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Author SHA1 Message Date
Ricardo Wurmus
902fb15d92
gnu: Add r-genomicfiles. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
 2017-11-07 23:32:41 +01:00
Marius Bakke
cd215877a0
gnu: bdftopcf: Update to 1.1. 
* gnu/packages/xorg.scm (bdftopcf): Update to 1.1.
[native-inputs]: Change from LIBXFONT to LIBXFONT2.
 2017-11-07 23:29:23 +01:00
Marius Bakke
d469bc09bd
gnu: feh: Update to 2.22.2. 
* gnu/packages/image-viewers.scm (feh): Update to 2.22.2.
 2017-11-07 22:16:27 +01:00
Jan Nieuwenhuizen
625492ee1a
gnu: gcc-4.7: Resurrect building with gcc-5.4.0. 
* 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.
 2017-11-07 22:03:51 +01:00
Rutger Helling
a67f094671
gnu: Add websockify. 
* gnu/packages/web.scm (websockify): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:56:42 +01:00
Gábor Boskovits
75d342ffa9
gnu: Add python-networkx2. 
* 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>
 2017-11-07 21:17:20 +01:00
Gábor Boskovits
2b295f5a2f
gnu: Add python-pydot. 
* gnu/packages/graphviz.scm (python-pydot, python2-pydot): New variables.

Modified-by: Marius Bakke <mbakke@fastmail.com>
 2017-11-07 21:03:15 +01:00
Marius Bakke
38ad27da80
gnu: mercurial: Update to 4.4.1. 
* gnu/packages/version-control.scm (mercurial): Update to 4.4.1.
 2017-11-07 20:23:29 +01:00
Marius Bakke
4a30c1c0e2
gnu: vim: Update to 8.0.1274 [fixes CVE-2017-1000382]. 
* gnu/packages/vim.scm (vim): Update to 8.0.1274.
 2017-11-07 20:21:46 +01:00
Marius Bakke
31a963fe80
gnu: notmuch: Update to 0.25.2. 
* gnu/packages/mail.scm (notmuch): Update to 0.25.2.
 2017-11-07 20:01:03 +01:00
Efraim Flashner
9129804230
gnu: psm: Only use as an input on supported-systems. 
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.
 2017-11-07 20:41:08 +02:00
Efraim Flashner
b516b78002
gnu: psm: Limit supported systems. 
* gnu/packages/linux.scm (psm)[supported-systems]: New field, limit to
i686-linux and x86_64-linux.
 2017-11-07 20:41:05 +02:00
Efraim Flashner
174807b9a4
gnu: gnupg: Update to 2.2.2. 
* gnu/packages/gnupg.scm (gnupg): Update to 2.2.2.
 2017-11-07 19:34:29 +02:00
Efraim Flashner
2f17187ff3
gnu: mediainfo: Change order of custom phases. 
* gnu/packages/video.scm (mediainfo)[arguments]: Change to the build
directory before executing the autogen script.
 2017-11-07 19:34:25 +02:00
Mathieu Othacehe
6541673354
gnu: linux: Fix kconfig selection. 
* 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.
 2017-11-07 18:16:02 +01:00
Ludovic Courtès
b574cee361
hydra: Add jobs for all of '%final-inputs'. 
* 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.
 2017-11-07 18:09:13 +01:00
Dave Love
f4433d09a1
gnu: openmpi: Add dependency on PSM. 
* gnu/packages/mpi.scm (openmpi)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love
7bc05ef0ac
gnu: libfabric: Add dependency on PSM. 
* gnu/packages/linux.scm (libfabric)[inputs]: Add PSM.
 2017-11-07 18:09:13 +01:00
Dave Love
fd23d259cd
gnu: Add PSM. 
* 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
Gábor Boskovits
63b7fbe1bb
gnu: diffoscope: Update to 88. 
* 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
ng0
db0164b21f
gnu: awesome: Update to 4.2. 
* 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
Timothy Sample
3eda8dd614
services: gdm: Add environment variables. 
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
Timothy Sample
51bc8357e8
gnu: gdm: Add configure flags for better defaults. 
* 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
Timothy Sample
950d8e5d8c
gnu: gdm: Fix config file path. 
* 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
Ludovic Courtès
25a5b187e8
hydra: Build hidden packages. 
* build-aux/hydra/gnu-system.scm (all-packages): Pass #:select? to
'fold-packages'.
 2017-11-07 18:09:12 +01:00
Ludovic Courtès
b5033c5a9e
hydra: Factorize package list creation. 
* 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
Oleg Pykhalov
ad54924285
gnu: expect: Change home-page to http://expect.sourceforge.net/. 
* gnu/packages/tcl.scm (expect): Change home-page to
  http://expect.sourceforge.net/.
 2017-11-07 18:50:46 +03:00
Ricardo Wurmus
e160aa1f81
gnu: Add r-gage. 
* gnu/packages/bioinformatics.scm (r-gage): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus
3121814ef1
gnu: Add r-keggrest. 
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus
a9540107c6
gnu: antlr3-3.3: Prettify build phases. 
* gnu/packages/java.scm (antlr3-3.3)[arguments]: Prettify build phases
"bin-install" and "generate-grammar".
 2017-11-07 12:39:50 +01:00
Ricardo Wurmus
9ecc4c69eb
gnu: r-servr: Update to 0.8. 
* gnu/packages/web.scm (r-servr): Update to 0.8.
 2017-11-07 08:15:45 +01:00
Ricardo Wurmus
60ec9da3aa
gnu: r-tidyselect: Update to 0.2.3. 
* gnu/packages/statistics.scm (r-tidyselect): Update to 0.2.3.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
baa00ee90d
gnu: r-msnbase: Update to 2.4.0. 
* 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
Ricardo Wurmus
39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0. 
* 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
Ricardo Wurmus
14b3c71911
gnu: r-annotationhub: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus
15ca195979
gnu: r-mzr: Remove bundled copy of boost. 
* 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
Ricardo Wurmus
34b9675449
gnu: r-mzr: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
b500dbcdef
gnu: r-mzid: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
eeaa6967f9
gnu: r-chipseq: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
74248d22a0
gnu: Add r-rmysql. 
* gnu/packages/databases.scm (r-rmysql): New variable.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus
4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0. 
* 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
Ricardo Wurmus
a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
42e11d3301
gnu: r-biomart: Update to 2.34.0. 
* 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
Ricardo Wurmus
010ab2ffd2
gnu: r-edger: Update to 3.20.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus
eb3f5cc76a
gnu: r-gostats: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
2404cc4283
gnu: r-category: Update to 2.44.0. 
* 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
Ricardo Wurmus
65a8cd6676
gnu: r-lubridate: Update to 1.7.1. 
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
689edf1153
gnu: r-preprocesscore: Update to 1.40.0. 
* gnu/packages/statistics.scm (r-preprocesscore): Update to 1.40.0.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus
e7f680f071
gnu: r-r-utils: Update to 2.6.0. 
* gnu/packages/statistics.scm (r-r-utils): Update to 2.6.0.
 2017-11-07 08:15:41 +01:00