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172677 Commits

Author SHA1 Message Date
Ricardo Wurmus eb8fb07869 gnu: r-txdbmaker: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-txdbmaker)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: I35e1fb2dce920cb0a59a063eb2b511b636e46546
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus e5809f9dfe gnu: r-scrapper: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-scrapper)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: I25b29604508732e64a7efb72b9635e7bc8685356
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus d618b746ab gnu: r-plyranges: Enable all tests. 
* gnu/packages/bioconductor.scm (r-plyranges)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I7539e3c6f8ed26a66bf9d4ef65ecb11bee74421d
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus 81e7897426 gnu: r-transcriptr: Enable all tests. 
* gnu/packages/bioconductor.scm (r-transcriptr)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: Ic0781089808a2468797d03e968aa696553409801
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 139275f541 gnu: r-tcgautils: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-tcgautils)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: I29a788dc229c599207d89d7f4dbd49c3c9f06f1e
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 0d3e6c9067 gnu: r-screpertoire: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-screpertoire)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: Ieac662ca919889a71861cb6b1f08febab2487f54
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 170430ae56 gnu: r-chippeakanno: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-chippeakanno)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: Id7e7cd02d1b0b02f62022b9d55e69c867200e213
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 0d872d8feb gnu: r-msnid: Enable all tests. 
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: Iaf459f89d1f6d82a486a0dcd860cff746ee140a0
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 18514ac581 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
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 634e01e63c gnu: r-h5mread: Enable all tests. 
* gnu/packages/bioconductor.scm (r-h5mread)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I8a20a311a4c8c2177c07ab5d0b59c8ea5e369c73
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 0ba382ed46 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
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 3914c0b0d4 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
 2026-04-28 09:43:18 +02:00
Ricardo Wurmus 77926495b9 gnu: r-karyoploter: Enable all tests. 
* gnu/packages/bioconductor.scm (r-karyoploter)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I3d5727327d1da4ba30bd8cd8d9251100329e4cac
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus 24b4cac721 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
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus 736493c469 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
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus 2313cfe545 gnu: r-mutationalpatterns: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mutationalpatterns)[arguments]: Remove
phase 'skip-bad-tests.

Change-Id: I51ee4d02fd12e34100a6823a8ba71e117bc618a1
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus 20703c3798 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
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus 33fdbbf0ec 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
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus fb44842b2b 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
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus e6cea80a08 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
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus b1241b9837 gnu: r-hdf5array: Update comment. 
* gnu/packages/bioconductor.scm (r-hdf5array)[arguments]: Update comment on
why we delete a test.

Change-Id: Ibefbe960a12969337a63329d511d6c0891895c94
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus fa529d1008 gnu: r-basilisk: Patch to bypass Conda. 
* gnu/packages/bioconductor.scm (r-basilisk)[arguments]: Add phase
'patch-for-guix.

Change-Id: I8bcfd78da0818235a3ab1c00aae8dafdc8aa57aa
 2026-04-28 09:43:17 +02:00
Ricardo Wurmus 7a85759090 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
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus 3cd0fafdd1 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
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus b6e3f8e6b6 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
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus a43943d964 gnu: r-mscoreutils: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mscoreutils)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I6fa331a8110d3923f7f1394023cfa81aa2a1b837
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus c11f5915ed gnu: r-abn: Enable all tests. 
* gnu/packages/bioconductor.scm (r-abn)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I78978dfc6e606c90d24c6ef6b4cf0ed5f1af3492
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus 56f3be50c4 gnu: r-posterior: Update to 1.7.0. 
* gnu/packages/cran.scm (r-posterior): Update to 1.7.0.

Change-Id: I7053e29e54d42cbb82a45d19831accc849df796a
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus 1bb57f474b gnu: r-processx: Update to 3.8.7. 
* gnu/packages/cran.scm (r-processx): Update to 3.8.7.

Change-Id: I69d8e6a7d8627f851b066b00e4e74340767facfb
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus e5eae4c58a gnu: r-pkgload: Update to 1.5.1. 
* gnu/packages/cran.scm (r-pkgload): Update to 1.5.1.

