]: Add build phase "fix-check-for-display".
 2017-11-08 16:21:53 +01:00
Efraim Flashner
c8b38f8ea6
gnu: time: Update license. 
* gnu/packages/time.scm (time)[license]: Change to gpl3+.
 2017-11-08 10:52:09 +02:00
Efraim Flashner
dd00e0919f
gnu: time: Update to 1.8. 
* gnu/packages/time.scm (time): Update to 1.8.
[arguments]: Remove custom 'configure phase.
 2017-11-08 10:49:19 +02:00
Ricardo Wurmus
12a24ee878
gnu: Add glusterfs. 
* gnu/packages/file-systems.scm (glusterfs): New variable.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus
2e648d2bc4
gnu: r-prabclus: Update description. 
* gnu/packages/statistics.scm (r-prabclus)[description]: Fix grammar errors.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus
14e5f6b20a
gnu: r-fdrtool: Update description. 
* gnu/packages/statistics.scm (r-fdrtool)[description]: Use "@dfn" syntax.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus
738dda8330
gnu: Add r-bbmle. 
* gnu/packages/cran.scm (r-bbmle): New variable.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus
7b0569c0a9
gnu: Add r-rsofia. 
* gnu/packages/cran.scm (r-rsofia): New variable.
 2017-11-07 23:32:46 +01:00
Ricardo Wurmus
c49102ecca
gnu: Add r-hitc. 
* gnu/packages/bioinformatics.scm (r-hitc): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus
30eb4e37c8
gnu: Add r-fithic. 
* gnu/packages/bioinformatics.scm (r-fithic): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus
fbf5440637
gnu: Add r-sushi. 
* gnu/packages/bioinformatics.scm (r-sushi): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus
9232cac410
gnu: Add r-vioplot. 
* gnu/packages/cran.scm (r-vioplot): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus
3a22732cd8
gnu: Add r-sm. 
* gnu/packages/cran.scm (r-sm): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus
2e4ce60e7c
gnu: Add r-gwascat. 
* gnu/packages/bioinformatics.scm (r-gwascat): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus
4272000661
gnu: Add r-gviz. 
* gnu/packages/bioinformatics.scm (r-gviz): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus
794ff347a9
gnu: Add r-gqtlstats. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus
7fd5f60b8f
gnu: Add r-hardyweinberg. 
* gnu/packages/cran.scm (r-hardyweinberg): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus
10e16fa93d
gnu: Add r-mice. 
* gnu/packages/cran.scm (r-mice): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus
66c39102e5
gnu: Add r-ldblock. 
* gnu/packages/bioinformatics.scm (r-ldblock): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus
15f98b0d23
gnu: Add r-erma. 
* gnu/packages/bioinformatics.scm (r-erma): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
421c68e3f7
gnu: Add r-homo-sapiens. 
* gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
b52a866d14
gnu: Add r-org-hs-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
dd5fc8b78e
gnu: Add r-snpstats. 
* gnu/packages/bioinformatics.scm (r-snpstats): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
e2b927993e
gnu: Add r-gqtlbase. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus
96a392a0b2
gnu: Add r-gprofiler. 
* gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
60faf94597
gnu: Add r-ggbio. 
* gnu/packages/bioinformatics.scm (r-ggbio): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
7af1f40373
gnu: Add r-biovizbase. 
* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
2f6f61fd8e
gnu: Add r-organismdbi. 
* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
aa30ab5aee
gnu: Add r-ensembldb. 
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
763e98103a
gnu: Add r-annotationfilter. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus
04e2a2e969
gnu: Add r-dirichletmultinomial. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus
3af149f524
gnu: Add r-complexheatmap. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus
902fb15d92
gnu: Add r-genomicfiles. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
 2017-11-07 23:32:41 +01:00
Marius Bakke
cd215877a0
gnu: bdftopcf: Update to 1.1. 
* gnu/packages/xorg.scm (bdftopcf): Update to 1.1.
[native-inputs]: Change from LIBXFONT to LIBXFONT2.
 2017-11-07 23:29:23 +01:00
Marius Bakke
d469bc09bd
gnu: feh: Update to 2.22.2. 
* gnu/packages/image-viewers.scm (feh): Update to 2.22.2.
 2017-11-07 22:16:27 +01:00
Jan Nieuwenhuizen
625492ee1a
gnu: gcc-4.7: Resurrect building with gcc-5.4.0. 
