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* gnu: dico: Patch 'idxgcide' bug.Ludovic Courtès2016-07-28
| | | | | | * gnu/packages/patches/dico-idxgcide-bug.patch: New file. * gnu/packages/dico.scm (dico)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: vlc: Drop -ffast-math from the compilation flags.Ludovic Courtès2016-07-28
| | | | | * gnu/packages/video.scm (vlc)[arguments]: Add "ac_cv_c_fast_math=no" to #:configure-flags.
* gnu: r-bsgenome: Update to 1.40.1.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
* gnu: r-iranges: Update to 2.6.1.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
* gnu: r-limma: Update to 3.28.17.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
* gnu: r-xvector: Update to 0.12.1.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
* gnu: r-genomicranges: Update to 1.24.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
* gnu: r-annotationdbi: Update to 1.34.4.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
* gnu: r-biocparallel: Update to 1.6.3.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
* gnu: r-biostrings: Update to 2.40.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
* gnu: r-summarizedexperiment: Update to 1.2.3.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
* gnu: r-genomicalignments: Update to 1.8.4.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
* gnu: r-rtracklayer: Update to 1.32.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
* gnu: r-genomeinfodb: Update to 1.8.3.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
* gnu: r-genomicfeatures: Update to 1.24.5.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
* gnu: r-s4vectors: Update to 0.10.2.Ben Woodcroft2016-07-28
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
* gnu: asymptote: Add native input gs.Andreas Enge2016-07-28
| | | | | | * gnu/packages/plotutils.scm (asymptote)[native-inputs]: Add gs. This is a follow-up to commit d8eb912132ccdff955e3318fe549c5f7f674adf8.
* Merge remote-tracking branch 'origin/master' into core-updatesAndreas Enge2016-07-28
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| * gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}].Leo Famulari2016-07-28
| | | | | | | | | | | | * gnu/packages/patches/mysql-fix-failing-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/databases.scm (mysql): Update to 5.7.13.
| * gnu: the-silver-searcher: Update to 0.32.0.Tomáš Čech2016-07-28
| | | | | | | | * gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
| * gnu: imagemagick: Update to 6.9.5-3.Leo Famulari2016-07-27
| | | | | | | | * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3.
| * gnu: mariadb: Update to 10.1.16.Leo Famulari2016-07-27
| | | | | | | | * gnu/packages/databases.scm (mariadb): Update to 10.1.16.
| * gnu: calibre: Update to 2.63.0.Alex Griffin2016-07-27
| | | | | | | | | | | | | | | | | | | | | | * gnu/packages/ebook.scm (calibre): Update to 2.63.0. [inputs]: Remove unnecessary imagemagick dependency. [phases]: Use modify-phases. * gnu/packages/patches/calibre-drop-unrar.patch: Update for new version. Signed-off-by: Roel Janssen <roel@gnu.org>
| * system: Source /etc/environment before $HOME/.guix-profile/etc/profile.Carlos Sánchez de La Lama2016-07-27
| | | | | | | | | | | | | | * gnu/system.scm (operating-system-etc-service) <profile>: Move sourcing of /etc/environment before that of $HOME/.guix-profile/etc/profile. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: krona-tools: Update to 2.7.Ben Woodcroft2016-07-27
| | | | | | | | | | * gnu/packages/web.scm (krona-tools): Update to 2.7. [arguments]: Delete 'build' phase. Install new scripts.
| * gnu: diamond: Update to 0.8.16.Ben Woodcroft2016-07-27
| | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
| * gnu: guix: Update revision number in version.Andreas Enge2016-07-27
| | | | | | | | | | This is a follow-up to commit 95af24a2f1fb58eb9e6ee902c9330534f0aca9f3. Reported by Alex Kost <alezost@gmail.com>.
| * gnu: magit: Fix rebase commands that require perl.Alex Griffin2016-07-27
| | | | | | | | | | | | | | | | * gnu/packages/emacs.scm (magit)[inputs]: Add 'perl'. [arguments]: Adjust 'patch-exec-paths' phase to make some rebase commands find 'perl'. Signed-off-by: Alex Kost <alezost@gmail.com>
| * gnu: Add httping.Tobias Geerinckx-Rice2016-07-27
| | | | | | | | * gnu/packages/networking.scm (httping): New variable.
| * gnu: Add missing copyright symbol.Tobias Geerinckx-Rice2016-07-27
| | | | | | | | * gnu/packages/networking.scm: Add missing "©" to header comments.
| * gnu: gmime: Remove 'gpg' to 'gpg2' substitution.ng02016-07-26
| | | | | | | | | | | | | | * gnu/packages/mail.scm (gmime)[arguments]: Remove the substitution which previously changed 'gpg' to 'gpg2' in 'patch-paths-in-tests' phase. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: dmd: Remove package, superseded by shepherd.Andreas Enge2016-07-26
| | | | | | | | * gnu/packages/admin.scm (dmd): Remove variable.
