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426fe16e06cb7fd1de9a3fc51f22c69fecb2d314
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167144 Commits

Author SHA1 Message Date
Ricardo Wurmus
426fe16e06 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
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
90c4c3530f 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
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
c0297673a5 gnu: r-msnid: Enable all tests. 
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: Iaf459f89d1f6d82a486a0dcd860cff746ee140a0
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
42e77aa9d9 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
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
0c0c0ad77c gnu: r-h5mread: Enable all tests. 
* gnu/packages/bioconductor.scm (r-h5mread)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I8a20a311a4c8c2177c07ab5d0b59c8ea5e369c73
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
37ef398f0d 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
2eb83001aa 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
65f50393ca gnu: r-karyoploter: Enable all tests. 
* gnu/packages/bioconductor.scm (r-karyoploter)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I3d5727327d1da4ba30bd8cd8d9251100329e4cac
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
1c52e22203 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
446924b39c 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
c6e8991a5b gnu: r-mutationalpatterns: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mutationalpatterns)[arguments]: Remove
phase 'skip-bad-tests.

Change-Id: I51ee4d02fd12e34100a6823a8ba71e117bc618a1
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
34f26309a3 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
69060517ed 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
146ea07ee7 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
0cd49cf2b9 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
 2026-04-25 09:09:55 +02:00
Ricardo Wurmus
748393f2ac gnu: r-hdf5array: Update comment. 
* gnu/packages/bioconductor.scm (r-hdf5array)[arguments]: Update comment on
why we delete a test.

Change-Id: Ibefbe960a12969337a63329d511d6c0891895c94
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
eaf5a6fd72 gnu: r-basilisk: Patch to bypass Conda. 
* gnu/packages/bioconductor.scm (r-basilisk)[arguments]: Add phase
'patch-for-guix.

Change-Id: I8bcfd78da0818235a3ab1c00aae8dafdc8aa57aa
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
626e54b5b6 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
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
756acc0ab6 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
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
00c96a6b16 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
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
99fda25cd1 gnu: r-mscoreutils: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mscoreutils)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I6fa331a8110d3923f7f1394023cfa81aa2a1b837
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
4e0f21cb7f gnu: r-abn: Enable all tests. 
* gnu/packages/bioconductor.scm (r-abn)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I78978dfc6e606c90d24c6ef6b4cf0ed5f1af3492
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
0b3951e929 gnu: r-posterior: Update to 1.7.0. 
* gnu/packages/cran.scm (r-posterior): Update to 1.7.0.

Change-Id: I7053e29e54d42cbb82a45d19831accc849df796a
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
5474846261 gnu: r-processx: Update to 3.8.7. 
* gnu/packages/cran.scm (r-processx): Update to 3.8.7.

Change-Id: I69d8e6a7d8627f851b066b00e4e74340767facfb
 2026-04-25 09:09:54 +02:00
Ricardo Wurmus
fd99032c1a gnu: r-pkgload: Update to 1.5.1. 
* gnu/packages/cran.scm (r-pkgload): Update to 1.5.1.

Change-Id: Ib774f4e6a77be5d7358673485337248e47388700
 2026-04-25 09:09:53 +02:00
Ricardo Wurmus
3ffafb6b8a gnu: r-ps: Update to 1.9.2. 
* gnu/packages/cran.scm (r-ps): Update to 1.9.2.

Change-Id: I44542f83ac5880a79f940ab6702805812d3414e1
 2026-04-25 09:09:53 +02:00
Ricardo Wurmus
4e78b68934 gnu: r-conos: Update to 1.5.3. 
* gnu/packages/bioconductor.scm (r-conos): Update to 1.5.3.

Change-Id: I1f2b0773ab03051dd4c82f991196c0c7ac77063f
 2026-04-25 09:09:53 +02:00
Ricardo Wurmus
7ff0ad4111 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
 2026-04-25 09:09:53 +02:00
Ricardo Wurmus
343447bae6 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
 2026-04-25 09:09:53 +02:00
Ian Eure
fef9065259 gnu: emacs-firefox-release-notes: Update to 1.8. 
* gnu/packages/emacs-xyz.scm (emacs-firefox-release-notes): Update to 1.8.

