From 32519d54531867b9bbe8953a51155ecfacb9afbc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 2 Apr 2026 11:48:43 +0200
Subject: [PATCH] gnu: r-barcodetrackr: Replace custom phase with SKIPPED-TESTS
 argument.

* gnu/packages/bioconductor.scm (r-barcodetrackr)[arguments]: Remove phase
'disable-bad-tests; specify #:skipped-tests instead.

Change-Id: Ibe719fb6a2395c31c67788255d7df95988962b4c
---
 gnu/packages/bioconductor.scm | 47 ++++++++++++-----------------------
 1 file changed, 16 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 682c74ac43..ff6745ee6b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6026,37 +6026,22 @@ estimates for each correlation element.")
     ;; Bioconductor 3.23.
     (arguments
      (list
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'disable-bad-tests
-           (lambda _
-             (with-directory-excursion "tests/testthat"
-               (substitute* "test-clonal-bias-functions.R"
-                 ((".*bias_(histogram|ridge_plot|lineplot) works.*" m)
-                  (string-append m "skip('guix')\n")))
-               (substitute* "test-clonal-diversity-functions.R"
-                 ((".*rank_abundance works.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*clonal_diversity works.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*clonal_count works.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*mds_plot works.*" m)
-                  (string-append m "skip('guix')\n")))
-               (substitute* "test-clonal-pattern-functions.R"
-                 ((".*barcode_ggheatmap works.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*barcode_ggheatmap_stat works.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*barcode_binary_heatmap works.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*clonal_contribution works.*" m)
-                  (string-append m "skip('guix')\n")))
-               (substitute* "test-shared-clonality-functions.R"
-                 ((".*scatter_plot works.*" m)
-                  (string-append m "skip('guix')\n"))
-                 ((".*cor_plot works.*" m)
-                  (string-append m "skip('guix')\n")))))))))
+      #:skipped-tests
+      '(("test-clonal-bias-functions.R"
+         "bias_(histogram|ridge_plot|lineplot) works")
+        ("test-clonal-diversity-functions.R"
+         "clonal_count works"
+         "clonal_diversity works"
+         "mds_plot works"
+         "rank_abundance works")
+        ("test-clonal-pattern-functions.R"
+         "barcode_binary_heatmap works"
+         "barcode_ggheatmap works"
+         "barcode_ggheatmap_stat works"
+         "clonal_contribution works")
+        ("test-shared-clonality-functions.R"
+         "cor_plot works"
+         "scatter_plot works"))))
     (propagated-inputs
      (list r-circlize
            r-cowplot