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Author SHA1 Message Date
Ricardo Wurmus
b4ebd385cb gnu: r-mosdef: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-mosdef)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: Iadf53cbebf8e30b1cd8a4a793a7853b01318de39
 2026-04-27 09:08:44 +02:00
Ricardo Wurmus
8bc19a783e gnu: r-h5mread: Enable all tests. 
* gnu/packages/bioconductor.scm (r-h5mread)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I8a20a311a4c8c2177c07ab5d0b59c8ea5e369c73
 2026-04-27 09:08:44 +02:00
Ricardo Wurmus
0885dcbd28 gnu: r-immapex: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-immapex)[arguments]: Remove phase
'skip-bad-tests; specify #:skipped-tests instead.

Change-Id: Icb90decad077e6e2b9f68b618a983b8251954791
 2026-04-27 09:08:44 +02:00
Ricardo Wurmus
ce874aa2ec gnu: r-rcas: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-rcas)[arguments]: Remove phase
'skip-bad-tests; specify #:skipped-tests instead.

Change-Id: Ib4497fa70e0b61267b61d4fdf70e3e5abd0c1af9
 2026-04-27 09:08:43 +02:00
Ricardo Wurmus
a95926a0c6 gnu: r-karyoploter: Enable all tests. 
* gnu/packages/bioconductor.scm (r-karyoploter)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I3d5727327d1da4ba30bd8cd8d9251100329e4cac
 2026-04-27 09:08:43 +02:00
Ricardo Wurmus
6979e90a06 gnu: r-sanssouci: Update to 0.16.2-1.fcd60da. 
* gnu/packages/bioconductor.scm (r-sanssouci): Update to 0.16.2-1.fcd60da.
[arguments]: Remove phase 'delete-bad-tests.
[propagated-inputs]: Remove r-rcpp and r-rcpparmadillo; add r-matrixtests and
r-rlang.
[native-inputs]: Remove r-ggplot2; add r-knitr.

Change-Id: I30fa708d0a1873d78fa2350e5933e807ccaae821
 2026-04-27 09:08:43 +02:00
Ricardo Wurmus
6a27c193e6 gnu: r-cicero-monocle3: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-cicero-monocle3)[arguments]: Remove phase
'skip-bad-tests; specify #:skipped-tests instead.

Change-Id: I3ab92000982c97e95e4b157dcf3cfe1d49f056f3
 2026-04-27 09:08:43 +02:00
Ricardo Wurmus
df58ecce45 gnu: r-mutationalpatterns: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mutationalpatterns)[arguments]: Remove
phase 'skip-bad-tests.

Change-Id: I51ee4d02fd12e34100a6823a8ba71e117bc618a1
 2026-04-27 09:08:43 +02:00
Ricardo Wurmus
dabf458672 gnu: r-bamsignals: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-bamsignals)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: Ifbb26ef31debc2ad43eb1265c7916b24bfa140ae
 2026-04-27 09:08:43 +02:00
Ricardo Wurmus
334b06c51b gnu: r-biomart: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-biomart)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: I98c167685c07453fd8fa8b8c7700c21591d043af
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
0e337d2ac8 gnu: r-biocset: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-biocset)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: Ibcdfdca6e35869e260a8f02deddacaa59002c7f1
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
485afefd34 gnu: r-zellkonverter: Enable tests by bypassing Conda. 
* gnu/packages/bioconductor.scm (r-zellkonverter)[arguments]: Enable all tests
but one; add phase 'basilisk-configuration.
[inputs]: Add python-anndata, python-h5py, python-natsort, python-numpy,
python-pandas, python-scipy, and python-wrapper.

Change-Id: I4eb5e34ab540bdeea64f6b8629bb8f17d24c3663
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
2b11327ca1 gnu: r-hdf5array: Update comment. 
* gnu/packages/bioconductor.scm (r-hdf5array)[arguments]: Update comment on
why we delete a test.

Change-Id: Ibefbe960a12969337a63329d511d6c0891895c94
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
91b7e40c48 gnu: r-basilisk: Patch to bypass Conda. 
* gnu/packages/bioconductor.scm (r-basilisk)[arguments]: Add phase
'patch-for-guix.

