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Author SHA1 Message Date
Tobias Geerinckx-Rice
2a91494ed1
gnu: ruby-redcloth: Update to 4.3.2. 
* gnu/packages/ruby.scm (ruby-redcloth): Update to 4.3.2.
 2017-08-11 00:20:46 +02:00
Tobias Geerinckx-Rice
a3179a7338
gnu: ruby-connection-pool: Update to 2.2.1. 
* gnu/packages/ruby.scm (ruby-connection-pool): Update to 2.2.1.
 2017-08-11 00:20:46 +02:00
Tobias Geerinckx-Rice
56822223c1
gnu: ruby-fivemat: Update to 1.3.5. 
* gnu/packages/ruby.scm (ruby-fivemat): Update to 1.3.5.
 2017-08-11 00:20:45 +02:00
Tobias Geerinckx-Rice
8d10918a43
gnu: ruby-daemons: Update to 1.2.4. 
* gnu/packages/ruby.scm (ruby-daemons): Update to 1.2.4.
 2017-08-11 00:20:44 +02:00
Tobias Geerinckx-Rice
e2fcef3913
gnu: ruby-diff-lcs: Update to 1.3. 
* gnu/packages/ruby.scm (ruby-diff-lcs): Update to 1.3.
 2017-08-11 00:20:44 +02:00
Tobias Geerinckx-Rice
313dd5ddc0
gnu: ruby-thread-safe: Update to 0.3.6. 
* gnu/packages/ruby.scm (ruby-thread-safe): Update to 0.3.6.
 2017-08-11 00:20:43 +02:00
Tobias Geerinckx-Rice
884a80dd0a
gnu: ruby-pkg-config: Update to 1.2.5. 
* gnu/packages/ruby.scm (ruby-pkg-config): Update to 1.2.5.
 2017-08-11 00:20:43 +02:00
Tobias Geerinckx-Rice
30caad5080
gnu: ruby-eventmachine: Update to 1.2.5. 
* gnu/packages/ruby.scm (ruby-eventmachine): Update to 1.2.5.
 2017-08-11 00:20:42 +02:00
Tobias Geerinckx-Rice
f3a6311af4
gnu: ruby-term-ansicolor: Update to 1.6.0. 
* gnu/packages/ruby.scm (ruby-term-ansicolor): Update to 1.6.0.
 2017-08-11 00:20:41 +02:00
Tobias Geerinckx-Rice
0cd7b8164d
gnu: ruby-rake-compiler: Update to 1.0.4. 
* gnu/packages/ruby.scm (ruby-rake-compiler): Update to 1.0.4.
 2017-08-11 00:20:40 +02:00
Tobias Geerinckx-Rice
3b0e45c86d
gnu: ruby-useragent: Update to 0.16.8. 
* gnu/packages/ruby.scm (ruby-useragent): Update to 0.16.8.
 2017-08-11 00:20:40 +02:00
Tobias Geerinckx-Rice
5620bd456f
gnu: ruby-domain-name: Update to 0.5.20170404. 
* gnu/packages/ruby.scm (ruby-domain-name): Update to 0.5.20170404.
 2017-08-11 00:20:39 +02:00
Tobias Geerinckx-Rice
a7ca218cd5
gnu: ruby-notiffany: Update to 0.1.1. 
* gnu/packages/ruby.scm (ruby-notiffany): Update to 0.1.1.
 2017-08-11 00:20:39 +02:00
Tobias Geerinckx-Rice
d5489a618d
gnu: ruby-byebug: Update to 9.0.6. 
* gnu/packages/ruby.scm (ruby-byebug): Update to 9.0.6.
 2017-08-11 00:20:38 +02:00
Tobias Geerinckx-Rice
65a7f09ce0
gnu: ruby-sequel: Update to 4.49.0. 
* gnu/packages/ruby.scm (ruby-sequel): Update to 4.49.0.
 2017-08-11 00:20:38 +02:00
Tobias Geerinckx-Rice
d1c1f36803
gnu: ruby-shoulda-matchers: Update to 3.1.2. 
* gnu/packages/ruby.scm (ruby-shoulda-matchers): Update to 3.1.2.
 2017-08-11 00:20:37 +02:00
Tobias Geerinckx-Rice
8e5ff25042
gnu: ruby-arel: Update to 8.0.0. 
* gnu/packages/ruby.scm (ruby-arel): Update to 8.0.0.
 2017-08-11 00:20:37 +02:00
Tobias Geerinckx-Rice
56ccada3c1
gnu: ruby-rb-fsevent: Update to 0.10.2. 
* gnu/packages/ruby.scm (ruby-rb-fsevent): Update to 0.10.2.
 2017-08-11 00:20:36 +02:00
Tobias Geerinckx-Rice
cd698b6e20
gnu: ruby-utils: Update to 0.9.0. 
* gnu/packages/ruby.scm (ruby-utils): Update to 0.9.0.
 2017-08-11 00:20:35 +02:00
Tobias Geerinckx-Rice
e322222ab4
gnu: ruby-tzinfo: Update to 1.2.3. 
* gnu/packages/ruby.scm (ruby-tzinfo): Update to 1.2.3.
 2017-08-11 00:20:35 +02:00
Tobias Geerinckx-Rice
32bbfea811
gnu: ruby-rb-inotify: Update to 0.9.10. 
* gnu/packages/ruby.scm (ruby-rb-inotify): Update to 0.9.10.
 2017-08-11 00:20:34 +02:00
Tobias Geerinckx-Rice
8929f0a481
gnu: ruby-gherkin: Update to 4.1.3. 
* gnu/packages/ruby.scm (ruby-gherkin): Update to 4.1.3.
 2017-08-11 00:20:33 +02:00
Tobias Geerinckx-Rice
3d4a5eb555
gnu: ruby-timecop: Update to 0.9.1. 
* gnu/packages/ruby.scm (ruby-timecop): Update to 0.9.1.
 2017-08-11 00:20:33 +02:00
Tobias Geerinckx-Rice
483846ac6f
gnu: ruby-minitest: Update to 5.10.3. 
* gnu/packages/ruby.scm (ruby-minitest): Update to 5.10.3.
 2017-08-11 00:20:32 +02:00
Tobias Geerinckx-Rice
5ca48923f5
gnu: ruby-redcarpet: Update to 3.4.0. 
* gnu/packages/ruby.scm (ruby-redcarpet): Update to 3.4.0.
 2017-08-11 00:20:32 +02:00
Tobias Geerinckx-Rice
dc97df2ef4
gnu: ruby-cucumber-core: Update to 2.0.0. 
* gnu/packages/ruby.scm (ruby-cucumber-core): Update to 2.0.0.
 2017-08-11 00:20:31 +02:00
Tobias Geerinckx-Rice
ce5f523001
gnu: ruby-pg: Update to 0.21.0. 
* gnu/packages/ruby.scm (ruby-pg): Update to 0.21.0.
 2017-08-11 00:20:30 +02:00
Tobias Geerinckx-Rice
d14e5eaa19
gnu: ruby-slop: Update to 4.5.0. 
* gnu/packages/ruby.scm (ruby-slop): Update to 4.5.0.
 2017-08-11 00:20:29 +02:00
Marius Bakke
c2f93e9c07
gnu: openjpeg: Update to 2.2.0 [security fixes]. 
In addition to the patches we already had (which are not mentioned in the
ChangeLog, but verified by following their respective GitHub issues) this
release also fixes CVE-2016-9112, CVE-2016-5139, CVE-2016-5152, CVE-2016-5158,
CVE-2016-5159, CVE-2016-1626 and CVE-2016-1628.

