b93881b9c5
gnu: r-scales: Update to 0.5.0.
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* gnu/packages/statistics.scm (r-scales): Update to 0.5.0.
[propagated-inputs]: Add r-r6 and r-viridislite.
2017-09-01 15:11:48 +02:00
2d99a31607
gnu: r-mgcv: Update to 1.8-19.
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* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-19.
2017-09-01 15:11:48 +02:00
fefe9f4753
gnu: r-matrix: Update to 1.2-11.
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* gnu/packages/statistics.scm (r-matrix): Update to 1.2-11.
2017-09-01 15:11:48 +02:00
3c2a5bf299
gnu: r-servr: Update to 0.7.
...
* gnu/packages/web.scm (r-servr): Update to 0.7.
2017-09-01 15:11:47 +02:00
1cf306639c
gnu: php: Update to 7.1.9.
...
* gnu/packages/php.scm (php): Update to 7.1.9.
2017-09-01 14:17:46 +02:00
dcf7a8a660
gnu: java-slf4j-api: Fix tests.
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* gnu/packages/java.scm (java-slf4j-api)[arguments]: Enable tests
Adjust the jar content to prevent a test failure.
2017-09-01 14:17:24 +02:00
5fe2a139df
gnu: djvulibre: Remove timestamps from .svgz files.
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* gnu/packages/djvu.scm (djvulibre)[arguments]: New field.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01 11:05:32 +02:00
833ade67f1
gnu: Add emacs-tuareg.
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* gnu/packages/ocaml.scm (emacs-tuareg): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01 10:39:55 +02:00
4735393a76
gnu: emacs-ebuild-mode: Update to 1.37.
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* gnu/packages/emacs.scm (emacs-ebuild-mode): Update to 1.37.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01 10:34:50 +02:00
ab966b8f61
gnu: Add emacs-2048-game.
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* gnu/packages/emacs.scm (emacs-2048-game): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01 10:34:36 +02:00
5c5ae46c00
packages: 'fold-packages' takes an optional 'modules' parameter.
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Suggested by Christopher Baines <mail@cbaines.net>.
* gnu/packages.scm (fold-packages): Add optional 'modules' parameter and
honor it.
2017-09-01 10:29:39 +02:00
fe55199542
scripts: Remove 'max-silent-time' from the default options.
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Fixes <http://bugs.gnu.org/27157 >.
Having a finite default `max-silent-time' value for scripts such as 'guix
environment' could lead to timeouts when building subtitutes; this was
undesirable.
This change also fixes client behavior to match the documentation, which
is that by default the daemon's settings are honored.
* guix/scripts/archive.scm (%default-options): Remove max-silent-time entry.
* guix/scripts/copy.scm (%default-options): Likewise.
* guix/scripts/environment.scm (%default-options): Likewise.
* guix/scripts/pack.scm (%default-options): Likewise.
* guix/scripts/package.scm (%default-options): Likewise.
* guix/scripts/pull.scm (%default-options): Likewise.
* guix/scripts/system.scm (%default-options): Likewise.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01 10:29:39 +02:00
75690c9f6b
gnu: r-rcas: Correct license.
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* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
2017-09-01 10:26:31 +02:00
eda8f36cd6
gnu: r-rcas: Update to 1.3.3.
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* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
2017-09-01 10:26:30 +02:00
7d099cbe13
gnu: mysql: Enable tests on aarch64.
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* gnu/packages/databases.scm (mysql)[arguments]: Remove logic disabling
the tests on aarch64-linux.
2017-09-01 10:50:39 +03:00
f4bf420c84
gnu: vsearch: Update to 2.4.4.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
2017-09-01 14:45:57 +08:00
25bd1fc1c1
gnu: metabat: Update to 2.12.1.
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* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1.
[source]: Remove it. Use url-fetch.
2017-09-01 14:45:57 +08:00
43d01672a1
gnu: netcdf: Fix reproducibility issue; remove unneeded references.
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* gnu/packages/maths.scm (netcdf) [arguments]: Add phase to fix the embedded
'Configured On' date; truncate reference to compiler store item.
2017-09-01 08:34:32 +02:00
e464b4550e
gnu: hdf4: Avoid unneeded store references to compilers.