* gnu/packages/patches/gcc-4-compile-with-gcc-5.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gcc.scm (gcc-4.7): Use it.
 2017-11-07 22:03:51 +01:00
Rutger Helling
a67f094671
gnu: Add websockify. 
* gnu/packages/web.scm (websockify): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:56:42 +01:00
Gábor Boskovits
75d342ffa9
gnu: Add python-networkx2. 
* gnu/packages/python.scm (python-networkx2, python2-networkx2): New variables.
* gnu/local.mk (dist_patch_DATA): Register 'python-networkx2-reproducible-build.patch'.
* gnu/packages/patches/python-networkx2-reproducible-build.patch: New file.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:17:20 +01:00
Gábor Boskovits
2b295f5a2f
gnu: Add python-pydot. 
* gnu/packages/graphviz.scm (python-pydot, python2-pydot): New variables.

Modified-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:03:15 +01:00
Marius Bakke
38ad27da80
gnu: mercurial: Update to 4.4.1. 
* gnu/packages/version-control.scm (mercurial): Update to 4.4.1.
 2017-11-07 20:23:29 +01:00
Marius Bakke
4a30c1c0e2
gnu: vim: Update to 8.0.1274 [fixes CVE-2017-1000382]. 
* gnu/packages/vim.scm (vim): Update to 8.0.1274.
 2017-11-07 20:21:46 +01:00
Marius Bakke
31a963fe80
gnu: notmuch: Update to 0.25.2. 
* gnu/packages/mail.scm (notmuch): Update to 0.25.2.
 2017-11-07 20:01:03 +01:00
Efraim Flashner
9129804230
gnu: psm: Only use as an input on supported-systems. 
Syntax help supplied by bavier@member.fsf.org

* gnu/packages/linux.scm (libfabric)[inputs]: Only use psm as an input
on systems where psm is supported.
* gnu/packages/mpi.scm (openmpi)[inputs]: Same.
 2017-11-07 20:41:08 +02:00
Efraim Flashner
b516b78002
gnu: psm: Limit supported systems. 
* gnu/packages/linux.scm (psm)[supported-systems]: New field, limit to
i686-linux and x86_64-linux.
 2017-11-07 20:41:05 +02:00
Efraim Flashner
174807b9a4
gnu: gnupg: Update to 2.2.2. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.2.
 2017-11-07 19:34:29 +02:00
Efraim Flashner
2f17187ff3
gnu: mediainfo: Change order of custom phases. 
* gnu/packages/video.scm (mediainfo)[arguments]: Change to the build
directory before executing the autogen script.
 2017-11-07 19:34:25 +02:00
Mathieu Othacehe
6541673354
gnu: linux: Fix kconfig selection. 
* gnu/packages/linux.scm (make-linux-libre): When cross-compiling,
  "kconfig" field is in native-inputs variable. So config is always #f
  when cross-compiling linux.
 2017-11-07 18:16:02 +01:00
Dave Love
f4433d09a1
gnu: openmpi: Add dependency on PSM. 
* gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love
7bc05ef0ac
gnu: libfabric: Add dependency on PSM. 
* gnu/packages/linux.scm (libfabric)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love
fd23d259cd
gnu: Add PSM. 
* gnu/packages/linux.scm (psm): New variable.
* gnu/packages/patches/psm-arch.patch,
gnu/packages/patches/psm-ldflags.patch,
gnu/packages/patches/psm-repro.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
 2017-11-07 18:09:13 +01:00
Gábor Boskovits
63b7fbe1bb
gnu: diffoscope: Update to 88. 
* gnu/packages/package-management.scm (diffoscope): Update to 88.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
ng0
db0164b21f
gnu: awesome: Update to 4.2. 
* gnu/packages/wm.scm (awesome): Update to 4.2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample
3eda8dd614
services: gdm: Add environment variables. 
While not an optimal solution (see comment), this makes GDM functional.

* gnu/services/xorg.scm (gdm-shepherd-service): Set PATH and XDG_DATA_DIRS
environment variables.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample
51bc8357e8
gnu: gdm: Add configure flags for better defaults. 
* gnu/packages/gnome.scm (gdm)[arguments]<#:configure-flags>: Add
--with-initial-vt=7 and --enable-gdm-xsession.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Timothy Sample
950d8e5d8c
gnu: gdm: Fix config file path. 
