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

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

Change-Id: Ieac662ca919889a71861cb6b1f08febab2487f54
This commit is contained in:
Ricardo Wurmus
2026-04-05 08:54:02 +02:00
parent b77880875b
commit f247a08a4f
1 changed files with 15 additions and 24 deletions
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39
gnu/packages/bioconductor.scm
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@@ -13739,30 +13739,21 @@ for downstream analysis and data visualization.")
(build-system r-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'disable-bad-tests
(lambda _
;; These attempt to connect to the Internet.
(substitute* "tests/testthat/test-getContigDoublets.R"
((".*getContigDoublets works for no doublets.*" m)
(string-append m "skip('guix')\n"))
((".*getContigDoublets works for inputs with doublets.*" m)
(string-append m "skip('guix')\n")))
(substitute* "tests/testthat/test-loadContigs.R"
((".*loadContigs correctly auto-detects and processes various formats.*" m)
(string-append m "skip('guix')\n"))
((".*loadContigs correctly processes various formats from URL.*" m)
(string-append m "skip('guix')\n")))
;; There is code running outside of testthat that tries to
;; download files off the Internet.
(delete-file "tests/testthat/test-combineContigs.R")
;; These fail with: Unknown property set: 'kideraFactors'.
(substitute* "tests/testthat/test-positionalProperty.R"
((".*positionalProperty: Output structure is correct.*" m)
(string-append m "skip('guix')\n"))
((".*positionalProperty: ggplot object is correctly formed.*" m)
(string-append m "skip('guix')\n"))))))))
#:skipped-tests
;; There is code running outside of testthat that tries to
;; download files off the Internet.
'("test-combineContigs.R"
;; These attempt to connect to the Internet.
("test-getContigDoublets.R"
"getContigDoublets works for no doublets"
"getContigDoublets works for inputs with doublets")
("test-loadContigs.R"
"loadContigs correctly auto-detects and processes various formats"
"loadContigs correctly processes various formats from URL")
;; These fail with: Unknown property set: 'kideraFactors'.
("test-positionalProperty.R"
"positionalProperty: Output structure is correct"
"positionalProperty: ggplot object is correctly formed"))))
(propagated-inputs
(list r-dplyr
r-evmix