fd23d259cd
gnu: 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.
2017-11-07 18:09:13 +01:00
63b7fbe1bb
gnu: diffoscope: Update to 88.
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* gnu/packages/package-management.scm (diffoscope): Update to 88.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 18:09:13 +01:00
db0164b21f
gnu: awesome: Update to 4.2.
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* gnu/packages/wm.scm (awesome): Update to 4.2.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-11-07 18:09:13 +01:00
3eda8dd614
services: gdm: Add environment variables.
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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>
2017-11-07 18:09:13 +01:00
51bc8357e8
gnu: gdm: Add configure flags for better defaults.
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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>
2017-11-07 18:09:13 +01:00
950d8e5d8c
gnu: gdm: Fix config file path.
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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>
2017-11-07 18:09:13 +01:00
25a5b187e8
hydra: Build hidden packages.
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* build-aux/hydra/gnu-system.scm (all-packages): Pass #:select? to
'fold-packages'.
2017-11-07 18:09:12 +01:00
b5033c5a9e
hydra: Factorize package list creation.
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* build-aux/hydra/gnu-system.scm (all-packages): New procedure, with
body taken from...
(hydra-jobs): ... here. Use it.
2017-11-07 18:09:12 +01:00
ad54924285
gnu: expect: Change home-page to http://expect.sourceforge.net/ .
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* gnu/packages/tcl.scm (expect): Change home-page to
http://expect.sourceforge.net/ .
2017-11-07 18:50:46 +03:00
e160aa1f81
gnu: Add r-gage.
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* gnu/packages/bioinformatics.scm (r-gage): New variable.
2017-11-07 12:39:51 +01:00
3121814ef1
gnu: Add r-keggrest.
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* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
2017-11-07 12:39:51 +01:00
a9540107c6
gnu: antlr3-3.3: Prettify build phases.
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* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases
"bin-install" and "generate-grammar".
2017-11-07 12:39:50 +01:00
9ecc4c69eb
gnu: r-servr: Update to 0.8.
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* gnu/packages/web.scm (r-servr): Update to 0.8.
2017-11-07 08:15:45 +01:00
60ec9da3aa
gnu: r-tidyselect: Update to 0.2.3.
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* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
2017-11-07 08:15:44 +01:00
baa00ee90d
gnu: r-msnbase: Update to 2.4.0.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
2017-11-07 08:15:44 +01:00
39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0.
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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.
2017-11-07 08:15:44 +01:00
14b3c71911
gnu: r-annotationhub: Update to 2.10.0.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
2017-11-07 08:15:44 +01:00
15ca195979
gnu: r-mzr: Remove bundled copy of boost.
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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.
2017-11-07 08:15:44 +01:00
34b9675449
gnu: r-mzr: Update to 2.12.0.
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* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
2017-11-07 08:15:43 +01:00
b500dbcdef
gnu: r-mzid: Update to 1.16.0.
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* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
2017-11-07 08:15:43 +01:00
eeaa6967f9
gnu: r-chipseq: Update to 1.28.0.
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* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
2017-11-07 08:15:43 +01:00
158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
2017-11-07 08:15:43 +01:00
74248d22a0
gnu: Add r-rmysql.
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* gnu/packages/databases.scm (r-rmysql): New variable.
2017-11-07 08:15:43 +01:00
4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
2017-11-07 08:15:42 +01:00
a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
2017-11-07 08:15:42 +01:00
42e11d3301
gnu: r-biomart: Update to 2.34.0.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
2017-11-07 08:15:42 +01:00
010ab2ffd2
gnu: r-edger: Update to 3.20.1.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
2017-11-07 08:15:42 +01:00
eb3f5cc76a
gnu: r-gostats: Update to 2.44.0.
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* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
2017-11-07 08:15:41 +01:00
2404cc4283
gnu: r-category: Update to 2.44.0.
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* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
2017-11-07 08:15:41 +01:00
65a8cd6676
gnu: r-lubridate: Update to 1.7.1.
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* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1.
[propagated-inputs]: Add r-rcpp.
2017-11-07 08:15:41 +01:00
689edf1153
gnu: r-preprocesscore: Update to 1.40.0.
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* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.40.0.
2017-11-07 08:15:41 +01:00
e7f680f071
gnu: r-r-utils: Update to 2.6.0.
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* gnu/packages/statistics.scm (r-r-utils): Update to 2.6.0.
2017-11-07 08:15:41 +01:00
ecfe98a17a
gnu: r-openssl: Update to 0.9.8.
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* gnu/packages/statistics.scm (r-openssl): Update to 0.9.8.
2017-11-07 08:15:40 +01:00
aced057fbc
gnu: r-rlang: Update to 0.1.4.
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* gnu/packages/statistics.scm (r-rlang): Update to 0.1.4.
2017-11-07 08:15:40 +01:00
1be0f53664
gnu: r-vsn: Update to 3.46.0.
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* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0.
[propagated-inputs]: Remove r-hexbin.
2017-11-07 08:15:40 +01:00
007424b5a5
gnu: r-motifrg: Rename input label.
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* gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]:
Rename label of r-bsgenome-hsapiens-ucsc-hg19.
2017-11-07 08:15:40 +01:00
ce59d62519
gnu: r-motifrg: Update to 1.22.0.
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* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
2017-11-07 08:15:40 +01:00
98791c25c8
gnu: r-qvalue: Update to 2.10.0.
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* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
2017-11-07 08:15:39 +01:00
87fa5aface
gnu: r-fastseq: Update to 1.24.0.
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* gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
2017-11-07 08:15:39 +01:00
1567c8d91b
gnu: r-interactivedisplaybase: Update to 1.16.0.
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* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.16.0.
2017-11-07 08:15:39 +01:00
0096127974
gnu: r-edaseq: Update to 2.12.0.
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* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
2017-11-07 08:15:39 +01:00
22752bef3b
gnu: r-msnid: Update to 1.11.0.
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* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
2017-11-07 08:15:38 +01:00
8140f680ad
gnu: r-deseq: Update to 1.30.0.
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* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
2017-11-07 08:15:38 +01:00
531e80903f
gnu: r-aroma-light: Update to 3.8.0.
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* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
2017-11-07 08:15:38 +01:00
a998c9a464
gnu: r-pcamethods: Update to 1.70.0.
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* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
2017-11-07 08:15:38 +01:00
8a8138d248
gnu: r-affyio: Update to 1.48.0.
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* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
2017-11-07 08:15:38 +01:00
dad5f83817
gnu: r-affy: Update to 1.56.0.
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* gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
2017-11-07 08:15:37 +01:00
9a665dfb6f
gnu: r-protgenerics: Update to 1.10.0.
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* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.10.0.
2017-11-07 08:15:37 +01:00
617700895b
gnu: r-seqlogo: Update to 1.44.0.
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* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.44.0.
2017-11-07 08:15:37 +01:00
e127c918f8
gnu: r-genomation: Update to 1.10.0.
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* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.10.0.
[propagated-inputs]: Remove r-rhtslib.
[inputs]: Remove zlib.
2017-11-07 08:15:37 +01:00
Dave Love