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23777 Commits

Author SHA1 Message Date
Ricardo Wurmus 347cab66b6
gnu: r-fastcluster: Update to 1.1.24. 
* gnu/packages/statistics.scm (r-fastcluster): Update to 1.1.24.
 2017-09-01 15:11:52 +02:00
Ricardo Wurmus d574d6bcc2
gnu: r-rcpparmadillo: Update to 0.7.960.1.2. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.960.1.2.
 2017-09-01 15:11:52 +02:00
Ricardo Wurmus 2dda8fca6f
gnu: r-plotrix: Update to 3.6-6. 
* gnu/packages/statistics.scm (r-plotrix): Update to 3.6-6.
 2017-09-01 15:11:51 +02:00
Ricardo Wurmus 7d60652ebe
gnu: r-httr: Update to 1.3.1. 
* gnu/packages/statistics.scm (r-httr): Update to 1.3.1.
[propagated-inputs]: Remove r-digest and r-stringr.
 2017-09-01 15:11:51 +02:00
Ricardo Wurmus e3323e0707
gnu: r-commonmark: Update to 1.4. 
* gnu/packages/statistics.scm (r-commonmark): Update to 1.4.
 2017-09-01 15:11:51 +02:00
Ricardo Wurmus 5d84369bda
gnu: r-ade4: Update to 1.7-8. 
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-8.
 2017-09-01 15:11:50 +02:00
Ricardo Wurmus fb10c923b3
gnu: r-tibble: Update to 1.3.4. 
* gnu/packages/statistics.scm (r-tibble): Update to 1.3.4.
 2017-09-01 15:11:50 +02:00
Ricardo Wurmus edd5fd7208
gnu: r-rlang: Update to 0.1.2. 
* gnu/packages/statistics.scm (r-rlang): Update to 0.1.2.
 2017-09-01 15:11:49 +02:00
Ricardo Wurmus 5a00ef0950
gnu: r-knitr: Update to 1.17. 
* gnu/packages/statistics.scm (r-knitr): Update to 1.17.
 2017-09-01 15:11:49 +02:00
Ricardo Wurmus 3949aef601
gnu: r-bh: Update to 1.65.0-1. 
* gnu/packages/statistics.scm (r-bh): Update to 1.65.0-1.
 2017-09-01 15:11:49 +02:00
Ricardo Wurmus b93881b9c5
gnu: r-scales: Update to 0.5.0. 
* 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
Ricardo Wurmus 2d99a31607
gnu: r-mgcv: Update to 1.8-19. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-19.
 2017-09-01 15:11:48 +02:00
Ricardo Wurmus fefe9f4753
gnu: r-matrix: Update to 1.2-11. 
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-11.
 2017-09-01 15:11:48 +02:00
Ricardo Wurmus 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
Julien Lepiller 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
Julien Lepiller dcf7a8a660
gnu: java-slf4j-api: Fix tests. 
* 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
Z. Ren 5fe2a139df
gnu: djvulibre: Remove timestamps from .svgz files. 
* gnu/packages/djvu.scm (djvulibre)[arguments]: New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-09-01 11:05:32 +02:00
Oleg Pykhalov 833ade67f1
gnu: Add emacs-tuareg. 
* gnu/packages/ocaml.scm (emacs-tuareg): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-09-01 10:39:55 +02:00
ng0 4735393a76
gnu: emacs-ebuild-mode: Update to 1.37. 
* 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
ng0 ab966b8f61
gnu: Add emacs-2048-game. 
* 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
Ludovic Courtès 5c5ae46c00
packages: 'fold-packages' takes an optional 'modules' parameter. 
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
Maxim Cournoyer fe55199542
scripts: Remove 'max-silent-time' from the default options. 
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
Ricardo Wurmus 75690c9f6b
gnu: r-rcas: Correct license. 
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
 2017-09-01 10:26:31 +02:00
Ricardo Wurmus eda8f36cd6
gnu: r-rcas: Update to 1.3.3. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
 2017-09-01 10:26:30 +02:00
Efraim Flashner 7d099cbe13
gnu: mysql: Enable tests on aarch64. 
* gnu/packages/databases.scm (mysql)[arguments]: Remove logic disabling
the tests on aarch64-linux.
 2017-09-01 10:50:39 +03:00
Ben Woodcroft f4bf420c84
gnu: vsearch: Update to 2.4.4. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
 2017-09-01 14:45:57 +08:00
Ben Woodcroft 25bd1fc1c1
gnu: metabat: Update to 2.12.1. 
* 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
Thomas Danckaert 43d01672a1
gnu: netcdf: Fix reproducibility issue; remove unneeded references. 
* 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
Thomas Danckaert e464b4550e
gnu: hdf4: Avoid unneeded store references to compilers. 
* 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
Thomas Danckaert fd0378a147
gnu: hdf5: Avoid unneeded store references to compilers. 
* 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
Thomas Danckaert e3a1a1deda
gnu: hdf5: Add output for fortran interface. 
* 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
Arun Isaac 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
Arun Isaac f618086220
gnu: python2-ttystatus: Enable tests. 
* gnu/packages/python.scm (python2-ttystatus)[arguments]: Replace 'check'
phase with custom function.
 2017-09-01 11:14:16 +05:30
Arun Isaac 689042e526
gnu: python2-cliapp: Enable tests. 
* gnu/packages/python.scm (python2-cliapp)[arguments]: Replace 'check' phase
with custom function.
 2017-09-01 11:14:16 +05:30
Mark H Weaver fe36ecf5c8
gnu: linux-libre: Update to 4.12.10. 
* 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
Mark H Weaver 2131663a76
gnu: linux-libre@4.9: Update to 4.9.46. 
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.46.
 2017-09-01 00:31:16 -04:00
Mark H Weaver d215e41a26
gnu: linux-libre@4.4: Update to 4.4.85. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.85.
 2017-09-01 00:30:17 -04:00
Marius Bakke 1b3f5fc387
gnu: libxml2/fixed: Use patches from inherited package. 
This is a followup to 76fed2b3c4.

