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Author SHA1 Message Date
Andreas Enge
dceba1c19b
gnu: zsh: Update to 5.2. 
* gnu/packages/zsh.scm (zsh): Update to 5.2.
 2016-07-31 17:05:36 +02:00
Andreas Enge
ce430bd637
gnu: tcc: Use "kernel-headers" instead of "linux-headers" to designate input. 
* gnu/packages/c.scm (tcc)[arguments]: Use "kernel-headers" as identifier
for an input.

This is a follow-up to commit 55de892b43.
 2016-07-31 16:50:12 +02:00
Andreas Enge
70a967209c
gnu: dealii: Unregister deleted patch. 
* gnu/local.mk (dist_patch_DATA): Drop deleted patch.

This is a follow-up to commit 101e847294.
 2016-07-31 16:37:39 +02:00
Andreas Enge
101e847294
gnu: dealii: Update to 8.4.1. 
* gnu/packages/maths.scm (dealii): Update to 8.4.1.
* gnu/packages/patches/dealii-p4est-interface.patch: Remove file.
 2016-07-31 15:22:41 +02:00
Andreas Enge
7b995c7bcb
gnu: wine: Update to 1.9.15. 
* gnu/packages/wine.scm (wine): Update to 1.9.15.
 2016-07-31 12:11:05 +02:00
Andreas Enge
bb484529cc
gnu: python-alembic: Update to 0.8.7. 
* gnu/packages/python.scm (python-alembic): Update to 0.8.7.
 2016-07-31 11:18:53 +02:00
Andreas Enge
33906d54c1
gnu: perl-xml-libxml: Update to 2.0128. 
* gnu/packages/xml.scm (perl-xml-libxml): Update to 2.0128.
 2016-07-31 09:55:14 +02:00
宋文武
85860fdf82
gnu: glibc-locales: Fix build. 
* gnu/packages/patches/glibc-locales.patch: Adjust to glibc-2.23.
* gnu/packages/base.scm (glibc-locales)[arguments]:
Pass 'lib_cv_complocaledir'.
 2016-07-31 10:42:47 +08:00
Tomáš Čech
2fa66f451a
gnu: mutt: Update to 1.6.2. 
* gnu/packages/mail.scm(mutt): Update to 1.6.2.
 2016-07-30 22:37:56 +02:00
Kei Kebreau
4bc37bf0c3
gnu: Add python-pygame. 
* gnu/packages/game-development.scm (python-pygame): New variable.
 2016-07-30 14:32:49 -04:00
Kei Kebreau
d8841cc52e
gnu: Add libsmpeg. 
* gnu/packages/video.scm (libsmpeg): New variable.
 2016-07-30 14:31:58 -04:00
Leo Famulari
6661db4e97
gnu: stellarium: Improve description. 
Suggested by Danny Milosavljevic <dannym@scratchpost.org>.

* gnu/packages/education.scm (stellarium)[description]: Mention telescope
tracking.
 2016-07-30 10:05:44 -04:00
Ludovic Courtès
c2c54ebd91
gnu: Add glibc 2.22. 
* gnu/packages/base.scm (glibc-2.22): New variable.
(glibc-2.21): Inherit from it; remove 'arguments' field.
 2016-07-30 15:47:28 +02:00
Ludovic Courtès
716753cb97
tests: base: Correct invalid merge. 
Fixes a regression introduced by merge commit
7575655212.

