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* gnu: boost: Update to 1.60.0.Eric Bavier2016-01-12
| | | | | | | | | | | | | | | | | | | | | | * gnu/packages/boost.scm (boost): Update to 1.60.0. [source]: Remove patch. * gnu/packages/patches/boost-mips-avoid-m32.patch: Delete patch * gnu-system.am (dist_patch_DATA): Remove patch. Also fix dependent packages: * gnu/packages/patches/csound-header-ordering.patch: New patch. * gnu/packages/audio.scm (csound)[source]: Use it. [arguments]: Add 'set-flags phase. * gnu/packages/patches/libcmis-fix-test-onedrive.patch: New patch. * gnu/packages/libreoffice.scm (libcmis)[source]: Use it. (libreoffice)[arguments]: Add LDFLAGS to #:configure-flags. (librevenge)[inputs]: Move boost from here... [propogated-inputs]: to here. [arguments]: Add LDFLAGS to #:configure-flags. * gnu/packages/patches/openimageio-boost-1.60.patch: New patch. * gnu/packages/graphics.scm (openimageio): Use it. * gnu-system.am (dist_patch_DATA): Add patches.
* gnu: boost: Use modify-phases.Eric Bavier2016-01-12
| | | | * gnu/packages/boost.scm (boost)[arguments]: Use modify-phases.
* gnu: sudo: Add fix for CVE-2015-5602.Mark H Weaver2016-01-12
| | | | | | * gnu/packages/patches/sudo-CVE-2015-5602.patch: New file. * gnu-system.am (dist_patch_DATA): Add it. * gnu/packages/admin.scm (sudo)[source]: Add patch.
* gnu: global: Use modify-phases syntax.Efraim Flashner2016-01-12
| | | | * gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax.
* gnu: global: Update to 6.5.2.Efraim Flashner2016-01-12
| | | | * gnu/packages/code.scm (global): Update to 6.5.2.
* gnu: icedtea-6: Fix directory name in "unpack" phase.Ricardo Wurmus2016-01-12
| | | | | * gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-".
* gnu: linux-libre: Update to 4.4.Mark H Weaver2016-01-11
| | | | | | | * gnu/packages/linux.scm (linux-libre): Update to 4.4. * gnu/packages/linux-libre-i686.conf, gnu/packages/linux-libre-x86_64.conf: Update from <https://jxself.org/git/kernel-configs.git>.
* gnu: Add fxtract.Ben Woodcroft2016-01-12
| | | | * gnu/packages/bioinformatics.scm (fxtract): New variable.
* gnu: youtube-dl: Update to 2016.01.09.Efraim Flashner2016-01-11
| | | | * gnu/packages/video.scm (youtube-dl): Update to 2016.01.09.
* gnu: gp2c: Update to 0.0.9pl5.Andreas Enge2016-01-11
| | | | * gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5.
* gnu: texlive: Use modify-phases syntax.Andreas Enge2016-01-11
| | | | | * gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax.
* gnu: man-pages: Update to 4.04.Efraim Flashner2016-01-11
| | | | | * gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location.
* gnu: bedtools: Update to 2.25.0.Ben Woodcroft2016-01-11
| | | | | | | | | * gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
* gnu: bedtools: Use modify-phases.Ben Woodcroft2016-01-11
| | | | * gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
* gnu: r: Update to 3.2.3.Andreas Enge2016-01-09
| | | | * gnu/packages/statistics.scm (r): Update to 3.2.3.
* gnu: icecat: Update to 38.5.2-gnu1.Andreas Enge2016-01-09
| | | | * gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1.
* gnu: ruby-2.1: Update to 2.1.8.Ben Woodcroft2016-01-09
| | | | * gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8.
* gnu: i2c-tools: Update source and home-page URLs.Leo Famulari2016-01-08
| | | | | * gnu/packages/linux.scm (i2c-tools)[source]: Update URL. [home-page]: Update URL.
* gnu: lm-sensors: Update source and home-page URLs.Leo Famulari2016-01-08
| | | | | * gnu/packages/linux.scm (lm-sensors)[source]: Update URL. [home-page]: Update URL.
* gnu: nss: Update to 3.21 [fixes CVE-2015-7575].Mark H Weaver2016-01-08
| | | | | | * gnu/packages/gnuzilla.scm (nss): Update to 3.21. [arguments]: In configure phase, setenv CC=gcc. * gnu/packages/patches/nss-pkgconfig.patch: Adapt to NSS 3.21.
* gnu: Add missing (gnu packages gcc) import.Mathieu Lirzin2016-01-08
| | | | | * gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'.
* gnu: xterm: Update to 322.Mathieu Lirzin2016-01-08
| | | | * gnu/packages/xorg.scm (xterm): Update to 322.
* gnu: epiphany: Update to 3.18.2.宋文武2016-01-08
| | | | * gnu/packages/gnome.scm (epiphany): Update to 3.18.2.
* gnu: webkitgtk: Update to 2.10.4.宋文武2016-01-08
| | | | * gnu/packages/webkit.scm (webkitgtk): Update to 2.10.4.
* gnu: Add Pfff.Pjotr Prins2016-01-07
| | | | * gnu/packages/textutils.scm (pfff): New variable.
* gnu: mpv: Remove 'samba' input.Alex Kost2016-01-07
| | | | | | | This is a heavy-weight and uncommon feature. See <http://lists.gnu.org/archive/html/guix-devel/2015-12/msg00701.html>. * gnu/packages/video.scm (mpv)[inputs]: Remove 'samba'.
* gnu: Add genomation.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomation): New variable.
* gnu: Add seqPattern.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
* gnu: Add impute.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-impute): New variable.
* gnu: Add BSgenome.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
* gnu: Add plotly.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-plotly): New variable.
* gnu: Add viridis.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-viridis): New variable.
* gnu: Add topGO.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-topgo): New variable.
* gnu: Add matrixStats.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-matrixstats): New variable.
* gnu: Add R.rsp.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-r-rsp): New variable.
* gnu: Add R.cache.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-r-cache): New variable.
* gnu: Add R.utils.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-r-utils): New variable.
* gnu: Add R.oo.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-r-oo): New variable.
* gnu: Add R.methodsS3.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-r-methodss3): New variable.
* gnu: Add base64enc.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-base64enc): New variable.
* gnu: Add DT.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-dt): New variable.
* gnu: Add SparseM.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/statistics.scm (r-sparsem): New variable.
* gnu: Add GO.db.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-go-db): New variable.
* gnu: Add GenomicFeatures.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
* gnu: Add rtracklayer.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
* gnu: Add GenomicAlignments.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
* gnu: Add SummarizedExperiment.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
* gnu: Add Rsamtools.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
* gnu: Add Biostrings.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): New variable.
* gnu: Add BiocParallel.Ricardo Wurmus2016-01-07
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
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