branch staging updated (4876226dd5 -> 99b25b1313)

[guix-commits]

apteryx pushed a change to branch staging
in repository guix.

    from 4876226dd5 gnu: go: Update home page URL.
     new 9eafe47e39 gnu: ruby-activesupport: Skip a failing test on i686-linux.
     new d80c5b936d gnu: python-geventhttpclient: Update to 2.0.9.
     new 3d9a57e128 gnu: python-locust: Update to 2.15.1.
     add a1d4e562f1 gnu: ddcutil: Update to 1.4.1.
     add a1b826b338 gnu: python-trustme: Update to 0.9.0.
     add 33f2e0dad1 gnu: Add python-sqlite-fts4.
     add 62cfe07f6a gnu: Add python-sqlite-utils.
     add 6d00909968 gnu: Add python-asgi-lifespan.
     add 4bff240e9b gnu: Add python-asgi-csrf.
     add d495b50444 gnu: Add python-cogapp.
     add ec628ef1c8 gnu: python-pytest-7.1: Depend on python-pluggy-next.
     add cd31437e9c gnu: Add datasette.
     add 05b4ae6ab6 gnu: Add texlive-glyphlist.
     add 3eb309b4d4 gnu: Add texlive-dvipdfmx.
     add 853bffb388 gnu: Add texlive-firstaid.
     add cbf731ae48 gnu: Add texlive-xetex.
     add 36f78676e5 import/texlive: Ignore architecture-dependent packages.
     add 03a83c2906 import/texlive: Only process description if it exists.
     add b849a47bdb import/texlive: Process license field only when it exists.
     add 739c257378 import/texlive: tlpdb->package: Ignore files outside of 
texmf-dist.
     add 5d6987f615 gnu: geeqie: Use libjpeg-turbo.
     add 631f19e43f gnu: flightgear: Update to 2020.3.18.
     add bd932c1855 services: configuration: Fix garbage output in 
configuration->documentation.
     add 4ba06192aa maint: Add icecat to the release manifest.
     add 2ab0c55e3f gnu: Add cl-flac.
     add 03387bd17f gnu: Add cl-vorbis.
     add c27301e827 gnu: Add libmixed.
     add c540336194 gnu: Add cl-mixed.
     add c5a943e016 gnu: Add cl-harmony.
     add 34ff1039a6 gnu: cl-trial: Activate trial-harmony system.
     add 314c599739 gnu: Add cl-collider.
     add 6f231e31a3 teams: lxqt: Add qt.scm to scope.
     add d8eccb6e7b teams: Add Andreas Enge to lxqt team.
     add 68d024ceff gnu: emacs-tramp: Update to 2.6.0.3.
     add 48fe02cc0a gnu: emacs-compat: Update to 29.1.4.1.
     add 127be8debb gnu: emacs-relint: Update to 1.22.
     add a9bd55214e gnu: emacs-corfu: Update to 0.36.
     add 088839d053 gnu: emacs-autocrypt: Update to 0.4.1.
     add 25bf823521 gnu: emacs-autocrypt: Fix license.
     add 23561595bd gnu: emacs-ebuild-mode: Update to 1.63.
     add 26fd5755a6 gnu: emacs-org: Update to 9.6.2.
     add 677cad5e1a gnu: emacs-rg: Update to 2.3.0.
     add 017caad572 gnu: Add emacs-pippel.
     add 6ba700e9e5 gnu: Add emacs-railscasts-theme.
     add 249781e93c gnu: emacs-lemon: Update to 2.1.0.
     add 9a180b905e gnu: emacs-lemon: Add tests
     add f3baa5da06 gnu: Add texlive-nth.
     add e42e4cecd0 gnu: Add r-flowai.
     add 3d74f1676b gnu: Add r-embedsom.
     add 3f1617da19 gnu: Add r-cytoexplorer.
     add 9e5a079eb4 gnu: Add r-illuminahumanmethylation450kmanifest.
     add a545bdd0c1 gnu: Add r-minfidata.
     add 4526e15cfd gnu: Add r-jade.
     add 09496d569a gnu: Add r-isva.
     add 7df926ee04 gnu: Add r-kpmt.
     add 2f9b2699b1 gnu: Add r-globaltest.
     add 884daf0f4b gnu: Add r-prettydoc.
     add fcc8b808e7 gnu: Add r-champdata.
     add a8ea4626ae gnu: Add r-ruv.
     add 1254ce1342 gnu: Add r-illumina450probevariants-db.
     add de1c49c25d gnu: Add r-illuminahumanmethylationepicanno-ilm10b4-hg19.
     add 6d1cc311e5 gnu: Add r-missmethyl.
     add a969d91ca5 gnu: Add r-dss.
     add bd35053677 gnu: Add r-dmrcate.
     add 418811783e gnu: Add r-rpmm.
     add 96e81b18b9 gnu: Add r-champ.
     add e93a570fd6 gnu: Add r-enmix.
     add 0024e4e6d4 gnu: Add r-flowsorted-blood-450k.
     add a5997202b8 gnu: Add r-flowsorted-blood-epic.
     add 928e9aa236 gnu: Add r-shinymethyl.
     add 033955b4e8 gnu: Add r-illuminahumanmethylationepicanno-ilm10b5-hg38.
     add caf163536a gnu: Add r-maxprobes.
     add a6f98c64f6 gnu: open-adventure: Update to 1.14.
     add 918ad58945 gnu: Add emacs-sphinx-doc.
     add 7ff5deda4d gnu: emacs-sphinx-doc: Run tests.
     add cca7d02463 gnu: Add emacs-tintin-mode.
     add 0c3d4cf38a gnu: Add emacs-beframe.
     add abf686239f gnu: Add emacs-exwm-modeline.
     add 1dcaa0fc30 guix: Shorten home page URL in texlive importer.
     add a30dcbffeb gnu: Add texlive-pict2e.
     add 65afc8fa44 gnu: Add texlive-halloweenmath.
     add 0a780005a7 gnu: r-covr: Update to 3.6.2.
     add d601d4ecf5 gnu: r-rgl: Update to 1.1.3.
     add b4960c9936 gnu: r-datawizard: Update to 0.7.0.
     add f54dc51b9a gnu: r-googledrive: Update to 2.1.0.
     add 2848f73fab gnu: r-googlesheets4: Update to 1.1.0.
     add bd4bf3c84c gnu: r-modelr: Update to 0.1.11.
     add 59914968d7 gnu: r-htmltools: Update to 0.5.5.
     add 9b95e9cfd4 gnu: r-spelling: Update to 2.2.1.
     add eab11487f1 gnu: r-ps: Update to 1.7.3.
     add 83a957e4a9 gnu: r-ctrdata: Update to 1.12.1.
     add 7d4a752afa gnu: r-dendextend: Update to 1.17.1.
     add 26a4304fc6 gnu: r-jomo: Update to 2.7-5.
     add a0ae32bb9c gnu: r-smurf: Update to 1.1.5.
     add 8fff272506 gnu: r-cli: Update to 3.6.1.
     add 620e7a53b1 gnu: r-xfun: Update to 0.38.
     add 3ded5e1b6e gnu: r-vctrs: Update to 0.6.1.
     add 15c8ac0509 gnu: r-pillar: Update to 1.9.0.
     add d3587e39b3 gnu: r-trend: Update to 1.1.5.
     add 9908de506b gnu: r-simplermarkdown: Update to 0.0.6.
     add a9585eea75 gnu: r-arules: Update to 1.7-6.
     add f986523017 gnu: r-dtplyr: Update to 1.3.1.
     add 8449d3ad7f gnu: r-ellipse: Update to 0.4.4.
     add eed688ea87 gnu: r-factominer: Update to 2.8.
     add c938338563 gnu: r-officer: Update to 0.6.2.
     add 2ccd430a4c gnu: r-nodbi: Update to 0.9.2.
     add a0f6305eb1 gnu: r-abctools: Update to 1.1.6.
     add d700fda57c gnu: r-gam: Update to 1.22-2.
     add 87070072b7 gnu: r-dofuture: Update to 1.0.0.
     add b23d3430f0 gnu: r-tmb: Update to 1.9.3.
     add 9d169137ff gnu: r-multidplyr: Update to 0.1.3.
     add 32db2dc977 gnu: r-parallelly: Update to 1.35.0.
     add 4519597494 gnu: r-imager: Update to 0.42.19.
     add d9e52d2124 gnu: r-caret: Update to 6.0-94.
     add 81ea6fa24e gnu: r-rstantools: Update to 2.3.1.
     add dddd4906ad gnu: r-zyp: Update to 0.11-1.
     add 516753cc10 gnu: r-rlecuyer: Update to 0.3-7.
     add 9dd47c2f13 gnu: r-distributional: Update to 0.3.2.
     add 9074ca5a74 gnu: r-hardhat: Update to 1.3.0.
     add 0c3a344570 gnu: r-mlr3pipelines: Update to 0.4.3.
     add 6eeebd8021 gnu: r-automap: Update to 1.1-9.
     add b748ea05cc gnu: r-gdtools: Update to 0.3.3.
     add d8fe4c68a6 gnu: r-dplyr: Update to 1.1.1.
     add 8ec84e8895 gnu: r-dbplyr: Update to 2.3.2.
     add ffcb110ad9 gnu: r-hms: Update to 1.1.3.
     add 8ad283c780 gnu: r-rmarkdown: Update to 2.21.
     add 082d5806ec gnu: r-gtable: Update to 0.3.3.
     add 3fa9594824 gnu: r-rcurl: Update to 1.98-1.12.
     add 5f416aa0e4 gnu: r-segmented: Update to 1.6-3.