* gnu/tests/base.scm (run-basic-test)[test]: Fix list of 'use-modules'
and 'test-begin' call.
 2016-07-30 15:47:28 +02:00
Ben Woodcroft
c4382cd18f
gnu: diamond: Update to 0.8.17. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.
 2016-07-30 23:02:57 +10:00
ng0
9b12bc7032
gnu: gnunet-gtk: Configure with gnunet path. 
* gnun/packages/gnunet.scm (gnunet-gtk)[arguments]: Add '--with-gnunet'
to #:configure-flags.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-07-30 15:33:57 +08:00
Eric Bavier
d25639731a
gnu: Add tuxpaint-config. 
* gnu/packages/games.scm (tuxpaint-config): New variable.
 2016-07-29 23:17:44 -05:00
Eric Bavier
c3d850f232
gnu: Add tuxpaint-stamps. 
* gnu/packages/games.scm (tuxpaint-stamps): New variable.
 2016-07-29 21:50:15 -05:00
Eric Bavier
9b1ada4e81
gnu: Add Tux Paint. 
* gnu/packages/games.scm (tuxpaint): New variable.
* gnu/packages/patches/tuxpaint-stamps-path.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-07-29 21:50:15 -05:00
Alex Griffin
23319ed674
gnu: beets: Update to 1.3.19. 
* gnu/packages/music.scm (beets): Update to 1.3.19.
[source]: Remove patch to skip failing tests.
* gnu/packages/patches/beets-image-test-failure.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-29 19:19:49 -04:00
Leo Famulari
d1c9d3bb42
gnu: python-protobuf: Update to 3.0.0. 
* gnu/packages/protobuf.scm (python-protobuf, python2-protobuf):
Update to 3.0.0.
 2016-07-29 19:04:31 -04:00
Leo Famulari
48b7e4a6c1
gnu: btrfs-progs: Update to 4.6.1 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.6.1.
[native-inputs]: Add WHICH.
 2016-07-29 18:58:48 -04:00
Mark H Weaver
359aba76b6
Merge branch 'master' into core-updates 2016-07-29 18:29:58 -04:00
Mark H Weaver
9bdf56dc13
gnu: gd: Add fix for gd2_read test. 
* gnu/packages/patches/gd-fix-gd2-read-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Add patch.
 2016-07-29 18:28:40 -04:00
Leo Famulari
de30a6e0f0
gnu: protobuf: Update to 2.6.1. 
* gnu/packages/protobuf.scm (protobuf): Update to 2.6.1.
[source]: Update to new upstream URL.
 2016-07-29 16:41:06 -04:00
Mark H Weaver
31c995f8af
Revert "gnu: gd: Add fix for gd2_read test." 
This reverts commit ce290354ec.
 2016-07-29 16:17:35 -04:00
Mark H Weaver
ce290354ec
gnu: gd: Add fix for gd2_read test. 
* gnu/packages/patches/gd-fix-gd2-read-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Add patch.
 2016-07-29 16:06:43 -04:00
Leo Famulari
814572aff5
gnu: wireshark: Update to 2.0.5. 
* gnu/packages/networking.scm (wireshark): Update to 2.0.5.
 2016-07-29 15:08:55 -04:00
Leo Famulari
d260015062
gnu: perl-dbd-mysql: Update to 4.035 [fixes CVE-2015-8949]. 
* gnu/packages/databases.scm (perl-dbd-mysql): Update to 4.035.
 2016-07-29 14:49:30 -04:00
Mark H Weaver
0bab3af078
Merge branch 'master' into core-updates 2016-07-29 14:18:07 -04:00
Mark H Weaver
682a7d2338
gnu: linux-libre@4.4: Update to 4.4.16. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.16.
 2016-07-29 14:14:25 -04:00
Mark H Weaver
a81445737d
gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]. 
* gnu/packages/patches/gd-CVE-2016-5766.patch,
gnu/packages/patches/gd-CVE-2016-6128.patch,
gnu/packages/patches/gd-CVE-2016-6132.patch,
gnu/packages/patches/gd-CVE-2016-6214.patch,
gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files.
* gnu/packages/patches/gd-fix-tests-on-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gd.scm (gd): Update to 2.2.3.
[source]: Update patches field accordingly.
 2016-07-29 13:56:39 -04:00
Leo Famulari
f54510d29b
gnu: virt-viewer: Remove SPICE-PROTOCOL from inputs. 
This is a followup to ba9e2ee64a.

* gnu/packages/spice.scm (virt-viewer)[inputs]: Remove SPICE-PROTOCOL.
 2016-07-29 12:50:29 -04:00
Leo Famulari
3c4a8f03a2
gnu: spice-gtk: Remove LIBUSB from inputs. 
This is a followup to 0d05a739d2.

