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8971 Commits

Author SHA1 Message Date
Patrick Hetu 9b381643f0
gnu: Add Guile-GNOME. 
* gnu/packages/gtk.scm (guile-gnome): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-28 18:06:15 +02:00
Ben Woodcroft 9fcc3509a7 gnu: Update diamond to 0.8.3. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
 2016-05-28 23:44:16 +10:00
宋文武 68e9ee725a
gnu: Add gcide. 
* gnu/packages/dictionaries.scm (gcide): New variable.
 2016-05-28 12:53:01 +08:00
宋文武 de477809d7
gnu: wxmaxima: Wrap with GSETTINGS_SCHEMA_DIR and XDG_DATA_DIRS. 
Fixes <http://bugs.gnu.org/22709> and <http://bugs.gnu.org/23260>.

* gnu/packages/math.scm (wxmaxima)[arguments]: Wrap with
GSETTINGS_SCHEMA_DIR and XDG_DATA_DIRS.
 2016-05-28 07:29:10 +08:00
宋文武 1a6d3cd374
gnu: gprolog: Don't install files into "$out/gprolog-1.4.4". 
* gnu/packages/gprolog.scm (gprolog)[arguments]: Pass '--with-install-dir'
to #:configure-flags.
 2016-05-28 07:27:46 +08:00
宋文武 6242b314c2
gnu: Add wiredtiger. 
* gnu/packages/database.scm (wiredtiger): New variable.
 2016-05-28 07:27:46 +08:00
Leo Famulari b5d08d7c28
gnu: gd: Update to 2.2.1 [fixes CVE-2015-{8874, 8877}]. 
* gnu/packages/patches/gd-CVE-2016-3074.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/gd.scm (gd): Update to 2.2.1.
[source]: Remove patch. Update source URL.
 2016-05-27 12:33:42 -04:00
Efraim Flashner 9da459f350
gnu: scrot: Add source mirror. 
* gnu/packages/xdisorg.scm (scrot)[source]: Add fossies mirror.
 2016-05-27 16:49:12 +03:00
Efraim Flashner 6d22653e39
gnu: serf: Update project source. 
* gnu/packages/web.scm (serf)[source]: Releases are now hosted by Apache.
[home-page]: Project is now hosted by Apache.
 2016-05-27 16:40:05 +03:00
Efraim Flashner e4ddf924e5
gnu: xlockmore: Update to 5.47. 
* gnu/packages/xdisorg.scm (xlockmore): Update to 5.47.
 2016-05-27 16:35:47 +03:00
Efraim Flashner a60c705bd8
gnu: t1lib: Add source mirror. 
* gnu/packages/fontutils.scm (t1lib)[souce]: Add fossies mirror.
 2016-05-27 16:23:21 +03:00
Efraim Flashner 63ae20da16
gnu: synergy: Update to 1.7.6. 
* gnu/packages/synergy.scm (synergy): Update to 1.7.6.
 2016-05-27 16:07:20 +03:00
Efraim Flashner a3025a4490
gnu: synergy: Use 'modify-phases'. 
* gnu/packages/synergy.scm (synergy)[arguments]; Use 'modify-phases'.
 2016-05-27 15:54:10 +03:00
Efraim Flashner cecaee420e
gnu: synergy: Update project source. 
* gnu/packages/synergy.scm (synergy)[source]: Use new location.
[home-page]: Use project's new website.
 2016-05-27 14:56:49 +03:00
Efraim Flashner ea3d5291cc
gnu: eyed3: Update to 0.7.9. 
* gnu/packages/mp3.scm (eyed3): Update to 0.7.9.
 2016-05-27 11:37:53 +03:00
Efraim Flashner 1a847b708d
gnu: mpc123: Use 'modify-phases'. 
* gnu/packages/mp3.scm (mpc123)[arguments]: Use 'modify-phases'.
 2016-05-27 11:37:53 +03:00
Efraim Flashner d1cd67af5d
gnu: mpc123: Add new source location. 
* gnu/packages/mp3.scm (mpc123)[source]: Add Debian mirror.
[home-page]: Project has moved to Github.