See <https://github.com/uclouvain/openjpeg/blob/v2.2.0/CHANGELOG.md> for details.

* gnu/packages/patches/openjpeg-CVE-2016-9572-CVE-2016-9573.patch,
  gnu/packages/patches/openjpeg-CVE-2016-9850-CVE-2016-9851.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
* gnu/packages/image.scm (openjpeg): Update to 2.2.0.
[source](patches): Remove.
* gnu/packages/gstreamer.scm (gst-plugins-bad)[arguments]: Add phase to patch
hard-coded openjpeg-2.1 path.
 2017-08-10 22:23:31 +02:00
Marius Bakke
1a1558e88f
gnu: postgresql: Update to 9.6.4 [fixes CVE-2017-{7546,7547,7548}]. 
See <https://www.postgresql.org/about/news/1772/> for more information.

* gnu/packages/databases.scm (postgresql): Update to 9.6.4.
 2017-08-10 22:23:31 +02:00
Leo Famulari
1e07daa27a
gnu: mercurial: Update to 4.2.3 [fixes CVE-2017-1000116]. 
* gnu/packages/version-control.scm (mercurial): Update to 4.2.3.
 2017-08-10 15:02:04 -04:00
Leo Famulari
38f8a882ab
gnu: git: Update to 2.14.1 [fixes CVE-2017-1000117]. 
* gnu/packages/version-control.scm (git): Update to 2.14.1.
 2017-08-10 15:02:04 -04:00
Leo Famulari
5993f7c455
gnu: subversion: Update to 1.8.19 [fixes CVE-2017-9800]. 
* gnu/packages/version-control.scm (subversion): Update to 1.8.19.
[source]: Add alternate URL.
 2017-08-10 15:02:04 -04:00
Oleg Pykhalov
f262f44683
gnu: Add emacs-engine-mode. 
* gnu/packages/emacs.scm (emacs-engine-mode): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-10 22:25:25 +05:30
Leo Famulari
783daa4982
gnu: libsoup: Update to 2.58.2 (fixes CVE-2017-2885). 
* gnu/packages/gnome.scm (libsoup): Update to 2.58.2.
 2017-08-10 12:25:31 -04:00
Tobias Geerinckx-Rice
ddde3f6be1
gnu: catimg: Update to 2.4.0. 
* gnu/packages/image-viewers.scm (catimg): Update to 2.4.0.
 2017-08-10 17:26:08 +02:00
Tobias Geerinckx-Rice
226685faa5
gnu: cppcheck: Update to 1.80. 
* gnu/packages/check.scm (cppcheck): Update to 1.80.
 2017-08-10 17:26:07 +02:00
Tobias Geerinckx-Rice
c63b83a40f
gnu: vdirsyncer: Update to 0.16.1. 
* gnu/packages/dav.scm (vdirsyncer): Update to 0.16.1.
 2017-08-10 17:26:07 +02:00
Ben Woodcroft
37b08547e4
gnu: ruby-bio-commandeer: Update to 0.4.0. 
* gnu/packages/ruby.scm (ruby-bio-commandeer): Update to 0.4.0.
 2017-08-10 22:20:38 +10:00
Oleg Pykhalov
27feda65e7
gnu: Add emacs-erc-hl-nicks. 
* gnu/packages/emacs.scm (emacs-erc-hl-nicks): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-10 14:55:09 +05:30
Oleg Pykhalov
1ee879e967
gnu: Add emacs-gitpatch. 
By the way, “gitpatch.el” says different version than release tarball.
Do I need to ask a developer?
--8<---------------cut here---------------start------------->8---
;; Author: Feng Shu <tumashu@163.com>
;; Homepage: https://github.com/tumashu/gitpatch
;; Keywords: convenience
;; Package-Requires: ((emacs "24.3"))
;; Version: 0.10
--8<---------------cut here---------------end--------------->8---

>From 9eddf07fa401468738c2f48a25e51ddef2a3ceed Mon Sep 17 00:00:00 2001
From: Oleg Pykhalov <go.wigust@gmail.com>
Date: Sat, 29 Jul 2017 14:22:48 +0300
Subject: [PATCH] gnu: Add emacs-gitpatch.

* gnu/packages/emacs.scm (emacs-gitpatch): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-10 14:37:17 +05:30
Oleg Pykhalov
a88adeb343
gnu: Add emacs-git-messenger. 
gnu/packages/emacs.scm (emacs-git-messenger): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-10 13:27:05 +05:30
Christopher Baines
1012056625
services: admin: Simplify the handling of the Tailon debug? option. 
* gnu/services/admin.scm (tailon-configuration-file-compiler): Simplify the
  handling of debug?.
 2017-08-09 23:50:35 +01:00
Christopher Baines
91fdc8a574
services: Update the Tailon service for Tailon 1.3.0. 
Tailon 1.3.0 (upgraded from 1.1.1) adds support for HTTP authentication.

* gnu/services/admin.scm (<tailon-configuration-file>): Add http-auth and
  users configuration values.
  (tailon-configuration-file-http-auth, tailon-configuration-file-users): New
  procedures.
  (tailon-configuration-file-compiler): Add support for the http-auth and
  users configuration options.
* doc/guix.texi (Monitoring Services): Document authentication for Tailon.
 2017-08-09 23:50:31 +01:00
Christopher Baines
f2d8e7f720
services: Add missing wrap-lines option to tailon. 
* gnu/services/admin.scm (<tailon-configuration-file>): Add wrap-lines.
  (tailon-configuration-wrap-lines): New procedure.
  (tailon-configuration-file-compiler): Add support for wrap-lines.
* doc/guix.texi (Monitoring Services): Document the wrap-lines Tailon
  configuration option.
 2017-08-09 23:50:27 +01:00
Christopher Baines
761f5865c8
gnu: Update tailon to version 1.3.0. 
From version 1.1.1.

* gnu/packages/logging.scm (tailon)[version]: Change to 1.3.0.
  [inputs]: Add python-tornado-http-auth.
 2017-08-09 23:50:23 +01:00
Christopher Baines
c795bc79d9
gnu: Add python-tornado-http-auth. 
* gnu/packages/python.scm (python-tornado-http-auth): New variable.
 2017-08-09 23:50:10 +01:00
Marius Bakke
4c6c683862
gnu: nmap: Update to 7.60. 
* gnu/packages/admin.scm (nmap): Update to 7.60.
 2017-08-10 00:15:35 +02:00
Marius Bakke
79d9525071
gnu: curl: Update replacement to 7.55.0. [security fixes] 
Fixes CVE-2017-1000099, CVE-2017-1000100, and CVE-2017-100101.
See <https://curl.haxx.se/docs/security.html> for details.

