rekado pushed a commit to branch master
in repository guix.
commit b8c1cde50ae3faba29c1ebe1fddf9a782ae895c1
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Thu May 15 10:19:58 2025 +0200
gnu: r-msigdbr: Update to 24.1.0.
* gnu/packages/cran.scm (r-msigdbr): Update to 24.1.0.
[arguments]: Disable some tests.
[propagated-inputs]: Add r-curl.
Change-Id: I90c3c0bf9c9842b13e7b95030b6bfec6b5d71099
---
gnu/packages/cran.scm | 24 ++++++++++++++++++++++--
1 file changed, 22 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8e6d4b5d6a..95d4e46e41 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -36162,18 +36162,38 @@ compiled by the HGNC Comparison of Orthology
Predictions (HCOP).")
(define-public r-msigdbr
(package
(name "r-msigdbr")
- (version "10.0.2")
+ (version "24.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "msigdbr" version))
(sha256
(base32
- "00pf6s688zskrwciddd520ns8zqkvkgbyn7gib2lr5ns6pszwvcj"))))
+ "0rii1fmwg09in67s2f6cw482093n320703si6ksjjlda5d8p0i1a"))))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'disable-bad-tests
+ (lambda _
+ ;; These tests attempt to download a data file.
+ (substitute* "tests/testthat/test-msigdbr-collections.R"
+ ((".*msigdbr_collections\\(\\).*" m)
+ (string-append m "skip('skip');\n")))
+ (substitute* "tests/testthat/test-msigdbr.R"
+ ((".*collections and subcollections.*" m)
+ (string-append m "skip('skip');\n"))
+ ((".*msigdbr\\(\\) subcollection partial match.*" m)
+ (string-append m "skip('skip');\n"))
+ ((".*deprecated parameters.*" m)
+ (string-append m "skip('skip');\n"))
+ ((".*species.*" m)
+ (string-append m "skip('skip');\n"))))))))
(propagated-inputs
(list r-assertthat
r-babelgene
+ r-curl
r-dplyr
r-lifecycle
r-rlang