Change-Id: Ib774f4e6a77be5d7358673485337248e47388700
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus 27d8040bb8 gnu: r-ps: Update to 1.9.2. 
* gnu/packages/cran.scm (r-ps): Update to 1.9.2.

Change-Id: I44542f83ac5880a79f940ab6702805812d3414e1
 2026-04-28 09:43:16 +02:00
Ricardo Wurmus 0ac03eb38c gnu: r-conos: Update to 1.5.3. 
* gnu/packages/bioconductor.scm (r-conos): Update to 1.5.3.

Change-Id: I1f2b0773ab03051dd4c82f991196c0c7ac77063f
 2026-04-28 09:43:15 +02:00
Ricardo Wurmus 6601fd0402 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
 2026-04-28 09:43:15 +02:00
Ricardo Wurmus 363ad0fc8c 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
 2026-04-28 09:43:15 +02:00
André Batista 02421ea3fb gnu: mullvadbrowser: Update to 15.0.10. 
Fixes CVEs: 2026-6746, 2026-6747, 2026-6748, 2026-6749, 2026-6750,
2026-6751, 2026-6752, 2026-6753, 2026-6754, 2026-6757, 2026-6759,
2026-6761, 2026-6762, 2026-6763, 2026-6764, 2026-6765, 2026-6766,
2026-6767, 2026-6769, 2026-6770, 2026-6771, 2026-6772, 2026-6776,
2026-6785 and 2026-6786.

See:
<https://www.mozilla.org/en-US/security/advisories/mfsa2026-32/> for
details.

* gnu/packages/tor-browsers.scm (%mullvadbrowser-build-date): Update to
20260420133000.
(%mullvadbrowser-version): Update to 15.0.10.
(%mullvadbrowser-firefox-version): Update to 140.10.0esr-15.0-1-build2.
(mullvadbrowser-translation-base): Update to b09d79a755.

Change-Id: I7ca71425b6135ca9649d52b577b3278e64250674
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-28 09:01:45 +02:00
André Batista 48f6b21f1c gnu: torbrowser: Update to 15.0.10. 
Fixes CVEs: 2026-6746, 2026-6747, 2026-6748, 2026-6749, 2026-6750,
2026-6751, 2026-6752, 2026-6753, 2026-6754, 2026-6757, 2026-6759,
2026-6761, 2026-6762, 2026-6763, 2026-6764, 2026-6765, 2026-6766,
2026-6767, 2026-6769, 2026-6770, 2026-6771, 2026-6772, 2026-6776,
2026-6785 and 2026-6786.

See:
<https://www.mozilla.org/en-US/security/advisories/mfsa2026-32/> for
details.

* gnu/packages/tor-browsers.scm (%torbrowser-build-date): Update to
20260420133000.
(%torbrowser-version): Update to 15.0.10.
(%torbrowser-firefox-version): Update to 140.10.0esr-15.0-1-build2.
(torbrowser-translation-base): Update to b09d79a755.
(torbrowser-translation-specific): Update to acc7524bf4.

Change-Id: If87a8147f55da7dba625d3cb976085a65b97ed09
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-28 09:01:38 +02:00
Cayetano Santos 8227c6e7b3 gnu: mu: Update to 1.14.1. 
* gnu/packages/mail.scm (mu): Update to 1.14.1.

Change-Id: I555df29c96b047ce2bbc0ac7903c220adbd69694
 2026-04-28 08:53:28 +02:00
Mattia Bunel abaf568edf services: postgresql: Change default authentification method. 
* gnu/services/databases.scm (%default-postgres-hba):
  Change the authentification method from the deprecated md5
  to the recommended scram-sha-256.

