From d7ccc1dfe3907283d1f15c934807c29232c02dd7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 27 Nov 2024 16:55:17 +0100 Subject: [PATCH] gnu: r-flowclust: Add missing input. * gnu/packages/bioconductor.scm (r-flowclust)[native-inputs]: Add r-flowworkspace. [properties]: Tell updater not to add r-opencyto. [arguments]: Add phases 'delete-bad-tests. Change-Id: Ie82854c0ff52c290e7482f67771aa9ef82a83343 --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1c8129384f..e61a3057a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -20184,11 +20184,23 @@ (define-public r-flowclust (sha256 (base32 "0li9vcgk82vn5wqzmz6hbn04vqa5l0mwsb6vyb537mkcg45dhcr3")))) - (properties `((upstream-name . "flowClust"))) + (properties + `((upstream-name . "flowClust") + ;; Avoid dependency cycle. + (updater-ignored-native-inputs . ("r-opencyto")))) (build-system r-build-system) (arguments - `(#:configure-flags - (list "--configure-args=--enable-bundled-gsl=no"))) + (list + #:configure-flags + '(list "--configure-args=--enable-bundled-gsl=no") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'delete-bad-tests + (lambda _ + ;; "invalid subscript type 'list'" + (delete-file "tests/testthat/test_2d.R") + ;; "argument is of length zero" + (delete-file "tests/testthat/test_1d_gated_data.R")))))) (propagated-inputs (list r-biobase r-biocgenerics @@ -20197,7 +20209,7 @@ (define-public r-flowclust (inputs (list gsl)) (native-inputs - (list pkg-config r-knitr r-testthat)) + (list pkg-config r-flowworkspace r-knitr r-testthat)) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description