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

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

Change-Id: Icb2170c300d80dc5f955b4ff1b97f1e33385a7c2
This commit is contained in:
Ricardo Wurmus
2026-04-07 06:28:59 +02:00
parent 32132def1e
commit 41204a6d85
1 changed files with 28 additions and 30 deletions
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58
gnu/packages/bioconductor.scm
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@@ -11942,6 +11942,33 @@ containers.")
(build-system r-build-system)
(arguments
(list
#:skipped-tests
;; These all need Internet access
'("test_MSmap.R"
("test_MzTab.R"
"MzTab creation and accessors"
"MzTab-M creation and accessors"
"MzTab-M MS-Dial import"
"MzTab reading and writing"
"MzTab-M reading and writing"
"Conversion to MSnSetList")
("test_MzTab_09.R"
"read MzTab data v 0.9 and 1.0")
("test_fileNames.R"
"fileNames accessor MzTab")
;; Fails with: unable to find an inherited method for function
;; ‘pickPeaks’
("test_OnDiskMSnExp_other_methods.R"
"Compare OnDiskMSnExp and MSnExp pickPeaks"
"pickPeaks,OnDiskMSnExp works with refineMz")
;; Fails with: object 'hyperLOPIT2015' not found
("test_utils.R"
"merging and expanding features")
;; Fails with: invalid 'description' argument
("test_io.R"
"readMSnSet2: rownames and fnames")
;; Attempts to run "hostname"
"test_readMSData2.R")
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'set-HOME
@@ -11952,36 +11979,7 @@ containers.")
(lambda _
(substitute* "tests/testthat.R"
(("library\\(\"MSnbase\"\\)" m)
(string-append "XML::libxmlFeatures()\n" m)))))
(add-after 'unpack 'delete-bad-tests
(lambda _
;; Needs r-prolocdata
(for-each delete-file
'("tests/testthat/test_average.R"
"tests/testthat/test_fdata-selection.R"
"tests/testthat/test_foi.R"
"tests/testthat/test_nadata.R"
"tests/testthat/test_trimws.R"
"tests/testthat/test_MSnSet.R"))
;; Attempts to run "hostname"
(delete-file "tests/testthat/test_readMSData2.R")
;; Needs Internet access
(for-each delete-file
'("tests/testthat/test_fileNames.R"
"tests/testthat/test_MSmap.R"
"tests/testthat/test_MzTab.R"
"tests/testthat/test_MzTab_09.R"))
;; Fails with: object 'hyperLOPIT2015' not found
(delete-file "tests/testthat/test_utils.R")
;; Fails with: invalid 'description' argument
(delete-file "tests/testthat/test_io.R")
;; Fails with: unable to find an inherited method for function
;; ‘pickPeaks’
(substitute* "tests/testthat/test_OnDiskMSnExp_other_methods.R"
((".*pickPeaks,OnDiskMSnExp works with refineMz.*" m)
(string-append m "skip('guix')\n"))
((".*Compare OnDiskMSnExp and MSnExp pickPeaks.*" m)
(string-append m "skip('guix')\n"))))))))
(string-append "XML::libxmlFeatures()\n" m))))))))
(propagated-inputs
(list r-affy
r-biobase