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13858 commits

Author SHA1 Message Date
Ricardo Wurmus
4b005c7a75
gnu: Add r-spatial. 
* gnu/packages/statistics.scm (r-spatial): New variable.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
567b154fb0
gnu: r-rpart: Move to the set of recommended packages. 
* gnu/packages/statistics.scm (r-rpart): Move up to the set of recommended
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
a5a343656b
gnu: r-nnet: Move to set of recommended R packages. 
* gnu/packages/machine-learning.scm (r-nnet): Move from here...
* gnu/packages/statistics.scm (r-nnet): ...to here because the other
recommended R packages are here.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
ac8d738b97
gnu: r-mgcv: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-mgcv): Move up to set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
248f65269a
gnu: Add r-nlme. 
* gnu/packages/statistics.scm (r-nlme): New variable.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
69e14f9ec7
gnu: r-matrix: Move to set of recommended R packages. 
* gnu/packages/statistics.scm (r-matrix): Move to set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
060c12868b
gnu: r-lattice: Move to other recommended R packages. 
* gnu/packages/statistics.scm (r-lattice): Move to the set of recommended R
packages.
 2017-03-17 10:14:01 +01:00
Ricardo Wurmus
e88bad6ddb
gnu: Add r-kernsmooth. 
* gnu/packages/statistics.scm (r-kernsmooth): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
69fddd2d6e
gnu: Add r-foreign. 
* gnu/packages/statistics.scm (r-foreign): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
c1999c5910
gnu: Add r-codetools. 
* gnu/packages/statistics.scm (r-codetools): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
a27bfb8484
gnu: Add r-cluster. 
* gnu/packages/statistics.scm (r-cluster): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
7489258751
gnu: Add r-class. 
* gnu/packages/statistics.scm (r-class): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
c7e80a7e0d
gnu: Add r-mass. 
* gnu/packages/statistics.scm (r-mass): New variable.
 2017-03-17 10:14:00 +01:00
Ricardo Wurmus
8f0069170c
gnu: Add r-boot. 
* gnu/packages/statistics.scm (r-boot): New variable.
 2017-03-17 10:14:00 +01:00
Tobias Geerinckx-Rice
54d556bdd7
gnu: youtube-dl: Update to 2017.03.16. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.03.16.
 2017-03-17 03:11:35 +01:00
Kei Kebreau
3078821d13
gnu: asciidoc: Use local docbook-xml package. 
* gnu/packages/documentation.scm (asciidoc)[inputs]: Add docbook-xml.
[arguments]: Add 'make-local-docbook-xml' phase.
 2017-03-16 21:35:50 -04:00
Tobias Geerinckx-Rice
f9cdf1c15b
gnu: Add knot. 
* gnu/packages/dns.scm (knot): New variable.
 2017-03-17 02:32:01 +01:00
Tobias Geerinckx-Rice
754667f0eb
gnu: Add liburcu. 
* gnu/packages/datastructures.scm (liburcu): New variable.
 2017-03-17 02:32:00 +01:00
Tobias Geerinckx-Rice
366efcb2fb
gnu: dns: Fix typo and use @dfn in descriptions. 
* gnu/packages/dns.scm (bind)[description]: Use @dfn to expand acronyms.
(yadifa)[description]: Likewise, and fix a typo.
 2017-03-17 02:32:00 +01:00
Leo Famulari
2ec5ba859f
gnu: linux-libre: Update to 4.10.3. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.10.3.
(%linux-libre-hash): Update hash.
 2017-03-16 19:40:40 -04:00
Leo Famulari
2044306f05
gnu: linux-libre@4.4: Update to 4.4.54. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.54.
 2017-03-16 19:40:39 -04:00
Leo Famulari
bcc5b74173
gnu: linux-libre@4.9: Update to 4.9.15. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.15.
 2017-03-16 19:40:39 -04:00
Leo Famulari
49ac6dbb0a
gnu: qemu: Fix CVE-2017-{2620,2630}. 
* gnu/packages/patches/qemu-CVE-2017-2620.patch,
gnu/packages/patches/qemu-CVE-2017-2630.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/qemu.scm (qemu)[source]: Use them.
 2017-03-16 19:40:08 -04:00
Leo Famulari
1e5b8beeff
gnu: virglrenderer: Fix CVE-2017-6386. 
* gnu/packages/patches/virglrenderer-CVE-2017-6386.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/spice.scm (virglrenderer)[source]: Use it.
 2017-03-16 19:39:55 -04:00
Clément Lassieur
2c715a9223
gnu: password-store: Fix compatibility with GnuPG 2.1.19. 
* gnu/packages/patches/password-store-gnupg-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/password-utils.scm (password-store)[source]: Use it.