* gnu/packages/curl.scm (curl)[replacement]: Update to 7.55.0.
(curl-7.54.1): Rename to ...
(curl-7.55.0): ... this.
[source]: Update source URI to match upstream compression method change.
[arguments]: Add 'fix-Makefile' phase.
 2017-08-10 00:15:35 +02:00
Marius Bakke
2e8c61fcf0
gnu: samba: Update to 4.6.7. 
* gnu/packages/samba.scm (samba): Update to 4.6.7.
 2017-08-10 00:15:34 +02:00
Leo Famulari
ae7f246cf1
gnu: python-nbformat: Update to 4.3.0. 
* gnu/packages/python.scm (python-nbformat, python2-nbformat): Update to 4.3.0.
 2017-08-09 16:52:51 -04:00
Leo Famulari
10756b9ed1
gnu: gnupg: Update to 2.1.23. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.1.23.
[arguments]: Remove 'enable-gpg2-is-gpg' from #:configure-flags, since it is now
the default.
 2017-08-09 16:01:33 -04:00
Ricardo Wurmus
1b22ecdac4
gnu: r-wgcna: Update to 1.61. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61.
[propagated-inputs]: Add r-rcpp, r-robust, r-survival.
 2017-08-09 20:08:13 +02:00
Ricardo Wurmus
c5f744a68d
gnu: Add r-robust. 
* gnu/packages/statistics.scm (r-robust): New variable.
 2017-08-09 20:08:13 +02:00
Ricardo Wurmus
5d0afe8849
gnu: Add r-fit-models. 
* gnu/packages/statistics.scm (r-fit-models): New variable.
 2017-08-09 20:08:13 +02:00
Ricardo Wurmus
0bae5fd6a7
gnu: Add r-rrcov. 
* gnu/packages/statistics.scm (r-rrcov): New variable.
 2017-08-09 20:08:13 +02:00
Ricardo Wurmus
23841b2573
gnu: Add r-pcapp. 
* gnu/packages/statistics.scm (r-pcapp): New variable.
 2017-08-09 20:08:13 +02:00
Ricardo Wurmus
0ecd065839
gnu: r-gdtools: Update to 0.1.5. 
* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.5.
 2017-08-09 20:08:12 +02:00
Ricardo Wurmus
c3317cd9fb
gnu: r-ggbeeswarm: Update to 0.6.0. 
* gnu/packages/statistics.scm (r-ggbeeswarm): Update to 0.6.0.
 2017-08-09 20:08:12 +02:00
Mark H Weaver
ea0277abcd
gnu: icecat: Add more fixes from upstream mozilla-esr52. 
* gnu/packages/gnuzilla.scm (icecat)[source]: Add fixes for CVE-2017-7802,
CVE-2017-7803, CVE-2017-7807, and the remaining 6 out of 23 changesets for
CVE-2017-7779.
 2017-08-09 13:16:52 -04:00
Mark H Weaver
12025fb9b0
gnu: icecat: Rename patches to reflect CVE assignments. 
Document that our existing patches include fixes for CVE-2017-7753,
CVE-2017-7784, CVE-2017-7786, CVE-2017-7787, CVE-2017-7791, CVE-2017-7792,
CVE-2017-7798, CVE-2017-7798, CVE-2017-7800, CVE-2017-7801, and 17 out of 23
changesets for CVE-2017-7779.

* gnu/packages/gnuzilla.scm (icecat)[source]: Rename patches to reflect CVE
assignments.
 2017-08-09 13:16:43 -04:00
ng0
28e12d6c81
gnu: gnurl: Update to 7.55.0. 
* gnu/packages/gnunet.scm (gnurl): Update to 7.55.0.

Signed-off-by: Tobias Geerinckx-Rice <me@tobias.gr>
 2017-08-09 18:16:51 +02:00
Tobias Geerinckx-Rice
a4afc536f9
gnu: virt-manager: Update to 1.4.2. 
* gnu/packages/virtualization.scm (virt-manager): Update to 1.4.2.
 2017-08-09 16:45:32 +02:00
Tobias Geerinckx-Rice
448052b713
gnu: libgdata: Disable failing tests. 
* gnu/packages/gnome.scm (libgdata)[arguments]: Add ‘disable-failing-tests’
phase.
 2017-08-09 16:31:06 +02:00
Ricardo Wurmus
18f5d2a70a
gnu: Add reference to (gnu packages graph). 
This is a follow-up to 1738138cb3.
 2017-08-09 15:43:35 +02:00
Ricardo Wurmus
1738138cb3
gnu: r-igraph: Move to (gnu packages graph). 
* gnu/packages/statistics.scm (r-igraph): Move from here...
* gnu/packages/graph.scm (r-igraph): ...to here.
 2017-08-09 14:47:47 +02:00
Ricardo Wurmus
31476df32e
gnu: Add python-igraph. 
* gnu/packages/graph.scm (python-igraph): New variable.
 2017-08-09 14:47:47 +02:00
Ricardo Wurmus
e57fffad90
gnu: Add igraph. 
* gnu/packages/graph.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2017-08-09 14:47:47 +02:00
Efraim Flashner
ea77385c4c
gnu: viewnior: Don't build icon-theme.cache. 
* gnu/packages/image-viewers.scm (viewnior)[arguments]: Add phase to
disable building the icon-theme.cache.
 2017-08-09 14:09:43 +03:00
Manolis Ragkousis
2d5bf32b8a
gnu: googletest: Build shared libraries. 
* gnu/packages/check.scm (googletest)[arguments]: Pass "-DBUILD_SHARED_LIBS=ON"
  in #:configure-flags.
 2017-08-09 13:53:29 +03:00
Manolis Ragkousis
c608fe8cf3
gnu: Add ois. 
* gnu/packages/game-development.scm (ois): New variable.
 2017-08-09 13:53:16 +03:00
Eric Bavier
d84b09e937
gnu: dealii: Update to 8.5.0. 
* gnu/packages/maths.scm (dealii): Update to 8.5.0.
[arguments]: Delete 'hint-example-prefix phase, which would need adjusting for
this version.  Users can use e.g. 'export DEAL_II_DIR=$GUIX_ENVIRONMENT'.
Adjust configuration flags.
 2017-08-09 01:56:53 -05:00
Eric Bavier
05cca6ce90
gnu: stress-make: Patch default shell. 
* gnu/packages/debug.scm (stress-make)[arguments]: Add 'set-default-shell
phase.
 2017-08-09 01:56:53 -05:00
Eric Bavier
bd5b5ac0c5
gnu: suitesparse: Update to 4.5.5. 
* gnu/packages/maths.scm (suitesparse): Update to 4.5.5.
[source]: Add 'modules' and 'snippet' field to remove bundled source.
[arguments]: Remove 'prepare-out' phase.  Adjust #:make-flags for metis.
Make build parallel, since it now appears to be safe.
[inputs]: Add metis.
 2017-08-09 01:56:53 -05:00
Eric Bavier
2509522c4f
gnu: suitesparse: Use modify-phases. 
* gnu/packages/maths.scm (suitesparse)[arguments]: Use modify-phases.
 2017-08-09 01:56:53 -05:00
Eric Bavier
9731c412e9
gnu: petsc, slepc: Use 'parallel-job-count'. 
* gnu/packages/maths.scm (petsc, slepc)[arguments]: Set #:make-flags to
override default unlimited '-j'.
(petsc)[arguments]: Scrub build machine cores from installed files in
'clean-local-references' phase.
 2017-08-09 01:56:53 -05:00
Eric Bavier
baeaf8821d
gnu: slepc: Update to 3.7.4. 
* gnu/packages/maths.scm (slepc): Update to 3.7.4.
[source]: Use direct source link.  Remove 'file-name' field.
 2017-08-09 01:56:52 -05:00
Eric Bavier
41a46a5035
gnu: petsc: Update to 3.7.6. 
* gnu/packages/maths.scm (petsc): Update to 3.7.6.
 2017-08-09 01:56:46 -05:00
Tobias Geerinckx-Rice
026051953d
gnu: epiphany: Update to 3.24.3. 
* gnu/packages/gnome.scm (epiphany): Update to 3.24.3.
 2017-08-09 07:20:57 +02:00
Tobias Geerinckx-Rice
c762011e40
gnu: tracker: Update to 1.12.2. 
* gnu/packages/gnome.scm (tracker): Update to 1.12.2.
 2017-08-09 07:20:56 +02:00
Tobias Geerinckx-Rice
666901b298
gnu: gnome-online-accounts: Update to 3.24.2. 
* gnu/packages/gnome.scm (gnome-online-accounts): Update to 3.24.2.
 2017-08-09 07:20:56 +02:00
Tobias Geerinckx-Rice
a51fc34c28
gnu: mutter: Update to 3.24.4. 
* gnu/packages/gnome.scm (mutter): Update to 3.24.4.
 2017-08-09 07:20:55 +02:00
Tobias Geerinckx-Rice
0d2df50caf
gnu: gedit: Support gspell. 
* gnu/packages/gnome.scm (gedit)[arguments]: Remove #:configure-flags.
[inputs]: Add gspell.
 2017-08-09 07:20:55 +02:00
Tobias Geerinckx-Rice
e3705bb6ea
gnu: gedit: Update to 3.22.1. 
* gnu/packages/gnome.scm (gedit): Update to 3.22.1.
 2017-08-09 07:20:54 +02:00
Tobias Geerinckx-Rice
eccd35be3d
gnu: gspell: Propagate enchant dependency. 
* gnu/packages/gnome.scm (gspell)[inputs]: Move enchant from here...
[propagated-inputs]: ...to here.
 2017-08-09 07:20:09 +02:00
Tobias Geerinckx-Rice
a801ae4cae
gnu: gspell: Order inputs alphabetically. 
* gnu/packages/gnome.scm (gspell)[inputs, native-inputs]: Re-order.
 2017-08-09 07:20:09 +02:00
Tobias Geerinckx-Rice
9099bedfea
gnu: gnumeric: Update to 1.12.35. 
* gnu/packages/gnome.scm (gnumeric): Update to 1.12.35.
 2017-08-09 07:20:08 +02:00
Tobias Geerinckx-Rice
e2bf423ab4
gnu: brasero: Update to 3.12.2. 
* gnu/packages/gnome.scm (brasero): Update to 3.12.2.
 2017-08-09 07:20:08 +02:00
Tobias Geerinckx-Rice
f032d0be9c
gnu: Use HTTPS for gnome.org and subdomains. 
* gnu/packages/fonts.scm (font-bitstream-vera)[home-page]: Use HTTPS.
* gnu/packages/glib.scm (glib)[home-page]: Likewise.
* gnu/packages/gnome.scm (gcr, libgnome-keyring, gnome-keyring, evince)
(gnome-icon-theme, libgsf, gnome-mime-data, vala, vte, python2-rsvg)
(glib-networking, gnome-settings-daemon, libchamplain, grilo, grilo-plugins)
(gjs, zenity, mutter, network-manager, network-manager-applet, gdm)
[home-page]: Likewise.
* gnu/packages/gtk.scm (gtk-engines, murrine)[home-page]: Likewise.
 2017-08-09 00:49:41 +02:00
Christopher Baines
9bb47d7df8
gnu: 0ad: Update to 0.0.22-alpha. 
* gnu/packages/games.scm (0ad-data, 0ad): Update to 0.0.22-alpha.
 2017-08-08 21:24:01 +01:00
Christopher Baines
0642838b2e
services: herd: Add a stop-service procedure. 
* gnu/services/herd.scm (stop-service): New procedure.
 2017-08-08 20:49:08 +01:00
Christopher Baines
dc7b3e5633
services: herd: Fix matching ok responses from shepherd service. 
Previously the match expression case for a successful response
(where error is #f) required that the result component contained a list with a
single element.

