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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2019-07-12 23:58:22 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2019-07-12 23:58:22 +0000 |
| commit | df8230f473a59350229f2e498383a9029cfb1f82 (patch) | |
| tree | 1e1811a7ba47aa50c9edb3735760ce33ed6c1454 /biology | |
| parent | 96ec6abecd308e55bbffb19e603b179ebf9a14ab (diff) | |
| download | ports-df8230f473a59350229f2e498383a9029cfb1f82.tar.gz ports-df8230f473a59350229f2e498383a9029cfb1f82.zip | |
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
Notes
Notes:
svn path=/head/; revision=506497
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/ncbi-blast+/Makefile | 2 | ||||
| -rw-r--r-- | biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp | 14 |
2 files changed, 9 insertions, 7 deletions
diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index 06bc21a59392..f4570f142696 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -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}/ 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 index 64f24cecd4cc..f9320d36865f 100644 --- 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 @@ -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 |