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Author SHA1 Message Date
Ricardo Wurmus
146f0ba5d1
gnu: r-genomicranges: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.36.1.
 2019-09-14 23:39:12 +02:00
Ricardo Wurmus
7f518ef70b
gnu: r-s4vectors: Update to 0.22.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.22.1.
 2019-09-14 23:39:08 +02:00
Ricardo Wurmus
11f973e093
gnu: r-mixomics: Update to 6.8.4. 
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.4.
 2019-09-14 23:39:03 +02:00
Ricardo Wurmus
f8fb5b75c9
gnu: r-gtrellis: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.16.1.
 2019-09-14 23:38:58 +02:00
Ricardo Wurmus
ec0270b1e9
gnu: r-regioner: Update to 1.16.4. 
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.4.
 2019-09-14 23:38:51 +02:00
Björn Höfling
cd75c487c8
gnu: Add emacs-elixir-mode. 
* gnu/packages/emacs-xyz.scm (emacs-elixir-mode): New variable.
 2019-09-14 19:44:40 +02:00
Rutger Helling
fda8ed0eb1
gnu: wine-staging: Update to 4.16. 
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 4.16.
* gnu/packages/wine.scm (wine-staging): Update to 4.16.
 2019-09-14 13:01:28 +02:00
Ricardo Wurmus
6e377b8893
import/utils: beautify-description: Recognize more fragments. 
* guix/import/utils.scm (beautify-description): Handle additional common
initial sentence fragments in descriptions.
 2019-09-14 00:37:47 +02:00
Ricardo Wurmus
981dcc3b0c
gnu: r-tidyr: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-tidyr): Update to 1.0.0.
[propagated-inputs]: Add r-ellipsis, r-lifecycle, and r-vctrs.
 2019-09-14 00:37:47 +02:00
Ricardo Wurmus
17f3960f28
gnu: r-diffusionmap: Update to 1.2.0. 
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.2.0.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
fd399b7a83
gnu: r-seqinr: Update to 3.6-1. 
* gnu/packages/cran.scm (r-seqinr): Update to 3.6-1.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
f5b1354fdb
gnu: Add r-lifecycle. 
* gnu/packages/cran.scm (r-lifecycle): New variable.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
cd3ba9c8c7
gnu: r-huge: Update to 1.3.3. 
* gnu/packages/cran.scm (r-huge): Update to 1.3.3.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
ac50956f31
gnu: r-tidytree: Update to 0.2.7. 
* gnu/packages/cran.scm (r-tidytree): Update to 0.2.7.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
aef5e2aadd
gnu: r-activity: Update to 1.3. 
* gnu/packages/cran.scm (r-activity): Update to 1.3.
[propagated-inputs]: Add r-insol.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
d72da21d54
gnu: r-sjplot: Update to 2.7.1. 
* gnu/packages/cran.scm (r-sjplot): Update to 2.7.1.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
664e15ed8f
gnu: r-sjstats: Update to 0.17.6. 
* gnu/packages/cran.scm (r-sjstats): Update to 0.17.6.
[propagated-inputs]: Add r-parameters.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
28110e6842
gnu: r-emmeans: Update to 1.4.1. 
* gnu/packages/cran.scm (r-emmeans): Update to 1.4.1.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
3ab3f7f3bb
gnu: r-sjlabelled: Update to 1.1.1. 
* gnu/packages/cran.scm (r-sjlabelled): Update to 1.1.1.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
4557f44755
gnu: r-circlize: Update to 0.4.8. 
* gnu/packages/cran.scm (r-circlize): Update to 0.4.8.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
a1f4399438
gnu: r-httpuv: Update to 1.5.2. 
* gnu/packages/cran.scm (r-httpuv): Update to 1.5.2.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
5ad9da9ab3
gnu: Add r-insol. 
* gnu/packages/cran.scm (r-insol): New variable.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
a0244ef000
gnu: Add r-rgdal. 
* gnu/packages/cran.scm (r-rgdal): New variable.
 2019-09-14 00:37:46 +02:00
Ricardo Wurmus
a5a79dd0b8
gnu: Add r-parameters. 
* gnu/packages/cran.scm (r-parameters): New variable.
 2019-09-14 00:37:45 +02:00
Efraim Flashner
18a613fb29
gnu: gnujump: Add desktop file. 
This fixes bug#37069.

