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Bacon" Date: Mon, 11 Jan 2021 17:17:35 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r561233 - in head/biology/ncbi-blast+: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/ncbi-blast+: . files X-SVN-Commit-Revision: 561233 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.34 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: Mon, 11 Jan 2021 17:17:36 -0000 Author: jwb Date: Mon Jan 11 17:17:35 2021 New Revision: 561233 URL: https://svnweb.freebsd.org/changeset/ports/561233 Log: biology/ncbi-blast+: Drop dependency on gcc Replace compiler:openmp with compiler:c++14-lang Clang build also requires localbase:ldflags and a source patch to explicitly set variables to shared GCC-based platforms still require -latomic PR: port/247753, ports/252379 Added: head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp (contents, props changed) Modified: head/biology/ncbi-blast+/Makefile Modified: head/biology/ncbi-blast+/Makefile ============================================================================== --- head/biology/ncbi-blast+/Makefile Mon Jan 11 17:12:47 2021 (r561232) +++ head/biology/ncbi-blast+/Makefile Mon Jan 11 17:17:35 2021 (r561233) @@ -2,6 +2,7 @@ PORTNAME= ncbi-blast+ DISTVERSION= 2.11.0 +PORTREVISION= 1 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+/${PORTVERSION}/ @@ -32,7 +33,7 @@ LIB_DEPENDS= libpcre.so:devel/pcre \ RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \ p5-JSON>=0:converters/p5-JSON -USES= compiler:openmp gmake shebangfix perl5 python +USES= compiler:c++14-lang gmake localbase:ldflags shebangfix perl5 python USE_LDCONFIG= yes SHEBANG_FILES= src/app/blast/legacy_blast.pl \ @@ -47,15 +48,14 @@ GNU_CONFIGURE= yes # --libdir=${PREFIX}/lib/ncbi-tools++ doesn't respect DESTDIR, so do # a postinstall mv. CONFIGURE_ARGS= AR="ar cr" --without-boost --libdir=${PREFIX}/lib/ncbi-tools++ -LDFLAGS+= -latomic WRKSRC_SUBDIR= c++ .include -# Force newer GCC on platforms using GCC 4.2 as base .if ${CHOSEN_COMPILER_TYPE} == gcc -USE_GCC= yes +# In case of problems: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=220822 +LDFLAGS+= -latomic # Only exists in gcc libs .endif post-install: 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 Mon Jan 11 17:17:35 2021 (r561233) @@ -0,0 +1,22 @@ +--- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig 2021-01-10 02:28:53 UTC ++++ src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp +@@ -137,7 +137,8 @@ CSeqDBPerfApp::x_ScanDatabase() + } + LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences"); + +-#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) ++#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) || \ ++ defined(NCBI_COMPILER_LLVM_CLANG) + #pragma omp parallel default(none) num_threads(m_DbHandles.size()) \ + shared(oids2iterate,kScanUncompressed) if(m_DbHandles.size() > 1) + #else +@@ -208,7 +209,8 @@ CSeqDBPerfApp::x_InitApplicationData() + + + if (args["multi_threaded_creation"]) { +-#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) ++#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900) || \ ++ defined(NCBI_COMPILER_LLVM_CLANG) + #pragma omp parallel default(none) shared(kDbName, kNumThreads, kSeqType) num_threads(kNumThreads) + #else + #pragma omp parallel default(none) shared(kDbName, kNumThreads) num_threads(kNumThreads)