rna-star: Clean up

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Jul 23 12:51:51 2023 -0500
Changeset:	1807b7c6dd0b3347033eaa19df3cff8fc335d7ed

Modified Files:
	rna-star/Makefile
	rna-star/distinfo
	rna-star/patches/patch-SpliceGraph.cpp
	rna-star/patches/patch-SuffixArrayFuns.cpp
	rna-star/patches/patch-bamSortByCoordinate.cpp
	rna-star/patches/patch-opal_opal.cpp

Log Message:
rna-star: Clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1807b7c6dd0b3347033eaa19df3cff8fc335d7ed

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

diffstat:
 rna-star/Makefile                              | 23 ++++++++++++++++-------
 rna-star/distinfo                              |  8 ++++----
 rna-star/patches/patch-SpliceGraph.cpp         |  2 ++
 rna-star/patches/patch-SuffixArrayFuns.cpp     |  2 ++
 rna-star/patches/patch-bamSortByCoordinate.cpp |  2 ++
 rna-star/patches/patch-opal_opal.cpp           |  2 ++
 6 files changed, 28 insertions(+), 11 deletions(-)

diffs:
diff --git a/rna-star/Makefile b/rna-star/Makefile
index 90b3de6523..a97df01ee6 100644
--- a/rna-star/Makefile
+++ b/rna-star/Makefile
@@ -34,13 +34,13 @@ SUBST_STAGE.htslib=	pre-configure
 SUBST_SED.htslib+=	-e 's|"htslib/htslib/sam.h"|<htslib/sam.h>|g'
 SUBST_SED.htslib+=	-e 's|"htslib/htslib/kstring.h"|<htslib/kstring.h>|g'
 SUBST_SED.htslib+=	-e 's|"htslib/htslib/bgzf.h"|<htslib/bgzf.h>|g'
-SUBST_FILES.htslib+=	${WRKSRC}/BAMfunctions.cpp
-SUBST_FILES.htslib+=	${WRKSRC}/IncludeDefine.h
-SUBST_FILES.htslib+=	${WRKSRC}/STAR.cpp
-SUBST_FILES.htslib+=	${WRKSRC}/bamRemoveDuplicates.cpp
-SUBST_FILES.htslib+=	${WRKSRC}/bam_cat.c
-SUBST_FILES.htslib+=	${WRKSRC}/bam_cat.h
-SUBST_FILES.htslib+=	${WRKSRC}/signalFromBAM.h
+SUBST_FILES.htslib+=	BAMfunctions.cpp
+SUBST_FILES.htslib+=	IncludeDefine.h
+SUBST_FILES.htslib+=	STAR.cpp
+SUBST_FILES.htslib+=	bamRemoveDuplicates.cpp
+SUBST_FILES.htslib+=	bam_cat.c
+SUBST_FILES.htslib+=	bam_cat.h
+SUBST_FILES.htslib+=	signalFromBAM.h
 
 # Test and change if necessary.
 MAKE_JOBS_SAFE=	no
@@ -57,6 +57,15 @@ INSTALLATION_DIRS=	bin
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/STAR ${DESTDIR}${PREFIX}/bin
 
