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2020-03-24gnu: r-harmony: Update to 0.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-harmony): Update to 0.1. [native-inputs]: Add autoconf.
2020-03-24gnu: r-shiny: Update to 1.4.0.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-shiny): Update to 1.4.0.2.
2020-03-24gnu: r-multiassayexperiment: Update to 1.12.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.5. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-bigpint: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bigpint): Update to 1.2.2. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-biosigner: Update to 1.14.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.14.4.
2020-03-24gnu: r-gosemsim: Update to 2.12.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.12.1. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-tximport: Update to 1.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-caret: Update to 6.0-86.Ricardo Wurmus
* gnu/packages/cran.scm (r-caret): Update to 6.0-86. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-batchtools: Update to 0.9.13.Ricardo Wurmus
* gnu/packages/cran.scm (r-batchtools): Update to 0.9.13. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-mcmc: Update to 0.9-7.Ricardo Wurmus
* gnu/packages/cran.scm (r-mcmc): Update to 0.9-7.
2020-03-24gnu: r-proc: Update to 1.16.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-proc): Update to 1.16.2.
2020-03-24gnu: r-xgboost: Update to 1.0.0.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-xgboost): Update to 1.0.0.1. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-radiant-data: Update to 1.3.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-radiant-data): Update to 1.3.4. [propagated-inputs]: Remove r-gridextra; add r-mass, r-patchwork, and r-randomizr.
2020-03-24gnu: r-patchwork: Update to 1.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-patchwork): Update to 1.0.0. [source]: Fetch from CRAN. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-igraph: Update to 1.2.5.Ricardo Wurmus
* gnu/packages/graph.scm (r-igraph): Update to 1.2.5.
2020-03-24gnu: r-robustbase: Update to 0.93-6.Ricardo Wurmus
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-6.
2020-03-24gnu: r-hmisc: Update to 4.4-0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-hmisc): Update to 4.4-0.
2020-03-24gnu: r-pkgmaker: Update to 0.31.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-pkgmaker): Update to 0.31.1.
2020-03-24gnu: r-dt: Update to 0.13.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dt): Update to 0.13. [native-inputs]: Add r-knitr.
2020-03-24gnu: r-locfit: Update to 1.5-9.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.2.
2020-03-24gnu: Add r-randomizr.Ricardo Wurmus
* gnu/packages/cran.scm (r-randomizr): New variable.
2020-03-24gnu: sbcl: Increase maximum heap size to 2Gb.Guillaume Le Vaillant
* gnu/packages/lisp.scm (sbcl)[arguments]: Add the "--dynamic-space-size=2Gb" option in the build phase.
2020-03-23gnu: dialog: Update to 1.3-20200228.Michael Rohleder
* gnu/packages/ncurses.scm (dialog): Update to 1.3-20200228. Signed-off-by: Leo Famulari <leo@famulari.name>
2020-03-23gnu: Git: Update to 2.26.0.Leo Famulari
* gnu/packages/version-control.scm (git): Update to 2.26.0. [arguments]: Adjust the 'install-credential-netrc' phase to upstream changes.
2020-03-23Revert "gnu: youtube-dl: Add 'ffmpeg' as input."Mathieu Othacehe
This reverts commit 4233e74b39635d5ef4dde204ecc26dcc894d9467.
2020-03-23gnu: Mutt: Update to 1.13.4.Leo Famulari
* gnu/packages/mail.scm (mutt): Update to 1.13.4. [source]: Prefer HTTPS URL and replace FTP URL with HTTP.
2020-03-23gnu: sord: Add pcre to inputs.Alexandros Theodotou
* gnu/packages/rdf.scm (sord)[inputs]: Add pcre needed for sord_validate.
2020-03-23gnu: youtube-dl: Add zsh completion.Brice Waegeneire
* gnu/packages/video.scm (youtube-dl)[arguments]: Add phase install-completion. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2020-03-23gnu: youtube-dl: Add 'ffmpeg' as input.Brice Waegeneire
* gnu/packages/video.scm (youtube-dl)[arguments]: Add phase wrap-executable. [inputs]: Add ffmpeg. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2020-03-23system: Export 'operating-system-kernel-loadable-modules'.Brice Waegeneire
* gnu/system.scm: Export 'operating-system-kernel-loadable-modules'. Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
2020-03-23gnu: emacs-lua-mode: Update to 20191204.Maxim Cournoyer
* (emacs-lua-mode): Update to 20191204.
2020-03-23gnu: emacs-ert-runner: Update to 0.8.0.Maxim Cournoyer
* (emacs-ert-runner): Update to 0.8.0.
2020-03-23gnu: emacs-dash: Update to 2.17.0.Maxim Cournoyer
* (emacs-dash): Update to 2.17.0.
2020-03-23installer: Fix cow-store umount issue.Mathieu Othacehe
* gnu/installer/final.scm (kill-cow-users): Ignore exception that could be raised if a process disappears between reading its pid and its maps file.
2020-03-23gnu: parallel: Update to 20200322.Tobias Geerinckx-Rice
* gnu/packages/parallel.scm (parallel): Update to 20200322.
2020-03-23gnu: extremetuxracer: Update to 0.8.0.Tobias Geerinckx-Rice
* gnu/packages/games.scm (extremetuxracer): Update to 0.8.0.
