stacks: Add OpenMP support on Darwin

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Sep 26 07:52:37 2023 -0500
Changeset:	8aba046a1a05d2e4ab47137a3b72328fc4a6809c

Modified Files:
	stacks/DESCR
	stacks/Makefile

Log Message:
stacks: Add OpenMP support on Darwin

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8aba046a1a05d2e4ab47137a3b72328fc4a6809c

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

diffstat:
 stacks/DESCR    |  9 +++++----
 stacks/Makefile | 14 +++++++++-----
 2 files changed, 14 insertions(+), 9 deletions(-)

diffs:
diff --git a/stacks/DESCR b/stacks/DESCR
index 91c14fbc8d..2bff3e6960 100644
--- a/stacks/DESCR
+++ b/stacks/DESCR
@@ -1,4 +1,5 @@
-Stacks is a software pipeline for building loci from short-read sequences, such
-as those generated on the Illumina platform. Stacks was developed to work with
-restriction enzyme-based data, such as RAD-seq, for the purpose of building
-genetic maps and conducting population genomics and phylogeography.
+Stacks is a software pipeline for building loci from short-read
+sequences, such as those generated on the Illumina platform. Stacks
+was developed to work with restriction enzyme-based data, such as
+RAD-seq, for the purpose of building genetic maps and conducting
+population genomics and phylogeography.
diff --git a/stacks/Makefile b/stacks/Makefile
index 27d74bf8d7..2dfa19f0d3 100644
--- a/stacks/Makefile
+++ b/stacks/Makefile
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.10 2022/06/30 11:18:05 nia Exp $
+# $NetBSD: Makefile,v 1.11 2023/08/14 05:23:52 wiz Exp $
 
 DISTNAME=	stacks-2.60
-PKGREVISION=	2
+PKGREVISION=	3
 CATEGORIES=	biology
 MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
 
@@ -10,9 +10,10 @@ HOMEPAGE=	http://catchenlab.life.illinois.edu/stacks/
 COMMENT=	Software pipeline for building loci from short-read sequences
 LICENSE=	gnu-gpl-v2
 
-USE_LANGUAGES=	c c++14
-USE_TOOLS+=	bash perl:run
-GNU_CONFIGURE=	yes
+USE_LANGUAGES=		c c++
+USE_CXX_FEATURES=	c++14
+USE_TOOLS+=		bash perl:run
+GNU_CONFIGURE=		yes
 
 REPLACE_BASH+=		scripts/stacks-count-reads-per-sample-per-locus
 REPLACE_BASH+=		scripts/stacks-dist-extract
@@ -35,6 +36,9 @@ SUBST_CLASSES+=		sed
 SUBST_STAGE.sed=	pre-configure
 SUBST_FILES.sed=	Makefile.in
 SUBST_SED.sed=		-e 's|sed -i.bkp|/usr/bin/sed -i .bkp|'
+CFLAGS+=		-Xpreprocessor -fopenmp
+
+.include "../../parallel/openmp/buildlink3.mk"
 .else
 # macOS clang lacks OpenMP
 CFLAGS+=		-fopenmp