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2017-09-01gnu: r-shape: Update to 1.4.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-shape): Update to 1.4.3.
2017-09-01gnu: r-tclust: Update to 1.3-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tclust): Update to 1.3-1.
2017-09-01gnu: r-fastcluster: Update to 1.1.24.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fastcluster): Update to 1.1.24.
2017-09-01gnu: r-rcpparmadillo: Update to 0.7.960.1.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.960.1.2.
2017-09-01gnu: r-plotrix: Update to 3.6-6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-plotrix): Update to 3.6-6.
2017-09-01gnu: r-httr: Update to 1.3.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-httr): Update to 1.3.1. [propagated-inputs]: Remove r-digest and r-stringr.
2017-09-01gnu: r-commonmark: Update to 1.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-commonmark): Update to 1.4.
2017-09-01gnu: r-ade4: Update to 1.7-8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ade4): Update to 1.7-8.
2017-09-01gnu: r-tibble: Update to 1.3.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tibble): Update to 1.3.4.
2017-09-01gnu: r-rlang: Update to 0.1.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rlang): Update to 0.1.2.
2017-09-01gnu: r-knitr: Update to 1.17.Ricardo Wurmus
* gnu/packages/statistics.scm (r-knitr): Update to 1.17.
2017-09-01gnu: r-bh: Update to 1.65.0-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-bh): Update to 1.65.0-1.
2017-09-01gnu: r-scales: Update to 0.5.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-scales): Update to 0.5.0. [propagated-inputs]: Add r-r6 and r-viridislite.
2017-09-01gnu: r-mgcv: Update to 1.8-19.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-19.
2017-09-01gnu: r-matrix: Update to 1.2-11.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrix): Update to 1.2-11.
2017-09-01gnu: r-servr: Update to 0.7.Ricardo Wurmus
* gnu/packages/web.scm (r-servr): Update to 0.7.
2017-09-01gnu: php: Update to 7.1.9.Julien Lepiller
* gnu/packages/php.scm (php): Update to 7.1.9.
2017-09-01gnu: java-slf4j-api: Fix tests.Julien Lepiller
* gnu/packages/java.scm (java-slf4j-api)[arguments]: Enable tests Adjust the jar content to prevent a test failure.
2017-09-01gnu: djvulibre: Remove timestamps from .svgz files.Z. Ren
* gnu/packages/djvu.scm (djvulibre)[arguments]: New field. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01gnu: Add emacs-tuareg.Oleg Pykhalov
* gnu/packages/ocaml.scm (emacs-tuareg): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01gnu: emacs-ebuild-mode: Update to 1.37.ng0
* gnu/packages/emacs.scm (emacs-ebuild-mode): Update to 1.37. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01gnu: Add emacs-2048-game.ng0
* gnu/packages/emacs.scm (emacs-2048-game): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-09-01packages: 'fold-packages' takes an optional 'modules' parameter.Ludovic Courtès
Suggested by Christopher Baines <mail@cbaines.net>. * gnu/packages.scm (fold-packages): Add optional 'modules' parameter and honor it.
2017-09-01scripts: Remove 'max-silent-time' from the default options.Maxim Cournoyer
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>
2017-09-01gnu: r-rcas: Correct license.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
2017-09-01gnu: r-rcas: Update to 1.3.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
2017-09-01gnu: mysql: Enable tests on aarch64.Efraim Flashner
* gnu/packages/databases.scm (mysql)[arguments]: Remove logic disabling the tests on aarch64-linux.
2017-09-01gnu: vsearch: Update to 2.4.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
2017-09-01gnu: metabat: Update to 2.12.1.Ben Woodcroft
* 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.
2017-09-01gnu: netcdf: Fix reproducibility issue; remove unneeded references.Thomas Danckaert
* gnu/packages/maths.scm (netcdf) [arguments]: Add phase to fix the embedded 'Configured On' date; truncate reference to compiler store item.
2017-09-01gnu: hdf4: Avoid unneeded store references to compilers.Thomas Danckaert
* gnu/packages/maths.scm (hdf4) [arguments]: Add phase 'patch-settings to truncate hashes of compiler store items.
2017-09-01gnu: hdf5: Avoid unneeded store references to compilers.Thomas Danckaert
* gnu/packages/maths.scm (hdf5) [arguments]: Add phase to patch "libhdf5.settings", removing references to the C/C++/Fortran compilers.
2017-09-01gnu: hdf5: Add output for fortran interface.Thomas Danckaert
* 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.
2017-09-01gnu: python2-larch: Enable tests.Arun Isaac
* 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.
2017-09-01gnu: python2-ttystatus: Enable tests.Arun Isaac
* gnu/packages/python.scm (python2-ttystatus)[arguments]: Replace 'check' phase with custom function.
2017-09-01gnu: python2-cliapp: Enable tests.Arun Isaac
* gnu/packages/python.scm (python2-cliapp)[arguments]: Replace 'check' phase with custom function.
2017-09-01gnu: linux-libre: Update to 4.12.10.Mark H Weaver
* gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.10. (%linux-libre-hash): Update hash.
2017-09-01gnu: linux-libre@4.9: Update to 4.9.46.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.46.
2017-09-01gnu: linux-libre@4.4: Update to 4.4.85.Mark H Weaver
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.85.
2017-08-31gnu: libxml2/fixed: Use patches from inherited package.Marius Bakke
This is a followup to 76fed2b3c4e3703d1ad81c4330edd94d551b6334. * gnu/packages/xml.scm (libxml2/fixed)(patches): Inherit patches from LIBXML2.
2017-09-01gnu: graphicsmagick: Fix CVE-2017-{13775,13776,13777}.Efraim Flashner
* 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.
2017-09-01gnu: efl: Update to 1.20.3.Efraim Flashner
* gnu/packages/enlightenment.scm (efl): Update to 1.20.3.
2017-08-31gnu: Fix current-guix.Christopher Baines
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.
2017-08-31gnu: sddm: Update to 0.15.0.Marius Bakke
* 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.
2017-08-31gnu: libxml2: Fix CVE-2017-{0663,7375,7376,9047,9048,9049,9050}.Alex Vong
* 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>
2017-08-31gnu: postgresql: Update to 9.6.5.Marius Bakke
* 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
2017-08-31gnu: Remove python2-rpy2.Ricardo Wurmus
Python 2 is no longer supported. * gnu/packages/python.scm (python2-rpy2): Remove variable.
2017-08-31gnu: python-rpy2: Update to 2.9.0.Ricardo Wurmus
* 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.
2017-08-31gnu: python-rpy2: Update license.Ricardo Wurmus
* gnu/packages/python.scm (python-rpy2)[license]: Correct GPLv3+ to GPLv2+; list additional licenses.
2017-08-31gnu: Add r-dbplyr.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dbplyr): New variable.
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