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2016-09-27gnu: python-plastid: Update to 1.4.6.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to 1.4.6. [propagated-inputs]: Add python-termcolor.
2016-09-27gnu: Add python-termcolor.Ben J Woodcroft
* gnu/packages/python.scm (python-termcolor, python2-termcolor): New variables.
2016-09-27gnu: python-pysam: Enable tests.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from PyPi to source archive due to missing test data. [arguments]: Add check phase after install. [native-inputs]: Add python-nose, samtools and bcftools.
2016-09-27gnu: python-pysam: Delete bundled htslib.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet to delete htslib. [arguments]: Add htslib flags in 'set-flags phase. [propagated-inputs]: New field. Add htslib.
2016-09-27gnu: python-pysam: Use 'modify-phases'.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use 'modify-phases'.
2016-09-27gnu: Add bcftools.Marius Bakke
* gnu/packages/bioinformatics.scm (bcftools): New variable.
2016-09-27gnu: python2-pbcore: Update to 1.2.10.Marius Bakke
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10. [propagated-inputs]: New field. Add python2-pyxb.
2016-09-27gnu: Add python-pyxb.Marius Bakke
* gnu/packages/xml.scm (python-pyxb, python2-pyxb): New variables.
2016-09-27gnu: python-pysam: Update to 0.9.1.4.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update to 0.9.1.4.
2016-09-27guix build: Gracefully handle packages without source for '-S'.Ludovic Courtès
Fixes <http://bugs.gnu.org/22836>. Reported by Ricardo Wurmus <rekado@elephly.net>. * guix/scripts/build.scm (options->derivations): Gracefully handle (package-source p) = #f.
2016-09-27Add missing exports.Ludovic Courtès
Reported by Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> at <https://lists.gnu.org/archive/html/guix-devel/2016-09/msg01686.html>. * gnu/system/file-systems.scm (%tty-gid): Export. * guix/build-system/python.scm (default-python, default-python2): Export.
2016-09-26gnu: openssl-next: Update to 1.1.0b [fixes CVE-2016-6309].Leo Famulari
* gnu/packages/tls.scm (openssl-next): Update to 1.1.0b.
2016-09-26gnu: openssl: Update replacement to 1.0.2j [fixes CVE-2016-7052].Leo Famulari
* gnu/packages/tls.scm (openssl): Update replacement to 1.0.2j. (openssl-1.0.2i): Replace with... (openssl-1.0.2j): ... new variable.
2016-09-26gnu: libftdi: Propagate the libusb input.Danny Milosavljevic
* gnu/packages/libftdi.scm (libftdi): Change libusb from an input to a propagated-input. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-26gnu: ncbi-vdb: Only build on i686 and x86_64.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only build on i686 and x86_64. [arguments]: Add mandatory "-msse2" flag to CFLAGS.
2016-09-26gnu: ghc-pandoc: Update to 1.17.2.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-pandoc): Update to 1.17.2.
2016-09-26gnu: ghc-texmath: Update to 0.8.6.5.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-texmath): Update to 0.8.6.5.
2016-09-26gnu: ghc-cmark: Update to 0.5.3.1.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-cmark): Update to 0.5.3.1.
2016-09-26gnu: ghc-highlighting-kate: Update to 0.6.3.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-highlighting-kate): Update to 0.6.3.
2016-09-26gnu: ghc-pandoc-types: Update to 1.16.1.1.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-pandoc-types): Update to 1.16.1.1.
2016-09-26gnu: ghc-tagsoup: Update to 0.14.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-tagsoup): Update to 0.14.
2016-09-26gnu: tbb: Fail on test errors.Ricardo Wurmus
* gnu/packages/tbb.scm (tbb)[arguments]: Add phase "fail-on-test-errors".
2016-09-26gnu: ghc-tls: Update to 1.3.8.Ricardo Wurmus
* gnu/packages/haskell.scm (ghc-tls): Update to 1.3.8.
2016-09-26gnu: tbb: Use modify-phases syntax.Ricardo Wurmus
* gnu/packages/tbb.scm (tbb)[arguments]: Use "modify-phases" syntax.
2016-09-26gnu: vsearch: Update to 2.1.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
2016-09-26gnu: azr3: Fix libsigc++ build errors.Ricardo Wurmus
* gnu/packages/audio.scm (azr3)[arguments]: Add "-std=gnu++11" flag. [source]: Add patch. * gnu/packages/patches/azr3.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2016-09-26gnu: qtractor: Update to 0.7.9.Ricardo Wurmus
* gnu/packages/music.scm (qtractor): Update to 0.7.9.
2016-09-26profiles: Build GTK+ input module cache.Ricardo Wurmus
* guix/profiles.scm (gtk-im-modules): New procedure. (%default-profile-hooks): Add it.
2016-09-26profiles: manifest-lookup-package: Optionally match version prefix.Ricardo Wurmus
* guix/profiles.scm (manifest-lookup-package): Optionally filter store item matches by version prefix.
2016-09-26gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): New variable.
2016-09-26gnu: Add r-grohmm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
2016-09-26gnu: Add r-systempiper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
2016-09-26gnu: Add r-shortread.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
2016-09-26gnu: Add r-gostats.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
2016-09-26gnu: Add r-category.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): New variable.
2016-09-26gnu: Add r-gseabase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
2016-09-26gnu: Add r-rbgl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
2016-09-26gnu: Add r-annotationforge.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
2016-09-26gnu: Add r-batchjobs.Ricardo Wurmus
* gnu/packages/statistics.scm (r-batchjobs): New variable.
2016-09-26gnu: Add r-fail.Ricardo Wurmus
* gnu/packages/statistics.scm (r-fail): New variable.
2016-09-26gnu: Add r-bbmisc.Ricardo Wurmus
* gnu/packages/statistics.scm (r-bbmisc): New variable.
2016-09-26gnu: Add r-checkmate.Ricardo Wurmus
* gnu/packages/statistics.scm (r-checkmate): New variable.
2016-09-26gnu: Add r-backports.Ricardo Wurmus
* gnu/packages/statistics.scm (r-backports): New variable.
2016-09-26gnu: Add r-sendmailr.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sendmailr): New variable.
2016-09-26gnu: Add r-pheatmap.Ricardo Wurmus
* gnu/packages/statistics.scm (r-pheatmap): New variable.
2016-09-26gnu: Add r-matrix.Ricardo Wurmus
* gnu/packages/statistics.scm (r-matrix): New variable.
2016-09-26gnu: Add r-deseq2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
2016-09-26gnu: Add r-genefilter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
2016-09-26gnu: Add r-hmisc.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hmisc): New variable.
2016-09-26gnu: Add r-geneplotter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
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