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8844 Commits

Author SHA1 Message Date
Ricardo Wurmus 8d07dd9ef7 gnu: r-h5mread: Patch for compatibility with R 4.6.0. 
* gnu/packages/patches/r-h5mread-0001-h5mread-1.3.2-Get-rid-of-non-API-calls-to-R.patch:
New file.
* gnu/local.mk (dist_patch_DATA): Record it.
* gnu/packages/bioconductor.scm (r-h5mread)[source]: Register patch.

Change-Id: Iecbf0eb41b554169b36c00b74072b1fca7a31943
 2026-04-28 09:43:46 +02:00
Ricardo Wurmus e2173901c2 gnu: r-rsamtools: Patch for compatibility with R 4.6.0. 
* gnu/packages/patches/r-rsamtools-r-4.6.0-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Record it.
* gnu/packages/bioconductor.scm (r-rsamtools)[source]: Register patch.

Change-Id: I0c1eafe3c440f998d309174e4292061dbaf3eb34
 2026-04-28 09:43:46 +02:00
Ricardo Wurmus 9163b17ce9 gnu: r-sparsearray: Patch for compatibility with R 4.6.0. 
* gnu/packages/patches/r-sparsearray-r-4.6.0-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Record it.
* gnu/packages/bioconductor.scm (r-sparsearray)[source]: Register patch.

Change-Id: I569f7150d91393d8c7c9981ebe3db77c0cfa5356
 2026-04-28 09:43:46 +02:00
Ricardo Wurmus e72baf6d34 gnu: r-snpstats: Patch for compatibility with R 4.6.0. 
* gnu/packages/patches/r-snpstats-0001-fixed-non-API-except-for-IS_S4_OBJECT.patch,
gnu/packages/patches/r-snpstats-0002-fixed-IS_S4_OBJECT.patch: New files.
* gnu/local.mk (dist_patch_DATA): Record them.
* gnu/packages/bioconductor.scm (r-snpstats)[source]: Register patches.

Change-Id: I911f5833199448a16a23f9e715903a8427b08233
 2026-04-28 09:43:46 +02:00
Ricardo Wurmus 895605e489 gnu: r-biostrings: Patch for compatibility with R 4.6.0. 
* gnu/packages/patches/r-biostrings-r4.6.0-compat.patch: New file.
* gnu/local.mk (dist_patch_DATA): Record it.
* gnu/packages/bioconductor.scm (r-biostrings)[source]: Register patch.

Change-Id: Id0ba9e4340245c456e25e631ca372c1a6edb2bba
 2026-04-28 09:43:46 +02:00
Ricardo Wurmus afe281ae0f gnu: r-s4vectors: Patch for R 4.6.0. 
* gnu/packages/bioconductor.scm (r-s4vectors)[arguments]: Add phase
'R-4.6.0-compatibility.

Change-Id: I731250e9dcfc62cfb2cafbf88e2f1e2d6b932828
 2026-04-28 09:43:46 +02:00
Ricardo Wurmus 922c10243d gnu: r-gviz: Skip one test on 32-bit systems. 
* gnu/packages/bioconductor.scm (r-gviz)[arguments]: Conditionally skip a
test.

Change-Id: Ibd9a0e6b7f57474dba9158350f52a94f708cd442
 2026-04-28 09:43:41 +02:00
Ricardo Wurmus a71f019471 gnu: r-gsva: Update to 2.4.9. 
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.4.9.

Change-Id: I1cde12b64f22c76813ecf41f7553e132807c5def
 2026-04-28 09:43:40 +02:00
Ricardo Wurmus a356889513 gnu: r-ggpicrust2: Update to 2.5.12. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 2.5.12.

Change-Id: Ie625e6082c6e6ff615e5655ef4e99f92d968f574
 2026-04-28 09:43:33 +02:00
Ricardo Wurmus eb330ca8b4 gnu: r-samr: Update to 3.0.1. 
* gnu/packages/bioconductor.scm (r-samr): Update to 3.0.1.

Change-Id: Ia662ec72bbd8c9c28c954e5a57137b14d9627def
 2026-04-28 09:43:33 +02:00
Ricardo Wurmus 8d32c01209 gnu: r-universalmotif: Conditionally skip test on 32-bit platforms. 
* gnu/packages/bioconductor.scm (r-universalmotif)
[arguments]: On 32-bit platforms skip one test.

Change-Id: I66c046c20b0eefbaeb90c5fbf86233c175c096b4
 2026-04-28 09:43:30 +02:00
Ricardo Wurmus 4fba0cfdd6 gnu: r-ballgown: Adjust for testthat compatibility. 
* gnu/packages/bioconductor.scm (r-ballgown)[arguments]: Add phase
'testthat-compatibility.

