jackhill/guix/guix.git
8 years agobuild: Add 'EMACS' silent rule.
Mathieu Lirzin [Sun, 24 Jan 2016 17:57:49 +0000 (18:57 +0100)]
build: Add 'EMACS' silent rule.

* Makefile.am (AM_V_EMACS, AM_V_EMACS_, AM_V_EMACS_0): New variables.
* emacs.am [HAVE_EMACS] ($(AUTOLOADS)): Use $(AM_V_EMACS).

8 years agobuild: Add 'DOT' silent rule.
Mathieu Lirzin [Sun, 24 Jan 2016 17:55:38 +0000 (18:55 +0100)]
build: Add 'DOT' silent rule.

* Makefile.am (AM_V_DOT, AM_V_DOT_, AM_V_DOT_0): New variables.
* doc.am (.dot.png, .dot.pdf, .dot.eps): Use $(AM_V_DOT).

8 years agobuild: Add 'DL' silent rule.
Mathieu Lirzin [Sun, 24 Jan 2016 17:48:29 +0000 (18:48 +0100)]
build: Add 'DL' silent rule.

* Makefile.am (AM_V_DL, AM_V_DL_, AM_V_DL_0): New variables.
* gnu-system.am (gnu/packages/bootstrap/x86_64-linux/guile-2.0.9.tar.xz)
(gnu/packages/bootstrap/i686-linux/guile-2.0.9.tar.xz)
(gnu/packages/bootstrap/armhf-linux/guile-2.0.11.tar.xz)
(gnu/packages/bootstrap/mips64el-linux/guile-2.0.9.tar.xz): Use $(AM_V_DL).
* build-aux/download.scm: Print a line break between target and origin.

8 years agopackages: Use '@' in package record printers.
Mathieu Lirzin [Sun, 24 Jan 2016 16:42:39 +0000 (17:42 +0100)]
packages: Use '@' in package record printers.

* guix/packages.scm <package>: Use '@' in record printer.
* guix/import/cabal.scm <cabal-package>: Likewise
* guix/import/elpa.scm <elpa-package>: Likewise.
* tests/packages.scm: Adapt to it.

8 years agolint: Rewrite 'check-patch-file-names'.
Mathieu Lirzin [Sun, 24 Jan 2016 14:15:54 +0000 (15:15 +0100)]
lint: Rewrite 'check-patch-file-names'.

* guix/scripts/lint.scm (check-patch-file-names): Improve clarity by
reversing the logic.

8 years agolint: Remove an unneeded clause in 'check-patch-file-names'.
Mathieu Lirzin [Sun, 24 Jan 2016 14:21:10 +0000 (15:21 +0100)]
lint: Remove an unneeded clause in 'check-patch-file-names'.

* guix/scripts/lint.scm (check-patch-file-names): Don't check if patches
start with the package full name since matching the package name (which
is a prefix of the full name) is sufficient.

8 years agotests: Use 'dummy-origin' for lint tests when possible.
Mathieu Lirzin [Sun, 24 Jan 2016 15:28:51 +0000 (16:28 +0100)]
tests: Use 'dummy-origin' for lint tests when possible.

* guix/tests/lint.scm ("patches: file names", "patches: not found"): Use
'dummy-origin'.  'sha256' field was wrongly set to a string instead of a
bytevector.

8 years agognu: icedtea-7: Update to 2.6.4.
Leo Famulari [Thu, 28 Jan 2016 13:38:58 +0000 (08:38 -0500)]
gnu: icedtea-7: Update to 2.6.4.

Fixes CVE-2015-{7575, 8126, 8472} and CVE-2016-{0402, 0448, 0466, 0483,
0494}.

* gnu/packages/java.scm (icedtea-7): Update to 2.6.4.

8 years agognu: icedtea-6: Update to 1.13.10.
Leo Famulari [Thu, 28 Jan 2016 13:35:04 +0000 (08:35 -0500)]
gnu: icedtea-6: Update to 1.13.10.

Fixes CVE-2015-{8126, 8472} and CVE-2016-{0402, 0448, 0466, 0483, 0494}.

* gnu/packages/java.scm (icedtea-6): Update to 1.13.10.

