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

gnu: r-skitools: Update to 0.0.0.9000-2.ba322dc.

* gnu/packages/bioinformatics.scm (r-skitools): Update to 0.0.0.9000-2.ba322dc.

Change-Id: Ic006e4178ccaae57e7f4b25e07bb63db42585cb3

gnu: r-skitools: Disable one test.

* gnu/packages/bioinformatics.scm (r-skitools)[arguments]: Add phase
'disable-bad-test.

Change-Id: I5c79aa28e343266a83522afe6635b3a714dadcc1

gnu: r-sigfit: Fix build with GCC@14

* gnu/packages/bioinformatics.scm (r-sigfit)[arguments]: Add phase
'gcc-14-compatibility.

Change-Id: Iaa00ecdf00dcf76330f3b1f904da6263b82e0617

gnu: r-sdmtools: Replace removed constants.

R 4.5.0 removed previously deprecated definitions.

* gnu/packages/cran.scm (r-sdmtools)[arguments]: Add phase 'patch-constants.

Change-Id: I06125aeff8b7b1f219f8458b6c9aeeb696e33f11

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

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

Change-Id: I555f19d5bc749cdd458af4b55a2a5a2e89c7d190

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

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

Change-Id: Ifeb3667449e862826a402b8c1ce37e4bcc92f21b

gnu: r-xml: Use libxml2-with-zlib.

* gnu/packages/cran.scm (r-xml)[inputs]: Replace libxml2 with libxml2-with-zlib.

Change-Id: I16de722bec362b87e0518e91de10e7a02afd8c71

gnu: Add libxml2-with-zlib.

* gnu/packages/xml.scm (libxml2-with-zlib): New variable.

Change-Id: I2cc59d8f0758b4caf6f35dedabc9ee66f41ca11c

gnu: python-libxml2: Reintroduce simplified deprecation.

This is a fixup for commit c23b9a1 ("gnu: Remove libxml2-xpath0.") which
wrongly resolved a conflict.

* gnu/packages/xml.scm (python-libxml2): Reintroduce simplified deprecation.

Change-Id: Ia9e474329c0ec695e15571cbe99dbbb6ced0b3ab

gnu: Remove libxml2-xpath0.

* gnu/packages/xml.scm (libxml2-xpath0): Delete variable.

Fixes: #3516
Fixes: <https://bugs.gnu.org/79572>
Change-Id: I8fd49d0ce1394fc4e55a148e15c23388934524a4

gnu: distrobox: Update to 1.8.2.1.

* gnu/packages/containers.scm (distrobox): Update to 1.8.2.1.

Change-Id: Ic98a43b3b59136a74726df9dd23289e5750bb3b1

gnu: trealla: Update to 2.84.19.

* gnu/packages/prolog.scm (trealla): Update to 2.84.19.

Change-Id: Ibff6a882d9d410d2e6fe79a96b5b30c6a9d4d22d

graph: Add cyclonedx-json backend.

Validated with:

  guix graph guile -b cyclonedx-json > /tmp/cyc.json && \
    docker run -v /tmp/:/tmp/  cyclonedx/cyclonedx-cli validate --input-format json --input-file /tmp/cyc.json

* guix/graph.scm (emit-cyclonedx-prologue, emit-cyclonedx-epilogue,
emit-cyclonedx-node, emit-cyclonedx-edge): New procedures.
(%cyclonedx-backend): New variable.
(%graph-backends): Add %cyclonedx-backend.

Change-Id: Icc8c33cbc08da0137489d13bdad618ef55a14923

gnu: Remove references to deprecated ‘ruby-concurrent’.

* gnu/packages/ruby-xyz.scm (ruby-i18n)[propagated-inputs]: Use
‘ruby-concurrent-ruby’ instead of ‘ruby-concurrent’; remove label.
(ruby-asciidoctor-pdf, ruby-hamster, ruby-tzinfo)
(ruby-sucker-punch, ruby-sentry-core, ruby-sentry): Use ‘ruby-concurrent-ruby’
instead of ‘ruby-concurrent’.

Change-Id: I38761047bd6605e43839b8c3e31ec34d4e2c93c4

gnu: rofi-pass: Remove reference to deprecated input.

This is a followup to 79ff2b353aa3be6bd9e16f6de04e7edea05c51f1.

* gnu/packages/password-utils.scm (rofi-pass-wayland)[inputs]: Remove
‘replace’ clause.

Change-Id: Iee7393388e5d3396eb38cbc68a6cbe39623b4bfc

gnu: xfce4-volumed-pulse: Avoid deprecated input.

* gnu/packages/xfce.scm (xfce4-volumed-pulse)[inputs]: Change ‘keybinder-3.0’
to ‘keybinder’.

Change-Id: I2cabc125f3e4ff87ecbf983c6c324a42feb4146d