 2016-05-27 11:37:53 +03:00
humanitiesNerd d345491ab4
gnu: Add emacs-epl. 
* gnu/packages/emacs.scm (emacs-epl): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-27 11:02:54 +03:00
Alex Kost a8ce82aca2
gnu: emacs-async: Update to 1.9. 
* gnu/packages/emacs.scm (emacs-async): Update to 1.9.
 2016-05-27 10:50:37 +03:00
Alex Kost 847534e1d3
gnu: magit: Update to 2.7.0. 
* gnu/packages/emacs.scm (magit): Update to 2.7.0.
 2016-05-27 10:50:37 +03:00
Efraim Flashner be1e35055b
gnu: moreutils: Use 'modify-phases'. 
* gnu/packages/moreutils.scm (moreutils)[arguments]: Use 'modify-phases'.
 2016-05-27 07:06:02 +03:00
Efraim Flashner 0a20f40240
gnu: moreutils: Update to 0.58. 
* gnu/packages/moreutils.scm (moreutils): Update to 0.58.
 2016-05-27 07:03:52 +03:00
Ludovic Courtès de3bbf6543
gnu: qemu: Make tests more verbose. 
* gnu/packages/qemu.scm (qemu)[arguments]: Add 'make-gtester-verbose'
phase.
 2016-05-26 23:58:23 +02:00
Ludovic Courtès 8489d79d1b
gnu: qemu: Use 'install-file' instead of 'copy-file'. 
* gnu/packages/qemu.scm (qemu)[arguments]: Use 'install-file'.
 2016-05-26 23:58:23 +02:00
Ludovic Courtès 05051e8bb1
gnu: qemu: Use 'modify-phases'. 
* gnu/packages/qemu.scm (qemu)[arguments]: Use 'modify-phases'.
 2016-05-26 23:58:23 +02:00
Ludovic Courtès 219b45567a
gnu: qemu: Disable parallel tests again. 
* gnu/packages/qemu.scm (qemu)[arguments]: Re-add #:parallel-tests? #f,
which had been removed in a2ccaa0d79.
 2016-05-26 23:58:21 +02:00
Ludovic Courtès 159a5e0197
gnu: isc-dhcp: Specify CPE name. 
* gnu/packages/admin.scm (isc-dhcp)[properties]: New field.
 2016-05-26 22:56:51 +02:00
Ludovic Courtès 2ca55f939c
gnu: rush: Fix CVE-2013-6889. 
* gnu/packages/patches/rush-CVE-2013-6889.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/rush.scm (rush): Use it.
 2016-05-26 22:51:12 +02:00
David Thompson 9698f4b74b gnu: Add mitlm. 
* gnu/packages/speech.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2016-05-26 08:50:09 -04:00
David Thompson 6b0686fa93 gnu: Add autoconf-archive. 
* gnu/packages/autotools.scm (autoconf-archive): New variable.
 2016-05-26 08:50:09 -04:00
Manolis Ragkousis 38efbcbb79
gnu: hurd: Add hurd-core-headers package. 
* gnu/packages/hurd.scm (hurd-core-headers): New variable.
 2016-05-26 14:41:56 +03:00
Roel Janssen 4791876ce1
gnu: Add texmaker. 
* gnu/packages/tex.scm (texmaker): New variable.
 2016-05-26 10:24:13 +02:00
Roel Janssen 8f9ac90182
gnu: Rename texlive module to tex. 
* gnu/local.mk (GNU_SYSTEM_MODULES): Rename texlive.scm to tex.scm.
* gnu/packages/texlive.scm: Rename file to tex.scm.
* gnu/packages/tex.scm: Renamed from texlive.scm.
* gnu/packages/algebra.scm: Adjust accordingly.
* gnu/packages/docbook.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/gettext.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/lisp.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/photo.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/scheme.scm: Likewise.
 2016-05-26 10:22:05 +02:00
Efraim Flashner 5bed95efd4
gnu: aria2: Update to 1.23.0. 
* gnu/packages/bittorrent.scm (aria2): Update to 1.23.0.
[inputs]: Move cppunit ...
[native-inputs]: ... to here.
[home-page]: Update to new Github website.
