From f247a08a4f089ce16e8d3a6d266faec492743e17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 5 Apr 2026 08:54:02 +0200 Subject: [PATCH] gnu: r-screpertoire: Replace custom phase with SKIPPED-TESTS argument. * gnu/packages/bioconductor.scm (r-screpertoire)[arguments]: Remove phase 'disable-bad-tests; specify #:skipped-tests instead. Change-Id: Ieac662ca919889a71861cb6b1f08febab2487f54 --- gnu/packages/bioconductor.scm | 39 ++++++++++++++--------------------- 1 file changed, 15 insertions(+), 24 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 266fe274f7..b91ba32b31 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13739,30 +13739,21 @@ for downstream analysis and data visualization.") (build-system r-build-system) (arguments (list - #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'disable-bad-tests - (lambda _ - ;; These attempt to connect to the Internet. - (substitute* "tests/testthat/test-getContigDoublets.R" - ((".*getContigDoublets works for no doublets.*" m) - (string-append m "skip('guix')\n")) - ((".*getContigDoublets works for inputs with doublets.*" m) - (string-append m "skip('guix')\n"))) - (substitute* "tests/testthat/test-loadContigs.R" - ((".*loadContigs correctly auto-detects and processes various formats.*" m) - (string-append m "skip('guix')\n")) - ((".*loadContigs correctly processes various formats from URL.*" m) - (string-append m "skip('guix')\n"))) - ;; There is code running outside of testthat that tries to - ;; download files off the Internet. - (delete-file "tests/testthat/test-combineContigs.R") - ;; These fail with: Unknown property set: 'kideraFactors'. - (substitute* "tests/testthat/test-positionalProperty.R" - ((".*positionalProperty: Output structure is correct.*" m) - (string-append m "skip('guix')\n")) - ((".*positionalProperty: ggplot object is correctly formed.*" m) - (string-append m "skip('guix')\n")))))))) + #:skipped-tests + ;; There is code running outside of testthat that tries to + ;; download files off the Internet. + '("test-combineContigs.R" + ;; These attempt to connect to the Internet. + ("test-getContigDoublets.R" + "getContigDoublets works for no doublets" + "getContigDoublets works for inputs with doublets") + ("test-loadContigs.R" + "loadContigs correctly auto-detects and processes various formats" + "loadContigs correctly processes various formats from URL") + ;; These fail with: Unknown property set: 'kideraFactors'. + ("test-positionalProperty.R" + "positionalProperty: Output structure is correct" + "positionalProperty: ggplot object is correctly formed")))) (propagated-inputs (list r-dplyr r-evmix