     add 042dc3b65d gnu: r-glmnet: Update to 4.1-7.
     add 8a69976f6c gnu: r-hexbin: Update to 1.28.3.
     add 25e67fdc4f gnu: r-robustbase: Update to 0.95-1.
     add aadc68f297 gnu: r-car: Update to 3.1-2.
     add c029bac121 gnu: r-tclust: Update to 1.5-4.
     add 113146d31c gnu: r-mumin: Update to 1.47.5.
     add 57c3662ddd gnu: conan: Use gexps and remove input labels.
     add 7ceedc7df7 gnu: conan: Update to 2.0.2.
     add be5e280e5f Revert "gnu: network-manager: Update to 1.43.4."
     add 42b938ae8c gnu: Add audmes.
     add f4d7b901db gnu: matio: Add header file.
     add 13b2d110ee gnu: Add suitesparse-3.
     add 1984d56b0e gnu: Add scilab.
     add 59878230f4 system: Remove obsolete GUIX_LOCPATH workaround.
     add ed50531885 services: base: Deprecate 'pam-limits-service' procedure.
     add 6d0ad93020 services: pam-limits-service-type: Deprecate file-like 
object support in favour for lists as service value.
     add 8c76eb6168 gnu: Add zsh-history-substring-search
     add e7558d1647 gnu: Add zsh-completions
     add cb0ae06d76 gnu: icedove: Update to 102.9.1 [fixes CVE-2023-28427].
     add efcaa0d710 gnu: linux-libre: Update to 6.2.9.
     add 3967426686 gnu: linux-libre 6.1: Update to 6.1.22.
     add e914ae1571 gnu: linux-libre 5.15: Update to 5.15.105.
     add a368e3cf6b gnu: Add tree-sitter-heex.
     add 1c6238794b gnu: Add emu8051.
     add 56de91b712 gnu: Add fbautostart.
     add 2c3383e8d8 gnu: r-amaretto: Update to 1.14.0.
     add 473bd926cf gnu: r-anvil: Update to 1.10.2.
     add 91c41b8ce7 gnu: r-annotationforge: Update to 1.40.2.
     add 4afcef7847 gnu: r-biomart: Update to 2.54.1.
     add 44599e7966 gnu: r-rhdf5filters: Update to 1.10.1.
     add 04b87844df gnu: r-flowclust: Update to 3.36.1.
     add 11956155e5 gnu: r-bionero: Update to 1.6.1.
     add b8152d668d gnu: conan: Do not hard-code package versions.
     add 47ea688fd2 gnu: conan: Disable more flaky tests.
     new 99b25b1313 Merge branch 'master' into staging

The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 doc/guix.texi                       |  28 +-
 etc/release-manifest.scm            |   5 +-
 etc/teams.scm.in                    |   5 +-
 gnu/local.mk                        |   1 +
 gnu/packages/audio.scm              |  56 +++-
 gnu/packages/benchmark.scm          |  43 ++-
 gnu/packages/bioconductor.scm       | 527 +++++++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm     | 133 +++++++++
 gnu/packages/check.scm              |   7 +-
 gnu/packages/cran.scm               | 446 ++++++++++++++++++++++++------
 gnu/packages/databases.scm          | 155 +++++++++++
 gnu/packages/emacs-xyz.scm          | 352 ++++++++++++++++++------
 gnu/packages/emulators.scm          |  40 +++
 gnu/packages/engineering.scm        |  44 +++
 gnu/packages/games.scm              |  12 +-
 gnu/packages/gnome.scm              |   4 +-
 gnu/packages/gnuzilla.scm           |   8 +-
 gnu/packages/hardware.scm           |  21 +-
 gnu/packages/image-viewers.scm      |   2 +-
 gnu/packages/linux.scm              |  12 +-
 gnu/packages/lisp-xyz.scm           | 281 ++++++++++++++++++-
 gnu/packages/maths.scm              | 203 ++++++++++++++
 gnu/packages/package-management.scm | 234 ++++++++--------
 gnu/packages/python-crypto.scm      |  17 +-
 gnu/packages/python-web.scm         | 100 ++++++-
 gnu/packages/python-xyz.scm         |  18 ++
 gnu/packages/rails.scm              |   6 +
 gnu/packages/shellutils.scm         |  55 ++++
 gnu/packages/statistics.scm         |  64 ++---
 gnu/packages/tex.scm                | 253 ++++++++++++++++-
 gnu/packages/tree-sitter.scm        |   7 +
 gnu/packages/wm.scm                 |  22 ++
 gnu/services/base.scm               |  42 ++-
 gnu/services/configuration.scm      |   1 -
 gnu/system.scm                      |  10 +-
 gnu/tests/pam.scm                   |  97 +++++++
 guix/import/texlive.scm             |  55 ++--
 37 files changed, 2891 insertions(+), 475 deletions(-)
 create mode 100644 gnu/tests/pam.scm