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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>
2016-07-27system: Source /etc/environment before $HOME/.guix-profile/etc/profile.Carlos Sánchez de La Lama
* 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>
2016-07-27gnu: python-2.7: Disable test failing on mips64el-linux.Andreas Enge
* gnu/packages/python.scm (python-2.7)[source]: In a snippet, remove an additional test that fails on mips64el-linux.
2016-07-27gnu: krona-tools: Update to 2.7.Ben Woodcroft
* gnu/packages/web.scm (krona-tools): Update to 2.7. [arguments]: Delete 'build' phase. Install new scripts.
2016-07-27gnu: diamond: Update to 0.8.16.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
2016-07-27gnu: guix: Update revision number in version.Andreas Enge
This is a follow-up to commit 95af24a2f1fb58eb9e6ee902c9330534f0aca9f3. Reported by Alex Kost <alezost@gmail.com>.
2016-07-27gnu: skribilo: Add input ghostscript-gs.Andreas Enge
* gnu/packages/engineering.scm (lout)[native-inputs]: Add ghostscript-gs. This is a follow-up to commit d8eb912132ccdff955e3318fe549c5f7f674adf8.
2016-07-27tests: Use unbuffered input ports when decompressing from 'guix publish'.Ludovic Courtès
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'.
2016-07-27zlib: Protect against non-empty port internal buffers.Ludovic Courtès
* 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'.
2016-07-27zlib: Clarify when 'gzread!' can return zero.Ludovic Courtès
* 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.
2016-07-27gnu: magit: Fix rebase commands that require perl.Alex Griffin
* 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>
2016-07-27gnu: Add httping.Tobias Geerinckx-Rice
* gnu/packages/networking.scm (httping): New variable.
2016-07-27gnu: Add missing copyright symbol.Tobias Geerinckx-Rice
* gnu/packages/networking.scm: Add missing "©" to header comments.
2016-07-26gnu: gmime: Remove 'gpg' to 'gpg2' substitution.ng0
* 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>
2016-07-26gnu: lout: Add input ghostscript.Andreas Enge
* gnu/packages/lout.scm (lout)[native-inputs]: Add ghostscript, needed for ps2pdf.
2016-07-26gnu: lout: Make ghostscript-gs a native input.Andreas Enge
* gnu/packages/lout.scm (lout)[inputs]: Move to native-inputs.
2016-07-26gnu: lout: Build with ghostscript-gs.Andreas Enge
* gnu/packages/engineering.scm (lout)[inputs]: Replace GHOSTSCRIPT by GHOSTSCRIPT-GS. This is a follow-up to commit d8eb912132ccdff955e3318fe549c5f7f674adf8.
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