06/13: gnu: r-chromstar: Adjust R@4.5.0 and GCC@14.

[guix-commits]

guix_mirror_bot pushed a commit to branch r-team
in repository guix.

commit ae76a734d402ef30b47a5edd47498969544ed66a
Author: Simon Tournier <zimon.touto...@gmail.com>
AuthorDate: Tue Oct 28 16:51:01 2025 +0100

    gnu: r-chromstar: Adjust R@4.5.0 and GCC@14.
    
    * gnu/packages/bioinformatics.scm (r-chromstar)[arguments]: Add phase that
    replaces C-level facilities from R@4.5.0.
    
    Change-Id: I16deb4b68beaf5665d57bd2045dc91a043c46e82
---
 gnu/packages/bioconductor.scm | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 80377991a3..af99a8547c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -26995,6 +26995,23 @@ the earlier snpMatrix package, allowing for 
uncertainty in genotypes.")
          "071aipwk1awr71hvzflps49dzp83p12zm1pbyx4l8d2v3wbj0dlz"))))
     (properties `((upstream-name . "chromstaR")))
     (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/scalehmm.cpp"
+                             "src/utility.cpp")
+                (("Calloc\\(") "R_Calloc(")
+                (("Free\\(") "R_Free(")
+                (("Realloc\\(") "R_Realloc(")))))))
     (propagated-inputs
      (list r-bamsignals
            r-biocgenerics