From 32ea496b55e0e77acedd87c55b1590602af4964c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 10 Nov 2025 18:38:16 +0100 Subject: [PATCH] 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 9e80c5e7786db9558c99d2040ea1666a9a5335f4..b492a50a42ec022ff99f5454e5b2adf66bc88432 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"