8 years agoMerge branch 'core-updates'
Mark H Weaver [Thu, 28 Jan 2016 12:29:13 +0000 (07:29 -0500)]
Merge branch 'core-updates'

8 years agognu: shepherd: Update to 0.3.
Ludovic Courtès [Thu, 28 Jan 2016 10:45:03 +0000 (11:45 +0100)]
gnu: shepherd: Update to 0.3.

* gnu/packages/admin.scm (shepherd): Update to 0.3.

8 years agognu: icecat: Add fixes for CVE-2016-{1930,1935} and other bugs.
Mark H Weaver [Thu, 28 Jan 2016 05:22:49 +0000 (00:22 -0500)]
gnu: icecat: Add fixes for CVE-2016-{1930,1935} and other bugs.

* gnu/packages/patches/icecat-CVE-2016-1930-pt01.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt02.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt03.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt04.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt05.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt06.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt07.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt08.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt09.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt10.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt11.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt12.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt13.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt14.patch,
  gnu/packages/patches/icecat-CVE-2016-1930-pt15.patch,
  gnu/packages/patches/icecat-CVE-2016-1935.patch,
  gnu/packages/patches/icecat-bug-1146335-pt1.patch,
  gnu/packages/patches/icecat-bug-1146335-pt2.patch,
  gnu/packages/patches/icecat-limit-max-buffers-size-for-ANGLE.patch: New
  files.
* gnu-system.am (dist_patch_DATA): Add them.
* gnu/packages/gnuzilla.scm (icecat)[source]: Add patches.

8 years agoservices: guix: Provide Guix via 'profile-service-type'.
Ludovic Courtès [Wed, 27 Jan 2016 14:40:29 +0000 (15:40 +0100)]
services: guix: Provide Guix via 'profile-service-type'.

* gnu/services/base.scm (guix-service-type): Extend
PROFILE-SERVICE-TYPE.
* gnu/system.scm (%base-packages): Remove GUIX.

8 years agoservices: dmd: Provide dmd via 'profile-service-type'.
Ludovic Courtès [Wed, 27 Jan 2016 14:36:27 +0000 (15:36 +0100)]
services: dmd: Provide dmd via 'profile-service-type'.

* gnu/services/dmd.scm (dmd-root-service-type): Extend
PROFILE-SERVICE-TYPE.
* gnu/system.scm (%base-packages): Remove dmd.

8 years agognu: Add snapshot of the GNU Shepherd.
Ludovic Courtès [Wed, 27 Jan 2016 14:34:41 +0000 (15:34 +0100)]
gnu: Add snapshot of the GNU Shepherd.

* gnu/packages/admin.scm (shepherd): New variable.

8 years agognu: Add ruby-http-cookie.
Ben Woodcroft [Wed, 30 Dec 2015 23:27:51 +0000 (09:27 +1000)]
gnu: Add ruby-http-cookie.

* gnu/packages/ruby.scm (ruby-http-cookie): New variable.

8 years agognu: Add ruby-domain-name.
Ben Woodcroft [Wed, 30 Dec 2015 23:25:45 +0000 (09:25 +1000)]
gnu: Add ruby-domain-name.

* gnu/packages/ruby.scm (ruby-domain-name): New variable.

8 years agognu: Add ruby-unf.
Ben Woodcroft [Wed, 30 Dec 2015 23:23:55 +0000 (09:23 +1000)]
gnu: Add ruby-unf.

* gnu/packages/ruby.scm (ruby-unf): New variable.

8 years agognu: Add ruby-shoulda.
Ben Woodcroft [Wed, 30 Dec 2015 23:22:43 +0000 (09:22 +1000)]
gnu: Add ruby-shoulda.

* gnu/packages/ruby.scm (ruby-shoulda): New variable.

8 years agognu: Add ruby-shoulda-matchers-2.
Ben Woodcroft [Wed, 30 Dec 2015 23:21:51 +0000 (09:21 +1000)]
gnu: Add ruby-shoulda-matchers-2.

* gnu/packages/ruby.scm (ruby-shoulda-matchers-2): New variable.

8 years agognu: Add ruby-shoulda-matchers.
Ben Woodcroft [Wed, 30 Dec 2015 23:12:59 +0000 (09:12 +1000)]
gnu: Add ruby-shoulda-matchers.

* gnu/packages/ruby.scm (ruby-shoulda-matchers): New variable.

8 years agognu: Add ruby-shoulda-context.
Ben Woodcroft [Wed, 30 Dec 2015 23:11:35 +0000 (09:11 +1000)]
gnu: Add ruby-shoulda-context.

