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2016-07-28Merge branch 'master' into core-updatesLeo Famulari
2016-07-28Revert "gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207]."Leo Famulari
This reverts commit ae46cd0e4cfb1f06d099b2cda1f9e702e86c90e9.
2016-07-28Merge branch 'master' into core-updatesMark H Weaver
2016-07-28guix package: Suggest prefix search path settings.Ludovic Courtès
* guix/scripts/package.scm (build-and-use-profile): Pass #:kind 'prefix to 'display-search-paths'.
2016-07-28gnu: gd: Update to 2.2.3 [fixes CVE-2016-6207].Mark H Weaver
* 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.
2016-07-28gnu: commencement: 'guile-final' is now "hidden".Ludovic Courtès
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.
2016-07-28packages: Add 'hidden-package'.Ludovic Courtès
* 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.
2016-07-28gnu: Add asciinema.Alex Griffin
* gnu/packages/terminals.scm (asciinema): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28gnu: gnome: Propagate file-roller.Alex Griffin
* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28doc: Discourage software bundling.Ludovic Courtès
Fixes <http://bugs.gnu.org/24008>. Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add item about bundling.
2016-07-28doc: Send changes in your patch which are related.ng0
* doc/contributing.texi (Submitting Patches): New @item: This gives information about sending related changes and examples on what we view as related changes. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2016-07-28doc: Mention separate branch for packages with many dependents.Ludovic Courtès
Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add note on packages with more than 100 dependents.
2016-07-28gnu: dico: Patch 'idxgcide' bug.Ludovic Courtès
* 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.
2016-07-28gnu: vlc: Drop -ffast-math from the compilation flags.Ludovic Courtès
* gnu/packages/video.scm (vlc)[arguments]: Add "ac_cv_c_fast_math=no" to #:configure-flags.
2016-07-28gnu: r-genomicfeatures: Update to 1.24.5.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
2016-07-28gnu: r-bsgenome: Update to 1.40.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
2016-07-28gnu: r-iranges: Update to 2.6.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
2016-07-28gnu: r-limma: Update to 3.28.17.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
2016-07-28gnu: r-xvector: Update to 0.12.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
2016-07-28gnu: r-genomicranges: Update to 1.24.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
2016-07-28gnu: r-annotationdbi: Update to 1.34.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
2016-07-28gnu: r-biocparallel: Update to 1.6.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
2016-07-28gnu: r-biostrings: Update to 2.40.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
2016-07-28gnu: r-summarizedexperiment: Update to 1.2.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
2016-07-28gnu: r-genomicalignments: Update to 1.8.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
2016-07-28gnu: r-rtracklayer: Update to 1.32.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
2016-07-28gnu: r-genomeinfodb: Update to 1.8.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
2016-07-28gnu: r-bsgenome: Update to 1.40.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
2016-07-28gnu: r-iranges: Update to 2.6.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
2016-07-28gnu: r-limma: Update to 3.28.17.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
2016-07-28gnu: r-xvector: Update to 0.12.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
2016-07-28gnu: r-genomicranges: Update to 1.24.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
2016-07-28gnu: r-annotationdbi: Update to 1.34.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
2016-07-28gnu: r-biocparallel: Update to 1.6.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
2016-07-28gnu: r-biostrings: Update to 2.40.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
2016-07-28gnu: r-summarizedexperiment: Update to 1.2.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
2016-07-28gnu: r-genomicalignments: Update to 1.8.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
2016-07-28gnu: r-rtracklayer: Update to 1.32.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
2016-07-28gnu: r-genomeinfodb: Update to 1.8.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
2016-07-28gnu: r-genomicfeatures: Update to 1.24.5.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
2016-07-28gnu: r-s4vectors: Update to 0.10.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
2016-07-28gnu: r-s4vectors: Update to 0.10.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
2016-07-28gnu: asymptote: Add native input gs.Andreas Enge
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Add gs. This is a follow-up to commit d8eb912132ccdff955e3318fe549c5f7f674adf8.
2016-07-28Merge remote-tracking branch 'origin/master' into core-updatesAndreas Enge
2016-07-28gnu: mysql: Update to 5.7.13 [fixes CVE-2016-{3477,3521,3615,5440}].Leo Famulari
* 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.
2016-07-28gnu: the-silver-searcher: Update to 0.32.0.Tomáš Čech
* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0.
2016-07-27gnu: imagemagick: Update to 6.9.5-3.Leo Famulari
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3.
2016-07-27gnu: mariadb: Update to 10.1.16.Leo Famulari
* gnu/packages/databases.scm (mariadb): Update to 10.1.16.
2016-07-28gnu: python@2.7: Delete faulty test on mips64el only.Ludovic Courtès
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.
2016-07-27gnu: calibre: Update to 2.63.0.Alex Griffin
* 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>
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