gnu: go-github-com-shirou-gopsutil: Reformat with guix style.

* gnu/packages/golang-xyz.scm (go-github-com-shirou-gopsutil): Reformat with
guix style.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: go-github-com-shirou-gopsutil: Update to 2.21.11.

* gnu/packages/golang-xyz.scm (go-github-com-shirou-gopsutil): Update to
2.21.11.
[arguments]: Fix tests.
<#:go>: Update to go-1.18.
<#:phases>: Add 'remove-v3 and 'remove-failing-tests phases.
[propagated-inputs]: Add go-golang-org-x-sys.
[native-inputs]: Add go-github-com-stretchr-testify and procps.

* gnu/packages/golang-xyz.scm: Add (gnu packages linux) module.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: go-github-com-shirou-gopsutil: Move to golang-xyz.

* gnu/packages/golang.scm (go-github-com-shirou-gopsutil): Move from here ...
* gnu/packages/golang-xyz.scm: ... to here.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add go-numcpus.

* gnu/packages/golang-xyz.scm (go-numcpus): New variable.

Change-Id: I2edb2f355fd14f2f9a470c91519e7fe1581cc243

gnu: Add go-github-com-tklauser-go-sysconf.

* gnu/packages/golang-xyz.scm (go-github-com-tklauser-go-sysconf): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: Add go-github-com-tklauser-numcpus.

* gnu/packages/golang-xyz.scm (go-github-com-tklauser-numcpus): New variable.

Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: emacs-ess: Disable two bad tests.

These tests used to be disabled before and they do still fail.

* gnu/packages/statistics.scm (emacs-ess)[arguments]: Disable two more tests.

Change-Id: I44a18b43d4fa6af2c9244bb8f3697a01c6c8d255

gnu: r-with-tests: Update to 4.3.3.

* gnu/packages/statistics.scm (r-with-tests): Update to 4.3.3.

Change-Id: Ida43d1e7f747245b01aa6fc73716b79611f0bbfd

gnu: libtheora: Fix cross-compiling to riscv64-linux.

* gnu/packages/xiph.scm (libtheora):
[native-inputs]: When cross compiling to riscv64-linux-gnu, add config.
[arguments]: When target riscv64-linux-gnu, add update-config phase.

Change-Id: Ie055cd4f6cb9d2a4601b93d1f9db227598349c7c
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: libtheora: Use Gexps.

* gnu/packages/xiph.scm (libtheora): Use Gexps.

Change-Id: Ie055cd4f6cb9d2a4601b93d1f9db227598349c7c
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: home: dotfiles: Properly support both plain and Stow directory layouts.

Fixes <https://issues.guix.gnu.org/68848>.

The current implementation of the home-dotfiles-service-type contradicts
the Guix manual.  This patch properly implements both the plain and Stow
dotfiles directory layouts.

It does so by refactoring home-dotfiles-configuration adding a new
packages field to support GNU Stow's users workflow and introducing
a new layout field to switch between the two directory layouts.

* gnu/home/services/dotfiles (home-dotfiles-configuration): Migrate to
(gnu services configuration);
[packages]: new field;
[layout]: new field;
(strip-stow-dotfile): new variable;
(strip-plain-dotfile): new variable;
(home-dotfiles-configuration->files): use the new fields;
[directory-contents]: allow for
selecting a subset of application dotfile directories;
* doc/guix.texi: document the new layouts.

Change-Id: I2e96037608353e360828290f055ec5271cfdfd48
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

services: virtual-build-machine: Disable substitutes by default.

These are useless when offloading yet were causing problems on systems
where the default substitute servers are unreachable.

* gnu/services/virtualization.scm (%virtual-build-machine-operating-system):
Add ‘use-substitutes?’ field to ‘guix-configuration’.

Change-Id: I7d5e380a6f2e2d537de43fdb3c550958ed4db255

doc: Fix typo in “Getting Started with the System”.

* doc/guix.texi (Getting Started with the System): Fix typo.

Change-Id: Idc52b9a4d5f5003899613595b6b275e098f6a3a8

gnu: r-seuratdata: Update to 0.2.2.9001-1.4dc08e0.

* gnu/packages/cran.scm (r-seuratdata): Update to 0.2.2.9001-1.4dc08e0.
[propagated-inputs]: Add r-seurat and r-seuratobject.

Change-Id: I8bf21d23ec0bdfbc0b8930673ac5750d081ac780

gnu: r-snprelate: Update to 1.36.1.

* gnu/packages/bioconductor.scm (r-snprelate): Update to 1.36.1.

Change-Id: I5cf14d463c0f4ca3707a8ac33c7a06baa4337789

gnu: r-s4arrays: Update to 1.2.1.

* gnu/packages/bioconductor.scm (r-s4arrays): Update to 1.2.1.

Change-Id: I68c0ee03264073e8816fc92fbaa97ebb6c5036ed

gnu: r-ggcyto: Update to 1.30.2.

* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.30.2.

Change-Id: I29c123aa60347b491412631f036923c3bbb7d6c9

gnu: r-ggtree: Update to 3.10.1.

* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.10.1.

Change-Id: I62eec59a6be3f806261198a1d39eb38ee86a9a79

gnu: r-nebulosa: Update to 1.12.1.

* gnu/packages/bioconductor.scm (r-nebulosa): Update to 1.12.1.
[propagated-inputs]: Remove r-seurat; add r-ggrastr and r-seuratobject.

Change-Id: If301102ec02ce618ed1ebeff17a9d7e0845e847c

scripts: import: elpa: Unquote-splice package sexp contents.

* guix/scripts/import/elpa.scm (guix-import-elpa): Unquote-splice the contents
of the package sexp so the matched package definition is returned unchanged.

Change-Id: Iaaa7e72390c73c6d6671811fe9ac284d599b44c6
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>