* gnu/packages/ruby.scm (ruby-shoulda-context): New variable.

8 years agognu: Add ruby-sqlite3.
Ben Woodcroft [Wed, 30 Dec 2015 23:08:56 +0000 (09:08 +1000)]
gnu: Add ruby-sqlite3.

* gnu/packages/ruby.scm (ruby-sqlite3): New variable.

8 years agognu: Add ruby-mime-types.
Ben Woodcroft [Wed, 30 Dec 2015 23:05:55 +0000 (09:05 +1000)]
gnu: Add ruby-mime-types.

* gnu/packages/ruby.scm (ruby-mime-types): New variable.

8 years agognu: Add ruby-fivemat.
Ben Woodcroft [Wed, 30 Dec 2015 23:03:19 +0000 (09:03 +1000)]
gnu: Add ruby-fivemat.

* gnu/packages/ruby.scm (ruby-fivemat): New variable.

8 years agognu: Add ruby-mime-types-data.
Ben Woodcroft [Wed, 30 Dec 2015 23:01:01 +0000 (09:01 +1000)]
gnu: Add ruby-mime-types-data.

* gnu/packages/ruby.scm (ruby-mime-types-data): New variable.

8 years agognu: Add ruby-minitest-rg.
Ben Woodcroft [Wed, 30 Dec 2015 22:58:44 +0000 (08:58 +1000)]
gnu: Add ruby-minitest-rg.

* gnu/packages/ruby.scm (ruby-minitest-rg): New variable.

8 years agognu: Add ruby-minitest-bonus-assertions.
Ben Woodcroft [Wed, 30 Dec 2015 22:56:18 +0000 (08:56 +1000)]
gnu: Add ruby-minitest-bonus-assertions.

* gnu/packages/ruby.scm (ruby-minitest-bonus-assertions): New variable.

8 years agognu: Add ruby-minitest-moar.
Ben Woodcroft [Wed, 30 Dec 2015 21:30:37 +0000 (07:30 +1000)]
gnu: Add ruby-minitest-moar.

* gnu/packages/ruby.scm (ruby-minitest-moar): New variable.

8 years agognu: Add ruby-minitest-pretty-diff.
Ben Woodcroft [Wed, 30 Dec 2015 13:36:03 +0000 (23:36 +1000)]
gnu: Add ruby-minitest-pretty-diff.

* gnu/packages/ruby.scm (ruby-minitest-pretty-diff): New variable.

8 years agognu: Add ruby-minitest-focus.
Ben Woodcroft [Wed, 30 Dec 2015 13:22:05 +0000 (23:22 +1000)]
gnu: Add ruby-minitest-focus.

* gnu/packages/ruby.scm (ruby-minitest-focus): New variable.

8 years agognu: Add ruby-turn.
Ben Woodcroft [Wed, 30 Dec 2015 13:19:10 +0000 (23:19 +1000)]
gnu: Add ruby-turn.

* gnu/packages/ruby.scm (ruby-turn): New variable.

8 years agognu: Add aria2.
Efraim Flashner [Wed, 27 Jan 2016 11:59:49 +0000 (13:59 +0200)]
gnu: Add aria2.

* gnu/packages/bittorrent.scm (aria2): New variable.

8 years agognu: c-ares: Move to adns.scm.
Efraim Flashner [Wed, 27 Jan 2016 12:06:23 +0000 (14:06 +0200)]
gnu: c-ares: Move to adns.scm.

* gnu/packages/aria2.scm (c-ares): Move to...
* gnu/packages/adns.scm (c-ares): ... here.
* gnu/packages/aria2.scm: Remove file.
* gnu-system.am (GNU_SYSTEM_MODULES): Remove aria2.scm.

8 years agognu: libressl: Update to 2.2.5.
Andreas Enge [Tue, 26 Jan 2016 20:39:39 +0000 (21:39 +0100)]
gnu: libressl: Update to 2.2.5.

* gnu/packages/tls.scm (libressl): Update to 2.2.5.

8 years agognu: nginx: Update to 1.8.1 [fixes CVE-2016-{0742,0746,0747}].
Leo Famulari [Tue, 26 Jan 2016 20:27:58 +0000 (15:27 -0500)]
gnu: nginx: Update to 1.8.1 [fixes CVE-2016-{0742,0746,0747}].

