| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
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* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
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* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
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* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
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* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
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* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
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* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
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* gnu/packages/xorg.scm (bdftopcf): Update to 1.1.
[native-inputs]: Change from LIBXFONT to LIBXFONT2.
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* gnu/packages/image-viewers.scm (feh): Update to 2.22.2.
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* 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.
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* gnu/packages/web.scm (websockify): New variable.
Signed-off-by: Marius Bakke <mbakke@fastmail.com>
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* 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>
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* gnu/packages/graphviz.scm (python-pydot, python2-pydot): New variables.
Modified-by: Marius Bakke <mbakke@fastmail.com>
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* gnu/packages/version-control.scm (mercurial): Update to 4.4.1.
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* gnu/packages/vim.scm (vim): Update to 8.0.1274.
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* gnu/packages/mail.scm (notmuch): Update to 0.25.2.
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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.
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* gnu/packages/linux.scm (psm)[supported-systems]: New field, limit to
i686-linux and x86_64-linux.
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* gnu/packages/gnupg.scm (gnupg): Update to 2.2.2.
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* gnu/packages/video.scm (mediainfo)[arguments]: Change to the build
directory before executing the autogen script.
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* 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.
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* gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM.
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* gnu/packages/linux.scm (libfabric)[inputs]: Add PSM.
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* 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.
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* gnu/packages/package-management.scm (diffoscope): Update to 88.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* gnu/packages/wm.scm (awesome): Update to 4.2.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* 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>
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* 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>
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* gnu/packages/tcl.scm (expect): Change home-page to
http://expect.sourceforge.net/.
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* gnu/packages/bioinformatics.scm (r-gage): New variable.
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* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
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* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases
"bin-install" and "generate-grammar".
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* gnu/packages/web.scm (r-servr): Update to 0.8.
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* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0.
[propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
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* 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.
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* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
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* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
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* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
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* gnu/packages/databases.scm (r-rmysql): New variable.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
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* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
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* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
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* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1.
[propagated-inputs]: Add r-rcpp.
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