* gnu/packages/spice.scm (spice-gtk)[inputs]: Remove LIBUSB.
 2016-07-29 12:50:29 -04:00
David Craven
efcada41e7
gnu: Order module imports in (gnu packages qemu) alphabetically. 
* gnu/packages/qemu.scm: Order module imports alphabetically.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:43:55 +02:00
David Craven
6799ed7614
gnu: Add xf86-video-qxl. 
* gnu/packages/xorg.scm (xf86-video-qxl): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:41:30 +02:00
David Craven
c38fb02e9b
gnu: Add libinput-minimal. 
* gnu/packages/freedesktop.scm (libinput-minimal): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:40:24 +02:00
David Craven
66e076642c
gnu: Remove trailing periods from synopsis. 
* gnu/packages/emacs.scm (emacs-smart-mode-line): Update synopsis.
* gnu/packages/gnustep.scm (wmfire): Update synopsis.
* gnu/packages/haskell.scm (ghc-socks): Update synopsis.
* gnu/packages/kde-frameworks.scm (oxygen-icons): Update synopsis.
* gnu/packages/openstack.scm (python-bandit): Update synopsis.
* gnu/packages/perl.scm (perl-test-trap): Update synopsis.
* gnu/packages/python.scm (python-backports-abc): Update synopsis.
* gnu/packages/ruby.scm (python-cryptography-vectors): Update synopsis.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:37:22 +02:00
David Craven
0160458bf8
gnu: Use define-public to export packages. 
* gnu/packages/bison.scm (bison): Define public.
* gnu/packages/flex.scm (flex): Define public.
* gnu/packages/pulseaudio.scm (libsndfile, libsamplerate, pulseaudio): Define
public.
* gnu/packages/sdl.scm (sdl, sdl2, libmikmod, sdl-gfx, sdl-image, sdl-mixer,
sdl-net, sdl-ttf): Define public.
* gnu/packages/search.scm (xapian): Remove unnecessary #:export.
* gnu/packages/swig.scm (swig): Define public.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:35:20 +02:00
Ludovic Courtès
35e4b3d546
gnu: iptables: Mention "firewall". 
Suggested by ng0 <ng0@we.make.ritual.n0.is>.

* gnu/packages/linux.scm (iptables)[description]: Mention "firewall".
 2016-07-29 17:32:03 +02:00
Eric Le Bihan
7c6bdeec23
gnu: Add s6-networking. 
* gnu/packages/skarnet.scm (s6-networking): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan
798b776deb
gnu: Add s6-dns. 
* gnu/packages/skarnet.scm (s6-dns): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan
918cee467d
gnu: Add s6. 
* gnu/packages/skarnet.scm (s6): New variable.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan
2f016ac150
gnu: execline: Update to 2.1.5.0. 
* gnu/packages/skarnet.scm (execline): Update to 2.1.5.0.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Eric Le Bihan
892aa89477
gnu: skalibs: Update to 2.3.10.0. 
* gnu/packages/skarnet.scm (skalibs): Update to 2.3.10.0.

Signed-off-by: Eric Le Bihan <eric.le.bihan.dev@free.fr>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Danny Milosavljevic
2614de3c5a
gnu: Add stellarium. 
* gnu/local.mk: Include gnu/packages/education.scm .
* gnu/packages/education.scm: Add new file.
* gnu/packages/education.scm (stellarium): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 17:29:50 +02:00
Leo Famulari
ba9e2ee64a
gnu: spice-gtk: Propagate SPICE-PROTOCOL. 
* gnu/packages/spice.scm (spice-gtk)[inputs]: Move SPICE-PROTOCOL to...
[propagated-inputs]: ... here.
 2016-07-29 11:16:23 -04:00
Leo Famulari
0d05a739d2
gnu: usbredir: Propagate LIBUSB. 
* gnu/packages/spice.scm (usbredir)[inputs]: Replace field with ...
[propagated-inputs]: ... new field.
 2016-07-29 11:16:23 -04:00
Ludovic Courtès
6e6ddebf48
gnu: guix: Add dependency on zlib. 
* gnu/packages/package-management.scm (guix-0.10.0)[inputs]: Add ZLIB.
 2016-07-29 11:39:30 +02:00
Alex Griffin
61201e46a7
gnu: password-store: Wrap PATH. 
* gnu/packages/password-utils.scm (password-store)
[arguments]: Wrap PATH more thoroughly.
[native-inputs]: Move getopt to inputs.
[inputs]: Add sed.

