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11689 Commits

Author SHA1 Message Date
Pjotr Prins 552f5c009e gnu: Add slurm. 
* gnu/packages/parallel.scm (slurm): New variable.
* gnu/packages/patches/slurm-configure-remove-nonfree-contribs.patch:
  New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/parallel.scm: Introduce license name space.

Co-authored-by: Andreas Enge <andreas@enge.fr>
 2016-02-15 22:47:47 +01:00
Ben Woodcroft e70f7a2306 gnu: prodigal: Update to 2.6.3. 
* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
 2016-02-16 07:18:59 +10:00
Efraim Flashner 7fe8ad7616 gnu: polkit-qt: Build with qt-5. 
*gnu/packages/polkit.scm (polkit-qt)[propagated-inputs]: Use qt.
 2016-02-15 20:22:28 +02:00
Efraim Flashner d1cba090a8 gnu: bazaar: Update to 2.7.0. 
* gnu/packages/version-control.scm (bazaar): Update to 2.7.0.
 2016-02-15 19:53:27 +02:00
Ricardo Wurmus 258c0a365e gnu: r-annotationdbi: Update to 1.32.3. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
 2016-02-15 16:11:22 +01:00
Ricardo Wurmus 3d7a157c62 gnu: Add audit. 
* gnu/packages/admin.scm (audit): New variable.
 2016-02-15 16:06:09 +01:00
Efraim Flashner fdc1b2fd65 gnu: vera: Update to 1.23. 
* gnu/packages/dictionaries.scm (vera): Update to 1.23.
 2016-02-15 15:49:13 +02:00
Efraim Flashner e0ef3708f7 gnu: nano: Update to 2.5.2. 
* gnu/packages/nano.scm (nano): Update to 2.5.2.
 2016-02-15 15:49:13 +02:00
Efraim Flashner 4bc0c634b3 gnu: bitcoin-core: Update to 0.11.2. 
* gnu/packages/finance.scm (bitcoin-core): Update to 0.11.2.
[native-inputs]: Use python-2 instead of python-wrapper.
 2016-02-15 15:46:00 +02:00
Efraim Flashner 87062f75e4 gnu: owncloud-client: Update to 2.1.1. 
* gnu/packages/owncloud.scm (owncloud-client): Update to 2.1.1.
 2016-02-15 15:46:00 +02:00
Ben Woodcroft cf6edaba74 gnu: vsearch: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0.
[origin]: Adapt to changes in bundling of cityhash.
 2016-02-15 22:54:25 +10:00
Ben Woodcroft a64a8c465d gnu: cityhash: Install citycrc.h. 
* gnu/packages/textutils.scm (cityhash)[arguments]: Install citycrc.h.
[version]: Use standardised format, increment to 1.1-2.
 2016-02-15 22:54:12 +10:00
Mark H Weaver e86409c566 gnu: graphite2: Update to 1.3.5. Update home-page and source URI. 
* gnu/packages/fontutils.scm (graphite2): Update to 1.3.5.
  [source, home-page]: Update to reflect upstream move to github.
 2016-02-15 02:51:35 -05:00
Mark H Weaver 4373278ea5 gnu: libsndfile: Update to 1.0.26 [with follow-up fix CVE-2015-7805]. 
Note: The previous fix for CVE-2015-7805 was incomplete.

* gnu/packages/patches/libsndfile-CVE-2014-9496.patch,
  gnu/packages/patches/libsndfile-CVE-2015-7805.patch: Delete files.
* gnu-system.am (dist_patch_DATA): Remove them.
* gnu/packages/pulseaudio.scm (libsndfile): Update to 1.0.26.
  [source]: Remove patches.
 2016-02-15 02:51:35 -05:00
Christopher Allan Webber ea79dbb240 gnu: libgcrypt: Update to 1.6.5 [fixes CVE-2015-7511]. 
* gnu/packages/gnupg.scm (libgcrypt): Update to 1.6.5.
 2016-02-15 02:51:35 -05:00
Leo Famulari 68bcac6b62 gnu: btrfs-progs: Fix license. 
Reported by Tobias Geerinckx-Rice <tobias.geerinckx.rice@gmail.com>