2020-03-23gnu: Add zlfo.Alexandros Theodotou
* gnu/packages/music.scm (zlfo): New variable. Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
2020-03-23gnu: Add ztoolkit-rsvg.Alexandros Theodotou
* gnu/packages/audio.scm (ztoolkit-rsvg): New variable. Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net> [with modifications]
2020-03-23gnu: Add ztoolkit.Alexandros Theodotou
* gnu/packages/audio.scm (ztoolkit): New variable. Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
2020-03-23gnu: Add circos.Roel Janssen
* gnu/local.mk: Register circos-remove-findbin.patch. * gnu/packages/patches/circos-remove-findbin.patch: New file. * gnu/packages/perl.scm: New variable.
2020-03-23gnu: Add python-gcovr.Alexandros Theodotou
* gnu/packages/python-xyz.scm (python-gcovr): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-23gnu: Add lv2toweb.Alexandros Theodotou
* gnu/packages/audio.scm (lv2toweb): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-03-23machine: ssh: Better report missing initrd modules.Ludovic Courtès
* gnu/machine/ssh.scm (machine-check-initrd-modules): Improve message upon module mismatch.
2020-03-23machine: ssh: Make sanity checks in a single round trip.Ludovic Courtès
* gnu/machine/ssh.scm (<remote-assertion>): New record type. (remote-let): New macro. (machine-check-file-system-availability): Rewrite to use 'remote-let' instead of 'mlet' and 'machine-remote-eval'. (machine-check-initrd-modules): Likewise. (machine-check-building-for-appropriate-system): Make non-monadic. (check-deployment-sanity): Rewrite to gather all the assertions as a single gexp and pass it to 'machine-remote-eval'.
2020-03-23Re-order the armhf linux-libre kernel packages to fix the build.Leo Famulari
This is a followup to commit 37f8c50cdc2e99189c74999319f3a1854d419546. Previously, building Guix crashed like this: ------ In ice-9/eval.scm: 619:8 4 (_ #f) 626:19 3 (_ #<directory (gnu packages linux) 7fcf3e526c80>) 159:9 2 (_ #<directory (gnu packages linux) 7fcf3e526c80>) 223:20 1 (proc #<directory (gnu packages linux) 7fcf3e526c80>) In unknown file: 0 (%resolve-variable (7 . linux-libre-arm-generic) #<directory (gnu packages linux) 7fcf3e526c80>) ERROR: In procedure %resolve-variable: error: linux-libre-arm-generic: unbound variable ------ * gnu/packages/linux.scm (linux-libre-arm-veyron): Move after linux-libre-arm-generic.
2020-03-22gnu: Add linux-libre-arm64-generic.Vagrant Cascadian
* gnu/packages/linux (linux-libre-arm64-generic): New variable.
2020-03-22gnu: linux-libre-arm-veyron: Deprecate package.Vagrant Cascadian
* gnu/packages/linux (linux-libre-arm-veyron): Mark as deprecated package. (kernel-config-veyron): Remove obsolete function. * gnu/system/examples/asus-c201.tmpl: Update to use linux-libre-arm-generic. * gnu/packages/aux-files/linux-libre/5.4-arm-veyron.conf: Delete file. * Makefile.am (AUX_FILES): Update accordingly.
2020-03-22gnu: emacs-elpy: Update to 1.32.0.Maxim Cournoyer
* gnu/packages/emacs-xyz.scm (emacs-elpy): Update to 1.32.0. [phases]{fake-virtualenv}: Rename to 'do-not-use-virtualenv. Use the new ELPY_TEST_DONT_USE_VIRTUALENV environment variable to skip tests using virtualenv, and set the elpy-rpc-virtualenv-path default value to 'system so that a virtualenv is not needed. [native-inputs]: Move the Python dependencies to... [propagated] ...here. This is so that Elpy doesn't nag users with fetching those from PyPI. Add python-rope. Fixes <https://bugs.gnu.org/40079>. Reported-by: sirgazil <sirgazil@zoho.com>
2020-03-22gnu: emacs: Patch references to /bin/sh.Maxim Cournoyer
When attempting to run ert-runner in the build side environment where /bin/sh doesn't exist as part of the emacs-elpy test suite, Emacs was throwing the error "Searching for program: No such file or directory, /bin/sh". This is because the default shell when SHELL is not set was "/bin/sh", as can be seen in callproc.c: sh = getenv ("SHELL"); Vshell_file_name = build_string (sh ? sh : "/bin/sh"); Thus, patch the occurrences of "/bin/sh" in the source files of Emacs to refer to their correct store location. * gnu/packages/emacs.scm (emacs)[phases]{patch-program-file-names}: Add phase.
2020-03-22gnu: emacs-minimal: Install the custom site-start file.Maxim Cournoyer
This makes the EMACS-MINIMAL package more generally useful, by adding support to load autoload definitions. Note that this doesn't negatively impact the performance of the emacs-build-system, because at that time the --quick option is used, which disables loading site-start.el (which is the one calling GUIX-EMACS-AUTOLOAD-PACKAGES). * gnu/packages/emacs.scm (emacs-minimal)[phases]: Do not delete the 'install-site-start phase. [inputs]: Add the emacs/guix-emacs.el auxiliary file.
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