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Author SHA1 Message Date
Ricardo Wurmus
773c8d1635 gnu: r-variantfiltering: Enable all tests. 
* gnu/packages/bioconductor.scm (r-variantfiltering)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I76ef169743ecbd5c75fb115ab5adf8c46128d068
 2026-04-25 09:09:59 +02:00
Ricardo Wurmus
1fa2bc1f54 gnu: r-beachmat: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-beachmat)[arguments]: Remove
phase 'delete-bad-tests; specify #:skipped-tests
instead.

Change-Id: I17f4999f3747f4e72015ae64872e2c877a157267
 2026-04-25 09:09:59 +02:00
Ricardo Wurmus
c897dc7b5c gnu: r-rhdf5lib: Use G-expressions and fix test instead of disabling it. 
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Use G-expressions;
fix library version check instead of disabling the test.

Change-Id: I78e8cfd9d2588517b0911dde5fc8aa53d4f67892
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
f475d9728f gnu: r-sgseq: Enable all tests. 
* gnu/packages/bioconductor.scm (r-sgseq)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I25cfd6620b6573057c161200bd5fad99a19e2bdd
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
ce86f386cf gnu: r-metagenomeseq: Enable all tests. 
* gnu/packages/bioconductor.scm (r-metagenomeseq)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I17d0d965b6d7702dfd6eb24eef288a51915aa3f6
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
fbc13d9db0 gnu: r-graph: Enable tests. 
* gnu/packages/bioconductor.scm (r-graph)[arguments]: Enable tests.

Change-Id: I9307f27a1e36e439b3d0c5680faa558981dc5d3a
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
82a96ecc83 gnu: r-summarizedexperiment: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-summarizedexperiment)[arguments]: Remove
phase 'delete-bad-tests; specify #:test-directory and #:skipped-tests
instead.

Change-Id: I6229ec548d21f30534f9d279b3aae8847e55a77e
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
09048dad73 gnu: r-batchelor: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-batchelor)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: Icd8aaae97130eed2e3c1b1629ac1dd9d18287fee
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
991f528483 gnu: r-biocsingular: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-biocsingular)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: I8b8f91562233c9cca180eeda50f5d6dc4bc1cd37
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
82374c0f39 gnu: r-glmgampoi: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-glmgampoi)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead; enable tests.

Change-Id: I5de95bf59482d706bf80bb6fc4cdcf6da89d2afd
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
9f5339071d gnu: r-variantannotation: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-variantannotation)[arguments]: Remove phase
'delete-bad-tests; specify #:test-directory and #:skipped-tests instead.

Change-Id: I17532f8a6e23b52591f0593677e8cd88aacbfc23
 2026-04-25 09:09:58 +02:00
Ricardo Wurmus
30b92275be gnu: r-rhdf5: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-rhdf5)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead; enable tests.

Change-Id: I2a440a41b6d527c5c91786345db49532fdca5b2c
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
e42d0406af gnu: r-regioner: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-regioner)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: Ic90c620653ffa6d2ad6eab4ded05e4bbfe62d279
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
41204a6d85 gnu: r-msnbase: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-msnbase)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: Icb2170c300d80dc5f955b4ff1b97f1e33385a7c2
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
32132def1e gnu: r-genomicdatacommons: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-genomicdatacommons)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead.

Change-Id: I02a6f73db89104c90e6a4301240a1fd20e35a636
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
4145f305c8 gnu: r-escape: Enable all tests. 
* gnu/packages/bioconductor.scm (r-escape)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I6d0af6daaed7b5c142ccfdfc162ba57968d1ce17
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
7de1544807 gnu: r-category: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-category)[arguments]: Remove phase
'delete-bad-tests; specify #:test-directory and #:skipped-tests instead.

Change-Id: If573e4ea497fdd1f3654433d2854f0a821455bd6
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
c68c0d2eff gnu: r-treeio: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-treeio)[arguments]: Remove phase
'delete-bad-tests; specify #:skipped-tests instead; enable more tests.

Change-Id: I55fccf144c233bfd4115b9201c1550e9d477e6a4
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
2763e48f66 gnu: r-derfinder: Enable all tests. 
* gnu/packages/bioconductor.scm (r-derfinder)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: Ib4e5e8557209b5a46b48e77c52c6355676b3e577
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
9a2efa7b44 gnu: r-bumphunter: Disable tests instead of patching them. 
After patching we didn't run any tests anyway.

* gnu/packages/bioconductor.scm (r-bumphunter)[arguments]: Remove phase
'delete-bad-tests; disable tests instead.

Change-Id: I6ba13013c6038b272204ae4191111714d835be05
 2026-04-25 09:09:57 +02:00
Ricardo Wurmus
9cda0861de 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
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
70c4e88a6d 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
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
1bf19a4932 gnu: r-plyranges: Enable all tests. 
* gnu/packages/bioconductor.scm (r-plyranges)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: I7539e3c6f8ed26a66bf9d4ef65ecb11bee74421d
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
ebd8d41e27 gnu: r-transcriptr: Enable all tests. 
* gnu/packages/bioconductor.scm (r-transcriptr)[arguments]: Remove phase
'disable-bad-tests.

Change-Id: Ic0781089808a2468797d03e968aa696553409801
 2026-04-25 09:09:56 +02:00
Ricardo Wurmus
488d5e3d68 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
 2026-04-25 09:09:56 +02:00
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