 2016-05-26 08:59:41 +03:00
Efraim Flashner 25e0037a29
gnu: randomjungle: Add gfortran:lib to native-inputs. 
* gnu/packages/machine-learning.scm (randomjungle)[native-inputs]: Add
gfortran:lib.
 2016-05-25 21:49:08 +03:00
Efraim Flashner 68bf2f9d6b
gnu: enlightenment: Update to 0.20.8. 
* gnu/packages/enlightenment.scm (enlightenment): Update to 0.20.8.
 2016-05-25 20:52:25 +03:00
Efraim Flashner fac5065b8f
gnu: elementary: Update to 1.17.1. 
* gnu/packages/enlightenment.scm (elementary): Update to 1.17.1.
 2016-05-25 20:51:48 +03:00
Efraim Flashner cda20b86cf
gnu: efl: Update to 1.17.1. 
* gnu/packages/enlightenment.scm (efl): Update to 1.17.1.
 2016-05-25 20:51:48 +03:00
Leo Famulari 10240c7cbe
gnu: python-llfuse: Update to 1.1. 
* gnu/packages/python.scm (python-llfuse, python2-llfuse): Update to 1.1.
 2016-05-25 11:50:20 -04:00
Leo Famulari 0e9bc883b4
gnu: fuse: Update to 2.9.6. 
* gnu/packages/linux.scm (fuse): Update to 2.9.6.
[home-page]: Update home-page URL.
 2016-05-25 11:50:20 -04:00
Leo Famulari c99bf9b2ea
gnu: dnsmasq: Update to 2.76 [fixes CVE-2015-3294]. 
* gnu/packages/dns.scm (dnsmasq): Update to 2.76.
 2016-05-25 11:47:51 -04:00
Ben Woodcroft 803bcc81e2 gnu: ruby-mime-types: Update to 3.1. 
* gnu/packages/ruby.scm (ruby-mime-types): Update to 3.1.
[native-inputs]: Add 'ruby-minitest-hooks'.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft 2a96dbe6d6 gnu: Add ruby-minitest-hooks. 
* gnu/packages/ruby.scm (ruby-minitest-hooks): New variable.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft cbdd428cf4 gnu: Add ruby-sequel. 
* gnu/packages/ruby.scm (ruby-sequel): New variable.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft f1ae7c6218 gnu: ruby-nokogumbo: Update to 1.4.7-1. 
* gnu/packages/ruby.scm (ruby-nokogumbo): Update to 1.4.7-1.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft 59884b71e3 gnu: ruby-mini-portile-2: Update to 2.1.0. 
* gnu/packages/ruby.scm (ruby-mini-portile-2): Update to 2.1.0.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft 0907bf571d gnu: ruby-mime-types-data: Update to 3.2016.0221. 
* gnu/packages/ruby.scm (ruby-mime-types-data): Update to 3.2016.0221.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft 80756fa66b gnu: ruby-shoulda-matchers: Update to 3.1.1. 
* gnu/packages/ruby.scm (ruby-shoulda-matchers): Update to 3.1.1.
[arguments]: Remove 'fix-import' phase.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft 33a45ed652 gnu: ruby-domain-name: Update to 0.5.20160310. 
* gnu/packages/ruby.scm (ruby-domain-name): Update to 0.5.20160310.
 2016-05-25 22:34:29 +10:00
Ben Woodcroft 5e7f1b0b2a gnu: ruby-nokogiri: Update to 1.6.7.2. 
* gnu/packages/ruby.scm (ruby-nokogiri): Update to 1.6.7.2.
[arguments]: Relax 'mini_portile2' dependency.
 2016-05-25 22:34:29 +10:00
Mark H Weaver 2301195f2e
gnu: linux-libre: Update to 4.6. 
* gnu/packages/linux.scm (linux-libre): Update to 4.6.
* gnu/packages/linux-libre-4.6-x86_64.conf,
gnu/packages/linux-libre-4.6-i686.conf: New files.
* gnu/packages/linux-libre-4.5-x86_64.conf,
gnu/packages/linux-libre-4.5-i686.conf: Delete files.
* Makefile.am (KCONFIGS): Update accordingly.
