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2026-05-07gnu: r-cellid: Fix deprecated argument.Romain GARBAGE
r-seurat update (commit 51b1aea0bd633136c27ff082fc52de9f1fdec04c) broke this package as it is using deprecated arguments that were removed. * gnu/packages/bioconductor.scm (r-cellid)[arguments]: Add ’fix-deprecated-argument #:phase. Merges guix/guix!8414 Change-Id: I12aa8665aa694836ea21f199b521cc208af317a2 Signed-off-by: Cayetano Santos <csantosb@inventati.org> Modified-by: Cayetano Santos <csantosb@inventati.org>
2026-04-28gnu: r-mscoreutils: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* gnu/packages/patches/r-mscoreutils-0001-fix-non-API-call-to-R-SETLENGTH-by-using-lengthgets.patch: New file. * gnu/local.mk (dist_patch_DATA): Record it. * gnu/packages/bioconductor.scm (r-mscoreutils)[source]: Register patch. Change-Id: If288fed9c85d7a46d1938e7699e2a9bc57447a03
2026-04-28gnu: r-flowcore: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowcore)[arguments]: Add phase 'R-4.6.0-compatibility. Change-Id: Ic99953b3bf228928ab7ada1d36d2be2c1aae608b
2026-04-28gnu: r-shortread: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* gnu/packages/patches/r-shortread-0001-ShortRead-1.69.3-Get-rid-of-non-API-calls-to-R.patch: New file. * gnu/local.mk (dist_patch_DATA): Record it. * gnu/packages/bioconductor.scm (r-shortread)[source]: Register patch. Change-Id: I9fd85076db6a86b25f4389d3226e0fde8a38a3b5
2026-04-28gnu: r-h5mread: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* 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
2026-04-28gnu: r-rsamtools: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* 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
2026-04-28gnu: r-sparsearray: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* 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
2026-04-28gnu: r-snpstats: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* 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
2026-04-28gnu: r-biostrings: Patch for compatibility with R 4.6.0.Ricardo Wurmus
* 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
2026-04-28gnu: r-s4vectors: Patch for R 4.6.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4vectors)[arguments]: Add phase 'R-4.6.0-compatibility. Change-Id: I731250e9dcfc62cfb2cafbf88e2f1e2d6b932828
2026-04-28gnu: r-gviz: Skip one test on 32-bit systems.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gviz)[arguments]: Conditionally skip a test. Change-Id: Ibd9a0e6b7f57474dba9158350f52a94f708cd442
2026-04-28gnu: r-gsva: Update to 2.4.9.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-gsva): Update to 2.4.9. Change-Id: I1cde12b64f22c76813ecf41f7553e132807c5def
2026-04-28gnu: r-ggpicrust2: Update to 2.5.12.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 2.5.12. Change-Id: Ie625e6082c6e6ff615e5655ef4e99f92d968f574
2026-04-28gnu: r-samr: Update to 3.0.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-samr): Update to 3.0.1. Change-Id: Ia662ec72bbd8c9c28c954e5a57137b14d9627def
2026-04-28gnu: r-universalmotif: Conditionally skip test on 32-bit platforms.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-universalmotif) [arguments]: On 32-bit platforms skip one test. Change-Id: I66c046c20b0eefbaeb90c5fbf86233c175c096b4
2026-04-28gnu: r-ballgown: Adjust for testthat compatibility.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ballgown)[arguments]: Add phase 'testthat-compatibility. Change-Id: Id8d931ee79b55b82e977eb3822537f80b55108bf
2026-04-28gnu: r-biocstyle: Do not build self-contained reports on 32-bit platforms.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocstyle)[arguments]: Conditionally add phase 'prevent-pandoc-segfault. Change-Id: I84ea57c44ceedb21e03050b4c48c9c05beedc7d7
2026-04-28gnu: r-s4vectors: Update to 0.48.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.48.1. Change-Id: I8b856c0e0679262ec5be2a1ae655fd2aa9f6d263
2026-04-28gnu: r-biocviews: Update to 1.78.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocviews): Update to 1.78.2. Change-Id: I3aa91454ea13045bb4f4ebe36700c5c36ee28816
2026-04-28gnu: r-wiggleplotr: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-wiggleplotr): Update to 1.34.1. Change-Id: I3e9df308ff374a62d2ae41eed6df7297411ee665
2026-04-28gnu: r-enmix: Update to 1.46.2.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-enmix): Update to 1.46.2. Change-Id: I04675d3351d71cf7132918f3840a236ba64ad2c0
2026-04-28gnu: r-delayedarray: Update to 0.36.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.36.1. Change-Id: I36e6c48575213cbdac4c7351bfd5fc49d2ca1faf
2026-04-28gnu: r-flames: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flames)[arguments]: Remove phase 'disable-some-tests; specify #:skipped-tests instead. Change-Id: I75024c6b9c5316e1b4bef80c5e60d77699b71e9b
2026-04-28gnu: r-ncdfflow: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ncdfflow)[arguments]: Remove phase 'delete-bad-tests. Change-Id: I5c4c64f992b33af1ecaa42b833a8f2cb3f2b47d6
2026-04-28gnu: r-flowclust: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-flowclust)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead; disable one more test. Change-Id: I18369d410ad9cff4db7afcb15fd5292b3c6c0177