* gnu/packages/xml.scm (libxml2/fixed)(patches): Inherit patches from LIBXML2.
 2017-08-31 23:43:55 +02:00
Efraim Flashner 0ff44ba464
gnu: graphicsmagick: Fix CVE-2017-{13775,13776,13777}. 
* 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
Efraim Flashner d36212e94d
gnu: efl: Update to 1.20.3. 
* gnu/packages/enlightenment.scm (efl): Update to 1.20.3.
 2017-09-01 00:02:25 +03:00
Christopher Baines a9d5e4bed1
gnu: Fix current-guix. 
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
Marius Bakke fa9f5222a9
gnu: sddm: Update to 0.15.0. 
* 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
Alex Vong 76fed2b3c4
gnu: libxml2: Fix CVE-2017-{0663,7375,7376,9047,9048,9049,9050}. 
* 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
Marius Bakke ff54f194f3
gnu: postgresql: Update to 9.6.5. 
* 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
Ricardo Wurmus 59ff96aafd
gnu: Remove python2-rpy2. 
Python 2 is no longer supported.

* gnu/packages/python.scm (python2-rpy2): Remove variable.
 2017-08-31 18:24:52 +02:00
Ricardo Wurmus deee5ddaf4
gnu: python-rpy2: Update to 2.9.0. 
* 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
Ricardo Wurmus c92483bd63
gnu: python-rpy2: Update license. 
* gnu/packages/python.scm (python-rpy2)[license]: Correct GPLv3+ to GPLv2+;
list additional licenses.
 2017-08-31 18:24:51 +02:00
Ricardo Wurmus caa4e796e4
gnu: Add r-dbplyr. 
* gnu/packages/statistics.scm (r-dbplyr): New variable.
 2017-08-31 18:24:51 +02:00
Kei Kebreau 4eebfefe7e
gnu: retux: Update to 1.3.5. 
* gnu/packages/games.scm (retux): Update to 1.3.5.
 2017-08-31 11:38:00 -04:00
Kei Kebreau 95c1324adc
gnu: python-tmx: Update to 1.10. 
* gnu/packages/game-development.scm (python-tmx): Update to 1.10.
 2017-08-31 11:38:00 -04:00