 2016-05-25 04:54:06 -04:00
Mark H Weaver 92a7e46d58
gnu: python-libxml2: Drop replacement from inherited libxml2. 
This is a followup to commit 493e9a5a8f.

* gnu/packages/xml.scm (python-libxml2)[replacement]: Set to #f, overriding
inherited value.
 2016-05-25 04:54:06 -04:00
Efraim Flashner 19d6248634
gnu: freeipmi: Update to 1.5.2. 
* gnu/packages/freeipmi.scm (freeipmi): Update to 1.5.2.
 2016-05-25 09:13:13 +03:00
Mark H Weaver 796787a577
gnu: linux-libre-4.1: Update to 4.1.25. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.25.
 2016-05-25 00:26:40 -04:00
Mark H Weaver 6f82a7d40d
gnu: webkitgtk: Update to 2.12.3 [fixes CVE-2016-{1856,1857}]. 
* gnu/packages/webkit.scm (webkitgtk): Update to 2.12.3.
 2016-05-25 00:14:32 -04:00
Ludovic Courtès 493e9a5a8f
gnu: libxml2: Fix CVE-2016-3627 and CVE-2016-3705. 
* gnu/packages/patches/libxml2-CVE-2016-3627.patch,
gnu/packages/patches/libxml2-CVE-2016-3705.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xml.scm (libxml2)[replacement]: New field.
(libxml2/fixed): New variable.
 2016-05-24 14:15:18 +02:00
Mathieu Lirzin c0d2e7b197
build: Use "%D%" in Makefile fragments. 
* doc/local.mk: Use "%D%" for the directory of the fragment relative to
the base 'Makefile.am'.
* emacs/local.mk: Likewise.
* gnu/local.mk: Likewise.
* nix/local.mk: Likewise.
 2016-05-24 13:07:19 +02:00
humanitiesNerd 8eeb301de2
gnu: Add emacs-clojure-mode. 
* gnu/packages/emacs.scm (emacs-clojure-mode): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-24 11:32:42 +03:00
Alex Kost b8fc362239
gnu: Use 'emacs-minimal' instead of 'emacs-no-x'. 
* gnu/packages/code.scm (cflow)[native-inputs]: Use 'emacs-minimal'
  instead of 'emacs-no-x'.
* gnu/packages/databases.scm (recutils): Likewise.
* gnu/packages/finance.scm (ledger): Likewise
* gnu/packages/idutils.scm (idutils): Likewise.
* gnu/packages/mail.scm (mu): Likewise.
* gnu/packages/ocaml.scm (proof-general): Likewise.
* gnu/packages/package-management.scm (guix-0.10.0): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/scheme.scm (scmutils): Likewise.
* gnu/packages/version-control.scm (vc-dwim): Likewise.
* gnu/packages/emacs.scm (geiser): Likewise.
(paredit): Likewise.
(git-modes): Likewise.
(magit): Likewise.
(magit-svn): Likewise.
(haskell-mode): Likewise.
(let-alist): Likewise.
(emacs-w3m): Likewise.
(emacs-wget): Likewise.
(emms): Likewise.
(bbdb): Likewise.
(emacs-mmm-mode): Likewise.
(emacs-pdf-tools): Likewise.
(emacs-popup)[native-inputs]: Remove as it is not needed for
emacs-build-system.
(emacs-rfcview): Likewise.
(emacs-ffap-rfc-space): Likewise.
 2016-05-24 11:32:27 +03:00
Alex Kost 6aaf38992c
gnu: Move emacs for building from inputs to native-inputs. 
* gnu/packages/emacs.scm (geiser): Move "emacs" from inputs to native-inputs.
(paredit): Likewise.
(haskell-mode): Likewise.
(emacs-w3m): Likewise.
(emacs-wget): Likewise.
* gnu/packages/mail.scm (mu): Likewise.
* gnu/packages/version-control.scm (vc-dwim): Likewise.
 2016-05-24 11:32:27 +03:00
Alex Kost a6eafbed66
build-system/emacs: Use 'emacs-minimal' by default. 
* guix/build-system/emacs.scm (default-emacs): Use 'emacs-minimal'.
