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2019-09-14gnu: r-mixomics: Update to 6.8.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.8.4.
2019-09-14gnu: r-gtrellis: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gtrellis): Update to 1.16.1.
2019-09-14gnu: r-regioner: Update to 1.16.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-regioner): Update to 1.16.4.
2019-09-14gnu: Add emacs-elixir-mode.Björn Höfling
* gnu/packages/emacs-xyz.scm (emacs-elixir-mode): New variable.
2019-09-14gnu: wine-staging: Update to 4.16.Rutger Helling
* gnu/packages/wine.scm (wine-staging-patchset-data): Update to 4.16. * gnu/packages/wine.scm (wine-staging): Update to 4.16.
2019-09-14gnu: r-tidyr: Update to 1.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tidyr): Update to 1.0.0. [propagated-inputs]: Add r-ellipsis, r-lifecycle, and r-vctrs.
2019-09-14gnu: r-diffusionmap: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/graph.scm (r-diffusionmap): Update to 1.2.0.
2019-09-14gnu: r-seqinr: Update to 3.6-1.Ricardo Wurmus
* gnu/packages/cran.scm (r-seqinr): Update to 3.6-1.
2019-09-14gnu: Add r-lifecycle.Ricardo Wurmus
* gnu/packages/cran.scm (r-lifecycle): New variable.
2019-09-14gnu: r-huge: Update to 1.3.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-huge): Update to 1.3.3.
2019-09-14gnu: r-tidytree: Update to 0.2.7.Ricardo Wurmus
* gnu/packages/cran.scm (r-tidytree): Update to 0.2.7.
2019-09-14gnu: r-activity: Update to 1.3.Ricardo Wurmus
* gnu/packages/cran.scm (r-activity): Update to 1.3. [propagated-inputs]: Add r-insol.
2019-09-14gnu: r-sjplot: Update to 2.7.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-sjplot): Update to 2.7.1.
2019-09-14gnu: r-sjstats: Update to 0.17.6.Ricardo Wurmus
* gnu/packages/cran.scm (r-sjstats): Update to 0.17.6. [propagated-inputs]: Add r-parameters.
2019-09-14gnu: r-emmeans: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-emmeans): Update to 1.4.1.
2019-09-14gnu: r-sjlabelled: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-sjlabelled): Update to 1.1.1.
2019-09-14gnu: r-circlize: Update to 0.4.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-circlize): Update to 0.4.8.
2019-09-14gnu: r-httpuv: Update to 1.5.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-httpuv): Update to 1.5.2.
2019-09-14gnu: Add r-insol.Ricardo Wurmus
* gnu/packages/cran.scm (r-insol): New variable.
2019-09-14gnu: Add r-rgdal.Ricardo Wurmus
* gnu/packages/cran.scm (r-rgdal): New variable.
2019-09-14gnu: Add r-parameters.Ricardo Wurmus
* gnu/packages/cran.scm (r-parameters): New variable.
2019-09-13gnu: gnujump: Add desktop file.Efraim Flashner
This fixes bug#37069. * gnu/packages/games.scm (gnujump)[arguments]: Add custom 'create-desktop-entry phase to install a desktop file.
2019-09-13gnu: tipp10: Fix path in desktop entry.Efraim Flashner
* gnu/packages/patches/tipp10-fix-compiling.patch: Remove changes to hardcode executable path.
2019-09-13gnu: gmsh: Update home page.Paul Garlick
This addresses a 'guix lint' warning. * gnu/packages/maths.scm (gmsh)[home-page]: Update to avoid URL redirection.
2019-09-13gnu: mcron: Update to 1.1.2.Efraim Flashner
* 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.
2019-09-13gnu: shellutils.scm: Sort module inputs.Efraim Flashner
* gnu/packages/shellutils.scm: Sort module inputs alphabetically.