+.include "../../mk/bsd.prefs.mk"
+
+# Xcode supports -Xpreprocessor -fopenmp, but does not supply OpenMP libs
+# parallel/openmp installs an entire llvm
+# Maybe a libomp package would suffice?
+.if ${OPSYS} == Darwin
+.include "../../parallel/openmp/buildlink3.mk"
+.endif
+
 # Convert any _DEPENDS above that have a buildlink3.mk
 .include "../../biology/htslib/buildlink3.mk"
 # CentOS doesn't have zlib in the base, so uncomment if needed.
diff --git a/rna-star/distinfo b/rna-star/distinfo
index 44bbb3f8b0..1dc9009a61 100644
--- a/rna-star/distinfo
+++ b/rna-star/distinfo
@@ -6,7 +6,7 @@ Size (STAR-2.7.10b.tar.gz) = 12443703 bytes
 SHA1 (patch-Makefile) = 7dd8ef0ba12182a4cb2722aacfc6691b4f0a0cfe
 SHA1 (patch-SharedMemory.cpp) = 42cd862f58f45ea09e63487ef4bd6baa00bbb25f
 SHA1 (patch-SoloBarcode.cpp) = a939a97cadd05b1ec6b6dfcddb469acd5072b0e8
-SHA1 (patch-SpliceGraph.cpp) = 17f5b819985914d075cc15ef67f9b1625a1a6ca3
-SHA1 (patch-SuffixArrayFuns.cpp) = 219abac0885e2e710e634335228baadf16138429
-SHA1 (patch-bamSortByCoordinate.cpp) = 8c3db8dff990c3ff69be02fc86a4b7a8bed17bd6
-SHA1 (patch-opal_opal.cpp) = 69334ba211d2b371fcf96f86fb842d3e67acc9c0
+SHA1 (patch-SpliceGraph.cpp) = b51ff09c03c770ab39820159d76efebcddff12ec
+SHA1 (patch-SuffixArrayFuns.cpp) = b7c623c02277fdfc2bd9d6fa8068afafeb46b1cf
+SHA1 (patch-bamSortByCoordinate.cpp) = 8b6d1542c3168d37075d75fc76302eff074b5a77
+SHA1 (patch-opal_opal.cpp) = 0fe78b98336624cb03e4eb291a88b803eb6d7423
diff --git a/rna-star/patches/patch-SpliceGraph.cpp b/rna-star/patches/patch-SpliceGraph.cpp
index 374054d0c5..4181ef8b00 100644
--- a/rna-star/patches/patch-SpliceGraph.cpp
+++ b/rna-star/patches/patch-SpliceGraph.cpp
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- SpliceGraph.cpp.orig	2023-07-21 15:27:26 UTC
 +++ SpliceGraph.cpp
 @@ -1,7 +1,6 @@
diff --git a/rna-star/patches/patch-SuffixArrayFuns.cpp b/rna-star/patches/patch-SuffixArrayFuns.cpp
index 0906b36c1c..b751063081 100644
--- a/rna-star/patches/patch-SuffixArrayFuns.cpp
+++ b/rna-star/patches/patch-SuffixArrayFuns.cpp
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Drop obsolete modifier for c++17 compat
+
 --- SuffixArrayFuns.cpp.orig	2023-07-21 15:26:07 UTC
 +++ SuffixArrayFuns.cpp
 @@ -15,7 +15,7 @@ uint compareSeqToGenome(Genome &mapGen, char** s2, uin
diff --git a/rna-star/patches/patch-bamSortByCoordinate.cpp b/rna-star/patches/patch-bamSortByCoordinate.cpp
index 6d18a2d90e..6bcd1f813e 100644
--- a/rna-star/patches/patch-bamSortByCoordinate.cpp
+++ b/rna-star/patches/patch-bamSortByCoordinate.cpp
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability
+
 --- bamSortByCoordinate.cpp.orig	2021-11-26 16:17:37 UTC
 +++ bamSortByCoordinate.cpp
 @@ -64,7 +64,7 @@ void bamSortByCoordinate (Parameters &P, ReadAlignChun
diff --git a/rna-star/patches/patch-opal_opal.cpp b/rna-star/patches/patch-opal_opal.cpp
index d281b30e31..ef654b1470 100644
--- a/rna-star/patches/patch-opal_opal.cpp
+++ b/rna-star/patches/patch-opal_opal.cpp
@@ -1,5 +1,7 @@
 $NetBSD$
 
+# Portability to modern C++ compilers
+
 --- opal/opal.cpp.orig	2021-11-26 16:14:46 UTC
 +++ opal/opal.cpp
 @@ -5,10 +5,8 @@