* gnu/packages/emacs.scm (emacs-auctex): Use 'emacs'.
 2016-05-24 11:32:27 +03:00
Alex Kost b2eaf7bacd
gnu: Add emacs-minimal. 
* gnu/packages/emacs.scm (emacs-minimal): New variable.
 2016-05-24 11:32:27 +03:00
Alex Kost 486f36eb9e
gnu: emacs: Remove *.elc and autoloads from the tarball. 
* gnu/packages/emacs.scm (emacs)[source]: Add 'snippet' to remove
  compiled and generated elisp files.
 2016-05-24 11:11:26 +03:00
Efraim Flashner d16479c51e
gnu: enblend-enfuse: Update to 4.2. 
* gnu/packages/photo.scm (enblend-enfuse): Update to 4.2.
[native-inputs]: Add help2man, texlive-minimal.
 2016-05-24 08:49:23 +03:00
Leo Famulari 7febe3a282
gnu: grub: Re-enable test. 
* gnu/packages/grub.scm (grub)[arguments]: Re-enable test.
 2016-05-23 18:47:45 -04:00
Leo Famulari 88ac650c7b
gnu: vdirsyncer: Update to 0.11.0. 
* gnu/packages/dav.scm (vdirsyncer): Update to 0.11.0.
 2016-05-23 13:26:17 -04:00
Leo Famulari e1343994b0
gnu: git: Update to 2.8.3. 
* gnu/packages/version-control.scm (git): Update to 2.8.3.
(git-manpages)[source]: Update hash.
 2016-05-23 13:14:50 -04:00
Roel Janssen 031cf6b65e
gnu: Add r-zoo. 
* gnu/packages/statistics.scm (r-zoo): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-05-23 12:36:38 -04:00
Leo Famulari 148e8e8e75
gnu: borg: Update to 1.0.3. 
* gnu/packages/backup.scm (borg): Update to 1.0.3.
[source]: Remove pypi-uri.
 2016-05-23 12:27:12 -04:00
Roel Janssen f22debacb4
gnu: Add poppler-qt5. 
* gnu/packages/pdf.scm (poppler-qt5): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-05-23 14:35:23 +03:00
Ricardo Wurmus 524eee0298 gnu: Add slurm-drmaa. 
* gnu/packages/parallel.scm (slurm-drmaa): New variable.
 2016-05-23 12:55:40 +02:00
Ricardo Wurmus 0783787436 gnu: Add ParDRe. 
* gnu/packages/bioinformatics.scm (pardre): New variable.
 2016-05-23 12:55:09 +02:00
Efraim Flashner 624d4e2e6b
gnu: gnu-pw-mgr: Update to 2.0. 
* gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.0.
 2016-05-22 16:58:21 +03:00
Leo Famulari 13913c52d5
gnu: imagemagick: Update to 6.9.4-4. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-4.
 2016-05-22 03:51:57 -04:00
Lukas Gradl 88bb4197c4 gnu: Add python2-rope. 
* gnu/packages/python.scm (python2-rope): New variable.
 2016-05-22 14:19:52 +10:00
Kei Yamashita 3c47489766
gnu: Add gnome-calendar. 
* gnu/packages/gnome.scm (gnome-calendar): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Matthew Jordan 548994142f
gnu: Add envstore. 
* gnu/package/shellutils.scm: New file.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Jan Nieuwenhuizen b9b447be64
gnu: Add sicp. 
* gnu/packages/scheme.scm (sicp): New variable.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Roel Janssen a56be436d0
gnu: Add dia. 
* gnu/packages/gnome.scm (dia): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-21 23:30:37 +02:00
Mark H Weaver 3c9a7185e4
gnu: linux-libre: Update to 4.5.5. 
* gnu/packages/linux.scm (linux-libre): Update to 4.5.5.
 2016-05-20 18:58:15 -04:00
Mark H Weaver 4483a1185d
gnu: linux-libre-4.4: Update to 4.4.11. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.11.
 2016-05-20 18:58:06 -04:00
Ricardo Wurmus 987a118334
gnu: Add default gcc-objc++. 
* gnu/packages/gcc.scm (gcc-objc++): New variable.