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* gnu/packages/maths.scm (hdf4) [arguments]: Add phase 'patch-settings to
truncate hashes of compiler store items.
2017-09-01 08:34:32 +02:00
fd0378a147
gnu: hdf5: Avoid unneeded store references to compilers.
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* gnu/packages/maths.scm (hdf5) [arguments]: Add phase to patch
"libhdf5.settings", removing references to the C/C++/Fortran compilers.
2017-09-01 08:34:31 +02:00
e3a1a1deda
gnu: hdf5: Add output for fortran interface.
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* gnu/packages/maths.scm (hdf5) [native-inputs]: Add gfortran.
[outputs]: Add "fortran".
[arguments]: Enable Fortran compilation; add "/lib" directory of the fortran
output to the runpath of the Fortran libs; add a 'split phase to move
all Fortran-related files to the the Fortran output store location.
2017-09-01 08:34:24 +02:00
a0596a2f27
gnu: python2-larch: Enable tests.
...
* gnu/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python2-larch)[source]: Use it.
[arguments]: Move 'check' phase to before 'build' phase.
2017-09-01 11:14:16 +05:30
f618086220
gnu: python2-ttystatus: Enable tests.
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* gnu/packages/python.scm (python2-ttystatus)[arguments]: Replace 'check'
phase with custom function.
2017-09-01 11:14:16 +05:30
689042e526
gnu: python2-cliapp: Enable tests.
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* gnu/packages/python.scm (python2-cliapp)[arguments]: Replace 'check' phase
with custom function.
2017-09-01 11:14:16 +05:30
fe36ecf5c8
gnu: linux-libre: Update to 4.12.10.
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* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.10.
(%linux-libre-hash): Update hash.
2017-09-01 00:31:55 -04:00
2131663a76
gnu: linux-libre@4.9: Update to 4.9.46.
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* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.46.
2017-09-01 00:31:16 -04:00
d215e41a26
gnu: linux-libre@4.4: Update to 4.4.85.
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* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.85.
2017-09-01 00:30:17 -04:00
1b3f5fc387
gnu: libxml2/fixed: Use patches from inherited package.
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This is a followup to 76fed2b3c4
2017-08-31 23:43:55 +02:00
0ff44ba464
gnu: graphicsmagick: Fix CVE-2017-{13775,13776,13777}.
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* gnu/packages/imagemagick.scm (graphicsmagick)[source]: Add patches.
* gnu/packages/patches/graphicsmagick-CVE-2017-13775.patch,
gnu/packages/patches/graphicsmagick-CVE-2017-13776+CVE-2017-13777.patch:
New files.
* gnu/local.mk (dist_patch_DATA): Register them.
2017-09-01 00:02:27 +03:00
d36212e94d
gnu: efl: Update to 1.20.3.
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* gnu/packages/enlightenment.scm (efl): Update to 1.20.3.
2017-09-01 00:02:25 +03:00
a9d5e4bed1
gnu: Fix current-guix.
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Without this change, I get errors like:
ERROR: In procedure string-drop:
ERROR: Value out of range 0 to 35: 51
* gnu/packages/package-management.scm (current-guix): Pass exactly the same
path to git-predicate and local-file, to ensure that the select? function is
compatible.
2017-08-31 21:48:05 +01:00
fa9f5222a9
gnu: sddm: Update to 0.15.0.
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* gnu/packages/display-managers.scm (sddm): Update to 0.15.0.
[source]: Update tarball name.
[inputs]: Add ELOGIND.
[arguments]: Adjust #:configure-flags for elogind support. Add phase to
patch hard-coded loginctl reference.
2017-08-31 22:35:54 +02:00
76fed2b3c4
gnu: libxml2: Fix CVE-2017-{0663,7375,7376,9047,9048,9049,9050}.
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* gnu/packages/patches/libxml2-CVE-2017-0663.patch,
gnu/packages/patches/libxml2-CVE-2017-7375.patch,
gnu/packages/patches/libxml2-CVE-2017-7376.patch,
gnu/packages/patches/libxml2-CVE-2017-9047+CVE-2017-9048.patch,
gnu/packages/patches/libxml2-CVE-2017-9049+CVE-2017-9050.patch: New files.
* gnu/local.mk (dist_patch_DATA): Add them.
* gnu/packages/xml.scm (libxml2)[replacement]: New field.