Signed-off-by: Mathieu Lirzin <mthl@gnu.org>
 2016-07-29 11:00:31 +02:00
Ludovic Courtès
f33e71fca2
gnu: perl-dbd-pg: Add description. 
* gnu/packages/databases.scm (perl-dbd-pg)[description]: Add non-empty
description.
 2016-07-29 10:22:31 +02:00
Ludovic Courtès
a3947cb1b8
gnu: Sync GNU descriptions with upstream. 
From 'guix lint -c gnu-description'.

* gnu/packages/gnunet.scm (gnunet): Adjust description.
* gnu/packages/marst.scm (marst): Likewise.
* gnu/packages/maths.scm (c-graph): Likewise.
* gnu/packages/networking.scm (macchanger): Likewise.
 2016-07-29 10:13:12 +02:00
Nicolas Goaziou
c777570b57
gnu: Add sshpass. 
* gnu/packages/ssh.scm (sshpass): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-29 00:04:39 +02:00
Leo Famulari
cfbb3b0d00
gnu: python-beautifulsoup4: Update to 4.5.0. 
* gnu/packages/python.scm (python-beautifulsoup4, python2-beautifulsoup4):
Update to 4.5.0.
 2016-07-28 17:50:52 -04:00
ng0
adca268e97
gnu: perl-devel-symdump: Update to 2.17. 
* gnu/packages/perl.scm (perl-devel-symdump): Update to 2.17.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:41:06 -04:00
David Craven
6144dff516
gnu: Add virt-viewer. 
* gnu/packages/spice.scm (virt-viewer): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven
33b0f4a4b2
gnu: Add spice-vdagent. 
* gnu/packages/spice.scm (spice-vdagent): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven
3cbd37e440
gnu: Add spice. 
* gnu/packages/spice.scm (spice): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven
bb28cf90e9
gnu: Add spice-gtk. 
* gnu/packages/spice.scm (spice-gtk): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:42 -04:00
David Craven
289e472f56
gnu: Add spice-protocol. 
* gnu/packages/spice.scm (spice-protocol): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
David Craven
2ef2654de4
gnu: Add virglrenderer. 
* gnu/packages/spice.scm (virglrenderer): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
David Craven
1d2c67c11e
gnu: Add usbredir. 
* gnu/packages/spice.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-28 17:08:41 -04:00
Leo Famulari
49d725a108
Merge branch 'master' into core-updates 2016-07-28 16:46:27 -04:00
Leo Famulari
a1dfa02233
Revert "gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]." 
This reverts commit ae46cd0e4c.
 2016-07-28 16:45:02 -04:00
Mark H Weaver
622c22ccb4
Merge branch 'master' into core-updates 2016-07-28 14:13:26 -04:00
Mark H Weaver
ae46cd0e4c
gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]. 
* gnu/packages/patches/gd-CVE-2016-5766.patch,
gnu/packages/patches/gd-CVE-2016-6128.patch,
gnu/packages/patches/gd-CVE-2016-6132.patch,
gnu/packages/patches/gd-CVE-2016-6214.patch,
gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files.
* gnu/packages/patches/gd-fix-tests-on-i686.patch: New file.
* gnu/local.mk (dist_patch_DATA): Update accordingly.
* gnu/packages/gd.scm (gd): Update to 2.2.3.
[source]: Update patches field accordingly.
 2016-07-28 14:06:12 -04:00
Ludovic Courtès
386b71d1b9
gnu: commencement: 'guile-final' is now "hidden". 
This way, we no longer have this annoying warning:

  $ guix build guile -n
  guix build: warning: ambiguous package specification `guile'
  guix build: warning: choosing guile-2.0.11 from gnu/packages/guile.scm:128:2