* gnu/packages/gnome.scm (gdm)[arguments]<#:phases>: Fix the
'pre-configure phase so that GDM finds its config file.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 18:09:13 +01:00
Oleg Pykhalov
ad54924285
gnu: expect: Change home-page to http://expect.sourceforge.net/. 
* gnu/packages/tcl.scm (expect): Change home-page to
  http://expect.sourceforge.net/.
 2017-11-07 18:50:46 +03:00
Ricardo Wurmus
e160aa1f81
gnu: Add r-gage. 
* gnu/packages/bioinformatics.scm (r-gage): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus
3121814ef1
gnu: Add r-keggrest. 
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus
a9540107c6
gnu: antlr3-3.3: Prettify build phases. 
* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases
"bin-install" and "generate-grammar".
 2017-11-07 12:39:50 +01:00
Ricardo Wurmus
9ecc4c69eb
gnu: r-servr: Update to 0.8. 
* gnu/packages/web.scm (r-servr): Update to 0.8.
 2017-11-07 08:15:45 +01:00
Ricardo Wurmus
60ec9da3aa
gnu: r-tidyselect: Update to 0.2.3. 
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
baa00ee90d
gnu: r-msnbase: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0.
[propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
14b3c71911
gnu: r-annotationhub: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
15ca195979
gnu: r-mzr: Remove bundled copy of boost. 
* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source.
[arguments]: Add build phase "use-system-boost" to link with our boost
package and avoid building the bundled sources.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
34b9675449
gnu: r-mzr: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
b500dbcdef
gnu: r-mzid: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
eeaa6967f9
gnu: r-chipseq: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
74248d22a0
gnu: Add r-rmysql. 
* gnu/packages/databases.scm (r-rmysql): New variable.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
42e11d3301
gnu: r-biomart: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
010ab2ffd2
gnu: r-edger: Update to 3.20.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
eb3f5cc76a
gnu: r-gostats: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
2404cc4283
gnu: r-category: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
65a8cd6676
gnu: r-lubridate: Update to 1.7.1. 
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
689edf1153
gnu: r-preprocesscore: Update to 1.40.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.40.0.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
e7f680f071
gnu: r-r-utils: Update to 2.6.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.6.0.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
ecfe98a17a
gnu: r-openssl: Update to 0.9.8. 
* gnu/packages/statistics.scm (r-openssl): Update to 0.9.8.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
aced057fbc
gnu: r-rlang: Update to 0.1.4. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.1.4.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
1be0f53664
gnu: r-vsn: Update to 3.46.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0.
[propagated-inputs]: Remove r-hexbin.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
007424b5a5
gnu: r-motifrg: Rename input label. 
* gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]:
Rename label of r-bsgenome-hsapiens-ucsc-hg19.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
ce59d62519
gnu: r-motifrg: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus
98791c25c8
gnu: r-qvalue: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
87fa5aface
gnu: r-fastseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
1567c8d91b
gnu: r-interactivedisplaybase: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.16.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
0096127974
gnu: r-edaseq: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus
22752bef3b
gnu: r-msnid: Update to 1.11.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
8140f680ad
gnu: r-deseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
531e80903f
gnu: r-aroma-light: Update to 3.8.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
a998c9a464
gnu: r-pcamethods: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
8a8138d248
gnu: r-affyio: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus
dad5f83817
gnu: r-affy: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
9a665dfb6f
gnu: r-protgenerics: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.10.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
617700895b
gnu: r-seqlogo: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.44.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
e127c918f8
gnu: r-genomation: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.10.0.
[propagated-inputs]: Remove r-rhtslib.
