import/cran: Generate rudimentary ARGUMENTS field.

* guix/import/cran.scm (phases-for-inputs, maybe-arguments): New procedures.
(description->package): Splice in result of MAYBE-ARGUMENTS.

Change-Id: I578e1903f37c91bf865f0be49b04187ec372ed05

gnu: Add r-protgear.

* gnu/packages/bioconductor.scm (r-protgear): New variable.

Change-Id: Ic6d5cae65d4f76df4488ee2462071ba68b50c184

Revert "gnu: emacs-minimal: Update to 29.2."

This reverts commit b9bc400d85b1dbf3295f96aed9031527b6c59ba7.

Fixes: Too many rebuilds <http://logs.guix.gnu.org/guix/2024-01-21.log#095235>
Reported-by: Efraim Flashner <efraim@flashner.co.il>

gnu: gnome-shell-extension-paperwm: Use new package style.

* gnu/packages/gnome-xyz.scm (gnome-shell-extension-paperwm)[arguments]:
Convert to list of G-Expressions.
[native-inputs]: Drop labels.

Co-authored-by: Justin Veilleux <terramorpha@cock.li>
Co-authored-by: Vivien Kraus <vivien@planete-kraus.eu>

gnu: gnome-shell-extension-paperwm: Update to 44.17.0.

* gnu/packages/gnome-xyz.scm (gnome-shell-extension-paperwm): Update to 44.17.0.

Change-Id: I3d9923ccfdb35b9952c24d8dd3d064c3cba7b8c2
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: vcmi: Update to 1.4.2.

* gnu/packages/games.scm (vcmi): Update to 1.4.2.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>

gnu: emacs-minimal: Update to 29.2.

* gnu/packages/emacs.scm (emacs-minimal): Update to 29.2.

gnu: emacs-minimal: Set upstream-name to “emacs”.

* gnu/packages/emacs.scm (emacs-minimal)[properties]: Add ‘upstream-name’.

gnu: Add r-netgsa.

* gnu/packages/bioconductor.scm (r-netgsa): New variable.

Change-Id: I79b842854db80bbacdb8ff4c9fccfabdfc04d779

gnu: Add r-glassofast.

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

Change-Id: I6ec7a1f8d4391d7d93f23789f448476b866e4687

gnu: Add r-rcy3.

* gnu/packages/bioconductor.scm (r-rcy3): New variable.

Change-Id: Ia295e8a174f65c8378ae83bdc1dde2877a48ff45

gnu: torbrowser: Add support for language localisation.

* gnu/packages/gnuzilla.scm (all-mozilla-locales): Export it.
* gnu/packages/tor.scm (%torbrowser-locales, translation-base-browser,
translation-tor-browser): New variables.
(torbrowser)[arguments]: In ‘setenv’ phase, set MOZ_CHROME_MULTILOCALE.  Add
‘copy-firefox-locales’, ‘copy-basebrowser-locales’, ‘copy-torbrowser-locales’
and ‘build-locales’ phases.

Change-Id: Ia5b28fa5d885f24140893dc270e57e83b0250c67

gnu: r-cytolib: Update to 2.14.1.

* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.14.1.
[source]: Do not unbundle included boost.
[arguments]: Remove.
[inputs]: Remove boost.

Change-Id: Ibe26b9df3f73e67fb9f53676a2c27a5aed714895

gnu: python-pandera: Fix build.

* gnu/packages/python-science.scm (python-pandera): Fix build.
[source]: Delete tests/modin directory.
[native-inputs]: Remove python-modin.

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

gnu: python-pandas-stubs: Update to 1.5.3.230321.

* gnu/packages/python-science.scm (python-pandas-stubs): Update to
1.5.3.230321.
[arguments]<#:test-flags>: Ignore tests that require a version of
python-pyarrow with ORC integration.
[native-inputs]: Add python-odfpy.

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

gnu: xorg-server-xwayland: Update to 23.2.4 [security fixes].

Fixes CVE-2023-6816, CVE-2024-0229, CVE-2024-21885, CVE-2024-21886,
CVE-2024-0409, and CVE-2024-0408.  See the X.Org security advisory
<https://lists.x.org/archives/xorg/2024-January/061525.html> for more
information.

* gnu/packages/xorg.scm (xorg-server-xwayland): Update to 23.2.4.

Change-Id: Ie6343d34652ba0caf00940775b5b227dd9bc05bc
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>

gnu: xorg-server: Update to 21.1.11 [security fixes].

Fixes CVE-2023-6816, CVE-2024-0229, CVE-2024-21885, CVE-2024-21886,
CVE-2024-0409, and CVE-2024-0408.  See the X.Org security advisory
<https://lists.x.org/archives/xorg/2024-January/061525.html> for more
information.

Copyright line updated as followup to commits
3080abba40c819933d1857abe4abaaa3cf65baab and
158502e40d800407f1bd697dd5dd0437086730bf.

* gnu/packages/xorg.scm (xorg-server): Update to 21.1.11.

Change-Id: I07cb273e2a504f94f8f26624d26ad79c6e92f109
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>

gnu: gnutls: Update to 3.8.3 [security-fixes].

Fixes CVE-2024-0553 and CVE-2024-0567.

gnu/packages/tls.scm (gnutls-3.8.2): Rename to ...
(gnutls/fixed): ... this.  Update to 3.8.3.
(gnutls): Rename replacement to gnutls/fixed.

Change-Id: Ic44b3b0481ffd51cdc42a2d71a598f001b43c6f7
Signed-off-by: John Kehayias <john.kehayias@protonmail.com>
Co-authored-by: John Kehayias <john.kehayias@protonmail.com>

gnu: Add python-manimpango.

* gnu/packages/python-xyz.scm (python-manimpango): New variable.

Co-authored-by: Troy Figiel <troy@troyfigiel.com>
Change-Id: I80effb2412e7c35ddf69c0d3ff6e2f052f282840
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>

gnu: r-org-hs-eg-db: Update to 3.18.0.

* gnu/packages/bioconductor.scm (r-org-hs-eg-db): Update to 3.18.0.

Change-Id: Iaba83a413858a95e81b6488a2f8cde648f0bdeed