* gnu/packages/commencement.scm (guile-final): Use 'hidden-package'.
* tests/packages.scm ("fold-packages, hidden package"): New test.
 2016-07-28 18:53:13 +02:00
Ludovic Courtès
6980511b73
packages: Add 'hidden-package'. 
* guix/packages.scm (hidden-package, hidden-package?): New procedures.
* gnu/packages.scm (fold-packages): Filter out 'hidden-package?'.
* tests/packages.scm ("hidden-package"): New test.
 2016-07-28 18:50:43 +02:00
Alex Griffin
cb55f9c652
gnu: Add asciinema. 
* gnu/packages/terminals.scm (asciinema): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-28 15:43:40 +02:00
Alex Griffin
71d9b98078
gnu: gnome: Propagate file-roller. 
* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-28 15:42:30 +02:00
Ludovic Courtès
212163f8d5
gnu: dico: Patch 'idxgcide' bug. 
* gnu/packages/patches/dico-idxgcide-bug.patch: New file.
* gnu/packages/dico.scm (dico)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-07-28 14:18:59 +02:00
Ludovic Courtès
c6b3dc69bd
gnu: vlc: Drop -ffast-math from the compilation flags. 
* gnu/packages/video.scm (vlc)[arguments]: Add "ac_cv_c_fast_math=no" to
  #:configure-flags.
 2016-07-28 13:56:05 +02:00
Ben Woodcroft
6547708f71
gnu: r-genomicfeatures: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
 2016-07-28 21:54:44 +10:00
Ben Woodcroft
2c9f6251fc
gnu: r-bsgenome: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft
b0f0778a7c
gnu: r-iranges: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft
f403941f81
gnu: r-limma: Update to 3.28.17. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft
2b2ff0bd91
gnu: r-xvector: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft
a463055862
gnu: r-genomicranges: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft
bab15ccec4
gnu: r-annotationdbi: Update to 1.34.4. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft
a22999f245
gnu: r-biocparallel: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft
d104fc607d
gnu: r-biostrings: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft
1864e051c9
gnu: r-summarizedexperiment: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft
29b0cc8ad5
gnu: r-genomicalignments: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft
5131e21064
gnu: r-rtracklayer: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft
2a3e325f5e
gnu: r-genomeinfodb: Update to 1.8.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft
ae32c58e28
gnu: r-bsgenome: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
e426cd7421
gnu: r-iranges: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
1c4ad6076c
gnu: r-limma: Update to 3.28.17. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
bd0cc37834
gnu: r-xvector: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
362f39d667
gnu: r-genomicranges: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
ae60f3801a
gnu: r-annotationdbi: Update to 1.34.4. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
7a0594fb5d
gnu: r-biocparallel: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
658f36e569
gnu: r-biostrings: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
0d159d84e2
gnu: r-summarizedexperiment: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
722b4c919d
gnu: r-genomicalignments: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
380d3f8657
gnu: r-rtracklayer: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
303163c7b9
gnu: r-genomeinfodb: Update to 1.8.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
2d88825183
gnu: r-genomicfeatures: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
 2016-07-28 21:35:40 +10:00
Ben Woodcroft
d6dfc39f68
gnu: r-s4vectors: Update to 0.10.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
 2016-07-28 12:31:22 +02:00
Ben Woodcroft
f2e791750b
gnu: r-s4vectors: Update to 0.10.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
 2016-07-28 20:13:42 +10:00
Andreas Enge
4320c1c39f
gnu: asymptote: Add native input gs. 
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Add gs.

This is a follow-up to commit d8eb912132.
 2016-07-28 11:34:57 +02:00
Andreas Enge
e309c75610
Merge remote-tracking branch 'origin/master' into core-updates 2016-07-28 11:08:55 +02:00
Leo Famulari
e335b82c4e
gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}]. 
* gnu/packages/patches/mysql-fix-failing-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/databases.scm (mysql): Update to 5.7.13.
 2016-07-28 02:08:49 -04:00
Tomáš Čech
46e4e84ffc
gnu: the-silver-searcher: Update to 0.32.0. 
* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
 2016-07-28 08:05:04 +02:00
Leo Famulari
8e5d8b1880
gnu: imagemagick: Update to 6.9.5-3. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3.
 2016-07-27 23:25:13 -04:00
Leo Famulari
ff7172feae
gnu: mariadb: Update to 10.1.16. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.16.
 2016-07-27 23:25:08 -04:00
Ludovic Courtès
1bb163b0dd
gnu: python@2.7: Delete faulty test on mips64el only. 
This amends 8b732bf6d9 and avoids a
rebuild.

