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| author | Romain GARBAGE <romain.garbage@inria.fr> | 2026-05-07 14:26:34 +0200 |
|---|---|---|
| committer | Cayetano Santos <csantosb@inventati.org> | 2026-05-07 15:10:07 +0200 |
| commit | 363ea2f547c67926aa859520c028372eb74cc585 (patch) | |
| tree | 4bc7312538a02eef7dfe22be18f81167ca823f77 /gnu | |
| parent | 3d87fa6421116266b65ccd975ab7aac837a21452 (diff) | |
gnu: r-cellid: Fix deprecated argument.
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>
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 11 |
1 files changed, 11 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb4ef76607..6b5fcf7bc2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6272,6 +6272,17 @@ for clusters.") "1bvj7n2qxfvy1fmjqmm1w65fcj7fy5h74i0jgl0a0940mlhd7s9v")))) (properties `((upstream-name . "CelliD"))) (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; "The `slot` argument of `GetAssayData()` was deprecated in + ;; SeuratObject 5.0.0 and is now defunct.", i = "Please use + ;; the `layer` argument instead." + (add-after 'unpack 'fix-deprecated-argument + (lambda _ + (substitute* '("R/mca.R" "tests/testthat/test_CelliD.R") + (("slot") "layer"))))))) (propagated-inputs (list r-biocparallel r-data-table |