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171894 Commits

Author SHA1 Message Date
Ricardo Wurmus
c48ad5960a gnu: r-transcriptr: Enable all tests. 
* gnu/packages/bioconductor.scm (r-transcriptr)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: Ic0781089808a2468797d03e968aa696553409801
 2026-04-05 13:22:07 +02:00
Ricardo Wurmus
95349ce88f 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
 2026-04-05 10:00:54 +02:00
Ricardo Wurmus
f247a08a4f 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
 2026-04-05 10:00:54 +02:00
Ricardo Wurmus
b77880875b 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
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
722538254e gnu: r-msnid: Enable all tests. 
* gnu/packages/bioconductor.scm (r-msnid)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: Iaf459f89d1f6d82a486a0dcd860cff746ee140a0
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
514aafe814 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
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
945de29c83 gnu: r-h5mread: Enable all tests. 
* gnu/packages/bioconductor.scm (r-h5mread)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I8a20a311a4c8c2177c07ab5d0b59c8ea5e369c73
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
1366e268b5 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
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
967f30f154 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
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
1faabeb0fc gnu: r-karyoploter: Enable all tests. 
* gnu/packages/bioconductor.scm (r-karyoploter)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I3d5727327d1da4ba30bd8cd8d9251100329e4cac
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
caec87ac33 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
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
99657c7d39 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
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
0039438ddc gnu: r-mutationalpatterns: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mutationalpatterns)[arguments]: Remove
phase 'skip-bad-tests.

Change-Id: I51ee4d02fd12e34100a6823a8ba71e117bc618a1
 2026-04-05 10:00:53 +02:00
Ricardo Wurmus
253d9a3de5 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
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
7673e935e6 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
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
7f6e420283 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
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
92c05d76c3 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
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
3aca2db91d gnu: r-hdf5array: Update comment. 
* gnu/packages/bioconductor.scm (r-hdf5array)[arguments]: Update comment on
why we delete a test.

Change-Id: Ibefbe960a12969337a63329d511d6c0891895c94
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
63dbc9a7af gnu: r-basilisk: Patch to bypass Conda. 
* gnu/packages/bioconductor.scm (r-basilisk)[arguments]: Add phase
'patch-for-guix.

Change-Id: I8bcfd78da0818235a3ab1c00aae8dafdc8aa57aa
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
f4321b19f8 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
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
da55ed10a5 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
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
905137e885 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
 2026-04-05 10:00:52 +02:00
Ricardo Wurmus
96ffc6e6fe gnu: r-mscoreutils: Enable all tests. 
* gnu/packages/bioconductor.scm (r-mscoreutils)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I6fa331a8110d3923f7f1394023cfa81aa2a1b837
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
acd2265821 gnu: r-abn: Enable all tests. 
* gnu/packages/bioconductor.scm (r-abn)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I78978dfc6e606c90d24c6ef6b4cf0ed5f1af3492
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
2bc95c61a7 gnu: r-posterior: Update to 1.7.0. 
* gnu/packages/cran.scm (r-posterior): Update to 1.7.0.

Change-Id: I7053e29e54d42cbb82a45d19831accc849df796a
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
ff529218e4 gnu: r-processx: Update to 3.8.7. 
* gnu/packages/cran.scm (r-processx): Update to 3.8.7.

Change-Id: I69d8e6a7d8627f851b066b00e4e74340767facfb
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
a390f2deef gnu: r-pkgload: Update to 1.5.1. 
* gnu/packages/cran.scm (r-pkgload): Update to 1.5.1.

Change-Id: Ib774f4e6a77be5d7358673485337248e47388700
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
d5898eddd1 gnu: r-ps: Update to 1.9.2. 
* gnu/packages/cran.scm (r-ps): Update to 1.9.2.

Change-Id: I44542f83ac5880a79f940ab6702805812d3414e1
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
ff90d91ecf gnu: r-conos: Update to 1.5.3. 
* gnu/packages/bioconductor.scm (r-conos): Update to 1.5.3.

