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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-11-29 19:42:22 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-12-03 16:59:58 +0100 |
| commit | 169c4e612bc0cd498fddd0ffb039aa952cf5e8c0 (patch) | |
| tree | 11b3ae8beb3f79f09141b98f9d1d83701457c123 /gnu/packages/bioconductor.scm | |
| parent | 594d64569dcc680eaeecc9a73fbe294dfbb0c80b (diff) | |
| download | guix-169c4e612bc0cd498fddd0ffb039aa952cf5e8c0.tar.gz guix-169c4e612bc0cd498fddd0ffb039aa952cf5e8c0.zip | |
gnu: r-msnbase: Add missing inputs.
* gnu/packages/bioconductor.scm (r-msnbase)[native-inputs]: Add r-msdata,
r-rpx, r-summarizedexperiment, and r-xml.
[arguments]: Add phases 'set-HOME and 'delete-bad-tests.
[properties]: Tell updater to avoid a dependency cycle.
Change-Id: I49f6ec0c516f610785c3e79e0d4a4ad74a9ac38c
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 40 |
1 files changed, 38 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6c7006aa5c..728f1466df 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10923,8 +10923,39 @@ remote MS data sets.") (sha256 (base32 "0cykb5kk524i3ssps798c7wfpa3f8svdgxa8sfvc1pxm0fxypfgb")))) - (properties `((upstream-name . "MSnbase"))) + (properties + `((upstream-name . "MSnbase") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-prolocdata")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (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")))))) (propagated-inputs (list r-affy r-biobase @@ -10949,7 +10980,12 @@ remote MS data sets.") r-scales r-vsn)) (native-inputs - (list r-knitr r-testthat)) + (list r-knitr + r-msdata + r-rpx + r-summarizedexperiment + r-testthat + r-xml)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description |