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biology/ncbi-blast+: Upgrade to 2.10.0

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Numerous minor bug fixes, enhancements and dependency upgrades
Minor port clean-up
1 patch from previous version upstreamed

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2019-12-26 16:21:17 +00:00
parent de5a89eec4
commit de445f717c
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=520932
5 changed files with 49 additions and 29 deletions
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15
biology/ncbi-blast+/Makefile
View File

@ -1,8 +1,7 @@
# $FreeBSD$
PORTNAME= ncbi-blast+
DISTVERSION= 2.9.0
PORTREVISION= 3
DISTVERSION= 2.10.0
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+/${PORTVERSION}/
@ -27,7 +26,9 @@ LIB_DEPENDS= libpcre.so:devel/pcre \
libp11-kit.so:security/p11-kit \
libgcrypt.so:security/libgcrypt \
libgpg-error.so:security/libgpg-error \
libsqlite3.so:databases/sqlite3
libsqlite3.so:databases/sqlite3 \
libuv.so:devel/libuv \
libnghttp2.so:www/libnghttp2
RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils \
p5-JSON>=0:converters/p5-JSON
@ -36,8 +37,9 @@ USE_LDCONFIG= yes
SHEBANG_FILES= src/app/blast/legacy_blast.pl \
src/app/blast/update_blastdb.pl \
src/app/winmasker/windowmasker_2.2.22_adapter.py \
src/app/blast/get_species_taxids.sh
src/app/blast/cleanup-blastdb-volumes.py \
src/app/blast/get_species_taxids.sh \
src/app/winmasker/windowmasker_2.2.22_adapter.py
GNU_CONFIGURE= yes
# configure chooses /usr/local/bin/ar with no flags
@ -58,6 +60,9 @@ USE_GCC= yes
post-install:
@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
@${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/ncbi_build_ver.h.in
@${RM} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/common/ncbi_revision.h.in
@${RMDIR} ${STAGEDIR}${PREFIX}/lib/debug
${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/ncbi-tools++/*.so

6
biology/ncbi-blast+/distinfo
View File

@ -1,3 +1,3 @@
TIMESTAMP = 1560352108
SHA256 (ncbi-blast-2.9.0+-src.tar.gz) = a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257
SIZE (ncbi-blast-2.9.0+-src.tar.gz) = 25411110
TIMESTAMP = 1577200099
SHA256 (ncbi-blast-2.10.0+-src.tar.gz) = 3acdd9cec01c4f43e56aeaf89049cb8f8013d60b9c1705eced10166967f1d926
SIZE (ncbi-blast-2.10.0+-src.tar.gz) = 25547460

2
biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top
View File

@ -1,4 +1,4 @@
--- src/build-system/Makefile.in.top.orig 2018-03-27 03:40:40 UTC
--- src/build-system/Makefile.in.top.orig 2019-12-24 15:03:47 UTC
+++ src/build-system/Makefile.in.top
@@ -37,21 +37,21 @@ check: $(PROJECTS)
fi

16
biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp
View File

@ -1,16 +0,0 @@
--- src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp.orig 2018-10-23 19:28:52 UTC
+++ src/objtools/blast/seqdb_reader/test/seqdb_perf.cpp
@@ -137,8 +137,13 @@ CSeqDBPerfApp::x_ScanDatabase()
}
LOG_POST(Info << "Will go over " << oids2iterate.size() << " sequences");
+#if defined(NCBI_COMPILER_GCC) && (NCBI_COMPILER_VERSION >= 900)
#pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
+ shared(oids2iterate,kScanUncompressed) if(m_DbHandles.size() > 1)
+#else
+ #pragma omp parallel default(none) num_threads(m_DbHandles.size()) \
shared(oids2iterate) if(m_DbHandles.size() > 1)
+#endif
{
int thread_id = 0;
#ifdef _OPENMP

