gnu: abc-yosyshq: Update to 0.59.

* gnu/packages/electronics.scm (abc-yosyshq): Update to 0.59.

Change-Id: I5c8e346bbb3624bd5ad9efd0e10f4dda21044044
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: parallel: Update to 20251022.

* gnu/packages/parallel.scm (parallel): Update to 20251022.

Change-Id: I163a9ea614c34b26f975ae8a7762dba1a14b8821
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: Add --pid-file option to "guix system container" scripts.

* gnu/system/linux-container.scm (container-script): Accept pid-file command
line option to write out the container's process ID.
* doc/guix.texi (Invoking guix system): Document new option.

Change-Id: I93e8a99b39c1dd831f116104bf92c723d96c9965
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: ruby-activesupport: Fix build.

* gnu/packages/patches/ruby-activesupport-fix-deprecation-warning.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/rails.scm (ruby-activesupport): Apply it.

Change-Id: Ibeafb74ae93a42108ea5f383996756c43b0bc444
Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: python-pudb: Update to 2025.1.3.

* gnu/packages/python-xyz.scm (python-pudb): Update to 2025.1.3.
[propagated-inputs]: Add python-typing-extensions.

Change-Id: I10de9033343784803edf8e7a0e01648d8d5d21a3

gnu: trealla: Update to 2.84.22.

* gnu/packages/prolog.scm (trealla): Update to 2.84.22.

Change-Id: I696554fdff200e728542c47aaf1e5279bb0a74de

gnu: Add python-pytest-fail-slow.

* gnu/packages/python-check.scm (python-pytest-fail-slow): New variable.

Change-Id: I367efe9418a0792f9a1a64530fd1d83ef2cb992b
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: r-with-tests: Update to 4.5.2.

* gnu/packages/statistics.scm (r-with-tests): Update to 4.5.2.

Change-Id: I6b2fdde29812d9a7088cbd339771d4ee03b62467

gnu: r-with-tests: Update to 4.5.1.

* gnu/packages/statistics.scm (r-with-tests): Update to 4.5.1.

Change-Id: I0033a9827fa14b74659a2d037851ca1c52add701

gnu: r-bslib: Ensure that copied files are writable.

* gnu/packages/cran.scm (r-bslib)[arguments]: Add phase 'fix-file-permissions.

Change-Id: Idccb1ef5a271f04f50e60b4a639c87bf2ac87b4e

gnu: r-sass: Ensure that copied files are writable.

* gnu/packages/cran.scm (r-sass)[arguments]: Add phase 'fix-file-permissions.

Change-Id: If53ad242e5fcfa6951631ed7a1807a8930e92be3

gnu: r-bslib: Enable tests.

* gnu/packages/cran.scm (r-bslib)[arguments]: Enable most tests; add phase
'disable-bad-tests.
[native-inputs]: Add r-testthat and r-yaml.
[properties]: Record updater-extra-native-inputs.

Change-Id: I0221e3ee0dff309ba3f24e0d47b89efb59f7c9a1

gnu: r-swne: Replace deprecated r-liger by r-rliger.

* gnu/packages/statistics.scm (r-swne)[propagated-inputs]: Replace deprecated
r-liger by r-rliger.

Change-Id: If2aab2df369456518484edb3035e637ac0ca7c08

gnu: r-import: Update home-page

* gnu/packages/cran.scm (r-import)[home-page]: rticulate.org is
  no longer under the control of the package author. The official
  home page is now hosted at github.io. See
  <https://github.com/rticulate/import/issues/102#issuecomment-3376610296>
  for mor information.

Change-Id: I1513fcfea1ba8ad14813ad8929d06d3fc1fa36b0
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>

gnu: r-import: Update to 1.3.4.

* gnu/packages/cran.scm (r-import): Update to 1.3.4.

Change-Id: I61781fae0b164dc1ddd1a2f2a10c0d5b4dae7398
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>

gnu: r-rcppparallel: Update to 5.1.11-1.

* gnu/packages/cran.scm (r-rcppparallel): Update to 5.1.11-1.

Change-Id: Idb02209dc955a531ede00527fe0216a9ce5caafd

gnu: r-colorout: Update to 1.3-3.

* gnu/packages/cran.scm (r-colorout): Update to 1.3-3.

Change-Id: I4d6a6094061fab98fee8155c76ca760f3ef15cbe

gnu: r-msnbase: Restore tests that failed because of libxml2.

* gnu/packages/bioconductor.scm (r-msnbase)[arguments]: Restore two tests; fix
them by adding 'ensure-libxml2-works phase.

Change-Id: I555f19d5bc749cdd458af4b55a2a5a2e89c7d190

gnu: r-msnbase: Disable two tests.

* gnu/packages/bioconductor.scm (r-msnbase)[arguments]: Turn off two more
tests in 'delete-bad-tests phase.

Change-Id: I9bfa59a09db00e25c7b65cf4d642debfeb377f93

gnu: Remove r-spatstat-core.

In 2022 spatstat.core was replaced with spatstat.explore and spatstat.model.

See https://spatstat.org/2022/11/10/spatstat.core-split.html

* gnu/packages/cran.scm (r-spatstat-core): New variable.

Change-Id: I2193626f0c2346f3b2793026059c5fbc97d2c4d2