* gnu/packages/games.scm (gnujump)[arguments]: Add custom
'create-desktop-entry phase to install a desktop file.
 2019-09-13 17:07:16 +03:00
Efraim Flashner
dbb0b06eb4
gnu: tipp10: Fix path in desktop entry. 
* gnu/packages/patches/tipp10-fix-compiling.patch: Remove changes to
hardcode executable path.
 2019-09-13 17:07:13 +03:00
Paul Garlick
0746c33eff
gnu: gmsh: Update home page. 
This addresses a 'guix lint' warning.

* gnu/packages/maths.scm (gmsh)[home-page]: Update to avoid URL
redirection.
 2019-09-13 14:53:57 +01:00
Efraim Flashner
f61f424d5b
gnu: mcron: Update to 1.1.2. 
* gnu/packages/guile-xyz.scm (mcron): Update to 1.1.2.
[arguments]: Remove custom 'set-timezone phase.
[native-inputs]: Add autoconf, automake, help2man, texinfo.
[inputs]: Remove ed, which.
 2019-09-13 16:02:31 +03:00
Efraim Flashner
f0e149752a
gnu: shellutils.scm: Sort module inputs. 
* gnu/packages/shellutils.scm: Sort module inputs alphabetically.
 2019-09-13 15:39:43 +03:00
Collin J. Doering
8ebd56ea75
gnu: Add zsh-autosuggestions. 
* gnu/packages/shellutils.scm (zsh-autosuggestions): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-09-13 15:39:34 +03:00
Collin J. Doering
9c4cb1ef4c
gnu: Add ruby-rspec-wait. 
* gnu/packages/ruby.scm (ruby-rspec-wait): New variable.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2019-09-13 15:39:28 +03:00
Efraim Flashner
3af85f832d
build-system/cargo: Remove unused function. 
* guix/build/cargo-build-system.scm (touch): Remove it.
 2019-09-13 15:20:27 +03:00
Efraim Flashner
43ffa11fdc
build-system/cargo: Use 'strip-store-file-name'. 
This is a follow-up to f58b2f38e4.

* guix/build/cargo-build-system.scm (configure): Use bespoke
'strip-store-file-name' function.
 2019-09-13 15:20:16 +03:00
Collin J. Doering
f69f37d54a
gnu: Add sh-z shell tool 
* gnu/packages/shellutils.scm (sh-z): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-13 10:50:11 +02:00
L p R n d n
a00a3132c7
gnu: Thunar: Update to 1.8.9. 
* gnu/packages/xfce.scm (thunar): Update to 1.8.9.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-13 10:50:11 +02:00
Ludovic Courtès
ba05be2249
gnu: openblas: Set 'NUM_THREADS'. 
Until now, OpenBLAS would use at most the N threads, where N is the
number of cores that happened to be available on the build
machine (typically N=8).

* gnu/packages/maths.scm (openblas/fixed-num-threads): New variable.
(openblas)[replacement]: New field.
(openblas-ilp64): Use 'package/inherit'.
 2019-09-13 10:50:11 +02:00
Ricardo Wurmus
5ad0a45221
gnu: python-matplotlib-documentation: Add missing input. 
* gnu/packages/python-xyz.scm (python-matplotlib-documentation)[native-inputs]:
Add python-sphinx-copybutton.
(python2-matplotlib-documentation)[native-inputs]: Remove
python-sphinx-copybutton.
 2019-09-13 00:44:57 +02:00
Ricardo Wurmus
bcb22b3624
gnu: Add python-sphinx-copybutton. 
* gnu/packages/sphinx.scm (python-sphinx-copybutton): New variable.
 2019-09-13 00:44:57 +02:00
Ricardo Wurmus
5ea654cfe0
gnu: python-matplotlib: Update to 3.1.1. 
* gnu/packages/python-xyz.scm (python-matplotlib): Update to 3.1.1.
[native-inputs]: Remove python-nose; add python-pytest and unzip; add
jquery-ui.
[arguments]: Add build phases "fix-and-disable-failing-tests" and
"install-jquery-ui", and move the "check" phase after the "install" phase;
use the default backend in setup.cfg.
(python2-matplotlib): Keep at version 2.2.3.
(python-matplotlib-documentation)[arguments]: Remove "check" phase.
 2019-09-13 00:44:57 +02:00
Wiktor Żelazny
16fddf17f5
gnu: Add r-assertr. 
* gnu/packages/cran.scm (r-assertr): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-09-13 00:44:57 +02:00
Brian Leung
86ce3691e1
gnu: emacs-interactive-align: Update to 0.4.2. 
* gnu/packages/emacs-xyz.scm (emacs-interactive-align): Update to 0.4.2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-12 23:23:47 +02:00
Tim Gesthuizen
2151e04c1a
gnu: Add emacs-doom-themes. 
* gnu/packages/emacs-xyz.scm (emacs-doom-themes): New variable.