* gnu/packages/web.scm (nginx): Update to 1.8.1.

8 years agodoc: Show how to boot result of 'vm-image'.
Leo Famulari [Sun, 24 Jan 2016 21:04:35 +0000 (16:04 -0500)]
doc: Show how to boot result of 'vm-image'.

* doc/guix.texi (Running GuixSD in a VM): New node.
(Invoking guix system): Add reference to 'Running GuixSD in a VM'.

8 years agognu: alsa-modular-synth: Update to 2.1.2.
Ricardo Wurmus [Mon, 25 Jan 2016 16:07:39 +0000 (17:07 +0100)]
gnu: alsa-modular-synth: Update to 2.1.2.

* gnu/packages/audio.scm (alsa-modular-synth): Update to 2.1.2.

8 years agognu: hop: Add input avahi.
Andreas Enge [Tue, 26 Jan 2016 14:10:23 +0000 (15:10 +0100)]
gnu: hop: Add input avahi.

gnu/packages/scheme.scm (hop)[inputs]: Add avahi.

8 years agognu: Add ruby-ttfunk.
Ben Woodcroft [Tue, 29 Dec 2015 05:13:13 +0000 (15:13 +1000)]
gnu: Add ruby-ttfunk.

* gnu/packages/ruby.scm (ruby-ttfunk): New variable.

8 years agognu: Add ruby-ascii85.
Ben Woodcroft [Tue, 29 Dec 2015 05:05:18 +0000 (15:05 +1000)]
gnu: Add ruby-ascii85.

* gnu/packages/ruby.scm (ruby-ascii85): New variable.

8 years agognu: Add ruby-afm.
Ben Woodcroft [Tue, 29 Dec 2015 05:00:15 +0000 (15:00 +1000)]
gnu: Add ruby-afm.

* gnu/packages/ruby.scm (ruby-afm): New variable.

8 years agognu: Add ruby-rc4.
Ben Woodcroft [Tue, 29 Dec 2015 04:52:04 +0000 (14:52 +1000)]
gnu: Add ruby-rc4.

* gnu/packages/ruby.scm (ruby-rc4): New variable.

8 years agognu: Add ruby-hashery.
Ben Woodcroft [Tue, 29 Dec 2015 04:51:34 +0000 (14:51 +1000)]
gnu: Add ruby-hashery.

* gnu/packages/ruby.scm (ruby-hashery): New variable.

8 years agognu: Add ruby-rubytest-cli.
Ben Woodcroft [Tue, 29 Dec 2015 04:45:17 +0000 (14:45 +1000)]
gnu: Add ruby-rubytest-cli.

* gnu/packages/ruby.scm (ruby-rubytest-cli): New variable.

8 years agognu: Add ruby-lemon.
Ben Woodcroft [Tue, 29 Dec 2015 04:42:53 +0000 (14:42 +1000)]
gnu: Add ruby-lemon.

* gnu/packages/ruby.scm (ruby-lemon): New variable.

8 years agognu: Add ruby-ae.
Ben Woodcroft [Tue, 29 Dec 2015 04:37:45 +0000 (14:37 +1000)]
gnu: Add ruby-ae.

* gnu/packages/ruby.scm (ruby-ae): New variable.

8 years agognu: Add ruby-qed.
Ben Woodcroft [Tue, 29 Dec 2015 04:36:20 +0000 (14:36 +1000)]
gnu: Add ruby-qed.

* gnu/packages/ruby.scm (ruby-qed): New variable.

8 years agognu: Add ruby-brass.
Ben Woodcroft [Tue, 29 Dec 2015 04:16:42 +0000 (14:16 +1000)]
gnu: Add ruby-brass.

* gnu/packages/ruby.scm (ruby-brass): New variable.

8 years agognu: Add ruby-rubytest.
Ben Woodcroft [Tue, 29 Dec 2015 04:13:42 +0000 (14:13 +1000)]
gnu: Add ruby-rubytest.

* gnu/packages/ruby.scm (ruby-rubytest): New variable.

8 years agognu: sra-tools: Update to 2.5.7.
Ben Woodcroft [Tue, 26 Jan 2016 00:48:21 +0000 (10:48 +1000)]
gnu: sra-tools: Update to 2.5.7.

* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.

