From 7673e935e6fee11adfe0b8d92075fa99c4622ee5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 2 Apr 2026 18:41:40 +0200 Subject: [PATCH] gnu: r-biomart: Replace custom phase with SKIPPED-TESTS argument. * gnu/packages/bioconductor.scm (r-biomart)[arguments]: Remove phase 'delete-bad-tests; specify #:skipped-tests instead. Change-Id: I98c167685c07453fd8fa8b8c7700c21591d043af --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a9458aae01..428788d735 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8654,20 +8654,22 @@ on Bioconductor or which replace R functions.") (build-system r-build-system) (arguments (list - #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'delete-bad-tests - (lambda _ - ;; These tests attempt to download files. - (for-each delete-file - '("tests/testthat/test_ensemblFunctions.R" - "tests/testthat/test_ensemblGenomes.R" - "tests/testthat/test_getBM.R" - "tests/testthat/test-getGene.R" - "tests/testthat/test_utilityFunctions.R" - "tests/testthat/test_z_cache.R" - ;; This produces unexpected warnings. - "tests/testthat/test_ensembl_ssl_settings.R"))))))) + #:skipped-tests + '(("test_ensembl_ssl_settings.R" + ;; This produces unexpected warnings. + "SSL settings are stored in the cache") + ;; These tests attempt to download files. + ("test_ensemblFunctions.R" + "useEnsembl\\(\\) error handling is OK" + "useEnsembl\\(host = \\) is not necessary for ensembl.org" + "Ensembl URLs are constructed correctly") + ("test_getBM.R" + "getBM returns sensible things" + "getBM doesn't convert T/F alleles into TRUE/FALSE") + ("test-getGene.R" + "getGene\\(\\) recognizes new ensembl name as ensembl") + ;; Code run outside of testthat accesses www.ensembl.org + "test_z_cache.R"))) (propagated-inputs (list r-annotationdbi r-biocfilecache