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mirror of https://git.savannah.gnu.org/git/guix.git synced 2026-04-06 21:20:33 +02:00

gnu: r-biomart: Replace custom phase with SKIPPED-TESTS argument.

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

Change-Id: I98c167685c07453fd8fa8b8c7700c21591d043af
This commit is contained in:
Ricardo Wurmus
2026-04-02 18:41:40 +02:00
parent 7f6e420283
commit 7673e935e6

View File

@@ -8654,20 +8654,22 @@ on Bioconductor or which replace R functions.")
(build-system r-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'delete-bad-tests
(lambda _
;; These tests attempt to download files.
(for-each delete-file
'("tests/testthat/test_ensemblFunctions.R"
"tests/testthat/test_ensemblGenomes.R"
"tests/testthat/test_getBM.R"
"tests/testthat/test-getGene.R"
"tests/testthat/test_utilityFunctions.R"
"tests/testthat/test_z_cache.R"
;; This produces unexpected warnings.
"tests/testthat/test_ensembl_ssl_settings.R")))))))
#:skipped-tests
'(("test_ensembl_ssl_settings.R"
;; This produces unexpected warnings.
"SSL settings are stored in the cache")
;; These tests attempt to download files.
("test_ensemblFunctions.R"
"useEnsembl\\(\\) error handling is OK"
"useEnsembl\\(host = \\) is not necessary for ensembl.org"
"Ensembl URLs are constructed correctly")
("test_getBM.R"
"getBM returns sensible things"
"getBM doesn't convert T/F alleles into TRUE/FALSE")
("test-getGene.R"
"getGene\\(\\) recognizes new ensembl name as ensembl")
;; Code run outside of testthat accesses www.ensembl.org
"test_z_cache.R")))
(propagated-inputs
(list r-annotationdbi
r-biocfilecache