guix_mirror_bot pushed a commit to branch r-team
in repository guix.
commit dd8967cdcfa445802faf4db85f21ab7ebae6a019
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Mon Nov 10 18:38:43 2025 +0100
gnu: r-msnbase: Fix tests that failed because of libxml2.
* gnu/packages/bioconductor.scm (r-msnbase)[arguments]: Fix tests
by adding 'ensure-libxml2-works phase.
Change-Id: I555f19d5bc749cdd458af4b55a2a5a2e89c7d190
---
gnu/packages/bioconductor.scm | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b492a50a42..0d6bc9bc7d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11657,6 +11657,13 @@ containers.")
'(modify-phases %standard-phases
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp")))
+ ;; For unknown reasons, the libxml2 features are misreported without
+ ;; this call prior to running BiocGenerics:::testPackage("mzR").
+ (add-after 'unpack 'ensure-libxml2-works
+ (lambda _
+ (substitute* "tests/testthat.R"
+ (("library\\(\"MSnbase\"\\)" m)
+ (string-append "XML::libxmlFeatures()\n" m)))))
(add-after 'unpack 'delete-bad-tests
(lambda _
;; Needs r-prolocdata