8 years agognu: ncbi-vdb: Update to 2.5.7.
Ben Woodcroft [Tue, 26 Jan 2016 00:45:10 +0000 (10:45 +1000)]
gnu: ncbi-vdb: Update to 2.5.7.

gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.

8 years agognu: ngs-sdk: Update to 1.2.3.
Ben Woodcroft [Tue, 26 Jan 2016 00:40:26 +0000 (10:40 +1000)]
gnu: ngs-sdk: Update to 1.2.3.

gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.

8 years agognu: webkitgtk-2.4, webkitgtk/gtk+-2, qt: Disable parallel builds.
Andreas Enge [Mon, 25 Jan 2016 22:33:54 +0000 (23:33 +0100)]
gnu: webkitgtk-2.4, webkitgtk/gtk+-2, qt: Disable parallel builds.

* gnu/packages/webkit.scm (webkitgtk-2.4, webkitgtk/gtk+-2):
  Disable parallel builds as suggested in
  https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00837.html .
* gnu/packages/qt.scm (qt): Likewise.

8 years agognu: aspell-dict-en: Update to 2016.01.19-0.
Alex Kost [Sun, 24 Jan 2016 08:14:59 +0000 (11:14 +0300)]
gnu: aspell-dict-en: Update to 2016.01.19-0.

* gnu/packages/aspell.scm (aspell-dict-en): Update to 2016.01.19-0.

8 years agoemacs: Add interface for licenses.
Alex Kost [Thu, 21 Jan 2016 19:07:10 +0000 (22:07 +0300)]
emacs: Add interface for licenses.

* emacs/guix-main.scm (%license-param-alist): New variable.
  (license->sexp, find-licenses, license-entries): New procedures.
* emacs/guix-license.el (guix-license-get-entries)
  (guix-license-get-display, guix-license-insert-packages-button)
  (guix-license-insert-comment, guix-license-list-describe)
  (guix-license-list-show-packages): New procedures.
  (guix-licenses): New command.
* doc/emacs.texi (Emacs Licenses): New node.
  (Emacs Interface): Add it.
* doc/guix.texi (Top): Add it.
* NEWS: Mention new interface.

8 years agoemacs: list: Support displaying URL links.
Alex Kost [Thu, 21 Jan 2016 08:00:59 +0000 (11:00 +0300)]
emacs: list: Support displaying URL links.

* emacs/guix-list.el (guix-list-url): New face.
  (guix-list-get-url): New procedure.

8 years agoemacs: Add 'guix-packages-by-license' command.
Alex Kost [Wed, 20 Jan 2016 15:53:19 +0000 (18:53 +0300)]
emacs: Add 'guix-packages-by-license' command.

* emacs/guix-main.scm (packages-by-license): New procedure.
(%patterns-makers): Add 'license' search type.
* emacs/guix-messages.el (guix-message-packages-by-license): New procedure.
(guix-messages): Use it.
* emacs/guix-ui-package.el (guix-packages-by-license): New command.
* doc/emacs.texi (Emacs Commands): Document it.

8 years agoemacs: Buttonize licenses in "Package Info".
Alex Kost [Tue, 19 Jan 2016 19:16:20 +0000 (22:16 +0300)]
emacs: Buttonize licenses in "Package Info".

* emacs/guix-ui-package.el (guix-package-license): New button type.
  (guix-package-info-format, guix-output-info-format): Use it.
* doc/emacs.texi (Emacs Info buffer): Mention it.

8 years agoemacs: Add 'guix-browse-license-url' command.
Alex Kost [Tue, 19 Jan 2016 17:27:58 +0000 (20:27 +0300)]
emacs: Add 'guix-browse-license-url' command.

* emacs/guix-main.scm (%licenses): New variable.
(licenses, license-names, lookup-license, lookup-license-uri): New
procedures.
* emacs/guix-read.el (guix-license-names, guix-read-license-name): New
procedures.
* emacs/guix-license.el: New file.
(guix-lookup-license-url): New procedure.
(guix-browse-license-url): New command.
* emacs.am (ELFILES): Add new file.

8 years agoemacs: Rename 'file-path' to 'file-name'.
Alex Kost [Thu, 21 Jan 2016 07:59:50 +0000 (10:59 +0300)]
emacs: Rename 'file-path' to 'file-name'.

