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2017-11-07gnu: Add r-mice.Ricardo Wurmus
* gnu/packages/cran.scm (r-mice): New variable.
2017-11-07gnu: Add r-ldblock.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ldblock): New variable.
2017-11-07gnu: Add r-erma.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-erma): New variable.
2017-11-07gnu: Add r-homo-sapiens.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
2017-11-07gnu: Add r-org-hs-eg-db.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
2017-11-07gnu: Add r-snpstats.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-snpstats): New variable.
2017-11-07gnu: Add r-gqtlbase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
2017-11-07gnu: Add r-gprofiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
2017-11-07gnu: Add r-ggbio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggbio): New variable.
2017-11-07gnu: Add r-biovizbase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
2017-11-07gnu: Add r-organismdbi.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
2017-11-07gnu: Add r-ensembldb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
2017-11-07gnu: Add r-annotationfilter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
2017-11-07gnu: Add r-dirichletmultinomial.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
2017-11-07gnu: Add r-complexheatmap.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
2017-11-07gnu: Add r-genomicfiles.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
2017-11-07gnu: bdftopcf: Update to 1.1.Marius Bakke
* gnu/packages/xorg.scm (bdftopcf): Update to 1.1. [native-inputs]: Change from LIBXFONT to LIBXFONT2.
2017-11-07gnu: feh: Update to 2.22.2.Marius Bakke
* gnu/packages/image-viewers.scm (feh): Update to 2.22.2.
2017-11-07gnu: gcc-4.7: Resurrect building with gcc-5.4.0.Jan Nieuwenhuizen
* gnu/packages/patches/gcc-4-compile-with-gcc-5.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gcc.scm (gcc-4.7): Use it.
2017-11-07gnu: Add websockify.Rutger Helling
* gnu/packages/web.scm (websockify): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-11-07gnu: Add python-networkx2.Gábor Boskovits
* gnu/packages/python.scm (python-networkx2, python2-networkx2): New variables. * gnu/local.mk (dist_patch_DATA): Register 'python-networkx2-reproducible-build.patch'. * gnu/packages/patches/python-networkx2-reproducible-build.patch: New file. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2017-11-07gnu: Add python-pydot.Gábor Boskovits
* gnu/packages/graphviz.scm (python-pydot, python2-pydot): New variables. Modified-by: Marius Bakke <mbakke@fastmail.com>
2017-11-07gnu: mercurial: Update to 4.4.1.Marius Bakke
* gnu/packages/version-control.scm (mercurial): Update to 4.4.1.
2017-11-07gnu: vim: Update to 8.0.1274 [fixes CVE-2017-1000382].Marius Bakke
* gnu/packages/vim.scm (vim): Update to 8.0.1274.
2017-11-07gnu: notmuch: Update to 0.25.2.Marius Bakke
* gnu/packages/mail.scm (notmuch): Update to 0.25.2.
2017-11-07gnu: psm: Only use as an input on supported-systems.Efraim Flashner
Syntax help supplied by bavier@member.fsf.org * gnu/packages/linux.scm (libfabric)[inputs]: Only use psm as an input on systems where psm is supported. * gnu/packages/mpi.scm (openmpi)[inputs]: Same.
2017-11-07gnu: psm: Limit supported systems.Efraim Flashner
* gnu/packages/linux.scm (psm)[supported-systems]: New field, limit to i686-linux and x86_64-linux.
2017-11-07gnu: gnupg: Update to 2.2.2.Efraim Flashner
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.2.
2017-11-07gnu: mediainfo: Change order of custom phases.Efraim Flashner
* gnu/packages/video.scm (mediainfo)[arguments]: Change to the build directory before executing the autogen script.
2017-11-07gnu: linux: Fix kconfig selection.Mathieu Othacehe
* gnu/packages/linux.scm (make-linux-libre): When cross-compiling, "kconfig" field is in native-inputs variable. So config is always #f when cross-compiling linux.
2017-11-07gnu: openmpi: Add dependency on PSM.Dave Love
* gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM.
2017-11-07gnu: libfabric: Add dependency on PSM.Dave Love
* gnu/packages/linux.scm (libfabric)[inputs]: Add PSM.
2017-11-07gnu: Add PSM.Dave Love
* gnu/packages/linux.scm (psm): New variable. * gnu/packages/patches/psm-arch.patch, gnu/packages/patches/psm-ldflags.patch, gnu/packages/patches/psm-repro.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them.
2017-11-07gnu: diffoscope: Update to 88.Gábor Boskovits
* gnu/packages/package-management.scm (diffoscope): Update to 88. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: awesome: Update to 4.2.ng0
* gnu/packages/wm.scm (awesome): Update to 4.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07services: gdm: Add environment variables.Timothy Sample
While not an optimal solution (see comment), this makes GDM functional. * gnu/services/xorg.scm (gdm-shepherd-service): Set PATH and XDG_DATA_DIRS environment variables. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: gdm: Add configure flags for better defaults.Timothy Sample
* gnu/packages/gnome.scm (gdm)[arguments]<#:configure-flags>: Add --with-initial-vt=7 and --enable-gdm-xsession. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: gdm: Fix config file path.Timothy Sample
* gnu/packages/gnome.scm (gdm)[arguments]<#:phases>: Fix the 'pre-configure phase so that GDM finds its config file. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07gnu: expect: Change home-page to http://expect.sourceforge.net/.Oleg Pykhalov
* gnu/packages/tcl.scm (expect): Change home-page to http://expect.sourceforge.net/.
2017-11-07gnu: Add r-gage.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): New variable.
2017-11-07gnu: Add r-keggrest.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
2017-11-07gnu: antlr3-3.3: Prettify build phases.Ricardo Wurmus
* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases "bin-install" and "generate-grammar".
2017-11-07gnu: r-servr: Update to 0.8.Ricardo Wurmus
* gnu/packages/web.scm (r-servr): Update to 0.8.
2017-11-07gnu: r-tidyselect: Update to 0.2.3.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
2017-11-07gnu: r-msnbase: Update to 2.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0. [propagated-inputs]: Add r-lattice; remove r-reshape2.
2017-11-07gnu: r-mutationalpatterns: Update to 1.4.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0. [propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
2017-11-07gnu: r-annotationhub: Update to 2.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0. [propagated-inputs]: Add r-curl.
2017-11-07gnu: r-mzr: Remove bundled copy of boost.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source. [arguments]: Add build phase "use-system-boost" to link with our boost package and avoid building the bundled sources.
2017-11-07gnu: r-mzr: Update to 2.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
2017-11-07gnu: r-mzid: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
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