As far as I see when looking at the responses from the shepherd, this is not
normally the case. Therefore, to avoid treating successful responses as
errors, make the match requirement more permissive, accepting any value.

* gnu/services/herd.scm (invoke-action): Change match condition for ok responses.
 2017-08-08 20:48:53 +01:00
Efraim Flashner
65831c6425
gnu: babl: Update to 0.1.28. 
* gnu/packages/gimp.scm (babl): Update to 0.1.28.
 2017-08-08 18:43:07 +03:00
Efraim Flashner
3616ff51b3
gnu: gegl: Use 'modify-phases' syntax. 
* gnu/packages/gimp.scm (gegl)[arguments]: Use the 'modify-phases' syntax.
 2017-08-08 18:43:05 +03:00
Efraim Flashner
b0a21b56db
gnu: gegl: Fix building on aarch64. 
* gnu/packages/gimp.scm (gegl)[arguments]: Add '-lm' configure-flag.
 2017-08-08 18:43:03 +03:00
Ben Woodcroft
cc36165efa
gnu: ruby-activesupport: Update to 5.1.3. 
* gnu/packages/ruby.scm (ruby-activesupport): Update to 5.1.3.
 2017-08-08 21:54:20 +10:00
Tobias Geerinckx-Rice
b998781d24
gnu: pciutils: Update to 3.5.5. 
* gnu/packages/pciutils.scm (pciutils): Update to 3.5.5.
 2017-08-08 05:23:38 +02:00
Tobias Geerinckx-Rice
a40af5d0ad
gnu: hunspell: Update to 1.6.1. 
* gnu/packages/libreoffice.scm (hunspell): Update to 1.6.1.
[native-inputs]: Add autoconf, automake, and libtool.
[arguments]: Add ‘bootstrap’ phase.
 2017-08-08 05:23:37 +02:00
Tobias Geerinckx-Rice
fc3560fff1
gnu: hunspell: Update home page. 
* gnu/packages/libreoffice.scm (hunspell)[home-page]: Update it.
 2017-08-08 05:23:37 +02:00
Tobias Geerinckx-Rice
625761a502
gnu: aspell-dict-en: Update to 2017.01.22-0. 
Add missing copyright line for 2016.