* gnu/packages/python.scm (python-2.7)[arguments] <pre-check>:
When (%current-system) starts with "mips64el", delete
Lib/test/test_ctypes.py.
 2016-07-28 00:58:40 +02:00
Alex Griffin
b111bdb667
gnu: calibre: Update to 2.63.0. 
* gnu/packages/ebook.scm (calibre): Update to 2.63.0.
[inputs]: Remove unnecessary imagemagick dependency.
[phases]: Use modify-phases.

* gnu/packages/patches/calibre-drop-unrar.patch: Update
for new version.

Signed-off-by: Roel Janssen <roel@gnu.org>
 2016-07-27 23:45:16 +02:00
Carlos Sánchez de La Lama
cad7e6abaf
system: Source /etc/environment before $HOME/.guix-profile/etc/profile. 
* gnu/system.scm (operating-system-etc-service) <profile>: Move sourcing
of /etc/environment before that of $HOME/.guix-profile/etc/profile.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-27 23:08:20 +02:00
Andreas Enge
8b732bf6d9
gnu: python-2.7: Disable test failing on mips64el-linux. 
* gnu/packages/python.scm (python-2.7)[source]: In a snippet, remove
an additional test that fails on mips64el-linux.
 2016-07-27 18:24:12 +02:00
Ben Woodcroft
9712ef8d42
gnu: krona-tools: Update to 2.7. 
* gnu/packages/web.scm (krona-tools): Update to 2.7.
[arguments]: Delete 'build' phase.  Install new scripts.
 2016-07-27 23:39:56 +10:00
Ben Woodcroft
12c8f210ee
gnu: diamond: Update to 0.8.16. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
 2016-07-27 23:17:57 +10:00
Andreas Enge
fd6830b3a6
gnu: guix: Update revision number in version. 
This is a follow-up to commit 95af24a2f1.
Reported by Alex Kost <alezost@gmail.com>.
 2016-07-27 15:16:17 +02:00
Andreas Enge
0072b3d3f2
gnu: skribilo: Add input ghostscript-gs. 
* gnu/packages/engineering.scm (lout)[native-inputs]: Add ghostscript-gs.

This is a follow-up to commit d8eb912132.
 2016-07-27 14:47:15 +02:00
Alex Griffin
46bd451520
gnu: magit: Fix rebase commands that require perl. 
* gnu/packages/emacs.scm (magit)[inputs]: Add 'perl'.
[arguments]: Adjust 'patch-exec-paths' phase to make some rebase
commands find 'perl'.

Signed-off-by: Alex Kost <alezost@gmail.com>
 2016-07-27 11:15:45 +03:00
Tobias Geerinckx-Rice
82ee141bab
gnu: Add httping. 
* gnu/packages/networking.scm (httping): New variable.
 2016-07-27 03:59:47 +02:00
Tobias Geerinckx-Rice
42ff54d5fa
gnu: Add missing copyright symbol. 
* gnu/packages/networking.scm: Add missing "©" to header comments.
 2016-07-27 03:59:47 +02:00
ng0
ae83dcf6ba
gnu: gmime: Remove 'gpg' to 'gpg2' substitution. 
* gnu/packages/mail.scm (gmime)[arguments]: Remove the substitution which
previously changed 'gpg' to 'gpg2' in 'patch-paths-in-tests' phase.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-07-26 19:43:54 -04:00
Andreas Enge
5425269bf7
gnu: lout: Add input ghostscript. 
* gnu/packages/lout.scm (lout)[native-inputs]: Add ghostscript, needed for ps2pdf.
 2016-07-26 23:28:55 +02:00
Andreas Enge
02b934e2c6
gnu: lout: Make ghostscript-gs a native input. 
* gnu/packages/lout.scm (lout)[inputs]: Move to native-inputs.
 2016-07-26 23:09:01 +02:00
Andreas Enge
5ef469ce31
gnu: lout: Build with ghostscript-gs. 
* gnu/packages/engineering.scm (lout)[inputs]: Replace GHOSTSCRIPT by
GHOSTSCRIPT-GS.

