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| * packages: Add 'hidden-package'.•••* 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. Ludovic Courtès2016-07-28
| * gnu: Add asciinema.•••* gnu/packages/terminals.scm (asciinema): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Alex Griffin2016-07-28
| * gnu: gnome: Propagate file-roller.•••* gnu/packages/gnome.scm (gnome)[propagated-inputs]: Add file-roller. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Alex Griffin2016-07-28
| * doc: Discourage software bundling.•••Fixes <http://bugs.gnu.org/24008>. Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add item about bundling. Ludovic Courtès2016-07-28
| * doc: Send changes in your patch which are related.•••* 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> ng02016-07-28
| * doc: Mention separate branch for packages with many dependents.•••Suggested by ng0 <ng0@we.make.ritual.n0.is>. * doc/contributing.texi (Submitting Patches): Add note on packages with more than 100 dependents. Ludovic Courtès2016-07-28
| * gnu: r-genomicfeatures: Update to 1.24.5.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5. Ben Woodcroft2016-07-28
| * gnu: r-bsgenome: Update to 1.40.1.•••* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1. Ben Woodcroft2016-07-28
| * gnu: r-iranges: Update to 2.6.1.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1. Ben Woodcroft2016-07-28
| * gnu: r-limma: Update to 3.28.17.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17. Ben Woodcroft2016-07-28
| * gnu: r-xvector: Update to 0.12.1.•••* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1. Ben Woodcroft2016-07-28
| * gnu: r-genomicranges: Update to 1.24.2.•••* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2. Ben Woodcroft2016-07-28
| * gnu: r-annotationdbi: Update to 1.34.4.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4. Ben Woodcroft2016-07-28
| * gnu: r-biocparallel: Update to 1.6.3.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3. Ben Woodcroft2016-07-28
| * gnu: r-biostrings: Update to 2.40.2.•••* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2. Ben Woodcroft2016-07-28
| * gnu: r-summarizedexperiment: Update to 1.2.3.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3. Ben Woodcroft2016-07-28
| * gnu: r-genomicalignments: Update to 1.8.4.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4. Ben Woodcroft2016-07-28
| * gnu: r-rtracklayer: Update to 1.32.2.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2. Ben Woodcroft2016-07-28
| * gnu: r-genomeinfodb: Update to 1.8.3.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3. Ben Woodcroft2016-07-28
| * gnu: r-s4vectors: Update to 0.10.2.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2. Ben Woodcroft2016-07-28
* | gnu: dico: Patch 'idxgcide' bug.•••* 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. Ludovic Courtès2016-07-28
* | gnu: vlc: Drop -ffast-math from the compilation flags.•••* gnu/packages/video.scm (vlc)[arguments]: Add "ac_cv_c_fast_math=no" to #:configure-flags. Ludovic Courtès2016-07-28
* | gnu: r-bsgenome: Update to 1.40.1.•••* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1. Ben Woodcroft2016-07-28
* | gnu: r-iranges: Update to 2.6.1.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1. Ben Woodcroft2016-07-28
* | gnu: r-limma: Update to 3.28.17.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17. Ben Woodcroft2016-07-28
* | gnu: r-xvector: Update to 0.12.1.•••* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1. Ben Woodcroft2016-07-28
* | gnu: r-genomicranges: Update to 1.24.2.•••* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2. Ben Woodcroft2016-07-28
* | gnu: r-annotationdbi: Update to 1.34.4.•••* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4. Ben Woodcroft2016-07-28
* | gnu: r-biocparallel: Update to 1.6.3.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3. Ben Woodcroft2016-07-28
* | gnu: r-biostrings: Update to 2.40.2.•••* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2. Ben Woodcroft2016-07-28
* | gnu: r-summarizedexperiment: Update to 1.2.3.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3. Ben Woodcroft2016-07-28
* | gnu: r-genomicalignments: Update to 1.8.4.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4. Ben Woodcroft2016-07-28
* | gnu: r-rtracklayer: Update to 1.32.2.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2. Ben Woodcroft2016-07-28
* | gnu: r-genomeinfodb: Update to 1.8.3.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3. Ben Woodcroft2016-07-28
* | gnu: r-genomicfeatures: Update to 1.24.5.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5. Ben Woodcroft2016-07-28
* | gnu: r-s4vectors: Update to 0.10.2.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2. Ben Woodcroft2016-07-28
* | gnu: asymptote: Add native input gs.•••* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Add gs. This is a follow-up to commit d8eb912132ccdff955e3318fe549c5f7f674adf8. Andreas Enge2016-07-28
* | 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}].•••* 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. Leo Famulari2016-07-28
| * gnu: the-silver-searcher: Update to 0.32.0.•••* gnu/packages/code.scm(the-silver-searcher): Update to 0.32.0. Tomáš Čech2016-07-28
| * gnu: imagemagick: Update to 6.9.5-3.•••* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.5-3. Leo Famulari2016-07-27
| * gnu: mariadb: Update to 10.1.16.•••* gnu/packages/databases.scm (mariadb): Update to 10.1.16. Leo Famulari2016-07-27
| * gnu: calibre: Update to 2.63.0.•••* 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> Alex Griffin2016-07-27
| * system: Source /etc/environment before $HOME/.guix-profile/etc/profile.•••* 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> Carlos Sánchez de La Lama2016-07-27
| * gnu: krona-tools: Update to 2.7.•••* gnu/packages/web.scm (krona-tools): Update to 2.7. [arguments]: Delete 'build' phase. Install new scripts. Ben Woodcroft2016-07-27
| * gnu: diamond: Update to 0.8.16.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16. Ben Woodcroft2016-07-27
| * gnu: guix: Update revision number in version.•••This is a follow-up to commit 95af24a2f1fb58eb9e6ee902c9330534f0aca9f3. Reported by Alex Kost <alezost@gmail.com>. Andreas Enge2016-07-27
| * tests: Use unbuffered input ports when decompressing from 'guix publish'.•••Fixes <http://bugs.gnu.org/24060>. Reported by Chris Marusich <cmmarusich@gmail.com>. * tests/publish.scm (http-get-port): Explicitly call 'open-socket-for-uri' and add calls to 'setvbuf'. Ludovic Courtès2016-07-27
| * zlib: Protect against non-empty port internal buffers.•••* guix/zlib.scm (make-gzip-input-port)[gzfile]: Error out if (drain-input port) returns a non-empty string. * guix/zlib.scm (make-gzip-output-port)[gzfile]: Call 'force-output'. Ludovic Courtès2016-07-27
| * zlib: Clarify when 'gzread!' can return zero.•••* guix/zlib.scm (gzread!): Augment docstring to clarify when zero is returned (based on reading zlib code). (make-gzip-input-port)[read!]: Remove scary comment. Ludovic Courtès2016-07-27
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