Signed-off-by: Clément Lassieur <clement@lassieur.org>
 2017-03-16 19:58:43 +01:00
Raoul Jean Pierre Bonnal
2441c28414
gnu: Add r-seurat. 
* gnu/packages/bioinformatics.scm (r-seurat): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-03-16 14:54:58 +01:00
Ricardo Wurmus
79849358f8
gnu: sra-tools: Update to 2.8.2-1. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
 2017-03-16 13:40:36 +01:00
Ricardo Wurmus
d5e1716239
gnu: ncbi-vdb: Install configuration files. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
 2017-03-16 13:39:53 +01:00
Ricardo Wurmus
558e23074e
gnu: ncbi-vdb: Override search path for java-ngs. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
 2017-03-16 13:38:39 +01:00
Ricardo Wurmus
701111989e
gnu: ncbi-vdb: Use modify-phases syntax. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
 2017-03-16 10:20:56 +01:00
Ricardo Wurmus
5021f54787
gnu: ncbi-vdb: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
 2017-03-16 10:19:25 +01:00
Ricardo Wurmus
6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
 2017-03-16 10:18:48 +01:00
Tobias Geerinckx-Rice
0f03c53168
gnu: Add pzstd. 
* gnu/packages/compression.scm (pzstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice
f6ac3101ff
gnu: Add zstd. 
* gnu/packages/compression.scm (zstd): New variable.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice
9186216268
gnu: python-publicsuffix2: Update to 2.20160818. 
* gnu/packages/python.scm (python-publicsuffix2): Update to 2.20160818.
 2017-03-16 05:44:02 +01:00
Tobias Geerinckx-Rice
192b887a03
gnu: awscli: Update to 1.11.63. 
* gnu/packages/python.scm (awscli): Update to 1.11.63.
 2017-03-16 05:44:01 +01:00
Tobias Geerinckx-Rice
d93985fe22
gnu: python-botocore: Update to 1.5.26. 
* gnu/packages/python.scm (python-botocore): Update to 1.5.26.
 2017-03-16 05:44:01 +01:00
Tobias Geerinckx-Rice
70fc93cb28
gnu: python-ptyprocess: Update to 0.5.1. 
* gnu/packages/python.scm (python-ptyprocess): Update to 0.5.1.
 2017-03-16 05:44:01 +01:00
Kei Kebreau
26a657f06a
gnu: Add prboom-plus. 
* gnu/packages/games.scm (prboom-plus): New variable.
 2017-03-15 23:14:42 -04:00
Gábor Boskovits
5b5cf3c765
gnu: Add tftp-hpa. 
* gnu/packages/networking.scm (tftp-hpa): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 18:24:30 -04:00
Andy Wingo
80a725726d
gnu: guile-next: Update to 2.2.0. 
* gnu/packages/guile.scm (guile-next): Update to 2.2.0.
 2017-03-15 22:59:40 +01:00
Leo Famulari
dce8ac54b4
gnu: profanity: Make the source URL version-agnostic. 
* gnu/packages/messaging.scm (profanity)[source]: Use (version) in the source
URL.
 2017-03-15 17:20:27 -04:00
Tobias Geerinckx-Rice
cf8d068775
gnu: units: Update to 2.14. 
* gnu/packages/maths.scm (units): Update to 2.14.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice
3d602acb13
gnu: no-more-secrets: Update to 0.3.2. 
* gnu/packages/games.scm (no-more-secrets): Update to 0.3.2.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice
7ea523853c
gnu: mailutils: Update to 3.2. 
* gnu/packages/mail.scm (mailutils): Update to 3.2.
 2017-03-15 22:19:40 +01:00
Tobias Geerinckx-Rice
f38607536e
gnu: Use INSTALL-FILE where appropriate. 
* gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler
INSTALL-FILE for COPY-FILE when invoked with redundant arguments.
* gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity,
edirect, fasttree, rsem, samtools-0.1): Likewise.
* gnu/packages/code.scm (withershins): Likewise.
* gnu/packages/conky.scm (conky): Likewise.
* gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise.
* gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise.
* gnu/packages/engineering.scm (librecad): Likewise.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice
618e4bfbad
gnu: cryptsetup: Update to 1.7.4. 
* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.4.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice
4e128dd582
gnu: man-pages: Update to 4.10. 
* gnu/packages/man.scm (man-pages): Update to 4.10.
[home-page]: Use HTTPS.
 2017-03-15 22:19:38 +01:00
Mekeor Melire
a829c6501b
gnu: Add profanity. 
* gnu/packages/messaging.scm (profanity): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00
Mekeor Melire
781d3b070c
gnu: Add libstrophe. 
* gnu/packages/messaging.scm (libstrophe): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2017-03-15 17:17:06 -04:00