guix_mirror_bot pushed a commit to branch r-team
in repository guix.
commit f100e269a49777fc765a12a55b5fbf31843864da
Author: Simon Tournier <[email protected]>
AuthorDate: Tue Oct 28 16:19:49 2025 +0100
gnu: r-aneufinder: Adjust [email protected] and GCC@14.
* gnu/packages/bioconductor.scm (r-aneufinder)[arguments]: Add phases that
relax GCC@14 strictness when using [email protected] C-level facilities.
Change-Id: If524806121e7b6f697b0cdee75cbe1aef3bb7b9a
---
gnu/packages/bioconductor.scm | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 39361e7f0a..80377991a3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4992,6 +4992,23 @@ create an alternative mapping from sequences.")
(base32
"0zx0brvcyi9id7xli9h5nk9an7j46p7zgjj3qmwr3jm4b95qahpl"))))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'install 'fix-r-4.5.0
+ ;; Changes in R 4.5.0: C-Level Facilities.
+ ;; Strict R headers are now the default. This removes the legacy
+ ;; definitions of PI, Calloc, Realloc and Free: use M_PI,
+ ;; R_Calloc, R_Realloc or R_Free instead.
+ ;; https://cran.r-project.org/doc/manuals/r-release/NEWS.html
+ (lambda _
+ (substitute* '("src/densities.cpp"
+ "src/loghmm.cpp"
+ "src/scalehmm.cpp"
+ "src/utility.cpp")
+ (("Calloc\\(") "R_Calloc(")
+ (("Free\\(") "R_Free(")))))))
(native-inputs
(list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
(propagated-inputs