Change-Id: Id8d931ee79b55b82e977eb3822537f80b55108bf
 2026-04-28 09:43:30 +02:00
Ricardo Wurmus dcb5c6797e gnu: r-biocstyle: Do not build self-contained reports on 32-bit platforms. 
* gnu/packages/bioconductor.scm (r-biocstyle)[arguments]: Conditionally add
phase 'prevent-pandoc-segfault.

Change-Id: I84ea57c44ceedb21e03050b4c48c9c05beedc7d7
 2026-04-28 09:43:29 +02:00
Ricardo Wurmus d04f8fddf1 gnu: r-s4vectors: Update to 0.48.1. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.48.1.

Change-Id: I8b856c0e0679262ec5be2a1ae655fd2aa9f6d263
 2026-04-28 09:43:26 +02:00
Ricardo Wurmus 84e69015d7 gnu: r-biocviews: Update to 1.78.2. 
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.78.2.

Change-Id: I3aa91454ea13045bb4f4ebe36700c5c36ee28816
 2026-04-28 09:43:26 +02:00
Ricardo Wurmus 2cd99842ce gnu: r-wiggleplotr: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.34.1.

Change-Id: I3e9df308ff374a62d2ae41eed6df7297411ee665
 2026-04-28 09:43:26 +02:00
Ricardo Wurmus 0ccb5c5601 gnu: r-enmix: Update to 1.46.2. 
* gnu/packages/bioconductor.scm (r-enmix): Update to 1.46.2.

Change-Id: I04675d3351d71cf7132918f3840a236ba64ad2c0
 2026-04-28 09:43:26 +02:00
Ricardo Wurmus c6a06616b1 gnu: r-delayedarray: Update to 0.36.1. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.36.1.

Change-Id: I36e6c48575213cbdac4c7351bfd5fc49d2ca1faf
 2026-04-28 09:43:26 +02:00
Ricardo Wurmus 0b3cb58286 gnu: r-flames: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-flames)[arguments]: Remove
phase 'disable-some-tests; specify #:skipped-tests instead.

Change-Id: I75024c6b9c5316e1b4bef80c5e60d77699b71e9b
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus 19e629f0cc gnu: r-ncdfflow: Enable all tests. 
* gnu/packages/bioconductor.scm (r-ncdfflow)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I5c4c64f992b33af1ecaa42b833a8f2cb3f2b47d6
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus 5b5c6e5089 gnu: r-flowclust: Replace custom phase with SKIPPED-TESTS argument. 
* gnu/packages/bioconductor.scm (r-flowclust)[arguments]: Remove
phase 'delete-bad-tests; specify #:skipped-tests instead; disable one more
test.

Change-Id: I18369d410ad9cff4db7afcb15fd5292b3c6c0177
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus f745fcd2dd gnu: r-variantfiltering: Enable all tests. 
* gnu/packages/bioconductor.scm (r-variantfiltering)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I76ef169743ecbd5c75fb115ab5adf8c46128d068
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus 46f41339ea 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
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus dc4c04a435 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
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus 958d5387bb gnu: r-sgseq: Enable all tests. 
* gnu/packages/bioconductor.scm (r-sgseq)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I25cfd6620b6573057c161200bd5fad99a19e2bdd
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus 3074ef6ae5 gnu: r-metagenomeseq: Enable all tests. 
* gnu/packages/bioconductor.scm (r-metagenomeseq)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I17d0d965b6d7702dfd6eb24eef288a51915aa3f6
 2026-04-28 09:43:21 +02:00
Ricardo Wurmus 6a39be4de0 gnu: r-graph: Enable tests. 
* gnu/packages/bioconductor.scm (r-graph)[arguments]: Enable tests.

Change-Id: I9307f27a1e36e439b3d0c5680faa558981dc5d3a
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus 4f373dc2d4 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
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus e4973ce3ec 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
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus 74958d45f5 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
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus 00fd60c839 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
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus d2a00bf5a7 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
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus 4eb595f98e 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
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus 039f42cacf 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
 2026-04-28 09:43:20 +02:00
Ricardo Wurmus 300ad1eae1 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
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus e91add3e5d 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
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus b623f93a1c gnu: r-escape: Enable all tests. 
* gnu/packages/bioconductor.scm (r-escape)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: I6d0af6daaed7b5c142ccfdfc162ba57968d1ce17
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus ff0ac745a3 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
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus 79caf62e0e 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
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus 2427e2c927 gnu: r-derfinder: Enable all tests. 
* gnu/packages/bioconductor.scm (r-derfinder)[arguments]: Remove phase
'delete-bad-tests.

Change-Id: Ib4e5e8557209b5a46b48e77c52c6355676b3e577
 2026-04-28 09:43:19 +02:00
Ricardo Wurmus ade48de757 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
 2026-04-28 09:43:19 +02:00
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