guix_mirror_bot pushed a commit to branch r-team
in repository guix.
commit 585b23e522458963dad41aea98d3053d9ccaadb0
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Mon Nov 10 18:38:16 2025 +0100
gnu: r-mzr: Restore tests that failed because of libxml2.
* gnu/packages/bioconductor.scm (r-mzr)[arguments]: Restore two tests; fix
them by adding 'ensure-libxml2-works phase.
Change-Id: Ifeb3667449e862826a402b8c1ce37e4bcc92f21b
---
gnu/packages/bioconductor.scm | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9e80c5e778..b492a50a42 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11838,12 +11838,13 @@ specific parser.")
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-after 'unpack 'skip-bad-tests
+ ;; For unknown reasons, the libxml2 features are misreported without
+ ;; this call prior to running BiocGenerics:::testPackage("mzR").
+ (add-after 'unpack 'ensure-libxml2-works
(lambda _
- ;; These tests need Internet access to load XML schemas.
- (with-directory-excursion "inst/unitTests/"
- (delete-file "test_isolationWindow.R")
- (delete-file "test_mzid.R"))))
+ (substitute* "tests/runTests.R"
+ (("library\\(\"mzR\"\\)" m)
+ (string-append "XML::libxmlFeatures()\n" m)))))
(add-after 'unpack 'use-system-boost
(lambda _
(substitute* "src/Makevars"