 2016-05-20 15:19:48 +02:00
Ricardo Wurmus a5948c0d41
gnu: Add gcc-objc++-4.9. 
* gnu/packages/gcc.scm (gcc-objc++-4.9): New variable.
 2016-05-20 15:19:48 +02:00
Ricardo Wurmus 8b196ad208
gnu: Add default gcc-objc. 
* gnu/packages/gcc.scm (gcc-objc): New variable.
 2016-05-20 15:19:48 +02:00
Ricardo Wurmus 2d69c1616d
gnu: Add gcc-objc-4.9. 
* gnu/packages/gcc.scm (gcc-objc-4.9): New variable.
 2016-05-20 15:19:33 +02:00
Ricardo Wurmus 813efdded1
gnu: r-rcpparmadillo: Update to 0.6.700.6.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.6.700.6.0.
* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to
6.700.6.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 945eef85c5
gnu: armadillo: Update to 6.700.7. 
* gnu/packages/maths.scm (armadillo): Update to 6.700.7.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 7740f58128
gnu: r-genomation: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus f6225d135c
gnu: r-jsonlite: Update to 0.9.20. 
* gnu/packages/web.scm (r-jsonlite): Update to 0.9.20.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus c969453e1c
gnu: r-plotly: Update to 3.6.0. 
* gnu/packages/statistics.scm (r-plotly): Update to 3.6.0.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 95513f284f
gnu: r-matrixstats: Update to 0.50.2. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 0.50.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus b8f6a97ebd
gnu: r-r-rsp: Update to 0.30.0. 
* gnu/packages/statistics.scm (r-r-rsp): Update to 0.30.0.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus f0c56a2411
gnu: r-rmarkdown: Update to 0.9.6. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 0.9.6.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 2f7ac060ff
gnu: r-plotrix: Update to 3.6-2. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.6-2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 133f27b06a
gnu: r-devtools: Update to 1.11.1. 
* gnu/packages/statistics.scm (r-devtools): Update to 1.11.1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 3624ad7150
gnu: r-git2r: Update to 0.15.0. 
* gnu/packages/statistics.scm (r-git2r): Update to 0.15.0.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus c1e2c9d41a
gnu: r-openssl: Update to 0.9.3. 
* gnu/packages/statistics.scm (r-openssl): Update to 0.9.3.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 383f6337a0
gnu: r-testthat: Update to 1.0.2. 
* gnu/packages/statistics.scm (r-testthat): Update to 1.0.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 1b206aeb00
gnu: r-knitr: Update to 1.13. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.13.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus d5130e6345
gnu: r-highr: Update to 0.6. 
* gnu/packages/statistics.scm (r-highr): Update to 0.6.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus df25b0048a
gnu: r-formatr: Update to 1.4. 
* gnu/packages/statistics.scm (r-formatr): Update to 1.4.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 84e5368719
gnu: r-evaluate: Update to 0.9. 
* gnu/packages/statistics.scm (r-evaluate): Update to 0.9.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 9a0ccf43cc
gnu: r-bh: Update to 1.60.0-2. 
* gnu/packages/statistics.scm (r-bh): Update to 1.60.0-2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus a76b3f6914
gnu: r-dbi: Update to 0.4-1. 
* gnu/packages/statistics.scm (r-dbi): Update to 0.4-1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus eb1a5b65c0
gnu: r-rcpp: Update to 0.12.5. 
* gnu/packages/statistics.scm (r-rcpp): Update to 0.12.5.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus d7420566a9
gnu: r-biocparallel: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 73af676feb
gnu: r-annotationdbi: Update to 1.34.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 679e670b36
gnu: r-variantannotation: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
 2016-05-20 15:18:23 +02:00
Ricardo Wurmus 186ed87337
gnu: r-genomeinfodb: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
 2016-05-20 15:18:23 +02:00
Leo Famulari 0fc4a8afba
gnu: btrfs-progs: Update to 4.5.3. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3.
 2016-05-19 21:04:22 -04:00
Jelle Licht 0e40755d35
gnu: jemalloc: Update to 4.2.0. 
* gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-05-19 20:43:13 +03:00
Leo Famulari 119b83989d
gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283. 
