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

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

Change-Id: I16deb4b68beaf5665d57bd2045dc91a043c46e82
This commit is contained in:
Simon Tournier 2025-10-28 16:51:01 +01:00
parent 6ea5c58a1f
commit 8c4c02db2a
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1 changed files with 17 additions and 0 deletions
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gnu/packages/bioconductor.scm
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@ -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