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biology/ncbi-blast+: Update to 2.16.0_3

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Fix build of seqdb_perf
Disable build system attempts to access NCBI file servers,
causing NFS timeouts where autofs is enabled
This commit is contained in:
Jason W. Bacon 2025-03-06 06:42:48 -06:00
parent 8c678f6b7d
commit 8de761e7d4
3 changed files with 25 additions and 8 deletions
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30
biology/ncbi-blast+/Makefile
View file

@ -1,6 +1,6 @@
PORTNAME= ncbi-blast+ PORTNAME= ncbi-blast+
DISTVERSION= 2.16.0 DISTVERSION= 2.16.0
PORTREVISION= 2 PORTREVISION= 3
CATEGORIES= biology perl5 python CATEGORIES= biology perl5 python
MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
@ -69,13 +69,29 @@ CONFIGURE_ARGS+= --without-openmp
LDFLAGS+= -latomic # Only exists in gcc libs LDFLAGS+= -latomic # Only exists in gcc libs
.endif .endif
# Build system attempts to access NCBI file server paths such as
# /net/snowman in many places. :-/
# This causes NFS timeouts if autofs is enabled.
pre-configure:
${REINPLACE_CMD} -e 's|/net/|/nonexistent/net/|g' \
${WRKSRC}/include/sra/readers/ncbi_traces_path.hpp \
${WRKSRC}/scripts/common/impl/create_flat_makefile.sh \
${WRKSRC}/src/objects/genomecoll/gc_cli/Makefile.in \
${WRKSRC}/src/objtools/blast/seqdb_reader/configuration.txt \
${WRKSRC}/src/objtools/align_format/unit_test/data/large_gi.asn \
${WRKSRC}/src/build-system/project_tree_builder.ini \
${WRKSRC}/src/build-system/cmake/CMake.NCBIptb.datatool.cmake \
${WRKSRC}/src/build-system/new_module.sh.in \
${WRKSRC}/src/build-system/Makefile.meta_l \
${WRKSRC}/src/build-system/config.site.ncbi
post-install: post-install:
@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra ${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
@${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11 ${RM} -rf ${STAGEDIR}${PREFIX}/lib/X11
@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in ${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in
@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_build_ver.h.in ${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_build_ver.h.in
@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_revision.h.in ${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_revision.h.in
@${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug ${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug
${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so
.include <bsd.port.post.mk> .include <bsd.port.post.mk>

2
biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
View file

@ -15,7 +15,7 @@
if (args["multi_threaded_creation"]) { 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_ICC) && (NCBI_COMPILER_VERSION >= 2100)) - (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100))
+ (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100)) || + (defined(NCBI_COMPILER_ICC) && (NCBI_COMPILER_VERSION >= 2100)) || \
+ defined(NCBI_COMPILER_LLVM_CLANG) + defined(NCBI_COMPILER_LLVM_CLANG)
#pragma omp parallel default(none) shared(kDbName, kNumThreads, kSeqType) num_threads(kNumThreads) #pragma omp parallel default(none) shared(kDbName, kNumThreads, kSeqType) num_threads(kNumThreads)
#else #else

1
biology/ncbi-blast+/pkg-plist
View file

@ -30,6 +30,7 @@ bin/run_with_lock
bin/seedtop bin/seedtop
bin/segmasker bin/segmasker
bin/seqdb_demo bin/seqdb_demo
bin/seqdb_perf
bin/tax4blast bin/tax4blast
bin/tblastn bin/tblastn
bin/tblastx bin/tblastx