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* gnu: vsearch: Update to 2.4.4.Ben Woodcroft2017-09-01
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
* gnu: metabat: Update to 2.12.1.Ben Woodcroft2017-09-01
| | | | | | | * 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.
* gnu: netcdf: Fix reproducibility issue; remove unneeded references.Thomas Danckaert2017-09-01
| | | | | * gnu/packages/maths.scm (netcdf) [arguments]: Add phase to fix the embedded 'Configured On' date; truncate reference to compiler store item.
* gnu: hdf4: Avoid unneeded store references to compilers.Thomas Danckaert2017-09-01
| | | | | * gnu/packages/maths.scm (hdf4) [arguments]: Add phase 'patch-settings to truncate hashes of compiler store items.
* gnu: hdf5: Avoid unneeded store references to compilers.Thomas Danckaert2017-09-01
| | | | | * gnu/packages/maths.scm (hdf5) [arguments]: Add phase to patch "libhdf5.settings", removing references to the C/C++/Fortran compilers.
* gnu: hdf5: Add output for fortran interface.Thomas Danckaert2017-09-01
| | | | | | | | * 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.
* gnu: python2-larch: Enable tests.Arun Isaac2017-09-01
| | | | | | | | * 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.
* gnu: python2-ttystatus: Enable tests.Arun Isaac2017-09-01
| | | | | * gnu/packages/python.scm (python2-ttystatus)[arguments]: Replace 'check' phase with custom function.
* gnu: python2-cliapp: Enable tests.Arun Isaac2017-09-01
| | | | | * gnu/packages/python.scm (python2-cliapp)[arguments]: Replace 'check' phase with custom function.
* gnu: linux-libre: Update to 4.12.10.Mark H Weaver2017-09-01
| | | | | * gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.10. (%linux-libre-hash): Update hash.
* gnu: linux-libre@4.9: Update to 4.9.46.Mark H Weaver2017-09-01
| | | | * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.46.
* gnu: linux-libre@4.4: Update to 4.4.85.Mark H Weaver2017-09-01
| | | | * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.85.
* gnu: libxml2/fixed: Use patches from inherited package.Marius Bakke2017-08-31
| | | | | | This is a followup to 76fed2b3c4e3703d1ad81c4330edd94d551b6334. * gnu/packages/xml.scm (libxml2/fixed)(patches): Inherit patches from LIBXML2.
* gnu: graphicsmagick: Fix CVE-2017-{13775,13776,13777}.Efraim Flashner2017-09-01
| | | | | | | | * 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.
* gnu: efl: Update to 1.20.3.Efraim Flashner2017-09-01
| | | | * gnu/packages/enlightenment.scm (efl): Update to 1.20.3.
* gnu: Fix current-guix.Christopher Baines2017-08-31
| | | | | | | | | | 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.
* gnu: sddm: Update to 0.15.0.Marius Bakke2017-08-31
| | | | | | | | * 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.
* gnu: libxml2: Fix CVE-2017-{0663,7375,7376,9047,9048,9049,9050}.Alex Vong2017-08-31
| | | | | | | | | | | | | * 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>
* gnu: postgresql: Update to 9.6.5.Marius Bakke2017-08-31
| | | | | | * 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
* gnu: Remove python2-rpy2.Ricardo Wurmus2017-08-31
| | | | | | Python 2 is no longer supported. * gnu/packages/python.scm (python2-rpy2): Remove variable.
* gnu: python-rpy2: Update to 2.9.0.Ricardo Wurmus2017-08-31
| | | | | | | * 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.
* gnu: python-rpy2: Update license.Ricardo Wurmus2017-08-31
| | | | | * gnu/packages/python.scm (python-rpy2)[license]: Correct GPLv3+ to GPLv2+; list additional licenses.
* gnu: Add r-dbplyr.Ricardo Wurmus2017-08-31
| | | | * gnu/packages/statistics.scm (r-dbplyr): New variable.
* gnu: retux: Update to 1.3.5.Kei Kebreau2017-08-31
| | | | * gnu/packages/games.scm (retux): Update to 1.3.5.
* gnu: python-tmx: Update to 1.10.Kei Kebreau2017-08-31
| | | | * gnu/packages/game-development.scm (python-tmx): Update to 1.10.
* gnu: python-sge-pygame: Update to 1.5.1.Kei Kebreau2017-08-31
| | | | | * gnu/packages/game-development.scm (python-sge-pygame, python2-sge-pygame): Update to 1.5.1.
* gnu: python-pyjwt: Update to 1.5.2 [fixes CVE-2017-11424].Marius Bakke2017-08-31
| | | | | | * 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.
* gnu: Add emacs-idris-mode.Peter Mikkelsen2017-08-31
| | | | | | * gnu/packages/emacs.scm (emacs-idris-mode): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add emacs-prop-menu.Peter Mikkelsen2017-08-31
| | | | | | * gnu/packages/emacs.scm (emacs-prop-menu): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: mpd: Remove the mpd-file field.Peter Mikkelsen2017-08-31
| | | | | | | | | | | | | | | 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>
* gnu: knot: Update to 2.5.4.Tobias Geerinckx-Rice2017-08-31
| | | | * gnu/packages/dns.scm (knot): Update to 2.5.4.
