From 363ea2f547c67926aa859520c028372eb74cc585 Mon Sep 17 00:00:00 2001
From: Romain GARBAGE <romain.garbage@inria.fr>
Date: Thu, 7 May 2026 14:26:34 +0200
Subject: [PATCH] gnu: r-cellid: Fix deprecated argument.
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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>
---
 gnu/packages/bioconductor.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fb4ef766079..6b5fcf7bc24 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