Change-Id: I4ae06bf2f77daa7a9339964182153c5f02897e4f
Merges: https://codeberg.org/guix/guix/pulls/7780
Reviewed-by: jgart <jgart@dismail.de>
Signed-off-by: Nguyễn Gia Phong <cnx@loang.net>
 2026-04-28 15:03:16 +09:00
Juliana Sims 75ea9c1857 gnu: xdg-desktop-portal-wlr: Cleanup and style. 
* gnu/packages/freedesktop.scm (xdg-desktop-portal-wlr): Cleanup and run guix
style.

Change-Id: I2ac138281b8be351000f0beabd2efb1d0cdcb29f
Signed-off-by: Noé Lopez <noelopez@free.fr>
 2026-04-27 22:53:53 +02:00
Juliana Sims c9652dcc06 gnu: xdg-desktop-portal-wlr: Use gexps. 
* gnu/packages/freedesktop.scm (xdg-desktop-portal-wlr): Use gexps.

Change-Id: I23356906c439dd2e4ba24e3ecf6244a7c5bf1942
Signed-off-by: Noé Lopez <noelopez@free.fr>
 2026-04-27 22:53:53 +02:00
Juliana Sims 4fd78658a7 gnu: xdg-desktop-portal-wlr: Fix screencast. 
Logic for handling output and window selection moved into a separate file
which needs to have its hardcoded paths correct.

* gnu/packages/freedesktop.scm (xdg-desktop-portal-wlr): Fix screencast.

Change-Id: Idad5bc7fa75b926cf48dfa6cb8dc95cf92e5bd5a
Signed-off-by: Noé Lopez <noelopez@free.fr>
 2026-04-27 22:53:50 +02:00
jgart da514e3e8f gnu: Remove ecl-mcclim. 
* gnu/packages/lisp-xyz.scm (ecl-mcclim): Delete variable.

Change-Id: I294e2cd132195a38719596f63e406251de203e80
 2026-04-27 15:45:47 -04:00
aecepoglu 9ae428f9ca gnu: sbcl-slime-swank: update to 2.32 
* gnu/packages/lisp-xyz.scm (sbcl-slime-swank): update to 2.32

Change-Id: Ie41a24f723dbe92a786f6cdd9695baba02eee9ff
Signed-off-by: jgart <jgart@dismail.de>
 2026-04-27 15:45:47 -04:00
Simen Endsjø 3ce60cd35e gnu: evdi: Update to 1.14.15. 
* gnu/packages/linux.scm (evdi): Update to 1.14.15.
[arguments]<#:phases>{embed-/etc/os-release}: New phase to remove
`include /etc/os-release' from Makefile.
[description]: Add a period.

Change-Id: Ica3290fdfbafe26e0f26604513a180b45d318275
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-27 15:27:04 +02:00
Simen Endsjø 80fcc26390 Revert "gnu: Remove libevdi." 
This reverts commit 8d6b041cb6.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-27 15:27:04 +02:00
Simen Endsjø 723dc0512c Revert "gnu: Remove evdi." 
This reverts commit 7619e82b35.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-27 15:27:04 +02:00
Cayetano Santos 66ca9d5331 gnu: verilator: Update to 5.048. 
* gnu/packages/electronics.scm (verilator): Update to 5.048.

Change-Id: I752a8d286fa0d6191450e4e40fe30780c8854774
 2026-04-27 14:44:13 +02:00
Cayetano Santos 7c93e85206 gnu: python-edalize: Update to 0.6.8. 
* gnu/packages/electronics.scm (python-edalize): Update to 0.6.8.

Change-Id: I753b5004a885386efcc8ede35ef948368a386311
 2026-04-27 14:42:57 +02:00
Cayetano Santos 19a2b2f026 gnu: nvc: Update to 1.20.1. 
* gnu/packages/electronics.scm (nvc): Update to 1.20.1.

Change-Id: Ia196440b823d38f371e3efe349b92226405c1cc3
 2026-04-27 14:20:18 +02:00
Andreas Enge e087bad5e9 gnu: Remove regrader. 
* gnu/packages/music.scm (regrader): Delete variable.

Fixes: guix/guix#7461
Change-Id: Id838f86be15353aff842afd54d793b21d146ff0e
 2026-04-27 14:03:58 +02:00