* emacs/guix-info.el (guix-info-file-path): Rename to...
  (guix-info-file-name): ... this.
* emacs/guix-list.el (guix-list-file-path): Rename to...
  (guix-list-file-name): ... this.
  (guix-list-get-file-path): Rename to...
  (guix-list-get-file-name): ... this.
* emacs/guix-ui-generation.el (guix-generation-list-format): Adjust
  accordingly.
* emacs/guix-ui-system-generation.el (guix-system-generation-list-format):
  Likewise.
* NEWS: Mention faces renaming.

8 years agognu: Add python-efl.
Efraim Flashner [Sun, 15 Nov 2015 11:54:22 +0000 (13:54 +0200)]
gnu: Add python-efl.

* gnu/packages/enlightenment.scm (python-efl, python2-efl): New variables.

8 years agognu: cmocka: New variable.
Efraim Flashner [Mon, 21 Dec 2015 09:11:01 +0000 (11:11 +0200)]
gnu: cmocka: New variable.

* gnu/packages/check.scm (cmocka): New variable.

8 years agognu: Add pixz.
Ben Woodcroft [Sun, 24 Jan 2016 22:31:14 +0000 (08:31 +1000)]
gnu: Add pixz.

* gnu/packages/compression.scm (pixz): New variable.

8 years agoMerge branch 'master' into core-updates
Mark H Weaver [Mon, 25 Jan 2016 02:04:54 +0000 (21:04 -0500)]
Merge branch 'master' into core-updates

8 years agodoc: Add policy about version numbers for VCS snapshots.
Ludovic Courtès [Sun, 24 Jan 2016 20:42:32 +0000 (21:42 +0100)]
doc: Add policy about version numbers for VCS snapshots.

* doc/guix.texi (Version Numbers): Add paragraphs about VCS snapshot
version numbers.

8 years agodoc: Remove unneeded backslashes.
Ludovic Courtès [Sun, 24 Jan 2016 20:38:09 +0000 (21:38 +0100)]
doc: Remove unneeded backslashes.

* doc/guix.texi (Networking Services): Remove unneeded backslashes.

8 years agognu: grue-hunter: Use 'https' URL.
Ludovic Courtès [Sat, 23 Jan 2016 21:52:49 +0000 (22:52 +0100)]
gnu: grue-hunter: Use 'https' URL.

* gnu/packages/grue-hunter.scm (grue-hunter): Use 'https' URL.

8 years agodoc: 'base-initrd' has #:virtio? default to #t.
Ludovic Courtès [Fri, 22 Jan 2016 08:23:39 +0000 (09:23 +0100)]
doc: 'base-initrd' has #:virtio? default to #t.

This is a followup to e26d507.

* doc/guix.texi (Initial RAM Disk): #:virtio? defaults to #t.

8 years agognu: Add sortmerna.
Ben Woodcroft [Sat, 16 Jan 2016 03:33:08 +0000 (13:33 +1000)]
gnu: Add sortmerna.

* gnu/packages/bioinformatics.scm (sortmerna): New variable.

8 years agodoc: Fix typo in section on offloading.
Andreas Enge [Sun, 24 Jan 2016 22:25:38 +0000 (23:25 +0100)]
doc: Fix typo in section on offloading.

* doc/guix.texi (Daemon Offload Setup): Fix quoting typo in command.

8 years agognu: calibre: Update to 2.49.0.
Andreas Enge [Sun, 24 Jan 2016 19:12:05 +0000 (20:12 +0100)]
gnu: calibre: Update to 2.49.0.

* gnu/packages/ebook.scm (calibre): Update to 2.49.0.

8 years agognu: cross-gcc-arguments: Enable C++, disable building of libstdc++-v3.
Ricardo Wurmus [Mon, 11 Jan 2016 18:43:25 +0000 (19:43 +0100)]
gnu: cross-gcc-arguments: Enable C++, disable building of libstdc++-v3.

* gnu/packages/cross-base.scm (cross-gcc-arguments)[arguments]: Disable
  building libstdc++-v3 and enable building C++ compiler.

8 years agognu: Add Qtractor.
Ricardo Wurmus [Sun, 17 Jan 2016 16:10:31 +0000 (17:10 +0100)]
gnu: Add Qtractor.

* gnu/packages/music.scm (qtractor): New variable.