Co-authored-by: Brett Gilio <brettg@posteo.net>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2019-09-12 23:22:19 +02:00
Ludovic Courtès
d236cd16a7
linux-container: "run-container" scripts shows the container's PID. 
* gnu/build/linux-container.scm (call-with-container): Add
 #:process-spawned-hook and honor it.
* gnu/system/linux-container.scm (container-script)[script]:
Define 'explain' and pass it as #:process-spawned-hook'.
 2019-09-12 23:07:43 +02:00
Ludovic Courtès
3d8424a5ad
services: Fix /usr/bin/env special file target. 
This is a followup to a916215597.

* gnu/services/base.scm (%base-services): Fix "/usr/bin/env" target.
 2019-09-12 23:07:42 +02:00
Ludovic Courtès
da966a7a3d
linux-container: Exclude more services when sharing networking with the host. 
* gnu/system/linux-container.scm (containerized-operating-system)[useless-services]:
Add more services to the list when SHARED-NETWORK? is true.
 2019-09-12 23:07:42 +02:00
Ludovic Courtès
5ccec77176
file-systems: Add /var/run/nscd to '%network-file-mappings'. 
This allows containers created by "guix environment -CN" or by
"guix system container -N" to talk to the host nscd.

* gnu/system/file-systems.scm (%network-file-mappings): Add
"/var/run/nscd".
* gnu/build/shepherd.scm (default-mounts)[nscd-socket]: Remove.
* gnu/system/linux-container.scm (container-script)[nscd-run-directory]
[nscd-mapping, nscd-os, nscd-specs]: Remove.
[script]: Filter out from SPECS bind-mounts where the device does not
exist.
* guix/scripts/environment.scm (launch-environment/container)
[optional-mapping->fs]: New procedure.
[mappings]: Remove %NETWORK-FILE-MAPPINGS.
[file-systems]: Add %NETWORK-FILE-MAPPINGS here, filtered through
'optional-mapping->fs'.
 2019-09-12 23:07:42 +02:00
Efraim Flashner
f58b2f38e4
build: cargo-build-system: Strip store hash from vendor-dir. 
* guix/build/cargo-build-system.scm (configure): When copying the
sources into the vendor-dir strip off the hash before the package name.
 2019-09-12 20:22:46 +03:00
Paul Garlick
abed5df777
gnu: gmsh: Fetch source from Git. 
* gnu/packages/maths.scm (gmsh)[source]: Switch to GIT-FETCH.
 2019-09-12 16:21:31 +01:00
Maxim Cournoyer
e2fb29b792
gnu: python-pytest-virtualenv: Enable tests. 
* gnu/packages/python-check.scm (python-pytest-virtualenv)
[phases]{patch-virtualenv-executable}: New phase.
[propagated-inputs]: Move python-virtualenv from here...
[inputs]: ...to here.
 2019-09-13 00:10:35 +09:00
Maxim Cournoyer
01a53e0b37
gnu: python-pathpy: Add a missing propagated input. 
This fixes the build of 'python-pytest-shutil', amongst others.

* gnu/packages/python-xyz.scm (python-pathpy)[propagated-inputs]: Add
python-importlib-metadata.
 2019-09-13 00:09:50 +09:00