| * gnu: Add perl-db-file.Danny Milosavljevic2016-07-26
| | | | | | | | | | | | * gnu/packages/databases.scm (perl-db_file): New variable. Signed-off-by: Andreas Enge <andreas@enge.fr>
| * gnu: icecat: Install icons.Alex Griffin2016-07-26
| | | | | | | | | | | | | | * gnu/packages/gnuzilla.scm (icecat)[arguments]: Add 'install-icons' phase. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: Add haveged.Tobias Geerinckx-Rice2016-07-26
| | | | | | | | * gnu/packages/linux.scm (haveged): New variable.
| * gnu: Add perceptualdiff.Tobias Geerinckx-Rice2016-07-26
| | | | | | | | * gnu/packages/image.scm (perceptualdiff): New variable.
| * gnu: linux-libre@4.1: Update to 4.1.28.Mark H Weaver2016-07-26
| | | | | | | | * gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.28.
| * gnu: linux-libre: Update to 4.7.Mark H Weaver2016-07-26
| | | | | | | | | | | | | | | | | | * gnu/packages/linux.scm (linux-libre): Update to 4.7. * gnu/packages/linux-libre-4.7-x86_64.conf, gnu/packages/linux-libre-4.7-i686.conf: New files. * gnu/packages/linux-libre-4.6-x86_64.conf, gnu/packages/linux-libre-4.6-i686.conf: Delete files. * Makefile.am (KCONFIGS): Update accordingly.
| * gnu: calibre: Build with non-modular Qt.Andreas Enge2016-07-26
| | | | | | | | | | | | | | | | | | * gnu/packages/ebook.scm (calibre)[native-inputs]: Replace QTBASE by QT. [inputs]: Replace QTBASE by QT and PYTHON2-PYQT by PYTHON2-PYQT-5.5. This essentially reverts commit 76806c54ed72f8f04079bbb187b186b833c103e1. Reported by Roel Janssen <roel@gnu.org>.
| * gnu: pyqt: Add versions based on non-modular Qt 5.5.Andreas Enge2016-07-26
| | | | | | | | * gnu/packages/qt.scm (python-pyqt-5.5, python2-pyqt-5.5): New variables.
| * gnu: guix: Update development snapshot.Andreas Enge2016-07-25
| | | | | | | | * gnu/packages/package-management.scm (guix-devel): Update to 97c8aef.
| * system: Add mapped devices for RAID.Andreas Enge2016-07-25
| | | | | | | | | | | | | | | | | | * gnu/system/mapped-devices.scm (raid-device-mapping, open-raid-device, close-raid-device): New variables. * doc/guix.texi (Mapped Devices): Add documentation for RAID devices, reorganize documentation for LUKS devices. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
* | gnu: python@2.7: Delete faulty test on mips64el only.Ludovic Courtès2016-07-28
| | | | | | | | | | | | | | | | | | This amends 8b732bf6d93ad2cb529c3c5f886efe2625c5fb72 and avoids a rebuild. * gnu/packages/python.scm (python-2.7)[arguments] <pre-check>: When (%current-system) starts with "mips64el", delete Lib/test/test_ctypes.py.
* | gnu: python-2.7: Disable test failing on mips64el-linux.Andreas Enge2016-07-27
| | | | | | | | | | * gnu/packages/python.scm (python-2.7)[source]: In a snippet, remove an additional test that fails on mips64el-linux.
* | gnu: skribilo: Add input ghostscript-gs.Andreas Enge2016-07-27
| | | | | | | | | | | | * gnu/packages/engineering.scm (lout)[native-inputs]: Add ghostscript-gs. This is a follow-up to commit d8eb912132ccdff955e3318fe549c5f7f674adf8.
* | gnu: lout: Add input ghostscript.Andreas Enge2016-07-26
| | | | | | | | * gnu/packages/lout.scm (lout)[native-inputs]: Add ghostscript, needed for ps2pdf.
* | gnu: lout: Make ghostscript-gs a native input.Andreas Enge2016-07-26
| | | | | | | | * gnu/packages/lout.scm (lout)[inputs]: Move to native-inputs.
* | gnu: lout: Build with ghostscript-gs.Andreas Enge2016-07-26
| | | | | | | | | | | | | | * gnu/packages/engineering.scm (lout)[inputs]: Replace GHOSTSCRIPT by GHOSTSCRIPT-GS. This is a follow-up to commit d8eb912132ccdff955e3318fe549c5f7f674adf8.
* | gnu: lpsolve: Fix compilation issue.Ludovic Courtès2016-07-26
| | | | | | | | | | | | | | Reported by Andreas Enge <andreas@enge.fr> at <https://lists.gnu.org/archive/html/guix-devel/2016-07/msg01018.html>. * gnu/packages/maths.scm (lpsolve)[source]: Augment 'snippet'.
* | gnu: lpsolve: Fail as early as possible.Ludovic Courtès2016-07-26
| | | | | | | | | | * gnu/packages/maths.scm (lpsolve)[arguments]: In 'build' phase, check the return value of 'system*' and honor it.
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