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* gnu: isc-dhcp: Update to 4.3.3-P1 [fixes CVE-2015-8605].•••* gnu/packages/admin.scm (isc-dhcp): Update to 4.3.3-P1. Mark H Weaver2016-01-131-3/+3
* gnu: samtools: Update to 1.3.•••* gnu/packages/bioinformatics.scm (samtools): Update to 1.3. [arguments]: Enable tests for all architectures; set ncurses in configure-flags instead of make-flags; simplify "patch-tests" phase; restore "configure" phase. Ricardo Wurmus2016-01-131-27/+12
* gnu: skribilo: Update to 0.9.3.•••* gnu/packages/skribilo.scm (skribilo): Update to 0.9.3. [native-inputs]: New field. Ludovic Courtès2016-01-131-3/+6
* gnu: boost: Update to 1.60.0.•••* 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. Eric Bavier2016-01-128-26/+132
* gnu: boost: Use modify-phases.•••* gnu/packages/boost.scm (boost)[arguments]: Use modify-phases. Eric Bavier2016-01-121-24/+23
* gnu: sudo: Add fix for CVE-2015-5602.•••* 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. Mark H Weaver2016-01-122-1/+374
* gnu: global: Use modify-phases syntax.•••* gnu/packages/code.scm (global)[arguments]: Use modify-phases syntax. Efraim Flashner2016-01-121-12/+11
* gnu: global: Update to 6.5.2.•••* gnu/packages/code.scm (global): Update to 6.5.2. Efraim Flashner2016-01-121-2/+3
* gnu: icedtea-6: Fix directory name in "unpack" phase.•••* gnu/packages/java.scm (icedtea-6)[arguments]: Change the directory prefix in the "unpack" phase to "icedtea6-". Ricardo Wurmus2016-01-121-1/+1
* gnu: linux-libre: Update to 4.4.•••* 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>. Mark H Weaver2016-01-113-132/+344
* gnu: Add fxtract.•••* gnu/packages/bioinformatics.scm (fxtract): New variable. Ben Woodcroft2016-01-121-0/+66
* gnu: youtube-dl: Update to 2016.01.09.•••* gnu/packages/video.scm (youtube-dl): Update to 2016.01.09. Efraim Flashner2016-01-111-2/+2
* gnu: gp2c: Update to 0.0.9pl5.•••* gnu/packages/algebra.scm (gp2c): Update to 0.0.9pl5. Andreas Enge2016-01-111-3/+3
* gnu: texlive: Use modify-phases syntax.•••* gnu/packages/texlive.scm (texlive-bin, texlive-texmf): Use modify-phases syntax. Andreas Enge2016-01-111-61/+58
* gnu: man-pages: Update to 4.04.•••* gnu/packages/man.scm (man-pages): Update to 4.04. [source]: Add alternate location. Efraim Flashner2016-01-111-5/+10
* gnu: bedtools: Update to 2.25.0.•••* 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. Ben Woodcroft2016-01-112-185/+3
* gnu: bedtools: Use modify-phases.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases. Ben Woodcroft2016-01-111-19/+19
* gnu: r: Update to 3.2.3.•••* gnu/packages/statistics.scm (r): Update to 3.2.3. Andreas Enge2016-01-091-2/+2
* gnu: icecat: Update to 38.5.2-gnu1.•••* gnu/packages/gnuzilla.scm (icecat): Update to 38.5.2-gnu1. Andreas Enge2016-01-091-2/+2
* gnu: ruby-2.1: Update to 2.1.8.•••* gnu/packages/ruby.scm (ruby-2.1): Update to 2.1.8. Ben Woodcroft2016-01-091-2/+2
* gnu: i2c-tools: Update source and home-page URLs.•••* gnu/packages/linux.scm (i2c-tools)[source]: Update URL. [home-page]: Update URL. Leo Famulari2016-01-081-2/+2
* gnu: lm-sensors: Update source and home-page URLs.•••* gnu/packages/linux.scm (lm-sensors)[source]: Update URL. [home-page]: Update URL. Leo Famulari2016-01-081-2/+2