Change-Id: I974e2414bd4a9fd3e128ca8778f15f3c1360fa0a
 2026-04-24 19:39:20 -07:00
jadzi
31c2fc709b guile-web-middleware: Propagate ‘guile-compose’. 
* gnu/packages/guile-xyz.scm (guile-web-middleware)[inputs]: Move
‘guile-compose’ to…
[propagated-inputs]: … here.

Change-Id: I4b8ce3fd160dab7eb57f3565ff6f693b5cbdd36a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8088
 2026-04-24 22:57:13 +02:00
Ludovic Courtès
bbfb6f2c62 gnu: guile-git: Update to 0.11.1. 
* gnu/packages/guile.scm (guile-git): Update to 0.11.1.
[home-page]: Switch to codeberg.org.
[arguments]: Remove ‘skip-tests/hurd’ phase, which is no longer needed.

Fixes: guix/guix#4989
Change-Id: Ie6570df3d19c61acc165d4619445c4a55ed319cf
Reported-by: Yelninei <yelninei@tutamail.com>
Reported-by: brian cully <bjc@spork.org>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Merges: #8076
 2026-04-24 22:16:08 +02:00
Ludovic Courtès
0cbf963044 gnu: guile-variant-package-name: Don’t rename ‘guile-bootstrap’. 
Previously, ‘package-for-guile-2.2’ would sometimes create a variant
of (@ (gnu packages commencement) glibc-final) with a package called
“guile2.2-bootstrap” among its derivations, thereby causing an entirely
separate package graph to be built.

The reason ‘glibc-final’ would be modified despite the use of #:deep? #f is
because ‘texinfo’ depends on ‘libc-utf8-locales-for-target’, which depends on
‘glibc-final’.  This happened for ‘guile2.2-git’ because it depends on
‘texinfo’.

* gnu/packages/guile.scm (guile-variant-package-name): When ‘name’ is
“guile-bootstrap”, return it unchanged.

Change-Id: I6317927cf073085f36c4e07704469bb400b5a890
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2026-04-24 22:16:07 +02:00
Efraim Flashner
72ce4088da gnu: bottom: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
bottom.

Change-Id: I8deffd25b7876514997fe4c78b21b4fb89d37210
 2026-04-24 16:15:57 +03:00
Efraim Flashner
65eb271e6f gnu: rmpc: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
rmpc.

Change-Id: I27e90add392c04f5670957240bb86c80882359e6
 2026-04-24 16:15:57 +03:00
Efraim Flashner
0e0622edcc gnu: mollysocket: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
mollysocket.

Change-Id: If0acc613381141b1227cc3c5154e354c5bb6da8a
 2026-04-24 16:15:57 +03:00
Efraim Flashner
9a9b4c5674 gnu: espflash: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
espflash.

Change-Id: I001401f94c48b0a524da23fd04e2f790639fa036
 2026-04-24 16:15:56 +03:00
Efraim Flashner
f0c5f25cb4 gnu: cargo-nextest: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
cargo-nextest.

Change-Id: I97cd6068fed88ddd25eda6a6a32ab596f31c5882
 2026-04-24 16:15:56 +03:00
Efraim Flashner
869cd7fa03 gnu: python-cmsis-pack-manager: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
python-cmsis-pack-manager.

Change-Id: I16ec4aebec3a887d04a72e6518a369d3c7b4d530
 2026-04-24 16:15:56 +03:00
André Batista
08015b27ee gnu: mullvadbrowser: Update to 15.0.9. 
* gnu/packages/tor-browsers.scm (%mullvadbrowser-build-date): Update to
140.9.1esr-15.0-1-build1.
(%mullvadbrowser-version): Update to 15.0.9.
(%mullvadbrowser-firefox-version): Update to 140.9.1esr-15.0-1-build1.
(mullvadbrowser-translation-base): Update to ce651a6f8a.
(mullvadbrowser-translation-specific): Update to 4bf1989120.

