guix_mirror_bot pushed a commit to branch r-team
in repository guix.
commit af2b5507bc78ed0f2cc5ff81b895b33b12cba828
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Fri Feb 20 14:23:12 2026 +0100
gnu: r-voltron: Replace custom phase with #:skipped-tests.
* gnu/packages/bioinformatics.scm (r-voltron)[arguments]: Remove phase
'skip-bad-tests; provide #:skipped-tests argument.
Change-Id: I00ddc80185972d5bf7e01856b8ab0c47ffcf3fd2
---
gnu/packages/bioinformatics.scm | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ad15af0af2..771eea352d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22967,6 +22967,12 @@ patterns.")
(build-system r-build-system)
(arguments
(list
+ #:skipped-tests
+ '(("test_conversion.R"
+ ;; These fail to raise an error because of our patch in the
+ ;; 'do-not-use-conda phase, which falls back to Python from Guix.
+ "as.AnnData, python path"
+ "as.ometiff, python path"))
#:phases
#~(modify-phases %standard-phases
;; By default VoltRon will use Basilisk, which uses Conda to set
@@ -22980,14 +22986,6 @@ patterns.")
(string-append
"source(paste0(system.file(package=\"VoltRon\"),
\"/guix-refs.R\"));\n"
"return(guix_python);")))))
- (add-after 'unpack 'skip-bad-tests
- (lambda _
- (with-directory-excursion "tests/testthat"
- (substitute* "test_conversion.R"
- ((".*as.AnnData, python path.*" m)
- (string-append m "skip('skip');\n"))
- ((".*as.ometiff, python path.*" m)
- (string-append m "skip('skip');\n"))))))
;; We do this outside of the source code to ensure that
;; references are accessible to Guix.
(add-after 'install 'record-python-reference