2026-04-28gnu: r-variantfiltering: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variantfiltering)[arguments]: Remove phase 'delete-bad-tests. Change-Id: I76ef169743ecbd5c75fb115ab5adf8c46128d068
2026-04-28gnu: r-beachmat: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-beachmat)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: I17f4999f3747f4e72015ae64872e2c877a157267
2026-04-28gnu: r-rhdf5lib: Use G-expressions and fix test instead of disabling it.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Use G-expressions; fix library version check instead of disabling the test. Change-Id: I78e8cfd9d2588517b0911dde5fc8aa53d4f67892
2026-04-28gnu: r-sgseq: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-sgseq)[arguments]: Remove phase 'delete-bad-tests. Change-Id: I25cfd6620b6573057c161200bd5fad99a19e2bdd
2026-04-28gnu: r-metagenomeseq: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-metagenomeseq)[arguments]: Remove phase 'delete-bad-tests. Change-Id: I17d0d965b6d7702dfd6eb24eef288a51915aa3f6
2026-04-28gnu: r-graph: Enable tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-graph)[arguments]: Enable tests. Change-Id: I9307f27a1e36e439b3d0c5680faa558981dc5d3a
2026-04-28gnu: r-summarizedexperiment: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-summarizedexperiment)[arguments]: Remove phase 'delete-bad-tests; specify #:test-directory and #:skipped-tests instead. Change-Id: I6229ec548d21f30534f9d279b3aae8847e55a77e
2026-04-28gnu: r-batchelor: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-batchelor)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: Icd8aaae97130eed2e3c1b1629ac1dd9d18287fee
2026-04-28gnu: r-biocsingular: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocsingular)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: I8b8f91562233c9cca180eeda50f5d6dc4bc1cd37
2026-04-28gnu: r-glmgampoi: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-glmgampoi)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead; enable tests. Change-Id: I5de95bf59482d706bf80bb6fc4cdcf6da89d2afd
2026-04-28gnu: r-variantannotation: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-variantannotation)[arguments]: Remove phase 'delete-bad-tests; specify #:test-directory and #:skipped-tests instead. Change-Id: I17532f8a6e23b52591f0593677e8cd88aacbfc23
2026-04-28gnu: r-rhdf5: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead; enable tests. Change-Id: I2a440a41b6d527c5c91786345db49532fdca5b2c
2026-04-28gnu: r-regioner: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-regioner)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: Ic90c620653ffa6d2ad6eab4ded05e4bbfe62d279
2026-04-28gnu: r-msnbase: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-msnbase)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: Icb2170c300d80dc5f955b4ff1b97f1e33385a7c2
2026-04-28gnu: r-genomicdatacommons: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-genomicdatacommons)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: I02a6f73db89104c90e6a4301240a1fd20e35a636
2026-04-28gnu: r-escape: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-escape)[arguments]: Remove phase 'delete-bad-tests. Change-Id: I6d0af6daaed7b5c142ccfdfc162ba57968d1ce17
2026-04-28gnu: r-category: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-category)[arguments]: Remove phase 'delete-bad-tests; specify #:test-directory and #:skipped-tests instead. Change-Id: If573e4ea497fdd1f3654433d2854f0a821455bd6
2026-04-28gnu: r-treeio: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-treeio)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead; enable more tests. Change-Id: I55fccf144c233bfd4115b9201c1550e9d477e6a4
2026-04-28gnu: r-derfinder: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-derfinder)[arguments]: Remove phase 'delete-bad-tests. Change-Id: Ib4e5e8557209b5a46b48e77c52c6355676b3e577
2026-04-28gnu: r-bumphunter: Disable tests instead of patching them.Ricardo Wurmus
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
2026-04-28gnu: r-txdbmaker: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-txdbmaker)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: I35e1fb2dce920cb0a59a063eb2b511b636e46546
2026-04-28gnu: r-scrapper: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-scrapper)[arguments]: Remove phase 'disable-bad-tests; specify #:skipped-tests instead. Change-Id: I25b29604508732e64a7efb72b9635e7bc8685356
2026-04-28gnu: r-plyranges: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-plyranges)[arguments]: Remove phase 'disable-bad-tests. Change-Id: I7539e3c6f8ed26a66bf9d4ef65ecb11bee74421d
2026-04-28gnu: r-transcriptr: Enable all tests.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-transcriptr)[arguments]: Remove phase 'disable-bad-tests. Change-Id: Ic0781089808a2468797d03e968aa696553409801
2026-04-28gnu: r-tcgautils: Replace custom phase with SKIPPED-TESTS argument.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgautils)[arguments]: Remove phase 'disable-bad-tests; specify #:skipped-tests instead. Change-Id: I29a788dc229c599207d89d7f4dbd49c3c9f06f1e
generated by cgit v1.3 (git 2.53.0) at 2026-07-09 05:28:50 +0000