Index: head/biology/ncbi-blast+/Makefile
===================================================================
--- head/biology/ncbi-blast+/Makefile	(revision 561232)
+++ head/biology/ncbi-blast+/Makefile	(revision 561233)
@@ -1,70 +1,70 @@
 # $FreeBSD$
 
 PORTNAME=	ncbi-blast+
 DISTVERSION=	2.11.0
+PORTREVISION=	1
 CATEGORIES=	biology perl5 python
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
 DISTNAME=	ncbi-blast-${PORTVERSION}+-src
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
 
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
 
 LIB_DEPENDS=	libpcre.so:devel/pcre \
 		liblmdb.so:databases/lmdb \
 		liblzo2.so:archivers/lzo2 \
 		libgnutls.so:security/gnutls \
 		libtspi.so:security/trousers \
 		libgmp.so:math/gmp \
 		libidn2.so:dns/libidn2 \
 		libnettle.so:security/nettle \
 		libhogweed.so:security/nettle \
 		libtasn1.so:security/libtasn1 \
 		libp11-kit.so:security/p11-kit \
 		libgcrypt.so:security/libgcrypt \
 		libgpg-error.so:security/libgpg-error \
 		libsqlite3.so:databases/sqlite3 \
 		libuv.so:devel/libuv \
 		libnghttp2.so:www/libnghttp2
 RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
 		p5-JSON>=0:converters/p5-JSON
 
-USES=		compiler:openmp gmake shebangfix perl5 python
+USES=		compiler:c++14-lang gmake localbase:ldflags shebangfix perl5 python
 USE_LDCONFIG=	yes
 
 SHEBANG_FILES=	src/app/blast/legacy_blast.pl \
 		src/app/blast/update_blastdb.pl \
 		src/app/blast/cleanup-blastdb-volumes.py \
 		src/app/blast/get_species_taxids.sh \
 		src/app/winmasker/windowmasker_2.2.22_adapter.py
 GNU_CONFIGURE=	yes
 
 # configure chooses /usr/local/bin/ar with no flags
 # FreeBSD boost port flagged by configure as untested version
 # --libdir=${PREFIX}/lib/ncbi-tools++ doesn't respect DESTDIR, so do
 # a postinstall mv.
 CONFIGURE_ARGS=	AR="ar cr" --without-boost --libdir=${PREFIX}/lib/ncbi-tools++
-LDFLAGS+=	-latomic
 
 WRKSRC_SUBDIR=		c++
 
 .include <bsd.port.pre.mk>
 
-# Force newer GCC on platforms using GCC 4.2 as base
 .if ${CHOSEN_COMPILER_TYPE} == gcc
-USE_GCC=	yes
+# In case of problems: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=220822
+LDFLAGS+=	-latomic # Only exists in gcc libs
 .endif
 
 post-install:
 	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
 	@${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11
 	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in
 	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_build_ver.h.in
 	@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_revision.h.in
 	@${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so
 
 .include <bsd.port.post.mk>
Index: head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
===================================================================
--- head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp	(nonexistent)
+++ head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp	(revision 561233)
@@ -0,0 +1,22 @@
+--- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig	2021-01-10 02:28:53 UTC
++++ src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
+@@ -137,7 +137,8 @@ CSeqDBPerfApp::x_ScanDatabase()
+     }
+     LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences");
+ 
+-#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)
++#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) || \
++    defined(NCBI_COMPILER_LLVM_CLANG)
+     #pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
+                          shared(oids2iterate,kScanUncompressed) if(m_DbHandles.size() > 1)
+ #else
+@@ -208,7 +209,8 @@ CSeqDBPerfApp::x_InitApplicationData()
+ 
+ 
+     if (args["multi_threaded_creation"]) {
+-#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)
++#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) || \
++    defined(NCBI_COMPILER_LLVM_CLANG)
+         #pragma omp parallel default(none) shared(kDbName, kNumThreads, kSeqType) num_threads(kNumThreads)
+ #else
+         #pragma omp parallel default(none) shared(kDbName, kNumThreads) num_threads(kNumThreads)

Property changes on: head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property