~ruther/guix-local: gnu: r-chipkernels: Adjust R@4.5.0 and GCC@14.

6ea5c58a1f443c4edfa95eefc385afd5a42a2f81 — Simon Tournier 8 months ago 2fef421

gnu: r-chipkernels: Adjust R@4.5.0 and GCC@14.

* gnu/packages/bioinformatics.scm (r-chipkernels)[arguments]: Add phase that
replaces C-level facilities from R@4.5.0.

Change-Id: Iac58b4d871160b4cbfd8b71d771c2f2fcf174240

patch browse .tar.gz .zip

1 files changed, 15 insertions(+), 0 deletions(-)

M gnu/packages/bioinformatics.scm

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +15 -0

@@ 15312,6 15312,21 @@ characteristic tag shift values in these assays.")
           (base32
            "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
       (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/hamming_distance.c"
+                (("Calloc") "R_Calloc")
+                (("Free") "R_Free")
+                (("Realloc") "R_Realloc")))))))
       (propagated-inputs
        (list r-iranges
              r-xvector