From owner-svn-ports-head@freebsd.org Thu Jul 11 13:53:31 2019 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 9F88215D4039; Thu, 11 Jul 2019 13:53:31 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4177F803EC; Thu, 11 Jul 2019 13:53:31 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 1BE17276CA; Thu, 11 Jul 2019 13:53:31 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id x6BDrUO5042027; Thu, 11 Jul 2019 13:53:30 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x6BDrUVl042026; Thu, 11 Jul 2019 13:53:30 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <201907111353.x6BDrUVl042026@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Thu, 11 Jul 2019 13:53:30 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r506409 - head/biology/ncbi-blast+/files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: head/biology/ncbi-blast+/files X-SVN-Commit-Revision: 506409 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 4177F803EC X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.96 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-1.000,0]; NEURAL_HAM_SHORT(-0.96)[-0.962,0]; NEURAL_HAM_LONG(-1.00)[-1.000,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 11 Jul 2019 13:53:31 -0000 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