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25422 Commits

Author SHA1 Message Date
Ricardo Wurmus b53755258a
gnu: r-systempiper: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus 9f52e53d5d
gnu: r-gseabase: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus fad7c0c7bd
gnu: r-sva: Update to 3.26.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus 91e1867972
gnu: r-methylkit: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus c126ba69db
gnu: r-copywriter: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus 598dacf657
gnu: r-annotationfilter: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus e6b332d43b
gnu: r-rhdf5: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus 19e8929cbd
gnu: r-tximport: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus da153b7f94
gnu: r-bamsignals: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus 5c18470008
gnu: r-zlibbioc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus 1d0263b44e
gnu: r-rhtslib: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus c25154e5cb
gnu: r-rbgl: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus 727706ad38
gnu: r-annotationforge: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus 3fd010ff30
gnu: r-dexseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 0166dc07ef
gnu: r-deseq2: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 554fac74aa
gnu: r-genefilter: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus cb4d3ff2c4
gnu: r-geneplotter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 2d4e887dc0
gnu: r-annotate: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 94fd86e5e1
gnu: r-dnacopy: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus c7782c3f1f
gnu: r-biocviews: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0.
[propagated-inputs]: Remove r-knitr.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus 7373b4167a
gnu: r-bioccheck: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0.
[native-inputs]: Remove which.
[propagated-inputs]: Add r-stringdist.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus a40a04fdbb
gnu: Add r-stringdist. 
* gnu/packages/cran.scm (r-stringdist): New variable.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus 8ca2b2b06e
gnu: r-rgraphviz: Update to 2.22.0. 
* gnu/packages/graph.scm (r-rgraphviz): Update to 2.22.0.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus 25e51b1c45
guix: Add archive support for bioconductor-uri. 
* guix/build-system/r.scm (bioconductor-uri): Also return the archive URL.
* guix/import/cran.scm (latest-bioconductor-release, fetch-description):
Adjust because bioconductor-uri now returns a list.
 2017-11-07 08:14:09 +01:00
Ricardo Wurmus 27baf50956
import: cran: Use Bioconductor 3.6 helpers. 
* guix/import/cran.scm (bioconductor-mirror-url): Remove procedure.
(fetch-description): Extract DESCRIPTION file from tarball for Bioconductor
packages.
(latest-bioconductor-release): Use latest-bioconductor-package-version.
 2017-11-07 08:13:35 +01:00
Ricardo Wurmus 84dfdc5759
import: cran: Add support for Bioconductor 3.6. 
* guix/import/cran.scm (%bioconductor-version,
%bioconductor-packages-list-url): New variables.
(bioconductor-packages-list, latest-bioconductor-package-version): New
procedures.
 2017-11-07 08:13:34 +01:00
Ricardo Wurmus 6b46b04f91
import: utils: Add string helpers. 
* guix/import/utils.scm (read-lines, chunk-lines): New procedures.
 2017-11-07 08:07:51 +01:00
Eric Bavier 89618fa8b8
build: Conditionally build json importer. 
* Makefile.am (MODULES): Add guix/scripts/import/json.scm when HAVE_GUILE_JSON.
 2017-11-06 17:27:43 -06:00
Ludovic Courtès a0e4b41b40
gnu: guile-git: Update snapshot. 
* gnu/packages/guile.scm (guile-git): Update to commit 951a32c.
 2017-11-07 00:12:11 +01:00
Brendan Tildesley fedde43b6d
gnu: moka-icon-theme: Fix license. 
* gnu/packages/gnome.scm (moka-icon-theme): Add cc-by-sa4.0 to license field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley 550281fb5f
gnu: moka-icon-theme: Add faba-icon-theme as propagated input. 
* gnu/packages/gnome.scm (moka-icon-theme)[propagated-inputs]: New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley 8b0e4177ee
gnu: moka-icon-theme: Simplify package definition. 
* gnu/packages/gnome.scm (moka-icon-theme): Inherit faba-icon-theme to avoid
  duplicating similar package definition.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Brendan Tildesley d935e6a12c
gnu: Add faba-icon-theme. 
* gnu/packages/gnome.scm (faba-icon-theme): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:11 +01:00
Carlo Zancanaro 47bd32d98e
gnu: electrum: Update to 3.0. 
gnu/packages/finance.scm (electrum): Update to 3.0.
[inputs]: Change to python3 inputs.
[arguments]: Remove python-2. Disable tests.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:10 +01:00
Carlo Zancanaro ea0421bbf6
gnu: Add python-jsonrpclib-pelix. 
* gnu/packages/python.scm (python-jsonrpclib-pelix, python2-jsonrpclib-pelix):
New variables.