(libxml2/fixed): New variable.
Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-08-31 21:45:36 +02:00
ff54f194f3
gnu: postgresql: Update to 9.6.5.
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* gnu/packages/databases.scm (postgresql): Update to 9.6.5.
Release-notes: https://www.postgresql.org/docs/9.6/static/release-9-6-5.html
2017-08-31 21:34:20 +02:00
59ff96aafd
gnu: Remove python2-rpy2.
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Python 2 is no longer supported.
* gnu/packages/python.scm (python2-rpy2): Remove variable.
2017-08-31 18:24:52 +02:00
deee5ddaf4
gnu: python-rpy2: Update to 2.9.0.
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* gnu/packages/python.scm (python-rpy2): Update to 2.9.0.
[arguments]: Run tests before install phase; add build phase "fix-tests".
[propagated-inputs]: Add python-jinja2 and python-pytz.
[inputs]: Add r-ggplot2, r-rsqlite, r-dplyr, r-dbplyr, and python-numpy.
2017-08-31 18:24:51 +02:00
c92483bd63
gnu: python-rpy2: Update license.
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* gnu/packages/python.scm (python-rpy2)[license]: Correct GPLv3+ to GPLv2+;
list additional licenses.
2017-08-31 18:24:51 +02:00
caa4e796e4
gnu: Add r-dbplyr.
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* gnu/packages/statistics.scm (r-dbplyr): New variable.
2017-08-31 18:24:51 +02:00
4eebfefe7e
gnu: retux: Update to 1.3.5.
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* gnu/packages/games.scm (retux): Update to 1.3.5.
2017-08-31 11:38:00 -04:00
95c1324adc
gnu: python-tmx: Update to 1.10.
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* gnu/packages/game-development.scm (python-tmx): Update to 1.10.
2017-08-31 11:38:00 -04:00
b1d1a10c7c
gnu: python-sge-pygame: Update to 1.5.1.
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* gnu/packages/game-development.scm (python-sge-pygame,
python2-sge-pygame): Update to 1.5.1.
2017-08-31 11:37:59 -04:00
7e31427ff0
gnu: python-pyjwt: Update to 1.5.2 [fixes CVE-2017-11424].
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* gnu/packages/python.scm (python-pyjwt): Update to 1.5.2.
[source]: Add snippet to remove pre-compiled files.
[native-inputs]: Change PYTHON-PYTEST to PYTHON-PYTEST-3.0.
2017-08-31 15:45:43 +02:00
5883bb76f8
gnu: Add emacs-idris-mode.
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* gnu/packages/emacs.scm (emacs-idris-mode): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-31 14:58:34 +02:00
b9dcaced16
gnu: Add emacs-prop-menu.
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* gnu/packages/emacs.scm (emacs-prop-menu): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-31 14:57:53 +02:00
b6dc69af1d
services: mpd: Remove the mpd-file field.
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Since MPD switches user, the pid-file must be in a writable dir. This
is now always /var/run/mpd/(user)/pid.
* gnu/services/audio.scm (mpd-service-type): Add a activation-service
extension.
(<mpd-configuration>)[pid-file]: Remove.
(mpd-service): Rename to...
(mpd-shepherd-service): ... this.
(mpd-file-name, mpd-service-activation): New procedure.
* doc/guix.texi (Audio Services): Document the changes.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-31 14:43:26 +02:00
79ada57ba9
gnu: knot: Update to 2.5.4.
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* gnu/packages/dns.scm (knot): Update to 2.5.4.
2017-08-31 13:53:04 +02:00
1c25a52c4a
gnu: Add pt-scotch32.
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* gnu/packages/maths.scm (pt-scotch32): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-31 12:34:50 +02:00
1c39f3b877
gnu: Add "scotch32".
...
* gnu/packages/maths.scm (scotch32): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-08-31 12:34:50 +02:00
0691851a64
gnu: bioinformatics: Work around more "dotless @INC" build failures.
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* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
2017-08-31 12:37:05 +08:00
c959e5a1dc
gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}.
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* gnu/packages/patches/ruby-2.2.7-rubygems-2613-ruby22.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/ruby.scm (ruby-2.2.7)[source]: Use it.
2017-08-31 10:43:19 +08:00
Ricardo Wurmus