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Author SHA1 Message Date
Ricardo Wurmus 1f2f01aed5
gnu: r-bigpint: Update to 1.2.2. 
* gnu/packages/bioconductor.scm (r-bigpint): Update to 1.2.2.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:01 +01:00
Ricardo Wurmus 4bcb38c801
gnu: r-biosigner: Update to 1.14.4. 
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.14.4.
 2020-03-24 11:06:01 +01:00
Ricardo Wurmus d5951dc43a
gnu: r-gosemsim: Update to 2.12.1. 
* gnu/packages/bioconductor.scm (r-gosemsim): Update to 2.12.1.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:01 +01:00
Ricardo Wurmus c649d31957
gnu: r-tximport: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus c10bef9bd3
gnu: r-caret: Update to 6.0-86. 
* gnu/packages/cran.scm (r-caret): Update to 6.0-86.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus 1e40a27465
gnu: r-batchtools: Update to 0.9.13. 
* gnu/packages/cran.scm (r-batchtools): Update to 0.9.13.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus 6005efa40f
gnu: r-mcmc: Update to 0.9-7. 
* gnu/packages/cran.scm (r-mcmc): Update to 0.9-7.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus d3836473de
gnu: r-proc: Update to 1.16.2. 
* gnu/packages/cran.scm (r-proc): Update to 1.16.2.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus c5036a4f39
gnu: r-xgboost: Update to 1.0.0.1. 
* gnu/packages/cran.scm (r-xgboost): Update to 1.0.0.1.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus 2f445f0da3
gnu: r-radiant-data: Update to 1.3.4. 
* 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.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus ff248f41cb
gnu: r-patchwork: Update to 1.0.0. 
* gnu/packages/cran.scm (r-patchwork): Update to 1.0.0.
[source]: Fetch from CRAN.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus d8dc2a7c1e
gnu: r-igraph: Update to 1.2.5. 
* gnu/packages/graph.scm (r-igraph): Update to 1.2.5.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus f7a21df523
gnu: r-robustbase: Update to 0.93-6. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.93-6.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus 7e349066e6
gnu: r-hmisc: Update to 4.4-0. 
* gnu/packages/statistics.scm (r-hmisc): Update to 4.4-0.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus 670cbe2c3c
gnu: r-pkgmaker: Update to 0.31.1. 
* gnu/packages/statistics.scm (r-pkgmaker): Update to 0.31.1.
 2020-03-24 11:06:00 +01:00
Ricardo Wurmus d16a4d1f96
gnu: r-dt: Update to 0.13. 
* gnu/packages/statistics.scm (r-dt): Update to 0.13.
[native-inputs]: Add r-knitr.
 2020-03-24 11:05:59 +01:00
Ricardo Wurmus f871696911
gnu: r-locfit: Update to 1.5-9.2. 
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.2.
 2020-03-24 11:05:59 +01:00
Ricardo Wurmus e0d6a7da74
gnu: Add r-randomizr. 
* gnu/packages/cran.scm (r-randomizr): New variable.
 2020-03-24 11:05:59 +01:00
Guillaume Le Vaillant 47a2306415
gnu: sbcl: Increase maximum heap size to 2Gb. 
* gnu/packages/lisp.scm (sbcl)[arguments]: Add the "--dynamic-space-size=2Gb"
  option in the build phase.
 2020-03-24 09:31:43 +01:00
Michael Rohleder 0f96fd6454
gnu: dialog: Update to 1.3-20200228. 
* gnu/packages/ncurses.scm (dialog): Update to 1.3-20200228.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2020-03-23 21:17:55 -04:00
Leo Famulari aae5f89db0
gnu: Git: Update to 2.26.0. 
* gnu/packages/version-control.scm (git): Update to 2.26.0.
[arguments]: Adjust the 'install-credential-netrc' phase to upstream changes.
 2020-03-23 21:17:46 -04:00
Mathieu Othacehe acd595c237
Revert "gnu: youtube-dl: Add 'ffmpeg' as input." 
This reverts commit 4233e74b39.
 2020-03-23 21:51:25 +01:00
Leo Famulari a11237e40a
gnu: Mutt: Update to 1.13.4. 
* gnu/packages/mail.scm (mutt): Update to 1.13.4.
[source]: Prefer HTTPS URL and replace FTP URL with HTTP.
 2020-03-23 15:53:11 -04:00
Alexandros Theodotou 0a6f68982b
gnu: sord: Add pcre to inputs. 
* gnu/packages/rdf.scm (sord)[inputs]: Add pcre needed for sord_validate.
 2020-03-23 20:48:49 +01:00
Brice Waegeneire 7884fc434f
gnu: youtube-dl: Add zsh completion. 
* gnu/packages/video.scm (youtube-dl)[arguments]: Add phase
install-completion.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
 2020-03-23 19:02:46 +01:00
Brice Waegeneire 4233e74b39
gnu: youtube-dl: Add 'ffmpeg' as input. 
* gnu/packages/video.scm (youtube-dl)[arguments]: Add phase
wrap-executable.
[inputs]: Add ffmpeg.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
 2020-03-23 19:02:44 +01:00
Brice Waegeneire 1a5443e86b
doc: Fix typo in example. 
* doc/guix.texi (Invoking guix deploy): Fix example to use '%user'
variable defined above.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
 2020-03-23 18:57:01 +01:00
Brice Waegeneire a9f2c210f3
system: Export 'operating-system-kernel-loadable-modules'. 
* gnu/system.scm: Export 'operating-system-kernel-loadable-modules'.

Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
 2020-03-23 18:52:31 +01:00
Maxim Cournoyer f2c698bd3e
gnu: emacs-lua-mode: Update to 20191204. 
* (emacs-lua-mode): Update to 20191204.
 2020-03-23 13:49:39 -04:00
Maxim Cournoyer 09c09c4c7c
gnu: emacs-ert-runner: Update to 0.8.0. 
* (emacs-ert-runner): Update to 0.8.0.
 2020-03-23 13:49:38 -04:00
Maxim Cournoyer 80168c4b5b
gnu: emacs-dash: Update to 2.17.0. 
* (emacs-dash): Update to 2.17.0.
 2020-03-23 13:49:38 -04:00
Mathieu Othacehe f9b6f75d1c
installer: Fix cow-store umount issue. 
* 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.
 2020-03-23 18:46:40 +01:00
Tobias Geerinckx-Rice 5490b2c733
gnu: parallel: Update to 20200322. 
* gnu/packages/parallel.scm (parallel): Update to 20200322.
 2020-03-23 18:35:27 +01:00
Tobias Geerinckx-Rice c2d468a111
gnu: extremetuxracer: Update to 0.8.0. 
* gnu/packages/games.scm (extremetuxracer): Update to 0.8.0.
 2020-03-23 18:35:27 +01:00
Alexandros Theodotou d3e7282ec3
gnu: Add zlfo. 
* gnu/packages/music.scm (zlfo): New variable.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
 2020-03-23 15:39:02 +01:00
Alexandros Theodotou 360ebe50b5
gnu: Add ztoolkit-rsvg. 
* gnu/packages/audio.scm (ztoolkit-rsvg): New variable.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net> [with modifications]
 2020-03-23 15:39:01 +01:00
Alexandros Theodotou 2f4faccc6f
gnu: Add ztoolkit. 
* gnu/packages/audio.scm (ztoolkit): New variable.

Signed-off-by: Jakub Kądziołka <kuba@kadziolka.net>
 2020-03-23 15:39:00 +01:00
Roel Janssen 7ff6395100
gnu: Add circos. 
* gnu/local.mk: Register circos-remove-findbin.patch.
* gnu/packages/patches/circos-remove-findbin.patch: New file.
* gnu/packages/perl.scm: New variable.
 2020-03-23 11:42:36 +01:00
Alexandros Theodotou 591faabd8c
gnu: Add python-gcovr. 
* gnu/packages/python-xyz.scm (python-gcovr): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-23 10:48:18 +01:00
Alexandros Theodotou 670da39888
gnu: Add lv2toweb. 
* gnu/packages/audio.scm (lv2toweb): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2020-03-23 10:48:18 +01:00
Ludovic Courtès 8bc745052e
machine: ssh: Better report missing initrd modules. 
* gnu/machine/ssh.scm (machine-check-initrd-modules): Improve message
upon module mismatch.
 2020-03-23 10:48:17 +01:00
Ludovic Courtès 1292372725
deploy: Write a message upon successful deployment. 
* guix/scripts/deploy.scm (guix-deploy): Write message upon successful
deployment.
 2020-03-23 10:48:17 +01:00
Ludovic Courtès 1bb248d0b1
deploy: Show what machines will be deployed. 
* guix/scripts/deploy.scm (show-what-to-deploy): New procedure.
(guix-deploy): Call it.
 2020-03-23 10:48:17 +01:00
Ludovic Courtès 7b322d3c4c
ui: Add 'indented-string'. 
* guix/scripts/pull.scm (display-news-entry): Remove extra space in
format string for 'indented-string'.
(indented-string): Remove.
(display-new/upgraded-packages)[pretty]: Pass #:initial-indent? to
'indented-string'.
* guix/ui.scm (indented-string): New procedure.
 2020-03-23 10:48:17 +01:00
Ludovic Courtès ea6e2299b4
machine: ssh: Make sanity checks in a single round trip. 
* 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'.
 2020-03-23 10:48:17 +01:00
Ludovic Courtès 8f53d73493
ssh: 'send-files' reports missing modules on the remote host. 
Reported by Mikael Djurfeldt <mikael@djurfeldt.com>
in <https://bugs.gnu.org/40125>.

* guix/ssh.scm (send-files)[inferior-remote-eval*]: New procedure.
[missing]: Use it.  Add an explicit 'resolve-module' call.
(report-inferior-exception): New procedure.
 2020-03-23 10:48:17 +01:00
Leo Famulari 1eb27d5cae
Re-order the armhf linux-libre kernel packages to fix the build. 
This is a followup to commit 37f8c50cdc.

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.
 2020-03-23 01:46:48 -04:00
Vagrant Cascadian 058e96c59f
gnu: Add linux-libre-arm64-generic. 
* gnu/packages/linux (linux-libre-arm64-generic): New variable.
 2020-03-22 20:55:42 -07:00
Vagrant Cascadian 37f8c50cdc
gnu: linux-libre-arm-veyron: Deprecate package. 
* 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.
 2020-03-22 20:55:37 -07:00
Maxim Cournoyer 4ef89d884d
gnu: emacs-elpy: Update to 1.32.0. 
* 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>
 2020-03-22 21:17:39 -04:00