* gnu/packages/linux.scm (btrfs-progs)[license]: Add GPL2 to list of licenses.
 2016-02-14 21:04:05 -05:00
Nils Gillmann acb381566c gnu: font-terminus: Update to 4.40 
* gnu/packages/fonts.scm (font-terminus): Update to 4.40.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-14 20:46:49 -05:00
Andreas Enge b6b07d9de3 gnu: python-ly: Update to 0.9.3. 
* gnu/packages/python.scm (python-ly): Update to 0.9.3.
 2016-02-14 21:49:56 +01:00
Mark H Weaver b042bdc8fd gnu: lxqt: Update source URLs to use HTTPS. 
* gnu/packages/lxqt.scm (libqtxdg, liblxqt, lxqt-common)
  (lxqt-session)[source]: Use HTTPS URLs.
 2016-02-14 08:48:13 -05:00
Efraim Flashner 38b209110e gnu: openbox: Update to 3.6.1. 
* gnu/packages/openbox.scm (openbox): Update to 3.6.1.
 2016-02-14 09:51:47 +02:00
Efraim Flashner 8826fb241e gnu: postgresql: Update to 9.3.11. [fixes CVE-2015-{5288,5289},CVE-2016-{0766,0773}] 
* gnu/packages/databases.scm (postgresql): Update to 9.3.11.
 2016-02-14 09:34:27 +02:00
Jochem Raat 3c697ffda3 gnu: Add baobab. 
* gnu/packages/gnome.scm (baobab): New variable.
 2016-02-13 21:09:42 -05:00
Al McElrath aa0edd3f5b gnu: Add pianobar. 
* gnu/packages/music.scm (pianobar): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-13 18:40:04 -05:00
Christopher Allan Webber cb34dc6c3e gnu: Add python-wtforms 
* gnu/packages/python.scm (python-wtforms, python2-wtforms): New variables.
 2016-02-13 15:03:10 -08:00
Andreas Enge f97c91757d doc: Correct typos. 
* doc/guix.texi: Correct typos, grammar and stylistic points.
 2016-02-13 19:58:22 +01:00
Alex Kost 75cd4b053e gnu: iproute: Update to 4.4.0. 
* gnu/packages/linux.scm (iproute): Update to 4.4.0.
 2016-02-13 20:39:34 +03:00
Alex Kost b53e44fb4e gnu: iproute: Use 'modify-phases'. 
* gnu/packages/linux.scm (iproute)[arguments]: Use 'modify-phases'.
 2016-02-13 20:39:34 +03:00
Andreas Enge a42d99f284 gnu: calibre: Update to 2.51.0. 
* gnu/packages/ebook.scm (calibre): Update to 2.51.0.
 2016-02-13 14:34:50 +01:00
Andreas Enge ec4130b7e7 gnu: gnuplot: Update to 5.0.2. 
* gnu/packages/maths.scm (gnuplot): Update to 5.0.2.
 2016-02-13 13:37:49 +01:00
Jan Nieuwenhuizen 8c1088bb0f gnu: lablgtk: Build cmxa libraries. 
* gnu/packages/ocaml.scm (lablgtk)[arguments]: Add the make target "opt"
  to also build *.cmxa files.
 2016-02-13 09:23:20 +01:00
Jan Nieuwenhuizen 6372e336a2 gnu: ocaml: Set search path. 
* gnu/packages/ocaml.scm (ocaml): Register OCAMLPATH as a search path.
 2016-02-13 09:21:58 +01:00
Jan Nieuwenhuizen a747baba00 gnu: Add ocaml-findlib. 
* gnu/packages/ocaml.scm (ocaml-findlib): New variable.
* gnu/packages/patches/ocaml-findlib-make-install.patch: New file.
* gnu-system.am (dist_patch_DATA): Register it.
 2016-02-13 09:15:55 +01:00
Mark H Weaver 3a7261bf96 gnu: gnupg: Add upstream fix for test failures on x86_64. 
Fixes <https://debbugs.gnu.org/22558>.

