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* gnu: Add r-biovizbase.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
* gnu: Add r-organismdbi.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
* gnu: Add r-ensembldb.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
* gnu: Add r-annotationfilter.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
* gnu: Add r-dirichletmultinomial.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
* gnu: Add r-complexheatmap.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
* gnu: Add r-genomicfiles.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
* gnu: bdftopcf: Update to 1.1.Marius Bakke2017-11-07
| | | | | * gnu/packages/xorg.scm (bdftopcf): Update to 1.1. [native-inputs]: Change from LIBXFONT to LIBXFONT2.
* gnu: feh: Update to 2.22.2.Marius Bakke2017-11-07
| | | | * gnu/packages/image-viewers.scm (feh): Update to 2.22.2.
* gnu: gcc-4.7: Resurrect building with gcc-5.4.0.Jan Nieuwenhuizen2017-11-07
| | | | | | * 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.
* gnu: Add websockify.Rutger Helling2017-11-07
| | | | | | * gnu/packages/web.scm (websockify): New variable. Signed-off-by: Marius Bakke <mbakke@fastmail.com>
* gnu: Add python-networkx2.Gábor Boskovits2017-11-07
| | | | | | | | * 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>
* gnu: Add python-pydot.Gábor Boskovits2017-11-07
| | | | | | * gnu/packages/graphviz.scm (python-pydot, python2-pydot): New variables. Modified-by: Marius Bakke <mbakke@fastmail.com>
* gnu: mercurial: Update to 4.4.1.Marius Bakke2017-11-07
| | | | * gnu/packages/version-control.scm (mercurial): Update to 4.4.1.
* gnu: vim: Update to 8.0.1274 [fixes CVE-2017-1000382].Marius Bakke2017-11-07
| | | | * gnu/packages/vim.scm (vim): Update to 8.0.1274.
* gnu: notmuch: Update to 0.25.2.Marius Bakke2017-11-07
| | | | * gnu/packages/mail.scm (notmuch): Update to 0.25.2.
* gnu: psm: Only use as an input on supported-systems.Efraim Flashner2017-11-07
| | | | | | | | 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.
* gnu: psm: Limit supported systems.Efraim Flashner2017-11-07
| | | | | * gnu/packages/linux.scm (psm)[supported-systems]: New field, limit to i686-linux and x86_64-linux.
* gnu: gnupg: Update to 2.2.2.Efraim Flashner2017-11-07
| | | | * gnu/packages/gnupg.scm (gnupg): Update to 2.2.2.
* gnu: mediainfo: Change order of custom phases.Efraim Flashner2017-11-07
| | | | | * gnu/packages/video.scm (mediainfo)[arguments]: Change to the build directory before executing the autogen script.
* gnu: linux: Fix kconfig selection.Mathieu Othacehe2017-11-07
| | | | | | * 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.
* gnu: openmpi: Add dependency on PSM.Dave Love2017-11-07
| | | | * gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM.
* gnu: libfabric: Add dependency on PSM.Dave Love2017-11-07
| | | | * gnu/packages/linux.scm (libfabric)[inputs]: Add PSM.
* gnu: Add PSM.Dave Love2017-11-07
| | | | | | | | * 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.
* gnu: diffoscope: Update to 88.Gábor Boskovits2017-11-07
| | | | | | * gnu/packages/package-management.scm (diffoscope): Update to 88. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: awesome: Update to 4.2.ng02017-11-07
| | | | | | * gnu/packages/wm.scm (awesome): Update to 4.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: gdm: Add environment variables.Timothy Sample2017-11-07
| | | | | | | | | 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>
* gnu: gdm: Add configure flags for better defaults.Timothy Sample2017-11-07
| | | | | | | * 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>
* gnu: gdm: Fix config file path.Timothy Sample2017-11-07
| | | | | | | * 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>
* gnu: expect: Change home-page to http://expect.sourceforge.net/.Oleg Pykhalov2017-11-07
| | | | | * gnu/packages/tcl.scm (expect): Change home-page to http://expect.sourceforge.net/.
* gnu: Add r-gage.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-gage): New variable.
* gnu: Add r-keggrest.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-keggrest): New variable.
* gnu: antlr3-3.3: Prettify build phases.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases "bin-install" and "generate-grammar".
* gnu: r-servr: Update to 0.8.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/web.scm (r-servr): Update to 0.8.
* gnu: r-tidyselect: Update to 0.2.3.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
* gnu: r-msnbase: Update to 2.4.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0. [propagated-inputs]: Add r-lattice; remove r-reshape2.
* gnu: r-mutationalpatterns: Update to 1.4.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0. [propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
* gnu: r-annotationhub: Update to 2.10.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0. [propagated-inputs]: Add r-curl.
* gnu: r-mzr: Remove bundled copy of boost.Ricardo Wurmus2017-11-07
| | | | | | * 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.
* gnu: r-mzr: Update to 2.12.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
* gnu: r-mzid: Update to 1.16.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
* gnu: r-chipseq: Update to 1.28.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0. [propagated-inputs]: Add r-lattice.
* gnu: r-genomicfeatures: Update to 1.30.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0. [propagated-inputs]: Add r-rmysql.
* gnu: Add r-rmysql.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/databases.scm (r-rmysql): New variable.
* gnu: r-rtracklayer: Update to 1.38.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0. [arguments]: Adjust patch to use system zlib.
* gnu: r-biocparallel: Update to 1.12.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0. [propagated-inputs]: Add r-bh.
* gnu: r-biomart: Update to 2.34.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0. [propagated-inputs]: Add r-progress and r-stringr.
* gnu: r-edger: Update to 3.20.1.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1. [propagated-inputs]: Add r-rcpp.
* gnu: r-gostats: Update to 2.44.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0. [propagated-inputs]: Add r-rgraphviz.
* gnu: r-category: Update to 2.44.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0. [propagated-inputs]: Remove r-rsqlite; add r-dbi.
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