gnu: simpleitk: Update to 2.5.4.

* gnu/packages/image-processing.scm (simpleitk): Update to 2.5.4.
[source]: Add patch.
* gnu/packages/patches/simpleitk-r-4.6.0.patch: New file.
* gnu/local.mk (dist_patch_DATA): Record it.

Change-Id: Id85b8a717046497bd8469c365c738ac984229e03

3 files changed, 52 insertions, 3 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index 49f2cfeb1fb..0ea10e65c57 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2454,6 +2454,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/shared-mime-info-xdgmime-path.patch      \
   %D%/packages/patches/sharutils-CVE-2018-1000097.patch         \
   %D%/packages/patches/showtime-python-3.11-compat.patch        \
+  %D%/packages/patches/simpleitk-r-4.6.0.patch                  \
   %D%/packages/patches/sipwitch-fix-build-with-exosip5.patch    \
   %D%/packages/patches/slim-config.patch                        \
   %D%/packages/patches/slim-gcc-14.patch                        \
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index 2df830ef3a4..bc69fb9b478 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -1923,7 +1923,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
 (define-public simpleitk
   (package
     (name "simpleitk")
-    (version "2.5.3")
+    (version "2.5.4")
     (source
      (origin
        (method git-fetch)
@@ -1932,7 +1932,9 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0fvacjfq0p8v7r2cmzwwh7bxb6ayavznhj0m81dah463x472qkd2"))))
+        (base32 "1bzj5naqbgv2b31iqgz7qqk9rixsvjqycjz6l7w3gm7v1aj14jpb"))
+       (patches
+        (search-patches "simpleitk-r-4.6.0.patch"))))
     (build-system cmake-build-system)
     (outputs '("out" "python" "r"))
     (arguments
@@ -2032,7 +2034,7 @@ and Scan Tailor Enhanced versions as well as including many more bug fixes.")
                    version "/SimpleITKData-" version ".tar.gz"))
              (sha256
               (base32
-               "0i4f87g1rh6xxisw06gwwyi8f216qqs6ih3gghi3k49vsl0h4g5d")))))
+               "0hryvi9fgqac00ng1bfhw3lm0al1dh0ka6jglba2q368nls428nx")))))
     (synopsis "Simplified interface to @acronym{ITK, Insight Toolkit}")
     (description
      "SimpleITK is an image analysis toolkit built on top of @acronym{ITK,
diff --git a/gnu/packages/patches/simpleitk-r-4.6.0.patch b/gnu/packages/patches/simpleitk-r-4.6.0.patch
new file mode 100644
index 00000000000..c5105e8b5a9
--- /dev/null
+++ b/gnu/packages/patches/simpleitk-r-4.6.0.patch
@@ -0,0 +1,46 @@
+From 1654599ea228efdd7b378ff44ed4e19d547641e0 Mon Sep 17 00:00:00 2001
+From: Bradley Lowekamp <blowekamp@mail.nih.gov>
+Date: Wed, 29 Apr 2026 16:22:49 +0000
+Subject: [PATCH 1/8] BUG: Replace removed CLOENV with R_ClosureEnv for R 4.6.0
+ compatibility
+
+R 4.6.0 removed the non-API macro CLOENV from its public headers.
+The replacement R_ClosureEnv() was added in R 4.5.0. Add a version-
+guarded backport so that builds against older R versions (< 4.5.0)
+continue to work.
+
+Fixes #2574
+---
+ Wrapping/R/sitkRCommand.cxx | 7 ++++++-
+ 1 file changed, 6 insertions(+), 1 deletion(-)
+
+diff --git a/Wrapping/R/sitkRCommand.cxx b/Wrapping/R/sitkRCommand.cxx
+index 216a9327b8..c3a62bead9 100644
+--- a/Wrapping/R/sitkRCommand.cxx
++++ b/Wrapping/R/sitkRCommand.cxx
+@@ -19,10 +19,15 @@
+ // The python header defines _POSIX_C_SOURCE without a preceding #undef
+ #include <iostream>
+ #include <Rinternals.h>
++#include <Rversion.h>
+ 
+ #include "sitkRCommand.h"
+ #include "sitkExceptionObject.h"
+ 
++// R_ClosureEnv was added in R 4.5.0, CLOENV was removed in R 4.6.0
++#if R_VERSION < R_Version(4, 5, 0)
++#  define R_ClosureEnv(x) CLOENV(x)
++#endif
+ 
+ namespace itk
+ {
+@@ -86,7 +91,7 @@ RCommand::SetFunctionClosure(SEXP FN)
+     // element
+     R_fcall = PROTECT(Rf_lang1(this->m_FunctionClosure));
+     this->SetCallbackRCallable(R_fcall);
+-    this->SetCallbackREnviron(CLOENV(this->m_FunctionClosure));
++    this->SetCallbackREnviron(R_ClosureEnv(this->m_FunctionClosure));
+     UNPROTECT(1);
+   }
+ }
+