* gnu/packages/patches/expat-CVE-2015-1283-refix.patch,
gnu/packages/patches/expat-CVE-2016-0718.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xml.scm (expat)[replacement]: New field.
(expat/fixed): New variable.
[source]: Use new patches.
 2016-05-19 10:27:18 -04:00
Ludovic Courtès 9684e30b9b
gnu: flann: Do not install .a files. 
* gnu/packages/maths.scm (flann)[arguments]: Add #:phases.
 2016-05-19 14:51:21 +02:00
Hartmut Goebel 458480235b
gnu: python: Add 'python' variables for different major/minor versions. 
* gnu/packages/python.scm (python-2): Rename variable to...
  (python-2.7): ...this.
  (python-2): Refer to "python-2.7".
  (python): Rename variable to...
  (python-3.4): ...this.
  (python-3): Refer to "python-3.4".
  (python): Refer to "python-3".

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-19 14:51:21 +02:00
Ludovic Courtès 39b3033731
gnu: flann: Strip .mex file. 
* gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories.
 2016-05-19 14:51:21 +02:00
Ben Woodcroft 0947698c42 gnu: Add r-biased-urn. 
* gnu/packages/statistics.scm (r-biased-urn): New variable.
 2016-05-19 22:13:43 +10:00
Efraim Flashner 44c5f0258d
gnu: giflib: Use 'modify-phases'. 
* gnu/packages/image.scm (giflib)[arguments]: Use 'modify-phases'.
 2016-05-19 13:06:49 +03:00
Efraim Flashner 3fdb2a84be
gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555, CVE-2016-3977]. 
* gnu/packages/image.scm (giflib): Update to 5.1.4.
 2016-05-19 13:01:55 +03:00
humanitiesNerd 5c447e280e
gnu: Add emacs-smartparens. 
*  gnu/packages/emacs.scm (emacs-smartparens): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-19 11:45:15 +03:00
Kei Kebreau 21f05134fc
Update name for Kei Kebreau. 
* .mailmap: Add Kei Kebreau.
* gnu/local.mk: Replace "Kei Yamashita" with "Kei Kebreau".
* gnu/packages/calendar.scm: Likewise.
* gnu/packages/dillo.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/game-development.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-19 11:42:03 +03:00
Kei Yamashita b7b27a8f28
gnu: octave: Update to 4.0.2. 
* gnu/packages/maths.scm (octave): Update to 4.0.2.
[inputs]: Added cyrus-sasl, openssl.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-05-19 04:32:23 +03:00
Ludovic Courtès 91231156ce
gnu: Add ntfs-3g. 
* gnu/packages/linux.scm (ntfs-3g): New variable.
 2016-05-18 23:41:03 +02:00
Kei Yamashita 64851f4a23
gnu: wmbattery: Fix UPower-related memory leak. 
* gnu/packages/gnustep.scm (wmbattery)[source](snippet): New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-05-18 23:41:03 +02:00
Efraim Flashner 65e46ca0ed
gnu: qtkeychain: Update to 0.6.2. 
* gnu/packages/qt.scm (qtkeychain): Update to 0.6.2.
 2016-05-18 18:06:47 +03:00
Ben Woodcroft bd9fe0f03b gnu: Add krona-tools. 
* gnu/packages/web.scm (krona-tools): New variable.
 2016-05-18 22:21:52 +10:00
Manolis Ragkousis 0affdfb805 gnu: hurd-headers: Update to 0.8. 
* gnu/packages/hurd.scm (hurd-headers): Update to version 0.8.
 2016-05-18 15:17:52 +03:00
Manolis Ragkousis eb3be3a791 gnu: mig: Update to 1.7. 
* gnu/packages/hurd.scm (mig): Update to version 1.7.
 2016-05-18 15:17:44 +03:00
Manolis Ragkousis 614f39271e gnu: gnumach-headers: Update to 1.7. 
* gnu/packages/hurd.scm (gnumach-headers): Update to version 1.7.
 2016-05-18 15:17:38 +03:00
Ben Woodcroft 7c544991dc gnu: diamond: Do not specify target architecture. 