Change-Id: I8bcfd78da0818235a3ab1c00aae8dafdc8aa57aa
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
9384694ed8 gnu: r-decoupler: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-decoupler)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: I40e3ba1539ee4dc5d471c547a5208317f2a7600e
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
876e740955 gnu: r-cner: Remove custom phases, enable all tests. 
* gnu/packages/bioconductor.scm (r-cner)[arguments]: Remove phases
'disable-bad-tests and 'fix-gcc-14-strictness.

Change-Id: I116538acce4dacad5550727dba14bb72bb8905f4
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
a54c1cce04 gnu: r-chromvar: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-chromvar)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: Ia5419e9be986c9600372de103c0ee5353a194346
 2026-04-27 09:08:42 +02:00
Ricardo Wurmus
db4ac307d3 gnu: r-mscoreutils: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mscoreutils)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I6fa331a8110d3923f7f1394023cfa81aa2a1b837
 2026-04-27 09:08:41 +02:00
Ricardo Wurmus
61d6237d50 gnu: r-abn: Enable all tests. 
* gnu/packages/bioconductor.scm (r-abn)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I78978dfc6e606c90d24c6ef6b4cf0ed5f1af3492
 2026-04-27 09:08:41 +02:00
Ricardo Wurmus
fcf0a97470 gnu: r-posterior: Update to 1.7.0. 
* gnu/packages/cran.scm (r-posterior): Update to 1.7.0.

Change-Id: I7053e29e54d42cbb82a45d19831accc849df796a
 2026-04-27 09:08:41 +02:00
Ricardo Wurmus
ce69ef9d5c gnu: r-processx: Update to 3.8.7. 
* gnu/packages/cran.scm (r-processx): Update to 3.8.7.

Change-Id: I69d8e6a7d8627f851b066b00e4e74340767facfb
 2026-04-27 09:08:41 +02:00
Ricardo Wurmus
1feeb06aff gnu: r-pkgload: Update to 1.5.1. 
* gnu/packages/cran.scm (r-pkgload): Update to 1.5.1.

Change-Id: Ib774f4e6a77be5d7358673485337248e47388700
 2026-04-27 09:08:41 +02:00
Ricardo Wurmus
5dc762a7ca gnu: r-ps: Update to 1.9.2. 
* gnu/packages/cran.scm (r-ps): Update to 1.9.2.

Change-Id: I44542f83ac5880a79f940ab6702805812d3414e1
 2026-04-27 09:08:41 +02:00
Ricardo Wurmus
a05f8cc7b0 gnu: r-conos: Update to 1.5.3. 
* gnu/packages/bioconductor.scm (r-conos): Update to 1.5.3.

Change-Id: I1f2b0773ab03051dd4c82f991196c0c7ac77063f
 2026-04-27 09:08:41 +02:00
Ricardo Wurmus
dce3a53259 gnu: r-barcodetrackr: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-barcodetrackr)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: Ibe719fb6a2395c31c67788255d7df95988962b4c
 2026-04-27 09:08:40 +02:00
Ricardo Wurmus
366a7fa3bb gnu: r-basics: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-basics)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: I2948991cebaab753c496ec272a9f82c5f359ca2d
 2026-04-27 09:08:40 +02:00
Efraim Flashner
c2b3c7a00b gnu: vim-full: Don't overwrite configure flags. 
* gnu/packages/vim.scm (vim-full)[arguments]: Adjust the inherited
configure-flags instead of prepending configure-flags to the inherited
arguments.

Fixes: guix/guix#8116
Change-Id: I522b03620ffe6668876843b30bb90f44e521484d
 2026-04-27 08:54:42 +03:00
jgart
0c1d342191 gnu: trealla: Update to 2.94.4. 
* gnu/packages/prolog.scm (trealla): Update to 2.94.4.

Change-Id: I1e3fd231fa11ac47ce89eeb986b2c2d0969ae7cf
 2026-04-26 21:59:16 -04:00
Maxim Cournoyer
ae50b34096 .guix-authorizations: Register Noé's key. 
* .guix-authorizations (baleine): Register Noé's key.

Voucher: Liliana Marie Prikler <liliana.prikler@gmail.com>
Voucher: Maxim Cournoyer <maxim@guixotic.coop>
Voucher: Andreas Enge <andreas@enge.fr>
Change-Id: Iaa262f753d73f5ecd15ecd883b7e905de647b476
 2026-04-27 09:35:25 +09:00
moksh
f90adbd63b gnu: syncthing: Update to 2.0.16. 
* gnu/packages/syncthing.scm (syncthing): Update to 2.0.16.