2019-09-13gnu: Add zsh-autosuggestions.Collin J. Doering
* gnu/packages/shellutils.scm (zsh-autosuggestions): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-09-13gnu: Add ruby-rspec-wait.Collin J. Doering
* gnu/packages/ruby.scm (ruby-rspec-wait): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2019-09-13gnu: Add sh-z shell toolCollin J. Doering
* gnu/packages/shellutils.scm (sh-z): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-09-13gnu: Thunar: Update to 1.8.9.L p R n d n
* gnu/packages/xfce.scm (thunar): Update to 1.8.9. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-09-13gnu: openblas: Set 'NUM_THREADS'.Ludovic Courtès
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'.
2019-09-13gnu: python-matplotlib-documentation: Add missing input.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-matplotlib-documentation)[native-inputs]: Add python-sphinx-copybutton. (python2-matplotlib-documentation)[native-inputs]: Remove python-sphinx-copybutton.
2019-09-13gnu: Add python-sphinx-copybutton.Ricardo Wurmus
* gnu/packages/sphinx.scm (python-sphinx-copybutton): New variable.
2019-09-13gnu: python-matplotlib: Update to 3.1.1.Ricardo Wurmus
* 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.
2019-09-13gnu: Add r-assertr.Wiktor Żelazny
* gnu/packages/cran.scm (r-assertr): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2019-09-12gnu: emacs-interactive-align: Update to 0.4.2.Brian Leung
* gnu/packages/emacs-xyz.scm (emacs-interactive-align): Update to 0.4.2. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-09-12gnu: Add emacs-doom-themes.Tim Gesthuizen
* 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>
2019-09-12linux-container: "run-container" scripts shows the container's PID.Ludovic Courtès
* 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'.
2019-09-12services: Fix /usr/bin/env special file target.Ludovic Courtès
This is a followup to a9162155975a131afa1e6a44262afbb7af91f7fd. * gnu/services/base.scm (%base-services): Fix "/usr/bin/env" target.
2019-09-12linux-container: Exclude more services when sharing networking with the host.Ludovic Courtès
* gnu/system/linux-container.scm (containerized-operating-system)[useless-services]: Add more services to the list when SHARED-NETWORK? is true.
2019-09-12file-systems: Add /var/run/nscd to '%network-file-mappings'.Ludovic Courtès
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'.
2019-09-12gnu: gmsh: Fetch source from Git.Paul Garlick
* gnu/packages/maths.scm (gmsh)[source]: Switch to GIT-FETCH.
2019-09-13gnu: python-pytest-virtualenv: Enable tests.Maxim Cournoyer
* gnu/packages/python-check.scm (python-pytest-virtualenv) [phases]{patch-virtualenv-executable}: New phase. [propagated-inputs]: Move python-virtualenv from here... [inputs]: ...to here.
2019-09-13gnu: python-pathpy: Add a missing propagated input.Maxim Cournoyer
This fixes the build of 'python-pytest-shutil', amongst others. * gnu/packages/python-xyz.scm (python-pathpy)[propagated-inputs]: Add python-importlib-metadata.
2019-09-12gnu: gfbgraph: Don't use NAME in source URI.Tobias Geerinckx-Rice
* gnu/packages/gnome.scm (gfbgraph)[source]: Hard-code NAME.
2019-09-12gnu: openconnect: Update to 8.05 [fixes CVE-2019-16239].Tobias Geerinckx-Rice
* gnu/packages/vpn.scm (openconnect): Update to 8.05.
2019-09-12gnu: hypre: Update texlive-union.Ricardo Wurmus
* gnu/packages/maths.scm (hypre)[native-inputs]: Replace texlive-generic-xypic and texlive-fonts-xypic with texlive-xypic; add texlive-cm to the texlive-union.
2019-09-12gnu: texlive-xypic: Install all files.Ricardo Wurmus
Reported by numerobis on the #guix IRC channel. * gnu/packages/tex.scm (texlive-xypic)[source]: Install "tex/generic/xypic" files. [arguments]: Remove #:tex-directory.
2019-09-12gnu: python-language-server: Update to 0.28.3-1.c3cab77.Brian Leung
* gnu/packages/python-xyz.scm (python-language-server): Update to 0.28.3-1.c3cab77. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2019-09-11gnu: r-bsgenome-celegans-ucsc-ce6: Permit substitution.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6)[arguments]: Remove field.
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