From 8f7196cbae1e96fdae62687a4fc661678256d983 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Nov 2024 22:41:41 +0100 Subject: [PATCH] gnu: r-rcas: Add missing inputs * gnu/packages/bioconductor.scm (r-rcas)[native-inputs]: Add r-biocmanager. [arguments]: Add phases 'skip-bad-tests and 'set-HOME. Change-Id: I952ae31347776dc35cf012aaa8146f38b375957a --- gnu/packages/bioconductor.scm | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 40d3b2853e9dc69ad942552302c619ef83a496a4..cef8721591f4fbc5e45a364141b8585fdf8f5fd9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11776,6 +11776,21 @@ the graph algorithms contained in the Boost library.") "0sg3ngb7jwh8gyhmmm7fkxn9ixj590j47rfcfdcnbbk9pwd9y07p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'unpack 'skip-bad-tests + (lambda _ + ;; These tests need Internet access. + (with-directory-excursion "tests/testthat" + (substitute* "test_database_functions.R" + ((".*Testing createDB function.*" m) + (string-append m "skip('guix')\n"))) + (delete-file "test_report.R") + (delete-file "test_motif.R"))))))) (inputs (list pandoc)) (propagated-inputs (list r-biocgenerics @@ -11806,7 +11821,7 @@ the graph algorithms contained in the Boost library.") r-seqlogo r-txdbmaker)) (native-inputs - (list r-knitr r-testthat)) + (list r-biocmanager r-knitr r-testthat)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides