svn commit: r506409 - head/biology/ncbi-blast+/files

[Jason W. Bacon]

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