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24150 Commits

Author SHA1 Message Date
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
Kei Kebreau b1d1a10c7c
gnu: python-sge-pygame: Update to 1.5.1. 
* gnu/packages/game-development.scm (python-sge-pygame,
python2-sge-pygame): Update to 1.5.1.
 2017-08-31 11:37:59 -04:00
Marius Bakke 7e31427ff0
gnu: python-pyjwt: Update to 1.5.2 [fixes CVE-2017-11424]. 
* 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
Peter Mikkelsen 5883bb76f8
gnu: Add emacs-idris-mode. 
* 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
Peter Mikkelsen b9dcaced16
gnu: Add emacs-prop-menu. 
* 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
Peter Mikkelsen b6dc69af1d
services: mpd: Remove the mpd-file field. 
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
Tobias Geerinckx-Rice 79ada57ba9
gnu: knot: Update to 2.5.4. 
* gnu/packages/dns.scm (knot): Update to 2.5.4.
 2017-08-31 13:53:04 +02:00
Paul Garlick 1c25a52c4a
gnu: Add pt-scotch32. 
* gnu/packages/maths.scm (pt-scotch32): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-08-31 12:34:50 +02:00
Paul Garlick 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
Ben Woodcroft 0691851a64
gnu: bioinformatics: Work around more "dotless @INC" build failures. 
* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
 2017-08-31 12:37:05 +08:00
Ben Woodcroft c959e5a1dc
gnu: ruby-2.2.7: Fix CVE-2017-{0899,0900,0901,0902}. 
* 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
Ben Woodcroft db542518b3
gnu: ruby-2.3.4: Fix CVE-2017-{0899,0900,0901,0902}. 
* 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.
 2017-08-31 10:43:19 +08:00
Ben Woodcroft 9770cbf9e2
gnu: ruby-2.4.1: Fix CVE-2017-{0899,0900,0901,0902}. 
* 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.
 2017-08-31 10:43:19 +08:00
Ben Woodcroft 690a904ad7
gnu: metabat: Update to 2.11.3. 
* 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.
 2017-08-31 10:43:18 +08:00
Marius Bakke 2d2e97bd71
gnu: vlc: Fix build and clean up expression. 
Commit 3e0c54bf4d 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.
 2017-08-31 03:43:54 +02:00
Marius Bakke 3e0c54bf4d
gnu: vlc: Recover lost phase. 
This is a followup to eb1f2420d5.

* gnu/packages/video.scm (vlc)[arguments]: Run the fix-livemedia-utils-prefix
phase before configure.
 2017-08-31 03:05:24 +02:00
Marius Bakke 4f68156140
gnu: gd: Replace with 2.2.5. 
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.
 2017-08-31 02:49:43 +02:00
Tobias Geerinckx-Rice cad88b8533
gnu: claws-mail: Update to 3.15.1. 
* gnu/packages/mail.scm (claws-mail): Update to 3.15.1.
 2017-08-31 00:57:46 +02:00
Ludovic Courtès 9ff7161a06
gnu: Add texlive-latex-acmart. 
* gnu/packages/tex.scm (texlive-latex-acmart): New variable.
 2017-08-31 00:03:20 +02:00
Marius Bakke 9749746544
gnu: mbedtls-apache: Update to 2.6.0 [fixes CVE-2017-14032]. 
* gnu/packages/tls.scm (mbedtls-apache): Update to 2.6.0.
 2017-08-30 22:41:40 +02:00
Marius Bakke eb1f2420d5
gnu: vlc: Remove obsolete test workaround. 
* gnu/packages/video.scm (vlc)[arguments]: Drop ac_cv_c_fast_math from
  #:configure-flags.  Remove related 'bootstrap' phase.
 2017-08-30 22:35:45 +02:00
Marius Bakke 552c3e95f3
gnu: vlc: Build with modular qt. 
* 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.
 2017-08-30 22:22:51 +02:00
Marius Bakke 2de7d137b3
gnu: qemu: Update to 2.10.0. 
* 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.
 2017-08-30 20:50:13 +02:00
Marius Bakke ffeeda6bab
gnu: jsoncpp: Update to 1.8.2. 
* gnu/packages/serialization.scm (jsoncpp): Update to 1.8.2.
 2017-08-30 20:36:40 +02:00
Ricardo Wurmus 799247d2d9
gnu: multiqc: Update to 1.2. 
* 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.
 2017-08-30 17:32:00 +02:00
Ricardo Wurmus 4a7d2009c8
gnu: Add python-spectra. 
* gnu/packages/python.scm (python-spectra, python2-spectra): New variables.
 2017-08-30 17:32:00 +02:00
Ricardo Wurmus beed6abc1d
gnu: Add python-colormath. 
* gnu/packages/python.scm (python-colormath, python2-colormath): New
variables.
 2017-08-30 17:31:59 +02:00
Ricardo Wurmus bac5fd21a1
gnu: python-jinja2: Update to 2.9.6. 
* gnu/packages/python.scm (python-jinja2): Update to 2.9.6.
[arguments]: Add build phase "delete-incompatible-files".
 2017-08-30 17:31:59 +02:00