8 years agognu: yoshimi: Update to 1.3.8.2.
Ricardo Wurmus [Sun, 24 Jan 2016 13:17:49 +0000 (14:17 +0100)]
gnu: yoshimi: Update to 1.3.8.2.

* gnu/packages/music.scm (yoshimi): Update to 1.3.8.2.

8 years agognu: privoxy: Update to 3.0.24.
Efraim Flashner [Sun, 24 Jan 2016 07:20:55 +0000 (09:20 +0200)]
gnu: privoxy: Update to 3.0.24.

* gnu/packages/tor.scm (privoxy): Update to 3.0.24.

8 years agognu: tor: Update to 0.2.7.6.
Efraim Flashner [Sun, 24 Jan 2016 05:21:33 +0000 (07:21 +0200)]
gnu: tor: Update to 0.2.7.6.

* gnu/packages/tor.scm (tor): Update to 0.2.7.6.

8 years agognu: myrepos: Update to 1.20160123.
Efraim Flashner [Sun, 24 Jan 2016 05:04:05 +0000 (07:04 +0200)]
gnu: myrepos: Update to 1.20160123.

* gnu/packages/version-control.scm (myrepos): Update to 1.20160123.

8 years agognu: nano: Update to 2.5.1.
Efraim Flashner [Sun, 24 Jan 2016 04:46:01 +0000 (06:46 +0200)]
gnu: nano: Update to 2.5.1.

* gnu/packages/nano.scm (nano): Update to 2.5.1.

8 years agobuild: container: Make 'unprivileged-user-namespace-supported?' more robust.
Mark H Weaver [Sat, 23 Jan 2016 23:40:33 +0000 (18:40 -0500)]
build: container: Make 'unprivileged-user-namespace-supported?' more robust.

* gnu/build/linux-container.scm (unprivileged-user-namespace-supported?): Only
  read and check the first character, to cope with a possible newline in the
  (pseudo-)file.

8 years agognu: letsencrypt and acme: Update to 0.2.0.
Leo Famulari [Sat, 23 Jan 2016 22:36:29 +0000 (17:36 -0500)]
gnu: letsencrypt and acme: Update to 0.2.0.

These packages should be updated together.

* gnu/packages/tls.scm (letsencrypt): Update to 0.2.0.
(acme): Update to 0.2.0.

8 years agognu: claws-mail: Update to 3.13.2.
Efraim Flashner [Sat, 23 Jan 2016 18:13:31 +0000 (20:13 +0200)]
gnu: claws-mail: Update to 3.13.2.

* gnu/packages/mail.scm (claws-mail): Update to 3.13.2.

8 years agognu: Add cufflinks.
Ricardo Wurmus [Wed, 16 Sep 2015 15:42:41 +0000 (17:42 +0200)]
gnu: Add cufflinks.

* gnu/packages/bioinformatics.scm (cufflinks): New variable.

8 years agognu: Add TopHat.
Ricardo Wurmus [Tue, 19 Jan 2016 13:29:19 +0000 (14:29 +0100)]
gnu: Add TopHat.

* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.

8 years agognu: star: Update to 2.5.1b.
Ricardo Wurmus [Tue, 19 Jan 2016 15:26:47 +0000 (16:26 +0100)]
gnu: star: Update to 2.5.1b.

* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".

8 years agognu: star: Use "modify-phases" syntax.
Ricardo Wurmus [Tue, 19 Jan 2016 15:04:01 +0000 (16:04 +0100)]
gnu: star: Use "modify-phases" syntax.

* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
  syntax.

8 years agognu: fuse: Update to 2.9.5 [fixes CVE-2016-1233].
Efraim Flashner [Fri, 22 Jan 2016 06:52:21 +0000 (08:52 +0200)]
gnu: fuse: Update to 2.9.5 [fixes CVE-2016-1233].

* gnu/packages/linux.scm (fuse): Update to 2.9.5.

8 years agognu: mozjs: Make milestone.pl compatible with Perl 5.22+.
宋文武 [Fri, 22 Jan 2016 06:33:07 +0000 (14:33 +0800)]
gnu: mozjs: Make milestone.pl compatible with Perl 5.22+.

* gnu/packages/gnuzilla.scm (mozjs, mozjs-24)[source]: Add snippet.

8 years agognu: american-fuzzy-lop: Update to 1.96b.
Eric Bavier [Fri, 22 Jan 2016 05:52:59 +0000 (23:52 -0600)]
gnu: american-fuzzy-lop: Update to 1.96b.

