From ee4f843e4673802a5b927cba762db60c110b4561 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 28 Apr 2023 19:01:22 +0200
Subject: [PATCH] gnu: r-bgmix: Update to 1.59.0.

* gnu/packages/bioconductor.scm (r-bgmix): Update to 1.59.0.
[arguments]: Add build phase 'avoid-naming-conflict.
---
 gnu/packages/bioconductor.scm | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 71b04e8066..d4d7147a69 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16736,16 +16736,27 @@ (define-public r-activepathways
 (define-public r-bgmix
   (package
     (name "r-bgmix")
-    (version "1.58.0")
+    (version "1.59.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BGmix" version))
        (sha256
         (base32
-         "0r4cxrjvf3qr5514lsw1s53h4by3djb9ipkz7bi979w343dn9xfx"))))
+         "16fzgxcy4sk0kd67vzdxqz81s84dvh4bqss9cbl9bn6vhpfsnfyf"))))
     (properties `((upstream-name . "BGmix")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; GCC's c++/bits/specfun.h (included by cmath) provides a std::beta
+         ;; procedure.
+         (add-after 'unpack 'avoid-naming-conflict
+           (lambda _
+             (substitute* "src/BGmix_main.cpp"
+               (("\\bbeta\\b") "::beta")
+               (("\\*\\*::beta,") "**beta,")))))))
     (propagated-inputs
      (list r-kernsmooth))
     (home-page "https://bioconductor.org/packages/BGmix/")