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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-01-11 17:17:35 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-01-11 17:17:35 +0000 |
| commit | ef665861634bf69e5cc2f940ce83a278cefbadc1 (patch) | |
| tree | cc762b2d8120c7c0eac0e36845c45dd544c38a02 /biology/ncbi-blast+ | |
| parent | 426575b8293c68a714fb3116b2ee4ea47557b34d (diff) | |
| download | ports-ef665861634bf69e5cc2f940ce83a278cefbadc1.tar.gz ports-ef665861634bf69e5cc2f940ce83a278cefbadc1.zip | |
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
Notes
Notes:
svn path=/head/; revision=561233
Diffstat (limited to 'biology/ncbi-blast+')
| -rw-r--r-- | biology/ncbi-blast+/Makefile | 8 | ||||
| -rw-r--r-- | biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp | 22 |
2 files changed, 26 insertions, 4 deletions
diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index 4da3f9e73a4b..f9dc2ba18175 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -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 <bsd.port.pre.mk> -# 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: 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 new file mode 100644 index 000000000000..f15e73c87671 --- /dev/null +++ b/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp @@ -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) |