* gnu/packages/debug.scm (american-fuzzy-lop): Update to 1.96b.
  [arguments]: Create symbolic link to custom qemu, rather than copying.

8 years agognu: american-fuzzy-lop: Fix qemu configure flags.
Eric Bavier [Fri, 22 Jan 2016 05:19:32 +0000 (23:19 -0600)]
gnu: american-fuzzy-lop: Fix qemu configure flags.

Fixes regression introduced in 06da1a6.

* gnu/packages/debug.scm (american-fuzzy-lop)[qemu]: Override inherited
  #:configure-flags.

8 years agognu: texi2html: Disable tests.
Eric Bavier [Fri, 22 Jan 2016 04:09:42 +0000 (22:09 -0600)]
gnu: texi2html: Disable tests.

* gnu/packages/texinfo.scm (texi2html): New 'arguments' field.

8 years agognu: Add iftop.
Leo Famulari [Fri, 22 Jan 2016 01:21:19 +0000 (20:21 -0500)]
gnu: Add iftop.

* gnu/packages/admin.scm (iftop): New variable.

8 years agoRevert "gnu: Add iftop."
Leo Famulari [Fri, 22 Jan 2016 01:11:21 +0000 (20:11 -0500)]
Revert "gnu: Add iftop."

This reverts commit 45da8c6dd10c93280277d17463d09fce6a25afe9.

8 years agognu: Add iftop.
Leo Famulari [Thu, 21 Jan 2016 07:12:40 +0000 (02:12 -0500)]
gnu: Add iftop.

* gnu/packages/admin.scm (iftop): New variable.

8 years agotests: Prevent 'http_proxy' from breaking Web server tests.
Ludovic Courtès [Thu, 21 Jan 2016 22:45:52 +0000 (23:45 +0100)]
tests: Prevent 'http_proxy' from breaking Web server tests.

* tests/lint.scm: Add call to 'unsetenv' to remove 'http_proxy'.
* tests/publish.scm: Likewise.

8 years agodoc: Fix typo in "Locales".
Ludovic Courtès [Thu, 21 Jan 2016 22:08:43 +0000 (23:08 +0100)]
doc: Fix typo in "Locales".

* doc/guix.texi (Locales): Add missing 's'.

8 years agosystem: grub: Search root device by label or UUID if possible.
Ludovic Courtès [Thu, 21 Jan 2016 21:45:54 +0000 (22:45 +0100)]
system: grub: Search root device by label or UUID if possible.

Fixes <http://bugs.gnu.org/22281>.
Reported by Christopher Allan Webber <cwebber@dustycloud.org>.

* gnu/system/grub.scm (eye-candy): Add 'root-fs' parameter.  Replace
'search --file' command in the output with whatever 'grub-root-search'
returns.
(grub-root-search): New procedure.
(grub-configuration-file): Add 'store-fs' parameter.  Use
'grub-root-search' instead of hard-coded 'search --file' commands.
* gnu/system.scm (store-file-system,
operating-system-store-file-system): New procedures.
(operating-system-grub.cfg): Use it, and adjust call to
'grub-configuration-file'.
* tests/system.scm: New file.
* Makefile.am (SCM_TESTS): Add it.

8 years agognu: ffmpeg: Update to 2.8.5.
Mark H Weaver [Fri, 15 Jan 2016 23:13:13 +0000 (18:13 -0500)]
gnu: ffmpeg: Update to 2.8.5.

* gnu/packages/video.scm (ffmpeg): Update to 2.8.5.

8 years agognu: gajim: Update to 0.16.5 [fixes CVE-2015-8688].
Mark H Weaver [Thu, 21 Jan 2016 15:23:19 +0000 (10:23 -0500)]
gnu: gajim: Update to 0.16.5 [fixes CVE-2015-8688].

* gnu/packages/messaging.scm (gajim): Update to 0.16.5.
  [arguments]: Disable tests.

8 years agognu: bind-utils: Build and install "nsupdate".
Ricardo Wurmus [Thu, 21 Jan 2016 10:42:17 +0000 (11:42 +0100)]
gnu: bind-utils: Build and install "nsupdate".

* gnu/packages/dns.scm (bind-utils)[arguments]: Build and install
  "nsupdate" executable.