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
 2016-05-18 21:25:06 +10:00
Ricardo Wurmus e62ffce538 gnu: Add Piranha. 
* gnu/packages/bioinformatics.scm (piranha): New variable.
 2016-05-18 11:59:34 +02:00
Efraim Flashner dbd40ac19d
gnu: python2-pandas: Fix native-inputs. 
* gnu/packages/python.scm (python2-pandas)[native-inputs]: Use python2-
versions of python-panda's native-inputs, not of inputs.
 2016-05-18 10:52:41 +03:00
Leo Famulari f1876bfc7a
gnu: Add signify. 
* gnu/packages/crypto.scm (signify): New variable.
 2016-05-17 17:52:59 -04:00
Leo Famulari ad42be8388
gnu: libndp: Update to 1.6 [fixes CVE-2016-3698]. 
* gnu/packages/networking.scm (libndp): Update to 1.6.
 2016-05-17 14:31:09 -04:00
humanitiesNerd 9576cc72dc gnu: Add emacs-zenburn-theme. 
* gnu/packages/emacs.scm (emacs-zenburn-theme): New variable.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-05-17 21:06:36 +03:00
Leo Famulari fb2b0f5c87
gnu: gd: Fix-CVE-2016-3074. 
* gnu/packages/patches/gd-CVE-2016-3074.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Use it.
 2016-05-17 13:18:15 -04:00
Ludovic Courtès bbb5d8aeea
gnu: gd: Specify 'cpe-name'. 
* gnu/packages/gd.scm (gd)[properties]: New field.
 2016-05-17 18:15:59 +02:00
Ludovic Courtès 99effc8faa
lint: Honor 'cpe-name' and 'cpe-version' package properties. 
* guix/scripts/lint.scm (package-name->cpe-name): Remove.
(package-vulnerabilities): Honor 'cpe-name' and 'cpe-version'
properties.
* gnu/packages/grub.scm (grub)[properties]: New field.
* gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and
'cpe-version'.
* doc/guix.texi (Invoking guix lint): Mention 'cpe-name'.
 2016-05-17 18:15:53 +02:00
Federico Beffa 1c29f3ef84 gnu: emacs-constants: Remove old patch. 
* gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it.
* gnu/local.mk (dist_patch_DATA): Remove entry for above patch.
 2016-05-17 14:17:38 +02:00
Federico Beffa f99f3f24ef gnu: emacs-constants: Update to 2.6. 
* gnu/packages/emacs.scm (emacs-constants): Change to versioned repository and
  update to 2.6.
 2016-05-17 14:01:20 +02:00
Ben Woodcroft 849485f5a0 gnu: sortmerna: Update to 2.1b. 
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
 2016-05-17 21:45:49 +10:00
Ben Woodcroft daaeed765a gnu: vsearch: Update to 1.11.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
 2016-05-17 21:36:46 +10:00
Ben Woodcroft 122395f9fc gnu: diamond: Update to 0.8.1. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
 2016-05-17 21:07:00 +10:00
Ludovic Courtès a9e41d2faf
gnu: emacs-constants: Factorize home-page in source URL. 
* gnu/packages/emacs.scm (emacs-constants): Move 'home-page' above.  Use
it in 'uri'.
 2016-05-17 09:41:40 +02:00
Ludovic Courtès 4f04243405
gnu: 'uncompressed-file-fetch' no longer depends on gzip. 
* gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on
GZIP.
 2016-05-17 09:41:40 +02:00
Efraim Flashner cb307c0833
gnu: cflow: Update to 1.5. 
* gnu/packages/code.scm (cflow): Update to 1.5.
 2016-05-17 09:04:38 +03:00
Christopher Allan Webber 11e4c1fd10 gnu: Add geiser-next. 
Also, I previously committed to this repository in 2015; add self to copyright
headers for that year too.

* gnu/packages/emacs.scm (geiser-next): New variable.
 2016-05-16 14:48:57 -05:00
Ricardo Wurmus 96101b6718
gnu: r-zlibbioc: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
 2016-05-16 20:59:50 +02:00
Ricardo Wurmus a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
 2016-05-16 20:59:38 +02:00