Date: Fri, 12 Jul 2019 23:58:22 +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: r506497 - in head/biology/ncbi-blast+: . files Message-ID: <201907122358.x6CNwMVd005178@repo.freebsd.org>
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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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