* gnu: Add pt-scotch32.Paul Garlick2017-08-31
| | | | | | * gnu/packages/maths.scm (pt-scotch32): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add "scotch32".Paul Garlick2017-08-31
| | | | | | * gnu/packages/maths.scm (scotch32): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: bioinformatics: Work around more "dotless @INC" build failures.Ben Woodcroft2017-08-31
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add 'set-perl-search-path' phase.
* gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}.Ben Woodcroft2017-08-31
| | | | | | * 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.
* gnu: ruby-2.3.4: Fix CVE-2017-{0899,0900,0901,0902}.Ben Woodcroft2017-08-31
| | | | | | * gnu/packages/patches/ruby-2.3.4-rubygems-2613-ruby23.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/ruby.scm (ruby-2.3.4)[source]: Use it.
* gnu: ruby-2.4.1: Fix CVE-2017-{0899,0900,0901,0902}.Ben Woodcroft2017-08-31
| | | | | | | * gnu/packages/patches/ruby-rubygems-2612-ruby24.patch, gnu/packages/patches/ruby-rubygems-2613-ruby24.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/ruby.scm (ruby-2.4.1)[source]: Use them.
* gnu: metabat: Update to 2.11.3.Ben Woodcroft2017-08-31
| | | | | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3. [source]: Use git-fetch. Remove boost-related patch. * gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: vlc: Fix build and clean up expression.Marius Bakke2017-08-31
| | | | | | | | | | | Commit 3e0c54bf4de0b5e9d77271613287457dbcd64103 touches 'configure.ac' which in turn regenerates 'po/Makefile.in.in' with the wrong SHELL and breaks install. While at it, consolidate the other patching phases and remove unneeded inputs. * gnu/packages/video.scm (vlc)[arguments]: Consolidate patching phases into a 'patch-source' phase and run it immediately after unpack. [native-inputs]: Remove AUTOCONF, AUTOMAKE and LIBTOOL.
* gnu: vlc: Recover lost phase.Marius Bakke2017-08-31
| | | | | | | This is a followup to eb1f2420d5d72bb5d178a744cffb4978c7446286. * gnu/packages/video.scm (vlc)[arguments]: Run the fix-livemedia-utils-prefix phase before configure.
* gnu: gd: Replace with 2.2.5.Marius Bakke2017-08-31
| | | | | | | | | | | Fixes CVE-2017-6362 and CVE-2017-7890. * gnu/packages/gd.scm (gd)[replacement]: New field. (gd-2.2.5): New variable. * gnu/packages/php.scm (gd-for-php): Remove variable (php)[inputs]: Replace GD-FOR-PHP with GD-2.2.5. * gnu/packages/patches/gd-CVE-2017-7890.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: claws-mail: Update to 3.15.1.Tobias Geerinckx-Rice2017-08-31
| | | | * gnu/packages/mail.scm (claws-mail): Update to 3.15.1.
* gnu: Add texlive-latex-acmart.Ludovic Courtès2017-08-31
| | | | * gnu/packages/tex.scm (texlive-latex-acmart): New variable.
* gnu: mbedtls-apache: Update to 2.6.0 [fixes CVE-2017-14032].Marius Bakke2017-08-30
| | | | * gnu/packages/tls.scm (mbedtls-apache): Update to 2.6.0.
* gnu: vlc: Remove obsolete test workaround.Marius Bakke2017-08-30
| | | | | * gnu/packages/video.scm (vlc)[arguments]: Drop ac_cv_c_fast_math from #:configure-flags. Remove related 'bootstrap' phase.
* gnu: vlc: Build with modular qt.Marius Bakke2017-08-30
| | | | | | * gnu/packages/video.scm (vlc)[inputs]: Remove QT. Add QTBASE and QTX11EXTRAS. [arguments]: Add CXXFLAGS=-std=gnu++11 to #:configure-flags. Add 'fix-qt-include' phase.
* gnu: qemu: Update to 2.10.0.Marius Bakke2017-08-30
| | | | | | | | | | | | | | | | | | * gnu/packages/patches/qemu-CVE-2017-10664.patch, gnu/packages/patches/qemu-CVE-2017-10806.patch, gnu/packages/patches/qemu-CVE-2017-10911.patch, gnu/packages/patches/qemu-CVE-2017-11334.patch, gnu/packages/patches/qemu-CVE-2017-11434.patch, gnu/packages/patches/qemu-CVE-2017-12809.patch: gnu/packages/patches/qemu-CVE-2017-7493.patch, gnu/packages/patches/qemu-CVE-2017-8112.patch, gnu/packages/patches/qemu-CVE-2017-8309.patch, gnu/packages/patches/qemu-CVE-2017-8379.patch, gnu/packages/patches/qemu-CVE-2017-8380.patch, gnu/packages/patches/qemu-CVE-2017-9524.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. * gnu/packages/virtualization.scm (qemu): Update to 2.10.0. [source](patches): Remove.
* gnu: jsoncpp: Update to 1.8.2.Marius Bakke2017-08-30
| | | | * gnu/packages/serialization.scm (jsoncpp): Update to 1.8.2.
* gnu: multiqc: Update to 1.2.Ricardo Wurmus2017-08-30
| | | | | | | | | | * gnu/packages/bioinformatics.scm (multiqc): Update to 1.2. [source]: Remove patches. [arguments]: Remove to enable tests. [propagated-inputs]: Add python-spectra, python-requests, python-markdown, python-lzstring. * gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: Add python-spectra.Ricardo Wurmus2017-08-30
| | | | * gnu/packages/python.scm (python-spectra, python2-spectra): New variables.
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