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gnu: r-gchain: Add missing inputs.

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* gnu/packages/bioinformatics.scm (r-gchain)[native-inputs]: Add
r-pwalign and r-testthat.
[arguments]: Add phase 'skip-bad-tests.

Change-Id: Ia11c6e50e0d2886762ec551df3e5d73ef98547f8
This commit is contained in:
Ricardo Wurmus 2024-11-28 11:29:40 +01:00
parent d2d2b4d4cb
commit e2561d2ec8
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1 changed files with 21 additions and 0 deletions
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gnu/packages/bioinformatics.scm
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@ -12133,6 +12133,26 @@ file formats, and ffTrack objects in multi-track panels.")
"105wgi5w2fhwq1grsvj6zjigwg0sny3z7zr577q8ki3qffjwdkj0"))))
(properties `((upstream-name . "gChain")))
(build-system r-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'skip-bad-tests
(lambda _
(substitute* "tests/testthat/test_gChain.R"
;; C stack usage 7973568 is too close to the limit
((".*'testing lift\\(\\) works'.*" m)
(string-append m "skip('guix')"))
;; C stack usage 7973568 is too close to the limit
((".*'testing \"\\*\" works'.*" m)
(string-append m "skip('guix')"))
;; Accuracy problem
((".*'testing cgChain\\(\\) works'.*" m)
(string-append m "skip('guix')"))
;; unable to find an inherited method for function ‘strand<-’
;; for signature ‘x = "GRangesList", value = "character"’
((".*'testing permute\\(\\) works'.*" m)
(string-append m "skip('guix')"))))))))
(propagated-inputs
(list r-bamutils
r-biostrings
@ -12143,6 +12163,7 @@ file formats, and ffTrack objects in multi-track panels.")
r-gutils
r-matrix
r-rtracklayer))
(native-inputs (list r-pwalign r-testthat))
(home-page "https://github.com/mskilab/gChain/")
(synopsis "Additional capabilities and speed for GenomicRanges operations")
(description