* gnu/packages/aspell.scm (aspell-dict-en): Update to 2017.01.22-0.
 2017-08-08 05:23:37 +02:00
Tobias Geerinckx-Rice
d459524713
gnu: moreutils: Update to 0.61. 
* gnu/packages/moreutils.scm (moreutils): Update to 0.61.
 2017-08-08 05:23:36 +02:00
Tobias Geerinckx-Rice
7fae2063f8
gnu: sudo: Use ‘modify-phases’ syntax. 
* gnu/packages/admin.scm (sudo)[arguments]: Use ‘modify-phases’.
 2017-08-08 05:23:36 +02:00
Mark H Weaver
4f4134c26d
gnu: linux-libre: Update to 4.12.5. 
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.5.
(%linux-libre-hash): Update hash.
 2017-08-07 21:33:03 -04:00
Mark H Weaver
99ccc74725
gnu: linux-libre@4.9: Update to 4.9.41. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.41.
 2017-08-07 21:32:13 -04:00
Mark H Weaver
c56b08b1e5
gnu: linux-libre@4.4: Update to 4.4.80. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.80.
 2017-08-07 21:31:36 -04:00
Mark H Weaver
c36e27d504
gnu: linux-libre@4.1: Update to 4.1.43. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.43.
 2017-08-07 21:30:47 -04:00
Ben Woodcroft
63755fcd65
gnu: ruby-puma: Update to 3.9.1. 
* gnu/packages/ruby.scm (ruby-puma): Update to 3.9.1.
[source]: Remove patch.
[arguments]: Disable tests.
[native-inputs]: Remove field.
* gnu/packages/patches/ruby-puma-ignore-broken-test.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-08-08 09:31:18 +10:00
Ben Woodcroft
5b0c223ae3
gnu: ruby-nokogiri-diff: Update to 0.2.0-1.a38491e4. 
* gnu/packages/ruby.scm (ruby-nokogiri-diff): Update to 0.2.0-1.a38491e4.
 2017-08-08 09:30:44 +10:00
Ben Woodcroft
5071f17b29
gnu: ruby-tdiff: Update to 0.3.3-1.b662a604. 
* gnu/packages/ruby.scm: Update to 0.3.3-1.b662a604
 2017-08-08 09:30:40 +10:00
Ben Woodcroft
e7ea30d59a
ruby: Replace with ruby-2.4.1. 
* gnu/packages/ruby.scm (ruby-2.4.1): New variable.
(ruby)[replacement]: New field.
 2017-08-08 09:30:02 +10:00
Efraim Flashner
57e96e48b1
gnu: propeller-gcc-4: Don't build on aarch64-linux. 
* gnu/packages/embedded.scm (propeller-gcc-4)[supported-system]: New field.
 2017-08-07 17:02:24 +03:00
Efraim Flashner
6eed26443f
gnu: nim: Update to 0.17.0. 
* gnu/packages/nim.scm (nim): Update to 0.17.0.
[source, home-page]: Use https.
[arguments]: Patch more shebangs, use custom build phase.
 2017-08-07 13:37:28 +03:00
Marius Bakke
83fef82b7c
gnu: cubicle: Fix evaluation. 
* gnu/packages/maths.scm (cubicle)[native-inputs]: Retrieve WHICH from
(gnu packages base).
 2017-08-07 12:02:33 +02:00
Efraim Flashner
cda20ee816
gnu: vapoursynth: Don't build on aarch64-linux. 
* gnu/packages/video.scm (vapoursynth)[supported-systems]: Remove
aarch64-linux from the supported-systems.
 2017-08-07 07:24:17 +03:00
Tobias Geerinckx-Rice
74033bbcc3
gnu: youtube-dl: Update to 2017.08.06. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.08.06.
 2017-08-07 05:28:34 +02:00
Tobias Geerinckx-Rice
d8af4f6dde
gnu: ntfs-3g: Update to 2017.3.23. 
* gnu/packages/linux.scm (ntfs-3g): Update to 2017.3.23.
[source]: Remove patch.
* gnu/packages/patches/ntfs-3g-CVE-2017-0358.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-08-07 02:01:34 +02:00
Tobias Geerinckx-Rice
8bad0c0bbb
gnu: ntfs-3g: Use HTTPS for the home page as well. 
* gnu/packages/linux.scm (ntfs-3g)[home-page]: Use HTTPS.
 2017-08-07 02:01:33 +02:00
Tobias Geerinckx-Rice
ea94aff7da
gnu: wimlib: Update to 1.12.0. 
* gnu/packages/backup.scm (wimlib): Update to 1.12.0.
 2017-08-07 02:01:32 +02:00
Tobias Geerinckx-Rice
9d217d277e
gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash. 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Restore hash from before the tarball changed in place.  It changed back.