* gnu/packages/patches/gnupg-simple-query-ignore-status-messages.patch: New
  file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/gnupg.scm (gnupg)[source]: Add patch.
 2016-02-12 21:02:24 -05:00
Jan Nieuwenhuizen 511539ae81 gnu: Add tclxml. 
* gnu/packages/patches/tclxml-3.2-install.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/tcl.scm (tclxml): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-12 19:13:05 -05:00
Leo Famulari 6cefd53d3e gnu: Split acme into python-acme and python2-acme. 
* gnu/packages/tls.scm (acme): Split variable into...
(python-acme, python2-acme): ...both Python variants.
(letsencrypt)[propagated-inputs]: Update user of renamed variable.
 2016-02-12 18:50:32 -05:00
Leo Famulari 8ad4ae204f gnu: python-wheel: Define 'python2-variant'. 
* gnu/packages/python.scm (python-wheel)[properties]: New field.
(python2-wheel): Use 'strip-python2-variant'.
(python2-requests): Take the result of 'package-with-python2' directly.
* gnu/packages/openstack.scm (python2-requests-mock): Likewise.
(python2-oslosphinx): Likewise.
 2016-02-12 18:50:32 -05:00
Leo Famulari a14600ecfa gnu: python-jsonschema: Define 'python2-variant'. 
* gnu/packages/python.scm (python-jsonschema)[properties]: New field.
(python2-jsonschema): Use 'strip-python2-variant'.
* gnu/packages/openstack.scm (python2-tempest-lib): Take the result of
'package-with-python2' directly.
 2016-02-12 18:50:32 -05:00
Leo Famulari 519e2f4fde gnu: python-cryptography: Define 'python2-variant'. 
* gnu/packages/python.scm (python-cryptography)[properties]: New field.
(python2-cryptography): Use 'strip-python2-variant'.
(python2-pyopenssl): Take the result of 'package-with-python2' directly.
 2016-02-12 18:50:32 -05:00
Jan Nieuwenhuizen 50fe318c3c gnu: Add tcllib. 
* gnu/packages/tcl.scm (tcllib): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-12 18:01:05 -05:00
Jan Nieuwenhuizen e4c38581f3 gnu: tcl: Use tcl/tk license. 
* gnu/packages/tcl.scm (tcl)[license]: Use the tcl/tk license variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-12 18:01:05 -05:00
Jan Nieuwenhuizen d29f647077 licenses: Add tcl/tk license. 
* guix/licenses.scm (tcl/tk): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-02-12 17:25:39 -05:00
David Thompson 779aa003fb scripts: environment: Build environments as profiles. 
Fixes <http://bugs.gnu.org/19816>.

* guix/scripts/environment.scm (evaluate-input-search-paths)
(build-inputs): Delete.
(evaluate-profile-search-paths, strip-input-name)
(package-or-package+output?, package-environment-inputs)
(build-environment, inputs->profile-derivations): New procedures.
(create-environment, show-search-paths, launch-environment)
(launch-environment/container): Replace 'inputs' argument
with 'profile' argument.
(package+propagated-inputs): Strip off names off of input tuples.
(options/resolve-packages): Handle input tuples that specify an output
in expressions.
(guix-environment): Convert inputs into a profile to use in the
environment.  Remove non-package inputs such as origins from
environment inputs.
* doc/guix.texi ("invoking guix environment"): Document package+output
tuples for --expression option.
* tests/guix-environment.sh: Update tests.
* tests/guix-environment-container.sh: Likewise.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2016-02-12 22:02:06 +01:00
Ludovic Courtès e5f04c2dde profiles: Add #:system argument to profile-derivation. 
Suggested by David Thompson <davet@gnu.org>.

* guix/profiles.scm (profile-derivation): Add #:system parameter and
honor it.
 2016-02-12 21:54:25 +01:00
Ludovic Courtès 98a7b528d6 store: Add monadic access to '%current-system'. 
* guix/store.scm (current-system, set-current-system): New procedures.
* tests/store.scm ("current-system"): New test.
 2016-02-12 21:54:25 +01:00
Ricardo Wurmus 0d0bcaa08e gnu: macs: Update to 2.1.0.20151222. 
* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
 2016-02-12 18:16:16 +01:00
Ricardo Wurmus 43ec07f17c gnu: macs: Use "pypi-uri". 
* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to
  build source URI.
 2016-02-12 18:16:16 +01:00
Ricardo Wurmus b074e7d486 gnu: python2-fastlmm: Update to 0.2.21. 
* gnu/packages/python.scm (python2-fastlmm): Update to 0.2.21.
 2016-02-12 10:58:46 +01:00
Ricardo Wurmus 3f2e9675fb gnu: python2-pysnptools: Update to 0.3.5. 
* gnu/packages/python.scm (python2-pysnptools): Update to 0.3.5.
 2016-02-12 10:58:46 +01:00
Ricardo Wurmus ef9b4c04a4 gnu: python-numpy-bootstrap: Update to 1.10.4. 
* gnu/packages/python.scm (python-numpy-bootstrap): Update to 1.10.4.
 2016-02-12 10:58:46 +01:00
Ricardo Wurmus 1b96f069e6 gnu: python-pandas: Update to 0.16.2. 
* gnu/packages/python.scm (python-pandas): Update to 0.16.2.
 2016-02-12 10:58:46 +01:00