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* Merge branch 'master' into core-updatesLeo Famulari2016-07-28
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| * Revert "gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]."Leo Famulari2016-07-28
| | | | | | | | This reverts commit ae46cd0e4cfb1f06d099b2cda1f9e702e86c90e9.
* | Merge branch 'master' into core-updatesMark H Weaver2016-07-28
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| * gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207].Mark H Weaver2016-07-28
| | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/patches/gd-CVE-2016-5766.patch, gnu/packages/patches/gd-CVE-2016-6128.patch, gnu/packages/patches/gd-CVE-2016-6132.patch, gnu/packages/patches/gd-CVE-2016-6214.patch, gnu/packages/patches/gd-fix-test-on-i686.patch: Delete files. * gnu/packages/patches/gd-fix-tests-on-i686.patch: New file. * gnu/local.mk (dist_patch_DATA): Update accordingly. * gnu/packages/gd.scm (gd): Update to 2.2.3. [source]: Update patches field accordingly.
| * gnu: commencement: 'guile-final' is now "hidden".Ludovic Courtès2016-07-28
| | | | | | | | | | | | | | | | | | | | | | This way, we no longer have this annoying warning: $ guix build guile -n guix build: warning: ambiguous package specification `guile' guix build: warning: choosing guile-2.0.11 from gnu/packages/guile.scm:128:2 * gnu/packages/commencement.scm (guile-final): Use 'hidden-package'. * tests/packages.scm ("fold-packages, hidden package"): New test.
| * packages: Add 'hidden-package'.Ludovic Courtès2016-07-28
| | | | | | | | | | | | * guix/packages.scm (hidden-package, hidden-package?): New procedures. * gnu/packages.scm (fold-packages): Filter out 'hidden-package?'. * tests/packages.scm ("hidden-package"): New test.
| * gnu: Add asciinema.Alex Griffin2016-07-28
| | | | | | | | | | | | * gnu/packages/terminals.scm (asciinema): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * gnu: gnome: Propagate file-roller.Alex Griffin2016-07-28
| | | | | | | | | | | | * gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| * 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-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-s4vectors: Update to 0.10.2.Ben Woodcroft2016-07-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
* | 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>
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