Change-Id: I1f2b0773ab03051dd4c82f991196c0c7ac77063f
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
32519d5453 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
 2026-04-05 10:00:51 +02:00
Ricardo Wurmus
f91b2f45fb 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
 2026-04-05 10:00:51 +02:00
Maxim Cournoyer
7473b051b6 gnu: Add pkgconf-as-pkg-config. 
* gnu/packages/pkg-config.scm (pkgconf-as-pkg-config): New variable.

Change-Id: If9ff93dbebde0c0d955cbe87af72e963913a6f45
 2026-04-05 10:25:16 +09:00
Liliana Marie Prikler
862fdaae31 gnu: gajim: Update GUIX_PYTHONPATH. 
* gnu/packages/messaging.scm (gajim)[native-search-paths]: Use “3.11” instead
of “3.10” as the python version.

Reported-by: Cayetano Santos <csantosb@inventati.org>
 2026-04-04 18:29:44 +02:00
Adrien 'neox' Bourmault
314cc3312e gnu: gajim: Update to 2.4.5. 
* gnu/packages/messaging.scm (gajim): Update to 2.4.5.

Change-Id: If3cbe09d84cfabf8ad979feb29e08f2a6310a04b
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:08 +02:00
Patrick Norton
f7d662c258 gnu: gimp: Update GI_TYPELIB_PATH. 
* gnu/packages/gimp.scm (gimp)[#:phases]<wrap>: Add “#$output/lib/girepository-1.0” to GI_TYPELIB_PATH.

Fixes: guix/guix#7546 (openttd-opengfx-8.0 fails to build)

Change-Id: Id7c2cc9e2a2de4107f50efa38e2926461d4074c1
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:04 +02:00
Sören Tempel
9a9c8f7304 gnu: louvain-community: Refer to library by path in CMake module. 
* gnu/packages/maths.scm (louvain-community)
[arguments]<#:phases>: Add 'cmake-lib-full-path phase.

Change-Id: I5f957c828f39b24a6fa8da8e3d19f16b5c328303
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:04 +02:00
Cayetano Santos
e946baf360 gnu: emacs-exwm-no-x-toolkit: Fix propagated-inputs. 
* gnu/packages/emacs-xyz.scm (emacs-exwm-no-x-toolkit)[propagated-inputs]:
Use ’modify-inputs.

Change-Id: I3708c6bd7f2ca6d132fe2e7e5a416fda80b6a299
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:04 +02:00
Noé Lopez
f78a0db28d services: Add gardenhostd-service-type. 
* gnu/services/desktop.scm (gardenhostd-service-type)
(gardenhostd-configuration): New variables.
* doc/guix.texi (Desktop Services): Document it.

Change-Id: Ied926c34b620cc8032a0b121c7419644746e2ce9
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
Noé Lopez
b6509681e2 gnu: Add gardenhostd. 
* gnu/packages/freedesktop.scm (gardenhostd): New variable.

Change-Id: Ic37b69c96dc00204d59f424dba3b757308271936
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
bdunahu
cb714dcd25 gnu: angband: Enable test suite. 
* gnu/packages/games.scm (angband)[arguments]:
<#:tests?>: Enable tests.
<#:phases>: Add phase 'skip-failing-tests.
[native-inputs]: Add perl.

Change-Id: I8af02d830e394190954d5d3374f5eaec2cfc6cf6
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
bdunahu
ddf9f96d91 gnu: angband: Update to 4.2.6. 
* gnu/packages/games.scm (angband): Update to 4.2.6.
[source]: Delete non-free and unused Windows libraries.
[arguments]:<#:phases>: Add 'fix-infinite-loop-on-sighup to prevent SIGHUP
from triggering an infinite loop.

Change-Id: I865d80f02e1ee815ea3fdabfe6999ae13e4120a9
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
Sören Tempel
37bb79a391 gnu: cadical: Update to 2.2.1. 
* gnu/packages/maths.scm (cadical): Update to 2.2.1.
[patches]: Remove cadical-add-shared-library.patch.
[arguments]<#:configure-flags>: Add "-shared".
<#:phases>: Remove replacement for 'check.
In 'configure no longer invoke setenv before configuring.
(cadical-2.1)[#:configure-flags]: Use empty list.
[#:phases]: Add 'set-shared-flags.  Replace 'check as before.

