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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-11-29 09:19:49 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-12-03 16:59:57 +0100 |
| commit | 18c5a3b3246d49b89c235ed6ad287c543b159d59 (patch) | |
| tree | aca5cf846d310d01160fd891955e3138e7f9b6cb /gnu/packages/bioconductor.scm | |
| parent | 8dd751f114f16ebfe9d8f5786502edebbe661e83 (diff) | |
gnu: r-variantfiltering: Add missing inputs.
* gnu/packages/bioconductor.scm (r-variantfiltering)[native-inputs]: Add
r-biocstyle, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db, and
r-txdb-hsapiens-ucsc-hg19-knowngene.
[properties]: Tell updater to keep extra inputs.
[arguments]: Add phase 'delete-bad-tests; disable vignettes.
Change-Id: I23e78f1bd49b348719c6e03a116228b5657ae379
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 26 |
1 files changed, 24 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ba33c4b405..48ac5ed1ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -21457,8 +21457,25 @@ provides methods for retrieving enriched pathways.") (base32 "0839ljb4fh1qrjk1xm89q2hwnbbxi2slaw3l36dk8kmpifhqqi16")))) (properties - `((upstream-name . "VariantFiltering"))) + `((upstream-name . "VariantFiltering") + (updater-extra-native-inputs + . ("r-biocstyle" + "r-bsgenome-hsapiens-1000genomes-hs37d5" + "r-org-hs-eg-db" + "r-txdb-hsapiens-ucsc-hg19-knowngene")))) (build-system r-build-system) + (arguments + (list + ;; Vignettes require an obscene amount of humongous annotation packages + ;; and *still* attempt to download additional files off the Internet. + ;; Enough is enough. + #:test-types '(list "tests") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; One test tries to connect to a website. + (delete-file "inst/unitTests/test_location-methods.R")))))) (propagated-inputs (list r-annotationdbi r-biobase @@ -21484,7 +21501,12 @@ provides methods for retrieving enriched pathways.") r-summarizedexperiment r-variantannotation r-xvector)) - (native-inputs (list r-runit)) + (native-inputs + (list r-biocstyle + r-bsgenome-hsapiens-1000genomes-hs37d5 + r-org-hs-eg-db + r-runit + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://github.com/rcastelo/VariantFiltering") (synopsis "Filtering of coding and non-coding genetic variants") (description |