Change Id: I6678167e836f66979f44a3c7f67ae499930abdd4

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-24 14:59:01 +02:00
André Batista
273a4433a6 gnu: torbrowser: Update to 15.0.9. 
* gnu/packages/tor-browsers.scm (firefox-locales): Update to 412690f136.
(%torbrowser-build-date): Update to 20260404073000.
(%torbrowser-version): Update to 15.0.9.
(%torbrowser-firefox-version): Update to 140.9.1esr-15.0-1-build1.
(torbrowser-translation-base): Update to ce651a6f8a.
(torbrowser-translation-specific): Update to 685a144cb5.
[arguments] <#:phases> 'fix-zucchini: New phase.

Change Id: I04a709936f40f32780d2a9fd31d395db727378d3

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-04-24 14:58:54 +02:00
Efraim Flashner
209874a88a gnu: ouch: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
ouch.

Change-Id: Ieef1dac04323f059afcfc1b4d814e81154fc3b09
 2026-04-24 15:01:10 +03:00
Efraim Flashner
d7f45831cf gnu: tectonic: Install shell completions. 
* gnu/packages/rust-apps.scm (tectonic)[arguments]: Add a phase to
generate the shell completions.

Change-Id: I9a624b1c44770325ff33567181440168c5b9a38f
 2026-04-24 15:01:09 +03:00
Efraim Flashner
b10d0fdaf0 gnu: tectonic: Update to 0.16.9. 
* gnu/packages/rust-apps.scm (tectonic): Update to 0.16.9.
[source]: Don't download recursively.  Remove snippet.
[arguments]: Skip a test.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
tectonic.

Change-Id: I293ba0f31567d0cedf918cdfbbcfd62692c46dec
 2026-04-24 15:01:09 +03:00
Efraim Flashner
af2b12e51f gnu: rust-crates: Remove some rust crates. 
These crates were mentioned specifically by cargo audit.

* gnu/packages/rust-crates.scm: Remove some unused crates.

Change-Id: Ic76e8fdaf47d1004e8f0fb2c28162d20ccb57004
 2026-04-24 15:01:09 +03:00
Efraim Flashner
cfa3de9ba4 gnu: hyperfine: Simplify installing shell completions. 
* gnu/packages/rust-apps.scm (hyperfine)[arguments]: Rewrite installing
the shell completions to use the copy-build-system's install phase.

Change-Id: I3113b1817a2a8ebeb63aa187f736def8babbb5c1
 2026-04-24 15:01:09 +03:00
Efraim Flashner
fd18daaa4d gnu: hyperfine: Update to 1.20.0. 
* gnu/packages/rust-apps.scm (hyperfine): Update to 1.20.0.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
hyperfine.

Change-Id: I285f911b3b1dbb5b8338e1b5d5f1153dfce0aeed
 2026-04-24 15:01:09 +03:00
Efraim Flashner
3c2ea3ba6a gnu: vtracer: Update rust dependencies. 
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
vtracer.

Change-Id: Iebf3a02aed85ef832ba2f57f696e45b9865f9983
 2026-04-24 15:01:09 +03:00
Efraim Flashner
d3a19b14a9 gnu: aw-watcher-window-wayland: Update rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
aw-watcher-window-wayland.

Change-Id: I03e5904c697be2d1dcb9a447c84aa80e30afc286
 2026-04-24 15:01:08 +03:00
Efraim Flashner
8a68d9f6c8 gnu: zed: Update some rust dependencies. 
Addresses rust security advisories.

* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
rust-dap-types-0.0.1.1b461b3, rust-gh-workflow-0.8.0.c9eac0e,
rust-livekit-0.7.8.5f04705, rust-notify-8.2.0.ce58c24,
rust-zed-xim-0.4.0-zed.16f35a2.

Change-Id: I489b0fbc53da10c38bb25e0a20a43065d1aafdd6
 2026-04-24 15:01:08 +03:00