svn commit: r506497 - in head/biology/ncbi-blast+: . files
Jason W. Bacon
jwb at FreeBSD.org
Fri Jul 12 23:58:23 UTC 2019
Author: jwb
Date: Fri Jul 12 23:58:22 2019
New Revision: 506497
URL: https://svnweb.freebsd.org/changeset/ports/506497
Log:
ncbi-blast+: Unbreak build with gcc8 following gcc9 patch
GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none). All const variables default to shared even with default(none)
present. 8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.
Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.
Reported by: jrm
Modified:
head/biology/ncbi-blast+/Makefile
head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
Modified: head/biology/ncbi-blast+/Makefile
==============================================================================
--- head/biology/ncbi-blast+/Makefile Fri Jul 12 23:55:54 2019 (r506496)
+++ head/biology/ncbi-blast+/Makefile Fri Jul 12 23:58:22 2019 (r506497)
@@ -2,7 +2,7 @@
PORTNAME= ncbi-blast+
DISTVERSION= 2.9.0
-PORTREVISION= 1
+PORTREVISION= 2
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}/
Modified: 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 Fri Jul 12 23:55:54 2019 (r506496)
+++ head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp Fri Jul 12 23:58:22 2019 (r506497)
@@ -1,14 +1,16 @@
---- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig 2019-07-10 10:11:51.713901000 -0500
-+++ src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp 2019-07-10 10:15:40.994964000 -0500
-@@ -137,8 +137,10 @@ CSeqDBPerfApp::x_ScanDatabase()
+--- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig 2018-10-23 19:28:52 UTC
++++ src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
+@@ -137,8 +137,13 @@ CSeqDBPerfApp::x_ScanDatabase()
}
LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences");
-+ // kScanUncompressed is read only and initialized before threading
-+ // so shared should be fine here
++#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)
#pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
-- shared(oids2iterate) if(m_DbHandles.size() > 1)
+ shared(oids2iterate,kScanUncompressed) if(m_DbHandles.size() > 1)
++#else
++ #pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
+ shared(oids2iterate) if(m_DbHandles.size() > 1)
++#endif
{
int thread_id = 0;
#ifdef _OPENMP
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