Merges: https://codeberg.org/guix/guix/pulls/8160
Change-Id: I3272857ea3d73b0a206ff878333e6339a2e815ca
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-26 22:45:13 +01:00
Sharlatan Hellseher
0791717950 gnu: go-github-com-openzipkin-zipkin-go: Enable build and tests. 
* gnu/packages/golang-web.scm (go-github-com-openzipkin-zipkin-go):
[arguments] <skip-build?, tests?>: Enable.
[propagated-inputs]: Add go-github-com-ibm-sarama and
go-github-com-rabbitmq-amqp091-go.
[description]: Provide URL with short explanation of what Zipkin is.

Change-Id: Ia3945e598b2868ab28b40ee7a4ff7937dc169558
 2026-04-26 22:35:23 +01:00
Sharlatan Hellseher
ab69b44f78 gnu: Add go-github-com-rabbitmq-amqp091-go. 
* gnu/packages/golang-web.scm (go-github-com-rabbitmq-amqp091-go): New variable.

Change-Id: I5f66448cc50ba88f84f1afdb571eb1e2d630451b
 2026-04-26 22:27:38 +01:00
Sharlatan Hellseher
d19d23ceba gnu: Add go-github-com-ibm-sarama. 
* gnu/packages/golang-web.scm (go-github-com-ibm-sarama, sarama-tools):
New variables.

Change-Id: I0022a5a435f5bb5001eba62b2ed59e45a0f4b0b0
 2026-04-26 22:22:53 +01:00
Sharlatan Hellseher
db8a17feea gnu: Add go-github-com-eapache-go-resiliency. 
* gnu/packages/golang-xyz.scm (go-github-com-eapache-go-resiliency): New variable.

Change-Id: I7b8c36c7c955c899e4212cb9248e7d9f86ce05b4
 2026-04-26 22:22:53 +01:00
Danny Milosavljevic
a1a82d2525 gnu: codex: Update to 0.124.0. 
* gnu/packages/patches/rust-codex-0.124.0-code-mode-stub-toolname.patch: New file.
* gnu/packages/patches/rust-codex-0.124.0-remove-patch-sections.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add references to them.
* gnu/packages/codex.scm (codex): Update to 0.124.0.
* gnu/packages/rust-crates.scm: Update.
* gnu/packages/rust-sources.scm (rust-codex-0.124.0): New variable.

Change-Id: I90570206d39c533edfc6d70e229ee3f7eda9dcf2
 2026-04-26 22:47:11 +02:00
Tobias Geerinckx-Rice
ecda809fd4 doc: Further elucidate(?) the bcachefs situation. 
This follows up on commit cd2d52bce2.

Said support is <https://codeberg.org/guix/guix/pulls/1917>, but linking
to PRs in the documentation is a bit much.  The git log is much better.

* doc/guix.texi (Keyboard Layout and Networking and Partitioning): One
cannot, in fact, load the bcachefs module on an unpatched Guix System.

Change-Id: Ib04cc97cf7cffc1e7d130d4dd43e422afaef55ee
 2026-04-19 02:00:00 +02:00
Tobias Geerinckx-Rice
6565cb39a9 gnu: psi-plus: Tweak description. 
* gnu/packages/messaging.scm (psi-plus)[description]: Prioritise.

Change-Id: Ica1695748628ba2ea7d06e2ebdaa871bf7cf09c1
 2026-04-19 02:00:00 +02:00
Tobias Geerinckx-Rice
d93269e925 gnu: psi-plus: Update to 1.5.2115. 
* gnu/packages/messaging.scm (psi-plus): Update to 1.5.2115.
[inputs]: Add libomemo-c.

Change-Id: Idc1ec0510a28420c659122f72ac832818be8e9b8
 2026-04-19 02:00:00 +02:00
Tobias Geerinckx-Rice
223b983c4f gnu: psi-plus: Update home page. 
* gnu/packages/messaging.scm (psi-plus)[home-page]: Update.

Change-Id: I27a0ef532455e1a352b19936a860ab0490217447
 2026-04-19 02:00:00 +02:00
Tobias Geerinckx-Rice
65d5abecf4 gnu: psi-plus: Simplify wrapping phase. 
* gnu/packages/messaging.scm (psi-plus)[arguments]: Rename the 'wrap-env phase
to 'wrap-executable and remove the single-element FOR-EACH complication.

