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* hydra: Add jobs for all of '%final-inputs'.Ludovic Courtès2017-11-07
| | | | | | | * build-aux/hydra/gnu-system.scm (package->job): Create a 'base.' job when PACKAGE is a member of BASE-PACKAGES. (all-packages)[adjust]: New procedure. Fold over %FINAL-INPUTS and add it to the result.
* 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>
* hydra: Build hidden packages.Ludovic Courtès2017-11-07
| | | | | * build-aux/hydra/gnu-system.scm (all-packages): Pass #:select? to 'fold-packages'.
* hydra: Factorize package list creation.Ludovic Courtès2017-11-07
| | | | | | * build-aux/hydra/gnu-system.scm (all-packages): New procedure, with body taken from... (hydra-jobs): ... here. Use it.
* 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.
* gnu: r-lubridate: Update to 1.7.1.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1. [propagated-inputs]: Add r-rcpp.
* gnu: r-preprocesscore: Update to 1.40.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/statistics.scm (r-preprocesscore): Update to 1.40.0.
* gnu: r-r-utils: Update to 2.6.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/statistics.scm (r-r-utils): Update to 2.6.0.
* gnu: r-openssl: Update to 0.9.8.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/statistics.scm (r-openssl): Update to 0.9.8.
* gnu: r-rlang: Update to 0.1.4.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/statistics.scm (r-rlang): Update to 0.1.4.
* gnu: r-vsn: Update to 3.46.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0. [propagated-inputs]: Remove r-hexbin.
* gnu: r-motifrg: Rename input label.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]: Rename label of r-bsgenome-hsapiens-ucsc-hg19.
* gnu: r-motifrg: Update to 1.22.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
* gnu: r-qvalue: Update to 2.10.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
* gnu: r-fastseq: Update to 1.24.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
* gnu: r-interactivedisplaybase: Update to 1.16.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.16.0.
* gnu: r-edaseq: Update to 2.12.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
* gnu: r-msnid: Update to 1.11.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
* gnu: r-deseq: Update to 1.30.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
* gnu: r-aroma-light: Update to 3.8.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
* gnu: r-pcamethods: Update to 1.70.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
* gnu: r-affyio: Update to 1.48.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
* gnu: r-affy: Update to 1.56.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
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