[inputs]: Remove zlib.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
e6ce4bf00d
gnu: r-impute: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.52.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus
0f948b116b
gnu: r-seqpattern: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.10.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
e67850b40d
gnu: r-bsgenome: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.46.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
d13a3fea7e
gnu: r-topgo: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
aeb73879f6
gnu: r-graph: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.56.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus
96fb465174
gnu: r-genomicalignments: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
6fcbed7329
gnu: r-summarizedexperiment: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
cb0a9a7493
gnu: r-delayedarray: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.4.1.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
f8068419a6
gnu: r-rsamtools: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.30.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
b719435ebb
gnu: r-biostrings: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.46.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus
0f8d98f294
gnu: r-annotationdbi: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.40.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
ca52123611
gnu: r-biobase: Update to 2.38.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.38.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
aa5c1f61f1
gnu: r-genomicranges: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
2b6ae8bfd5
gnu: r-xvector: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.18.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus
f642c0e4c7
gnu: r-limma: Update to 3.34.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
7f1bac3528
gnu: r-variantannotation: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
8aab0235e0
gnu: r-genomeinfodb: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
9e482c2069
gnu: r-iranges: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
41f0f94976
gnu: r-s4vectors: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus
2167eafc1d
gnu: r-biocstyle: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
3241461670
gnu: r-biocinstaller: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
d61fc4e104
gnu: r-biocgenerics: Update to 0.24.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
704fe4d115
gnu: r-grohmm: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus
843826e262
gnu: r-shortread: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
b53755258a
gnu: r-systempiper: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
9f52e53d5d
gnu: r-gseabase: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
fad7c0c7bd
gnu: r-sva: Update to 3.26.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
91e1867972
gnu: r-methylkit: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus
c126ba69db
gnu: r-copywriter: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
598dacf657
gnu: r-annotationfilter: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
e6b332d43b
gnu: r-rhdf5: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
19e8929cbd
gnu: r-tximport: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
da153b7f94
gnu: r-bamsignals: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus
5c18470008
gnu: r-zlibbioc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
1d0263b44e
gnu: r-rhtslib: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
c25154e5cb
gnu: r-rbgl: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
727706ad38
gnu: r-annotationforge: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus
3fd010ff30
gnu: r-dexseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
0166dc07ef
gnu: r-deseq2: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
554fac74aa
gnu: r-genefilter: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
cb4d3ff2c4
gnu: r-geneplotter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
2d4e887dc0
gnu: r-annotate: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus
94fd86e5e1
gnu: r-dnacopy: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
c7782c3f1f
gnu: r-biocviews: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0.
[propagated-inputs]: Remove r-knitr.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
7373b4167a
gnu: r-bioccheck: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0.
[native-inputs]: Remove which.
[propagated-inputs]: Add r-stringdist.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
a40a04fdbb
gnu: Add r-stringdist. 
* gnu/packages/cran.scm (r-stringdist): New variable.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus
8ca2b2b06e
gnu: r-rgraphviz: Update to 2.22.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.22.0.
 2017-11-07 08:15:27 +01:00
Ludovic Courtès
a0e4b41b40
gnu: guile-git: Update snapshot. 
* gnu/packages/guile.scm (guile-git): Update to commit 951a32c.
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
fedde43b6d
gnu: moka-icon-theme: Fix license. 
* gnu/packages/gnome.scm (moka-icon-theme): Add cc-by-sa4.0 to license field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
550281fb5f
gnu: moka-icon-theme: Add faba-icon-theme as propagated input. 
* gnu/packages/gnome.scm (moka-icon-theme)[propagated-inputs]: New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
8b0e4177ee
gnu: moka-icon-theme: Simplify package definition. 
* gnu/packages/gnome.scm (moka-icon-theme): Inherit faba-icon-theme to avoid
  duplicating similar package definition.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley
d935e6a12c
gnu: Add faba-icon-theme. 
* gnu/packages/gnome.scm (faba-icon-theme): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Carlo Zancanaro
47bd32d98e
gnu: electrum: Update to 3.0. 
gnu/packages/finance.scm (electrum): Update to 3.0.
[inputs]: Change to python3 inputs.
[arguments]: Remove python-2. Disable tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:10 +01:00
Carlo Zancanaro
ea0421bbf6
gnu: Add python-jsonrpclib-pelix. 
* gnu/packages/python.scm (python-jsonrpclib-pelix, python2-jsonrpclib-pelix):
New variables.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:10 +01:00
Ludovic Courtès
96dc8f3527
packages: 'fold-packages' takes #:select? parameter. 
* gnu/packages.scm (fold-packages): Add #:select? parameter and honor it.
 2017-11-07 00:12:10 +01:00
Ludovic Courtès
0ad5f80982
Fix ambiguous imports. 
* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1).
* guix/git.scm: Select 'mkdir-p' from (guix build utils).
 2017-11-07 00:12:10 +01:00
Efraim Flashner
913027f383
gnu: nnn: Update to 1.5. 
* gnu/packages/admin.scm (nnn): Update to 1.5.