Change-Id: Iabda6634f6f83cd8cd21bd26c2107b139030c575
 2026-04-19 02:00:00 +02:00
Sharlatan Hellseher
dd2c600e8f gnu: go-github-com-sigstore-rekor-tiles-v2: Add more missing inputs. 
* gnu/packages/golang-web.scm (go-github-com-sigstore-rekor-tiles-v2):
[arguments] <test-flags>: Run more tests.
[propagated-inputs]: Add go-cloud-google-com-go-spanner,
go-github-com-chainguard-dev-clog, and
go-github-com-transparency-dev-tessera.

Change-Id: I25d364114e8f4bc38a8aa3234f4952c5f6c58da9
 2026-04-26 12:59:22 +01:00
Patrick Norton
2a3492b086 gnu: Add go-github-com-alingse-asasalint. 
* gnu/packages/golang-check.scm (go-github-com-alingse-asasalint): New
variable.

Relates-to: https://codeberg.org/guix/guix/pulls/5417
Change-Id: Ia17d862ae911c00dac08256c0c2be61cbb422a8e
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-26 12:59:21 +01:00
Patrick Norton
850300f874 gnu: Add go-github-com-alexkohler-prealloc. 
* gnu/packages/golang-check.scm (go-github-com-alexkohler-prealloc): New
variable.

Relates-to: https://codeberg.org/guix/guix/pulls/5417
Change-Id: Ib7fffc1dbc1a026606dbd619b3db50b4c639eb8b
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-26 12:59:21 +01:00
Patrick Norton
0c05c14a1c gnu: Add go-github-com-akutz-memconn. 
* gnu/packages/golang-web.scm (go-github-com-akutz-memconn): New
variable.

Relates-to: https://codeberg.org/guix/guix/pulls/5417
Change-Id: I4983368885e32dbe8eb048ad40c2b4b244d5a691
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-26 12:59:21 +01:00
Patrick Norton
f340255ac3 gnu: Add go-fyne-io-systray. 
* gnu/packages/golang-xyz.scm (go-fyne-io-systray): New variable.

Relates-to: https://codeberg.org/guix/guix/pulls/5417
Change-Id: I026a0fc3045af9c3d6733973f88c8184d78596f6
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-26 12:59:21 +01:00
Patrick Norton
c60385e7f3 gnu: Add go-codeberg-org-chavacava-garif. 
* gnu/packages/golang-xyz.scm (go-codeberg-org-chavacava-garif): New
variable.

Relates-to: https://codeberg.org/guix/guix/pulls/5417
Change-Id: I701c4e3d7a55b7af146f6362d2ec1ff9060e54c5
Reviewed-by: Johannes Christ <jc@jchri.st>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-04-26 12:59:21 +01:00
Sharlatan Hellseher
11c071147e gnu: Add go-github-com-transparency-dev-tessera. 
* gnu/packages/golang-web.scm (go-github-com-transparency-dev-tessera): New variable.

Change-Id: I4424fb0e10dfd17b34e1c122f7aec78c1a83de67
 2026-04-26 12:59:21 +01:00
Sharlatan Hellseher
505d54e113 gnu: Add go-go-opentelemetry-io-contrib-detectors-aws-ecs. 
* gnu/packages/golang-web.scm (go-go-opentelemetry-io-contrib-detectors-aws-ecs): New variable.

Change-Id: I81e34bde1c85014bff5b3010dbb66453ba9d9f08
 2026-04-26 12:59:21 +01:00
Sharlatan Hellseher
adb6bc8174 gnu: Add go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2. 
* gnu/packages/golang-web.scm (go-go-opentelemetry-io-contrib-detectors-aws-ec2-v2): New variable.

Change-Id: I7dee3d4de6ef305e6ed8bafbedbba9754f008d17
 2026-04-26 12:59:21 +01:00
Sharlatan Hellseher
9572ef816c gnu: Add go-github-com-brunoscheufler-aws-ecs-metadata-go. 
* gnu/packages/golang-web.scm (go-github-com-brunoscheufler-aws-ecs-metadata-go): New variable.

Change-Id: I2862a77b66b0b78286dc4c3d0c799746e8e0978c
 2026-04-26 12:59:20 +01:00