rna-star: Fix build with macOS clang 17

[Jason Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Jun 6 19:59:20 2026 -0500
Changeset:	603bd4aac08339bbe7ec7e565f03932886e223ab

Modified Files:
	rna-star/Makefile
	rna-star/distinfo
Added Files:
	rna-star/patches/patch-Parameters__openReadsFiles.cpp

Log Message:
rna-star: Fix build with macOS clang 17

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=603bd4aac08339bbe7ec7e565f03932886e223ab

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 rna-star/Makefile                                     | 10 +++++++++-
 rna-star/distinfo                                     |  1 +
 rna-star/patches/patch-Parameters__openReadsFiles.cpp | 19 +++++++++++++++++++
 3 files changed, 29 insertions(+), 1 deletion(-)

diffs:
diff --git a/rna-star/Makefile b/rna-star/Makefile
index 62cfa5d7e9..302776ed70 100644
--- a/rna-star/Makefile
+++ b/rna-star/Makefile
@@ -52,7 +52,15 @@ do-install:
 # Maybe a libomp package would suffice?
 .if ${OPSYS} == Darwin
 SUBST_CLASSES+=		openmp
-SUBST_SED.openmp=	-e 's|-fopenmp|-Xpreprocessor &|g'
+
+# https://projects.blender.org/blender/blender/pulls/136816
+.include "../../mk/compiler/clang.mk"
+.if ${_CC_MAJOR} >= 17
+SUBST_SED.openmp=	-e 's|-fopenmp|-Xpreprocessor -fopenmp=libiomp5|g'
+.else
+SUBST_SED.openmp=	-e 's|-fopenmp|-Xpreprocessor -fopenmp|g'
+.endif
+
 SUBST_STAGE.openmp=	pre-configure
 SUBST_FILES.openmp=	Makefile
 LDFLAGS+= 		-L${PREFIX}/lib -lomp -lm
diff --git a/rna-star/distinfo b/rna-star/distinfo
index a5caa8ac5e..006c54defc 100644
--- a/rna-star/distinfo
+++ b/rna-star/distinfo
@@ -4,6 +4,7 @@ BLAKE2s (STAR-2.7.11b.tar.gz) = 8751942121396bc6ef7b16653caa87f0e16ed37395a1bcfe
 SHA512 (STAR-2.7.11b.tar.gz) = 5dabe5883139f5cc78f6b183d704fc34868282a68e71a14c4e3c5ff0276753f05879720b41f060180b65f4fe3cb48ed391891b85b7dbc8274c3f55db1aa55e61
 Size (STAR-2.7.11b.tar.gz) = 12466670 bytes
 SHA1 (patch-Makefile) = 7dd8ef0ba12182a4cb2722aacfc6691b4f0a0cfe
+SHA1 (patch-Parameters__openReadsFiles.cpp) = 7640c264f7b9e876cbe17718d54063e94b973a4d
 SHA1 (patch-SharedMemory.cpp) = e4b97d68ddeb7ed2c7da66378f253ff4cd42abee
 SHA1 (patch-SoloBarcode.cpp) = a939a97cadd05b1ec6b6dfcddb469acd5072b0e8
 SHA1 (patch-SuffixArrayFuns.cpp) = b7c623c02277fdfc2bd9d6fa8068afafeb46b1cf
diff --git a/rna-star/patches/patch-Parameters__openReadsFiles.cpp b/rna-star/patches/patch-Parameters__openReadsFiles.cpp
new file mode 100644
index 0000000000..e691a65fcf
--- /dev/null
+++ b/rna-star/patches/patch-Parameters__openReadsFiles.cpp
@@ -0,0 +1,19 @@
+$NetBSD$
+
+# vfork() is deprecated on macOS
+
+--- Parameters_openReadsFiles.cpp.orig	2026-06-07 00:57:24.777038819 +0000
++++ Parameters_openReadsFiles.cpp
+@@ -80,10 +80,10 @@ void Parameters::openReadsFiles()
+             readFilesCommandPID[imate]=0;
+ 
+             ostringstream errOut;
+-            pid_t PID=vfork();
++            pid_t PID=fork();
+             switch (PID) {
+                 case -1:
+-                    errOut << "EXITING: because of fatal EXECUTION error: Failed vforking readFilesCommand\n";
++                    errOut << "EXITING: because of fatal EXECUTION error: Failed forking readFilesCommand\n";
+                     errOut << errno << ": " << strerror(errno) << "\n";
+                     exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+                     break;