This is a follow-up to commit d8eb912132.
 2016-07-26 23:08:00 +02:00
Andreas Enge
d3896fc4ce
gnu: dmd: Remove package, superseded by shepherd. 
* gnu/packages/admin.scm (dmd): Remove variable.
 2016-07-26 22:50:26 +02:00
Danny Milosavljevic
90c2ee889b
gnu: Add perl-db-file. 
* gnu/packages/databases.scm (perl-db_file): New variable.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2016-07-26 22:43:48 +02:00
Alex Griffin
88a8ce87a4
gnu: icecat: Install icons. 
* gnu/packages/gnuzilla.scm (icecat)[arguments]: Add
'install-icons' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-26 14:53:16 +02:00
Tobias Geerinckx-Rice
2b76f13507
gnu: Add haveged. 
* gnu/packages/linux.scm (haveged): New variable.
 2016-07-26 11:20:52 +02:00
Tobias Geerinckx-Rice
af7aaaebab
gnu: Add perceptualdiff. 
* gnu/packages/image.scm (perceptualdiff): New variable.
 2016-07-26 11:20:27 +02:00
Mark H Weaver
ca80985c6c
gnu: linux-libre@4.1: Update to 4.1.28. 
* gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.28.
 2016-07-26 01:36:12 -04:00
Mark H Weaver
de348a0bb7
gnu: linux-libre: Update to 4.7. 
* gnu/packages/linux.scm (linux-libre): Update to 4.7.
* gnu/packages/linux-libre-4.7-x86_64.conf,
gnu/packages/linux-libre-4.7-i686.conf: New files.
* gnu/packages/linux-libre-4.6-x86_64.conf,
gnu/packages/linux-libre-4.6-i686.conf: Delete files.
* Makefile.am (KCONFIGS): Update accordingly.
 2016-07-26 00:46:40 -04:00
Ludovic Courtès
5dbfbef729
gnu: lpsolve: Fix compilation issue. 
Reported by Andreas Enge <andreas@enge.fr>
at <https://lists.gnu.org/archive/html/guix-devel/2016-07/msg01018.html>.

* gnu/packages/maths.scm (lpsolve)[source]: Augment 'snippet'.
 2016-07-26 00:43:52 +02:00
Ludovic Courtès
6689d09457
gnu: lpsolve: Fail as early as possible. 
* gnu/packages/maths.scm (lpsolve)[arguments]: In 'build' phase, check
the return value of 'system*' and honor it.
 2016-07-26 00:43:52 +02:00
Andreas Enge
0e5f606159
gnu: calibre: Build with non-modular Qt. 
* gnu/packages/ebook.scm (calibre)[native-inputs]: Replace QTBASE by QT.
[inputs]: Replace QTBASE by QT and PYTHON2-PYQT by PYTHON2-PYQT-5.5.

This essentially reverts commit 76806c54ed.

Reported by Roel Janssen <roel@gnu.org>.
 2016-07-26 00:38:39 +02:00
Andreas Enge
4a8c35e143
gnu: pyqt: Add versions based on non-modular Qt 5.5. 
* gnu/packages/qt.scm (python-pyqt-5.5, python2-pyqt-5.5): New variables.
 2016-07-26 00:38:20 +02:00
Andreas Enge
e83a13faa2
gnu: fastcap: Build with ghostscript-gs. 
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Replace GHOSTSCRIPT
by GHOST_SCRIPT-GS.

This is a follow-up to commit d8eb912132.
 2016-07-25 23:59:47 +02:00
Andreas Enge
95af24a2f1
gnu: guix: Update development snapshot. 
* gnu/packages/package-management.scm (guix-devel): Update to 97c8aef.
 2016-07-25 22:53:27 +02:00
Andreas Enge
97c8aef15d
system: Add mapped devices for RAID. 
* gnu/system/mapped-devices.scm (raid-device-mapping, open-raid-device,
close-raid-device): New variables.
* doc/guix.texi (Mapped Devices): Add documentation for RAID devices,
reorganize documentation for LUKS devices.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-25 22:22:21 +02:00
Andreas Enge
14656f4495
Merge remote-tracking branch 'origin/master' into core-updates 2016-07-25 21:58:36 +02:00
Alex Kost
090bdb9e91
gnu: emacs-solarized-theme: Remove unneeded dependencies. 
* gnu/packages/emacs.scm (emacs-solarized-theme)[propagated-inputs]:
Remove 'emacs-f' and 'emacs-s'.
 2016-07-25 17:18:53 +03:00
Alex Kost
c48899eba2
gnu: emacs: Install site-start.el in non-versioned directory. 
Reported by Ricardo Wurmus on #guix.

