From 6ea5c58a1f443c4edfa95eefc385afd5a42a2f81 Mon Sep 17 00:00:00 2001 From: Simon Tournier Date: Tue, 28 Oct 2025 16:45:46 +0100 Subject: [PATCH] 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 --- gnu/packages/bioinformatics.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 22fe9c565943c99052232b2ac5dbc86068467ea0..ca5fcfb884441e36ede4a01883856aec2d78fdc6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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