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| author | jwb <jwb@FreeBSD.org> | 2019-07-11 21:53:30 +0800 |
|---|---|---|
| committer | jwb <jwb@FreeBSD.org> | 2019-07-11 21:53:30 +0800 |
| commit | 5efe9777f4c93bba61c9f7fc094ef34b5a167ee2 (patch) | |
| tree | b78d72e4726e56dedd371694e59a111db13c06fa /biology | |
| parent | d2d5e458fb1ecef68ad243a68b0a7c4c81810302 (diff) | |
| download | freebsd-ports-gnome-5efe9777f4c93bba61c9f7fc094ef34b5a167ee2.tar.gz freebsd-ports-gnome-5efe9777f4c93bba61c9f7fc094ef34b5a167ee2.tar.zst freebsd-ports-gnome-5efe9777f4c93bba61c9f7fc094ef34b5a167ee2.zip | |
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
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp | 14 |
1 files changed, 14 insertions, 0 deletions
diff --git a/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp b/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp new file mode 100644 index 000000000000..64f24cecd4cc --- /dev/null +++ b/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp @@ -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 |