* gnu/packages/emacs.scm (emacs)[arguments]: Put "site-start.el" in
"/share/emacs/site-lisp" instead of "/share/emacs/<version>/site-lisp"
to let inherited package with another version find it.
 2016-07-25 17:18:53 +03:00
Alex Kost
07f7cc03ce
gnu: Add guile-daemon. 
* gnu/packages/guile.scm (guile-daemon): New variable.
 2016-07-25 17:18:53 +03:00
Alex Kost
bd9af61035
gnu: Add guile-xosd. 
* gnu/packages/guile.scm (guile-xosd): New variable.
 2016-07-25 17:18:53 +03:00
Alex Kost
6cfd1a687a
gnu: Add xdpyprobe. 
* gnu/packages/xdisorg.scm (xdpyprobe): New variable.
 2016-07-25 17:18:53 +03:00
Alex Kost
84b5d9075c
gnu: mkfontdir: Do not propagate 'mkfontscale'. 
* gnu/packages/xorg.scm (mkfontdir)[propagated-inputs]: Move
'mkfontscale' to ...
[inputs]: ... here.
[arguments]: Add 'wrap-mkfontdir' phase.
 2016-07-25 17:18:52 +03:00
Alex Kost
e48e31bcc8
gnu: Add xfd. 
* gnu/packages/xorg.scm (xfd): New variable.
 2016-07-25 17:18:52 +03:00
Alex Kost
f225ae7544
gnu: Add xfontsel. 
* gnu/packages/xorg.scm (xfontsel): New variable.
 2016-07-25 17:18:52 +03:00
Andy Patterson
1925a87926
gnu: sbcl: Update to 1.3.7. 
* gnu/packages/lisp.scm (sbcl): Update to 1.3.7.
[arguments]: During the patch-unix-tool-paths phase, avoid running
substitute* on a utf-16-be encoded file.

Signed-off-by: 宋文武 <iyzsong@gmail.com>
 2016-07-25 19:50:13 +08:00
Ludovic Courtès
d8eb912132
gnu: Use 'ghostscript-gs' in packages that need the 'gs' command. 
Fixes a regression introduced in
eb354bdacb.

Reported by Andreas Enge <andreas@enge.fr>.

* gnu/packages/gv.scm (gv)[propagated-inputs]: Change from GHOSTSCRIPT/X
to GHOSTSCRIPT-GS/X.
* gnu/packages/music.scm (lilypond): Use GHOSTSCRIPT-GS instead of
GHOSTSCRIPT.
* gnu/packages/ocaml.scm (unison): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/scheme.scm (chez-scheme): Likewise.
 2016-07-25 11:37:43 +02:00
Ludovic Courtès
71eba3ebc1
gnu: Add 'ghostscript-gs' and 'ghostscript-gs-with-x'. 
* gnu/packages/ghostscript.scm (ghostscript-wrapper): New procedure.
(ghostscript-gs, ghostscript-gs/x): New variables.
 2016-07-25 11:36:51 +02:00
Andy Patterson
54a43ff406
gnu: ecl: Wrap with PATH, CPATH, LIBRARY_PATH, and LD_LIBRARY_PATH. 
* gnu/packages/lisp.scm (ecl)[arguments]: Add 'wrap' phase.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-25 10:48:49 +02:00
Andy Patterson
60474cd114
gnu: ecl: Enable tests. 
* gnu/packages/lisp.scm (ecl): Enable tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-25 10:48:49 +02:00
Andy Patterson
e0524511ec
gnu: ecl: Update to 16.1.2. 
* gnu/packages/lisp.scm (ecl): Update to 16.1.2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-07-25 10:48:49 +02:00