* gnu: nss: Update to 3.21 [fixes CVE-2015-7575].•••* 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. Mark H Weaver2016-01-082-16/+16
* gnu: Add missing (gnu packages gcc) import.•••* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is required by 'r-impute' for 'gfortran'. Mathieu Lirzin2016-01-081-0/+1
* gnu: xterm: Update to 322.•••* gnu/packages/xorg.scm (xterm): Update to 322. Mathieu Lirzin2016-01-081-2/+3
* gnu: epiphany: Update to 3.18.2.•••* gnu/packages/gnome.scm (epiphany): Update to 3.18.2. 宋文武2016-01-081-2/+2
* gnu: webkitgtk: Update to 2.10.4.•••* gnu/packages/webkit.scm (webkitgtk): Update to 2.10.4. 宋文武2016-01-081-2/+4
* gnu: Add Pfff.•••* gnu/packages/textutils.scm (pfff): New variable. Pjotr Prins2016-01-071-1/+25
* gnu: mpv: Remove 'samba' input.•••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'. Alex Kost2016-01-071-2/+0
* gnu: Add genomation.•••* gnu/packages/bioinformatics.scm (r-genomation): New variable. Ricardo Wurmus2016-01-071-0/+43
* gnu: Add seqPattern.•••* gnu/packages/bioinformatics.scm (r-seqpattern): New variable. Ricardo Wurmus2016-01-071-0/+26
* gnu: Add impute.•••* gnu/packages/bioinformatics.scm (r-impute): New variable. Ricardo Wurmus2016-01-071-0/+20
* gnu: Add BSgenome.•••* gnu/packages/bioinformatics.scm (r-bsgenome): New variable. Ricardo Wurmus2016-01-071-0/+30
* gnu: Add plotly.•••* gnu/packages/statistics.scm (r-plotly): New variable. Ricardo Wurmus2016-01-071-0/+30
* gnu: Add viridis.•••* gnu/packages/statistics.scm (r-viridis): New variable. Ricardo Wurmus2016-01-071-0/+26
* gnu: Add topGO.•••* gnu/packages/bioinformatics.scm (r-topgo): New variable. Ricardo Wurmus2016-01-071-0/+29
* gnu: Add matrixStats.•••* gnu/packages/statistics.scm (r-matrixstats): New variable. Ricardo Wurmus2016-01-071-0/+24
* gnu: Add R.rsp.•••* gnu/packages/statistics.scm (r-r-rsp): New variable. Ricardo Wurmus2016-01-071-0/+31
* gnu: Add R.cache.•••* gnu/packages/statistics.scm (r-r-cache): New variable. Ricardo Wurmus2016-01-071-0/+26
* gnu: Add R.utils.•••* gnu/packages/statistics.scm (r-r-utils): New variable. Ricardo Wurmus2016-01-071-0/+22
* gnu: Add R.oo.•••* gnu/packages/statistics.scm (r-r-oo): New variable. Ricardo Wurmus2016-01-071-0/+23
* gnu: Add R.methodsS3.•••* gnu/packages/statistics.scm (r-r-methodss3): New variable. Ricardo Wurmus2016-01-071-0/+24
* gnu: Add base64enc.•••* gnu/packages/statistics.scm (r-base64enc): New variable. Ricardo Wurmus2016-01-071-0/+18
* gnu: Add DT.•••* gnu/packages/statistics.scm (r-dt): New variable. Ricardo Wurmus2016-01-071-0/+34
* gnu: Add SparseM.•••* gnu/packages/statistics.scm (r-sparsem): New variable. Ricardo Wurmus2016-01-071-0/+21
* gnu: Add GO.db.•••* gnu/packages/bioinformatics.scm (r-go-db): New variable. Ricardo Wurmus2016-01-071-0/+20
* gnu: Add GenomicFeatures.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable. Ricardo Wurmus2016-01-071-0/+41
* gnu: Add rtracklayer.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable. Ricardo Wurmus2016-01-071-0/+45
* gnu: Add GenomicAlignments.•••* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable. Ricardo Wurmus2016-01-071-0/+33
* gnu: Add SummarizedExperiment.•••* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable. Ricardo Wurmus2016-01-071-0/+29
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