svn commit: r561233 - in head/biology/ncbi-blast+: . files

[Jason W. Bacon]

Author: jwb
Date: Mon Jan 11 17:17:35 2021
New Revision: 561233
URL: https://svnweb.freebsd.org/changeset/ports/561233

Log:
  biology/ncbi-blast+: Drop dependency on gcc
  
  Replace compiler:openmp with compiler:c++14-lang
  Clang build also requires localbase:ldflags and a source patch to explicitly
  set variables to shared
  GCC-based platforms still require -latomic
  
  PR:             port/247753, ports/252379

Added:
  head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp   (contents, props changed)
Modified:
  head/biology/ncbi-blast+/Makefile

Modified: head/biology/ncbi-blast+/Makefile
==============================================================================
--- head/biology/ncbi-blast+/Makefile	Mon Jan 11 17:12:47 2021	(r561232)
+++ head/biology/ncbi-blast+/Makefile	Mon Jan 11 17:17:35 2021	(r561233)
@@ -2,6 +2,7 @@
 
 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}/
@@ -32,7 +33,7 @@ LIB_DEPENDS=	libpcre.so:devel/pcre \
 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 \
@@ -47,15 +48,14 @@ GNU_CONFIGURE=	yes
 # --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:

Added: head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp	Mon Jan 11 17:17:35 2021	(r561233)
@@ -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)