This reverts commit fd40857938.
 2017-08-07 01:58:39 +02:00
Leo Famulari
46f3c8f289
gnu: khal: Don't propagate vdirsyncer. 
* gnu/packages/calendar.scm (khal)[propagated-inputs]: Move vdirsyncer ...
[native-inputs]: ... here.
 2017-08-06 16:58:03 -04:00
Leo Famulari
fd8f946379
gnu: python-icalendar: Update to 3.11.6. 
* gnu/packages/python.scm (python-icalendar): Update to 3.11.6.
 2017-08-06 16:58:02 -04:00
Leo Famulari
03776ebd36
gnu: mpg123: Update to 1.25.4. 
* gnu/packages/mp3.scm (mpg123): Update to 1.25.4.
 2017-08-06 16:58:02 -04:00
Kei Kebreau
b0c95908c0
gnu: freedoom: Update to 0.11.3. 
* gnu/packages/games.scm (freedoom): Update to 0.11.3.
[arguments]: Remove unnecessary "no" phase.
 2017-08-06 14:13:07 -04:00
Kei Kebreau
f7b60fdc36
gnu: deutex: Update to 5.0.0. 
* gnu/packages/game-development.scm (deutex): Update to 5.0.0.
[source]: Change upstream URI.
[arguments]: Enable tests and restore normal "configure" and "install"
phases.
[native-inputs]: Add asciidoc.
 2017-08-06 14:13:07 -04:00
Efraim Flashner
403097d26d
gnu: Add motti. 
* gnu/packages/motti.scm (motti): New variable.
 2017-08-06 19:13:33 +03:00
Efraim Flashner
b7ac10e6da
gnu: keepassx: Superseded by keepassxc. 
* gnu/packages/password-utils.scm (keepassx)[properties]: New field.
 2017-08-06 19:13:32 +03:00
Efraim Flashner
99672f7b1d
gnu: Add keepassxc. 
* gnu/packages/password-utils.scm (keepassxc): New variable.
 2017-08-06 19:13:06 +03:00
Efraim Flashner
3ea2eaa8f3
gnu: python-efl: Update to 1.20.0. 
* gnu/packages/enlightenment.scm (python-efl): Update to 1.20.0.
[source]: Add alternate source uri.
[arguments]: Enable tests.
 2017-08-06 18:13:09 +03:00
Efraim Flashner
87cd1f5c2a
gnu: efl: Update to 1.20.1. 
* gnu/packages/enlightenment.scm (efl): Update to 1.20.1.
 2017-08-06 18:13:05 +03:00
Efraim Flashner
3bfee8ff02
gnu: make-u-boot-package: Don't unnecessarily cross-compile. 
* gnu/packages/bootloaders.scm (make-u-boot-package)[native-inputs]: Only
use cross-gcc and cross-binutils if compiling for a different
architecture.
[arguments]: Only use cross compiling make-flags if cross compiling.
 2017-08-06 18:13:03 +03:00
Danny Milosavljevic
18c6a7b4c8
gnu: Add python-flask-httpauth. 
* gnu/packages/python.scm (python-flask-httpauth, python2-flask-httpauth):
New variables.
 2017-08-06 13:35:07 +02:00
ng0
abd8825f90
gnu: Add font-open-dyslexic. 
* gnu/packages/fonts.scm (font-open-dyslexic): New variable.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-06 10:49:52 +05:30
Vasile Dumitrascu
799097e445
gnu: gnucash: Update to 2.6.17. 
* gnu/packages/gnucash.scm (gnucash): Update to 2.6.17.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-06 10:01:56 +05:30
Leo Famulari
01a61d7040
gnu: libtasn1: Fix CVE-2017-10790. 
* gnu/packages/patches/libtasn1-CVE-2017-10790.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/tls.scm (libtasn1/fixed)[source]: Use it.
 2017-08-05 20:17:53 -04:00
Danny Milosavljevic
9833bcfc08
build: Allow mounting of entire disks. 
* gnu/build/file-systems.scm (disk-partitions): Also return entire drives.
 2017-08-05 18:49:33 +02:00
Feng Shu
91d94e28ec
gnu: emacs-exwm-x: Do not set DISPLAY. 
* gnu/packages/emacs.scm (emacs-exwm-x): Do not set DISPLAY. The issue has
been fixed upstream in exwm-0.15.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-05 18:58:58 +05:30
Feng Shu
e78e38a4bb
gnu: emacs-exwm: Update to 0.15. 
* gnu/packages/emacs.scm (emacs-exwm): Update to 0.15.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2017-08-05 18:48:54 +05:30
Marius Bakke
7f171fdaad
gnu: git: Update to 2.14.0. 
* gnu/packages/version-control.scm (git): Update to 2.14.0.
 2017-08-05 14:07:43 +02:00
Marius Bakke
eedcfa704e
gnu: lftp: Update to 4.7.8. 
* gnu/packages/ftp.scm (lftp): Update to 4.7.8.
 2017-08-05 14:07:42 +02:00
Julien Lepiller
3d5d87a3ae
gnu: Add cubicle. 
* gnu/packages/maths.scm (cubicle): New variable.
 2017-08-05 10:11:42 +02:00
Julien Lepiller
1cec346232
gnu: php: Update to 7.1.8. 
* gnu/packages/patches/gd-CVE-2017-7890.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it
* gnu/packages/php.scm (php): Update to 7.1.8.
 2017-08-04 18:58:33 +02:00
Ricardo Wurmus
8d6c845d68
gnu: Add r-crosstalk. 
* gnu/packages/web.scm (r-crosstalk): New variable.
 2017-08-04 11:23:53 +02:00
Ricardo Wurmus
a3cd23b639
gnu: Add r-shiny. 
* gnu/packages/web.scm (r-shiny): New variable.
 2017-08-04 11:23:53 +02:00
Ricardo Wurmus
0b0aa76fa8
gnu: Add js-es5-shim. 
* gnu/packages/javascript.scm (js-es5-shim): New variable.
 2017-08-04 11:23:53 +02:00
Ricardo Wurmus
4f65067bde
gnu: Add js-selectize. 
* gnu/packages/javascript.scm (js-selectize): New variable.
 2017-08-04 11:23:53 +02:00
Ricardo Wurmus
c4abc94d2b
gnu: Add js-datatables. 
* gnu/packages/javascript.scm (js-datatables): New variable.
 2017-08-04 11:23:53 +02:00
Ricardo Wurmus
a6bbb2a0d8
gnu: Add js-highlight. 
* gnu/packages/javascript.scm (js-highlight): New variable.
 2017-08-04 11:23:53 +02:00
Ricardo Wurmus
3f48403aaf
gnu: Add js-strftime. 
* gnu/packages/javascript.scm (js-strftime): New variable.
 2017-08-04 11:23:52 +02:00
Ricardo Wurmus
68ffb6c586
gnu: Add js-json2. 
* gnu/packages/javascript.scm (js-json2): New variable.
 2017-08-04 11:23:52 +02:00
Ricardo Wurmus
ed69963b03
gnu: Add js-html5shiv. 
* gnu/packages/javascript.scm (js-html5shiv): New variable.
 2017-08-04 11:23:52 +02:00
Tobias Geerinckx-Rice
b316caaa9c
gnu: python-lz4: Fix typo in synopsis. 
* gnu/packages/compression.scm (python-lz4)[synopsis]: Fix typo.
 2017-08-04 05:00:26 +02:00
Tobias Geerinckx-Rice
e9f6a935fb
gnu: python-lz4: Update to 0.10.1. 
* gnu/packages/compression.scm (python-lz4): Update to 0.10.1.
[native-inputs]: Add python-setuptools-scm.
 2017-08-04 04:59:48 +02:00
Tobias Geerinckx-Rice
54360c917e
gnu: diffoscope: Use HTTPS. 
* gnu/packages/package-management.scm (diffoscope)[home-page]: Use HTTPS.
 2017-08-04 04:34:41 +02:00
Tobias Geerinckx-Rice
3b4018d6f2
gnu: sshoot: Update to 1.2.6. 
* gnu/packages/vpn.scm (sshoot): Update to 1.2.6.
[home-page]: Update to new project home.
 2017-08-04 04:34:41 +02:00
Tobias Geerinckx-Rice
f58be41761
gnu: fabric: Update to 1.13.2. 
* gnu/packages/admin.scm (fabric): Update to 1.13.2.  Remove outdated comments.
[source]: Remove ‘patches’.
* gnu/packages/patches/fabric-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-08-04 03:46:49 +02:00
Tobias Geerinckx-Rice
19dd5097d9
gnu: certbot, python-acme: Update to 0.17.0. 
* gnu/packages/tls.scm (certbot, python-acme, python2-acme): Update to 0.17.0.
 2017-08-04 02:32:53 +02:00
Tobias Geerinckx-Rice
9a7fd375a2
gnu: xonsh: Update to 0.5.12. 
* gnu/packages/shells.scm (xonsh): Update to 0.5.12.
 2017-08-04 02:06:39 +02:00
Tobias Geerinckx-Rice
b55d15e795
gnu: cmark: Update to 0.28.0. 
* gnu/packages/markup.scm (cmark): Update to 0.28.0.
 2017-08-04 01:51:23 +02:00
Tobias Geerinckx-Rice
0a3ecfd29c
gnu: thefuck: Update to 3.19. 
* gnu/packages/admin.scm (thefuck): Update to 3.19.
 2017-08-04 01:51:23 +02:00
Tobias Geerinckx-Rice
30ac4cc7e6
gnu: zerofree: Update to 1.1.0. 
* gnu/packages/linux.scm (zerofree): Update to 1.1.0.
[home-page, source]: Update from old, inaccessible location.
 2017-08-04 01:51:22 +02:00
Tobias Geerinckx-Rice
4de4a1cfcc
gnu: zerofree: Expand description. 
* gnu/packages/linux.scm (zerofree)[description]: Expand.
 2017-08-04 01:51:22 +02:00
Tobias Geerinckx-Rice
7a068459ba
gnu: zerofree: Use ‘install-file’. 
* gnu/packages/linux.scm (zerofree)[arguments]: Simplify install phase,
using ‘install-file’.
 2017-08-04 01:51:21 +02:00
Tobias Geerinckx-Rice
0f08917df3
gnu: zerofree: Use ‘modify-phases’ syntax. 
* gnu/packages/linux.scm (zerofree)[arguments]: Use ‘modify-phases’.
 2017-08-04 01:51:21 +02:00
Tobias Geerinckx-Rice
20f8d1dd78
gnu: sshfs-fuse: Update to 2.10. 
* gnu/packages/linux.scm (sshfs-fuse): Update to 2.10.
 2017-08-04 01:51:20 +02:00
Marius Bakke
c89091459f
gnu: freerdp: Update to 2.0.0-rc0 [security fixes]. 
Fixes CVE-2017-{2834,2835,2836,2837,2838,2839}.

Reported by Leo Famulari in <https://bugs.gnu.org/27939>.

* gnu/packages/rdesktop.scm (freerdp): Update to 2.0.0-rc0.
[source]: Use tarball release. Adjust file-name.
[arguments]: Remove #:phases.
 2017-08-04 00:52:52 +02:00
Marius Bakke
c9f4f56b24
gnu: git: Enable tests. 
* gnu/packages/version-control.scm (git)[arguments]: Remove #:tests?. Add
'patch-tests' phase.
 2017-08-04 00:52:13 +02:00
Leo Famulari
81ca29a6d6
gnu: gnupg@1.4: Update to 1.4.22 [fixes CVE-2017-7526]. 
* gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.22.
 2017-08-03 18:06:19 -04:00
Ricardo Wurmus
9e37e537a2
gnu: Add missing references to (gnu packages cran). 
This is a follow-up to commit a8cba9dd11.

Reported-by: Efraim Flashner <efraim@flashner.co.il>
 2017-08-03 22:15:57 +02:00
Efraim Flashner
7cb6155088
gnu: bioinformatics.scm: Use (gnu packages cran) module. 
This is a follow up to a8cba9dd11.

* gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
 2017-08-03 21:39:12 +03:00
Danny Milosavljevic
cf189709bc
vm: Use grub-hybrid's grub-mkrescue. 
* gnu/system/vm.scm (system-disk-image): Use grub-hybrid's grub-mkrescue.
* gnu/bootlader/grub.scm (grub-mkrescue-bootloader): New variable.
 2017-08-03 18:13:03 +02:00
Ricardo Wurmus
2267e4d3f6
gnu: r-purrr: Update to 0.2.3. 
* gnu/packages/statistics.scm (r-purrr): Update to 0.2.3.
[propagated-inputs]: Remove r-rcpp and r-lazyeval; add r-rlang.
 2017-08-03 17:53:55 +02:00
Ricardo Wurmus
ceb802a31c
gnu: r-desc: Update to 1.1.1. 
* gnu/packages/statistics.scm (r-desc): Update to 1.1.1.
 2017-08-03 17:53:55 +02:00
Ricardo Wurmus
5e0de29892
gnu: r-seqminer: Update to 6.0. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
4e0c847d59
gnu: r-wgcna: Update to 1.60. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
c8a9b2bcbf
gnu: r-qtl: Update to 1.41-6. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
023aa8ff58
gnu: r-seqinr: Update to 3.4-5. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus
7150f1c30c
gnu: r-optparse: Update to 1.4.4. 
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
 2017-08-03 17:53:53 +02:00
Ricardo Wurmus
3f6ec083ec
gnu: r-bookdown: Update to 0.4. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
 2017-08-03 17:53:53 +02:00
Ricardo Wurmus
85cd755417
gnu: r-tclust: Update to 1.2-7. 
* gnu/packages/statistics.scm (r-tclust): Update to 1.2-7.
 2017-08-03 17:53:53 +02:00
Ricardo Wurmus
6bb4bfa4bc
gnu: r-car: Update to 2.1-5. 
* gnu/packages/statistics.scm (r-car): Update to 2.1-5.
 2017-08-03 17:53:53 +02:00
Ricardo Wurmus
0f008abe7a
gnu: r-rcppeigen: Update to 0.3.3.3.0. 
* gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.3.0.
 2017-08-03 17:53:53 +02:00
Ricardo Wurmus
12c3bbb662
gnu: r-pbapply: Update to 1.3-3. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.3-3.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus
4431dd3a4e
gnu: r-vgam: Update to 1.0-4. 
* gnu/packages/statistics.scm (r-vgam): Update to 1.0-4.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus
41692b2963
gnu: r-mclust: Update to 5.3. 
* gnu/packages/statistics.scm (r-mclust): Update to 5.3.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus
60869fb2f8
gnu: r-flexmix: Update to 2.3-14. 
* gnu/packages/statistics.scm (r-flexmix): Update to 2.3-14.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus
62d3afc3d6
gnu: r-fastica: Update to 1.2-1. 
* gnu/packages/statistics.scm (r-fastica): Update to 1.2-1.
 2017-08-03 17:53:52 +02:00
Ricardo Wurmus
df03b6f90c
gnu: r-cowplot: Update to 0.8.0. 
* gnu/packages/statistics.scm (r-cowplot): Update to 0.8.0.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus
d58faa7f44
gnu: r-rann: Update to 2.5.1. 
* gnu/packages/statistics.scm (r-rann): Update to 2.5.1.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus
a8c2706de2
gnu: r-statmod: Update to 1.4.30. 
* gnu/packages/statistics.scm (r-statmod): Update to 1.4.30.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus
80d1185076
gnu: r-gdata: Update to 2.18.0. 
* gnu/packages/statistics.scm (r-gdata): Update to 2.18.0.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus
2c75199c56
gnu: r-sfsmisc: Update to 1.1-1. 
* gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-1.
 2017-08-03 17:53:51 +02:00
Ricardo Wurmus
1d256438c8
gnu: r-googlesheets: Update to 0.2.2. 
* gnu/packages/statistics.scm (r-googlesheets): Update to 0.2.2.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus
9b9fef0eaf
gnu: r-tidyr: Update to 0.6.3. 
* gnu/packages/statistics.scm (r-tidyr): Update to 0.6.3.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus
e1cd25bc78
gnu: r-glmnet: Update to 2.0-10. 
* gnu/packages/statistics.scm (r-glmnet): Update to 2.0-10.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus
1c576cbadb
gnu: r-irlba: Update to 2.2.1. 
* gnu/packages/statistics.scm (r-irlba): Update to 2.2.1.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus
81c057ced9
gnu: r-sparsem: Update to 1.77. 
* gnu/packages/statistics.scm (r-sparsem): Update to 1.77.
 2017-08-03 17:53:50 +02:00
Ricardo Wurmus
127b926bc1
gnu: r-segmented: Update to 0.5-2.1. 
* gnu/packages/statistics.scm (r-segmented): Update to 0.5-2.1.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus
fe9917284f
gnu: r-xml: Update to 3.98-1.9. 
* gnu/packages/statistics.scm (r-xml): Update to 3.98-1.9.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus
cc8ba9b69c
gnu: r-rmarkdown: Update to 1.6. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 1.6.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus
7c172eacfa
gnu: r-rcpparmadillo: Update to 0.7.900.2.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.900.2.0.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus
1c41d51743
gnu: r-plotrix: Update to 3.6-5. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.6-5.
 2017-08-03 17:53:49 +02:00
Ricardo Wurmus
76040b8561
gnu: r-readr: Update to 1.1.1. 
* gnu/packages/statistics.scm (r-readr): Update to 1.1.1.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus
d8048a1212
gnu: r-withr: Update to 2.0.0. 
* gnu/packages/statistics.scm (r-withr): Update to 2.0.0.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus
f212bf84ab
gnu: r-git2r: Update to 0.19.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.19.0.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus
58e1ce86ab
gnu: r-checkmate: Update to 1.8.3. 
* gnu/packages/statistics.scm (r-checkmate): Update to 1.8.3.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus
63f934e672
gnu: r-backports: Update to 1.1.0. 
* gnu/packages/statistics.scm (r-backports): Update to 1.1.0.
 2017-08-03 17:53:48 +02:00
Ricardo Wurmus
c832d326a1
gnu: r-formula: Update to 1.2-2. 
* gnu/packages/statistics.scm (r-formula): Update to 1.2-2.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus
f05c6275b7
gnu: r-r6: Update to 2.2.2. 
* gnu/packages/statistics.scm (r-r6): Update to 2.2.2.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus
b07c8c0156
gnu: r-knitr: Update to 1.16. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.16.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus
6dc86e8dfc
gnu: r-formatr: Update to 1.5. 
* gnu/packages/statistics.scm (r-formatr): Update to 1.5.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus
12cd797541
gnu: r-evaluate: Update to 0.10.1. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.10.1.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus
d5ce380711
gnu: r-dbi: Update to 0.7. 
* gnu/packages/statistics.scm (r-dbi): Update to 0.7.
 2017-08-03 17:53:47 +02:00
Ricardo Wurmus
831858a7d3
gnu: r-bit64: Update to 0.9-7. 
* gnu/packages/statistics.scm (r-bit64): Update to 0.9-7.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus
6fb21ed2a3
gnu: r-mgcv: Update to 1.8-18. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-18.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus
dbeda1b4a0
gnu: r-matrix: Update to 1.2-10. 
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-10.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus
74b037df64
gnu: r-foreign: Update to 0.8-69. 
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-69.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus
af1eeabe89
gnu: r-boot: Update to 1.3-20. 
* gnu/packages/statistics.scm (r-boot): Update to 1.3-20.
 2017-08-03 17:53:46 +02:00
Ricardo Wurmus
e584b9fc1b
gnu: r-curl: Update to 2.8.1. 
* gnu/packages/web.scm (r-curl): Update to 2.8.1.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus
53deffe5e9
gnu: r-htmlwidgets: Update to 0.9. 
* gnu/packages/web.scm (r-htmlwidgets): Update to 0.9.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus
850151058d
gnu: r-htmltools: Update to 0.3.6. 
* gnu/packages/web.scm (r-htmltools): Update to 0.3.6.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus
a1e54db2ac
gnu: r-servr: Update to 0.6. 
* gnu/packages/web.scm (r-servr): Update to 0.6.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus
9fe794f0f7
gnu: r-jsonlite: Update to 1.5. 
* gnu/packages/web.scm (r-jsonlite): Update to 1.5.
 2017-08-03 17:53:45 +02:00
Ricardo Wurmus
2d81bc16a9
gnu: r-httpuv: Update to 1.3.5. 
* gnu/packages/web.scm (r-httpuv): Update to 1.3.5.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus
0f2eee0d96
gnu: r-pracma: Update to 2.0.7. 
* gnu/packages/maths.scm (r-pracma): Update to 2.0.7.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus
64c6712d03
gnu: r-knitrbootstrap: Update to 1.0.1. 
* gnu/packages/statistics.scm (r-knitrbootstrap): Update to 1.0.1.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus
c628b8418a
gnu: r-ranger: Update to 0.8.0. 
* gnu/packages/statistics.scm (r-ranger): Update to 0.8.0.
[propagated-inputs]: Add r-matrix and r-rcppeigen.
 2017-08-03 17:53:44 +02:00
Ricardo Wurmus
cc9a778ecc
gnu: r-hmisc: Update to 4.0-3. 
* gnu/packages/statistics.scm (r-hmisc): Update to 4.0-3.
[propagated-inputs]: Remove r-base64.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus
f9b3760636
gnu: r-plotly: Update to 4.7.1. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.7.1.
[propagated-inputs]: Add r-crosstalk, r-data-table, r-htmltools, and
r-rcolorbrewer.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus
d59050823e
gnu: r-igraph: Update to 1.1.2. 
* gnu/packages/statistics.scm (r-igraph): Update to 1.1.2.
[propagated-inputs]: Remove r-nmf; add r-matrix and r-pkgconfig.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus
7b3688150b
gnu: r-purrr: Update to 0.2.2.2. 
* gnu/packages/statistics.scm (r-purrr): Update to 0.2.2.2.
[propagated-inputs]: Remove r-bh and r-dplyr; add r-tibble.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus
5fc74f24bf
gnu: r-devtools: Update to 1.13.3. 
* gnu/packages/statistics.scm (r-devtools): Update to 1.13.3.
[propagated-inputs]: Remove r-curl, r-digest, r-evaluate, r-roxygen2, and
r-rversions.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus
aad948a0ea
gnu: r-tibble: Update to 1.3.3. 
* gnu/packages/statistics.scm (r-tibble): Update to 1.3.3.
[propagated-inputs]: Remove r-lazyeval, add r-rlang.
 2017-08-03 17:53:43 +02:00
Ricardo Wurmus
a40b2c2129
gnu: r-dplyr: Update to 0.7.2. 
* gnu/packages/statistics.scm (r-dplyr): Update to 0.7.2.
[propagated-inputs]: Remove r-lazyeval, r-dbi; add r-rlang, r-plogr, r-glue,
r-pkgconfig, r-bindrcpp.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus
4bb0b4cc0a
gnu: Add r-bindrcpp. 
* gnu/packages/cran.scm (r-bindrcpp): New variable.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus
eed58a0886
gnu: Add r-bindr. 
* gnu/packages/cran.scm (r-bindr): New variable.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus
a8cba9dd11
gnu: r-rcpp: Move to (gnu packages cran). 
* gnu/packages/statistics.scm (r-rcpp): Move from here...
* gnu/packages/cran.scm (r-rcpp): ...to here.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus
736332c79c
gnu: r-rcpp: Update to 0.12.12. 
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.12.
 2017-08-03 17:53:42 +02:00
Ricardo Wurmus
847b457253
gnu: r-plogr: Move to (gnu packages cran). 
* gnu/packages/statistics.scm (r-plogr): Move from here...
* gnu/packages/cran.scm (r-plogr): ...to here.
 2017-08-03 17:53:41 +02:00
Ricardo Wurmus
5bee6bf409
gnu: Add r-glue. 
* gnu/packages/cran.scm (r-glue): New variable.
 2017-08-03 17:53:41 +02:00
Danny Milosavljevic
dd4b7476ec
gnu: Add grub-hybrid. 
* gnu/packages/bootloaders.scm (grub-hybrid): New variable.
 2017-08-03 16:35:34 +02:00
Ben Woodcroft
75e6639f36
gnu: htseq: Use PyPI URI. 
This is a follow-up to 92971d68ac.

* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
 2017-08-03 21:08:13 +10:00
Ben Woodcroft
92971d68ac
gnu: htseq: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package.  Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
 2017-08-03 21:02:30 +10:00
Efraim Flashner
a8ead6f91b
gnu: vc: Limit to x86_64 and i686. 
* gnu/packages/maths.scm (vc)[supported-systems]: New field.
 2017-08-03 13:34:18 +03:00
Manolis Ragkousis
5638d71502
gnu: openscenegraph: Add 'Release' configure flag. 
* gnu/packages/graphics.scm (openscenegraph)[arguments]: Add "-DCMAKE_BUILD_TYPE=Release".
 2017-08-03 10:35:31 +03:00
Eric Bavier
68a29ab8d0
gnu: Add LeoCAD. 
* gnu/packages/lego.scm (leocad): New variable.
 2017-08-03 00:33:02 -05:00
Tobias Geerinckx-Rice
5d8312f1c6
gnu: youtube-dl: Update to 2017.07.30.1. 
* gnu/packages/video.scm (youtube-dl): Update to 2017.07.30.1.
 2017-08-03 05:31:24 +02:00
Tobias Geerinckx-Rice
6862c72373
gnu: tor: Update to 0.3.0.10. 
* gnu/packages/tor.scm (tor): Update to 0.3.0.10.
 2017-08-03 01:56:22 +02:00
Ludovic Courtès
49962b15a1
activation: Make sure /etc exists. 
Fixes <http://bugs.gnu.org/27146>.
Reported by ng0 <ng0@pragmatique.xyz>.

* gnu/build/activation.scm (activate-etc): Add call to 'mkdir-p'.
 2017-08-03 00:35:59 +02:00
Efraim Flashner
edd08fb7ac
gnu: glibc@2.22: Fix security issues. 
Fixes CVE-2015-{5180,7547}, CVE-2016-{3075,3706,4429}.

* gnu/packages/base.scm (glibc@2.22)[source]: Add patches.
* gnu/packages/patches/glibc-CVE-2015-7547.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-08-02 21:51:35 +03:00
Efraim Flashner
a0ae64a334
gnu: glibc@2.23: Fix CVE-2015-5180, CVE-2016-{3075,3706,4429}. 
* gnu/packages/base.scm (glibc@2.23)[source]: Add patches.
* gnu/packages/patches/glibc-CVE-2016-3075.patch,
gnu/packages/patches/glibc-CVE-2016-3706.patch,
gnu/packages/patches/glibc-CVE-2016-4429.patch: New files.
* gnu/local.mk (dist_patch_DATA): Register them.
 2017-08-02 21:51:33 +03:00