Co-authored-by: Ludovic Courtès <ludo@gnu.org>
 2017-11-07 00:12:10 +01:00
Ludovic Courtès 8e57e416c0
refresh: Account for hidden packages. 
Suggested by Marius Bakke <mbakke@fastmail.com>
in <https://bugs.gnu.org/29177>.

* guix/scripts/refresh.scm (all-packages): Pass #:select? to
'fold-packages'.
 2017-11-07 00:12:10 +01:00
Ludovic Courtès 96dc8f3527
packages: 'fold-packages' takes #:select? parameter. 
* gnu/packages.scm (fold-packages): Add #:select? parameter and honor it.
 2017-11-07 00:12:10 +01:00
Ludovic Courtès c9405c461b
compile: Fix VPATH builds. 
Fixes <https://bugs.gnu.org/29091>.
Reported by Eric Bavier <bavier@cray.com>.

* guix/build/compile.scm (relative-file): New procedure.
(load-files): Use it before calling 'file-name->module-name'.
(compile-files): Likewise before calling 'scm->go'.
* guix/build/pull.scm (build-guix): Remove 'with-directory-excursion'
and file name hack from ce33c3af76.
Pass OUT to 'all-scheme-files'.
 2017-11-07 00:12:10 +01:00
Ludovic Courtès 0ad5f80982
Fix ambiguous imports. 
* gnu/packages/ocaml.scm: Hide 'zip' from (srfi srfi-1).
* guix/git.scm: Select 'mkdir-p' from (guix build utils).
 2017-11-07 00:12:10 +01:00
Efraim Flashner 913027f383
gnu: nnn: Update to 1.5. 
* gnu/packages/admin.scm (nnn): Update to 1.5.
 2017-11-06 23:07:19 +02:00
Efraim Flashner 6a534909fa
gnu: libuninameslist: Update to 20170807. 
* gnu/packages/fontutils.scm (libuninameslist): Update to 20170807.
 2017-11-06 23:07:13 +02:00
Efraim Flashner 10b159a303
gnu: u-boot: Only install 'MLO' output if it exists. 
* gnu/packages/bootloaders.scm (u-boot)[arguments]: Add 'MLO' to
uboot-files only if it has been built.
 2017-11-06 22:54:28 +02:00
Mathieu Othacehe b1a3079347
system: vm: Use 2^32 - 1 as hash size. 
* gnu/system/vm.scm (operating-system-uuid): Use 2^32 - 1 instead of
  2^32 as hash size.

On some 32 bit system (ARM for example), 2^32 exceeds hash max
size (ULONG_MAX = 2^32 - 1).
 2017-11-06 20:02:25 +01:00
Mathieu Othacehe dd208b936c
bootloaders: uboot: Add .img and MLO files to binary outputs. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Add .img and MLO files
  as binary output.
 2017-11-06 19:58:21 +01:00
Mathieu Othacehe f6948189a9
linux: Add omap2plus generic kernel. 
* gnu/packages/linux.scm (linux-libre-arm-omap2plus): New exported variable.
 2017-11-06 19:55:10 +01:00
Mathieu Othacehe 2ac42fe51f
gnu: uboot: Fix same-arch? check. 
* gnu/packages/bootloaders.scm (make-u-boot-package): Compare %current-system
  to system associated to given triplet. Comparing a system and a triplet
  didn't make sense.
 2017-11-06 19:53:13 +01:00
Efraim Flashner d298e7652a
gnu: perl-test-www-mechanize-psgi: Update source uri. 
* gnu/packages/web.scm (perl-test-www-mechanize-psgi)[source]: Update to
new source uri.
 2017-11-06 20:39:45 +02:00
Efraim Flashner 12c613b548
gnu: dtc: Build python bindings. 
* gnu/packages/bootloaders.scm (dtc)[native-inputs]: Add swig.
[inputs]: Add python-2.
[arguments]: Remove 'NO_PYTHON' from make-flags, add 'SETUP_PREFIX' to
set python bindings prefix.
 2017-11-06 20:39:45 +02:00
Efraim Flashner ab8757c5b1
gnu: dtc: Update to 1.4.5. 
* gnu/packages/bootloaders.scm (dtc): Update to 1.4.5.
[arguments]: Add NO_PYTHON flag to make-flags.
 2017-11-06 20:39:45 +02:00
Efraim Flashner 9371600ec8
gnu: libxres: Update to 1.2.0. 
* gnu/packages/xorg.scm (libxres): Update to 1.2.0.
 2017-11-06 20:02:45 +02:00