 2017-11-06 23:07:19 +02:00
Efraim Flashner
6a534909fa
gnu: libuninameslist: Update to 20170807. 
* gnu/packages/fontutils.scm (libuninameslist): Update to 20170807.
 2017-11-06 23:07:13 +02:00
Efraim Flashner
10b159a303
gnu: u-boot: Only install 'MLO' output if it exists. 
* gnu/packages/bootloaders.scm (u-boot)[arguments]: Add 'MLO' to
uboot-files only if it has been built.
 2017-11-06 22:54:28 +02:00
Mathieu Othacehe
b1a3079347
system: vm: Use 2^32 - 1 as hash size. 
* gnu/system/vm.scm (operating-system-uuid): Use 2^32 - 1 instead of
  2^32 as hash size.

On some 32 bit system (ARM for example), 2^32 exceeds hash max
size (ULONG_MAX = 2^32 - 1).
 2017-11-06 20:02:25 +01:00
Mathieu Othacehe
dd208b936c
bootloaders: uboot: Add .img and MLO files to binary outputs. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Add .img and MLO files
  as binary output.
 2017-11-06 19:58:21 +01:00
Mathieu Othacehe
f6948189a9
linux: Add omap2plus generic kernel. 
* gnu/packages/linux.scm (linux-libre-arm-omap2plus): New exported variable.
 2017-11-06 19:55:10 +01:00
Mathieu Othacehe
2ac42fe51f
gnu: uboot: Fix same-arch? check. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Compare %current-system
  to system associated to given triplet. Comparing a system and a triplet
  didn't make sense.
 2017-11-06 19:53:13 +01:00
Efraim Flashner
d298e7652a
gnu: perl-test-www-mechanize-psgi: Update source uri. 
* gnu/packages/web.scm (perl-test-www-mechanize-psgi)[source]: Update to
new source uri.
 2017-11-06 20:39:45 +02:00
Efraim Flashner
12c613b548
gnu: dtc: Build python bindings. 
* gnu/packages/bootloaders.scm (dtc)[native-inputs]: Add swig.
[inputs]: Add python-2.
[arguments]: Remove 'NO_PYTHON' from make-flags, add 'SETUP_PREFIX' to
set python bindings prefix.
 2017-11-06 20:39:45 +02:00
Efraim Flashner
ab8757c5b1
gnu: dtc: Update to 1.4.5. 
* gnu/packages/bootloaders.scm (dtc): Update to 1.4.5.
[arguments]: Add NO_PYTHON flag to make-flags.
 2017-11-06 20:39:45 +02:00
Efraim Flashner
9371600ec8
gnu: libxres: Update to 1.2.0. 
* gnu/packages/xorg.scm (libxres): Update to 1.2.0.
 2017-11-06 20:02:45 +02:00
Tobias Geerinckx-Rice
fd592a12e2
gnu: youtube-dl: Update to 2017.11.06. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.11.06.
 2017-11-06 18:18:41 +01:00
Efraim Flashner
8f4e3b95df
gnu: aria2: Update to 1.33.0. 
* gnu/packages/bittorrent.scm (aria2): Update to 1.33.0.
 2017-11-06 06:18:31 +02:00
Efraim Flashner
08e1f38ddd
gnu: emacs-undo-tree: Parameterize source uri. 
* gnu/packages/emacs.scm (emacs-undo-tree)[source]: Replace hard-coded
version with version parameter.
 2017-11-06 06:18:26 +02:00
Leo Famulari
73cd4022d6
gnu: borg: Update to 1.1.2. 
* gnu/packages/backup.scm (borg): Update to 1.1.2.
[arguments]: Disable another test in the 'check' phase.
 2017-11-05 20:36:05 -05:00
Eric Bavier
d8799bd0df
gnu: netsurf: Update to 3.7. 
For compatibility, dependents must be updated at the same time.

* gnu/packages/web.scm (libcss): Update to 0.7.0
(nsgenbind): Update to 0.5.
(netsurf): Update to 3.7.
[arguments]: Fix binary name in .desktop.  Adjust "docs" directory name.
* gnu/packages/patches/netsurf-system-utf8proc.patch: Adjust to new source.
 2017-11-05 07:46:08 -06:00
Eric Bavier
772588bd22
gnu: libnspsl: Update to 0.1.2. 
* gnu/packages/web.scm (libnspsl): Update to 0.1.2.
 2017-11-05 07:46:08 -06:00