Change-Id: I67c64cfe6de0b88d0fce5103a6dcc273a2b5f244
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
Sören Tempel
e91607864b gnu: Add cadical-2.1. 
With the latest 2.2.X version of cadical, lean4's test suite fails.
This can be mitigated by packaging the old version as cadical-2.1.

* gnu/packages/maths.scm (cadical-2.1): New variable.
* gnu/packages/lean.scm (lean4)[inputs]: Replace cadical with cadical-2.1.

Change-Id: Id5e4a06266e0688454040caf0766bf8d769bbd10
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
Sören Tempel
b2b885be52 gnu: cadical: Update to 2.1.3. 
* gnu/packages/maths.scm (cadical): Update to 2.1.3.
* gnu/packages/patches/cadical-add-shared-library.patch: Adjust accordingly.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
Yelninei
5119d7b1d6 gnu: d-tools: Fix tests on 32bit systems. 
* gnu/packages/dlang.scm (d-tools)[#:phases]: Build test executables for the
target bit size.

Change-Id: I49ea559c857757abb217ff896ebd6994ea4a90c0
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:03 +02:00
Yelninei
e1bf330763 gnu: ldc: Fix int128 alignment. 
* gnu/packages/patches/ldc-i686-int128-alignment.patch: New patches.
* gnu/local.mk (dist_patch_DATA): Register it.
* gnu/packages/dlang.scm (ldc-bootstrap)[patches]: Use it.

Change-Id: I21671c2a54634c284d8832f0627fe28494e1b0b8
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2026-04-04 18:27:02 +02:00
Tobias Geerinckx-Rice
5a44919bfd gnu: bcachefs-linux-module: Inherit more from -tools. 
Keep tools and driver in strict sync, as that is what upstream supports.
(‘Tightly coupled’ ain't even the word; it's the same source tree.)

* gnu/packages/file-systems.scm (bcachefs-linux-module)[version]:
Inherit from bcachefs-tools-minimal.
[source]: Likewise.

Change-Id: Ibe93f07ad1e7ebc995c4043fece3d4d0a1212d3c
 2026-03-29 01:00:00 +01:00
Tobias Geerinckx-Rice
f8828f568b gnu: bcachefs-tools-minimal: Update to 1.37.4. 
* gnu/packages/file-systems.scm (bcachefs-tools-minimal):
Update to 1.37.4.
* gnu/packages/rust-crates.scm (rust-anyhow-1.0.89, rust-clap-4.5.20)
(rust-clap-builder-4.5.20, rust-clap-complete-4.5.33)
(rust-clap-derive-4.5.18, rust-clap-lex-0.7.2, rust-fiemap-0.2.0)
(rust-fuser-0.17.0, rust-owo-colors-4.1.0, rust-prettyplease-0.2.22)
(rust-proc-macro2-1.0.87, rust-regex-1.11.0, rust-rustix-0.38.37)
(rust-terminal-size-0.4.0, rust-uuid-1.10.0): New machine-generated
variables.
(lookup-cargo-inputs): Update entry for bcachefs-tools.

Change-Id: I14a04ca31ca0e88c5244d8df7dd51138edff5799
 2026-03-29 01:00:00 +01:00
Tobias Geerinckx-Rice
e40cc524da gnu: bcachefs-linux-module: Update to 1.37.4. 
* gnu/packages/file-systems.scm (bcachefs-linux-module): Update to
1.37.4.
[arguments]: Remove the now-obsolete 'patch-source phase.  I'm surprised
that it ever worked as it broke Makefile syntax.

Change-Id: Ice76e94bca91901e565eef57469091a7fb891ab1
 2026-03-29 01:00:00 +01:00
Patrick Norton
442fff85d1 gnu: qpwgraph: Update to 1.0.0. 
* gnu/packages/audio.scm (qpwgraph): Update to 1.0.0.

Change-Id: Ie20ddebca2b897f64be75e9150d0ebeafd31792a
Merges: #7607
Signed-off-by: Sughosha <sughosha@disroot.org>
 2026-04-04 07:39:50 +05:30