Date: Thu, 11 Jul 2019 13:53:30 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r506409 - head/biology/ncbi-blast+/files Message-ID: <201907111353.x6BDrUVl042026@repo.freebsd.org>
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Author: jwb Date: Thu Jul 11 13:53:30 2019 New Revision: 506409 URL: https://svnweb.freebsd.org/changeset/ports/506409 Log: ncbi-blast+: Fix build with gcc9 GCC 9 requires OpenMP variables to be explicitly defined as shared or private where earlier versions fell back on default. New patch sent upstream. PR: 238471 Reported by: gerald Added: head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp (contents, props changed) 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 Thu Jul 11 13:53:30 2019 (r506409) @@ -0,0 +1,14 @@ +--- 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() + } + LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences"); + ++ // kScanUncompressed is read only and initialized before threading ++ // so shared should be fine here + #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) + { + int thread_id = 0; + #ifdef _OPENMP
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