39
biology/ncbi-blast+/pkg-plist
View File

@ -9,6 +9,7 @@ bin/blastdbcp
bin/blastn
bin/blastp
bin/blastx
bin/cleanup-blastdb-volumes.py
bin/convert2blastmask
bin/datatool
bin/deltablast
@ -262,18 +263,17 @@ include/ncbi-tools++/cgi/ref_args.hpp
include/ncbi-tools++/cgi/user_agent.hpp
include/ncbi-tools++/common/boost_skew_guard.hpp
include/ncbi-tools++/common/config/ncbiconf_msvc.h
include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in
include/ncbi-tools++/common/config/ncbiconf_universal.h
include/ncbi-tools++/common/config/ncbiconf_xcode.h
include/ncbi-tools++/common/header_template.hpp
include/ncbi-tools++/common/metamodules_doxygen.h
include/ncbi-tools++/common/ncbi_build_info.h
include/ncbi-tools++/common/ncbi_build_ver.h
include/ncbi-tools++/common/ncbi_build_ver.h.in
include/ncbi-tools++/common/ncbi_build_ver.h.last
include/ncbi-tools++/common/ncbi_export.h
include/ncbi-tools++/common/ncbi_package_ver.h
include/ncbi-tools++/common/ncbi_pch_impl.hpp
include/ncbi-tools++/common/ncbi_revision.h
include/ncbi-tools++/common/ncbi_skew_guard.h
include/ncbi-tools++/common/ncbi_source_ver.cmake_nodep
include/ncbi-tools++/common/ncbi_source_ver.h
@ -287,6 +287,7 @@ include/ncbi-tools++/connect/error_codes.hpp
include/ncbi-tools++/connect/impl/server_connection.hpp
include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
include/ncbi-tools++/connect/ncbi_base64.h
include/ncbi-tools++/connect/ncbi_blowfish.h
include/ncbi-tools++/connect/ncbi_buffer.h
include/ncbi-tools++/connect/ncbi_conn_exception.hpp
include/ncbi-tools++/connect/ncbi_conn_reader_writer.hpp
@ -319,6 +320,7 @@ include/ncbi-tools++/connect/ncbi_pipe_connector.hpp
include/ncbi-tools++/connect/ncbi_sendmail.h
include/ncbi-tools++/connect/ncbi_server_info.h
include/ncbi-tools++/connect/ncbi_service.h
include/ncbi-tools++/connect/ncbi_service.hpp
include/ncbi-tools++/connect/ncbi_service_connector.h
include/ncbi-tools++/connect/ncbi_service_cxx.hpp
include/ncbi-tools++/connect/ncbi_socket.h
@ -428,6 +430,7 @@ include/ncbi-tools++/corelib/ncbi_tree.hpp
include/ncbi-tools++/corelib/ncbi_url.hpp
include/ncbi-tools++/corelib/ncbi_xstr.hpp
include/ncbi-tools++/corelib/ncbiapp.hpp
include/ncbi-tools++/corelib/ncbiapp_api.hpp
include/ncbi-tools++/corelib/ncbiargs.hpp
include/ncbi-tools++/corelib/ncbiatomic.h
include/ncbi-tools++/corelib/ncbiatomic.hpp
@ -455,6 +458,7 @@ include/ncbi-tools++/corelib/ncbistl.hpp
include/ncbi-tools++/corelib/ncbistr.hpp
include/ncbi-tools++/corelib/ncbistr_util.hpp
include/ncbi-tools++/corelib/ncbistre.hpp
include/ncbi-tools++/corelib/ncbisys.hpp
include/ncbi-tools++/corelib/ncbithr.hpp
include/ncbi-tools++/corelib/ncbithr_conf.hpp
include/ncbi-tools++/corelib/ncbitime.hpp
@ -479,6 +483,7 @@ include/ncbi-tools++/corelib/tempstr.hpp
include/ncbi-tools++/corelib/test_boost.hpp
include/ncbi-tools++/corelib/test_mt.hpp
include/ncbi-tools++/corelib/version.hpp
include/ncbi-tools++/corelib/version_api.hpp
include/ncbi-tools++/db/error_codes.hpp
include/ncbi-tools++/db/sqlite/sqlitewrapp.hpp
include/ncbi-tools++/dbapi/cache/dbapi_blob_cache.hpp
@ -1290,6 +1295,8 @@ include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_SequenceInfo.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_SequenceInfo_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo_.hpp
include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLx.hpp
@ -3548,6 +3555,7 @@ include/ncbi-tools++/objtools/data_loaders/genbank/cache/writer_cache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/cache/writer_cache_entry.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gbloader.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gbloader_params.h
include/ncbi-tools++/objtools/data_loaders/genbank/gbnative.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gicache/reader_gicache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gicache/reader_gicache_entry.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/gicache/reader_gicache_params.h
@ -3564,12 +3572,14 @@ include/ncbi-tools++/objtools/data_loaders/genbank/impl/incr_time.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/info_cache.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/processor.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/processors.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id1_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_service.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/request_result.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/standalone_result.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/impl/statistics.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/psg_loader.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader_interface.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/reader_params.h
@ -3586,7 +3596,6 @@ include/ncbi-tools++/objtools/data_loaders/genbank/seqref.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/writer.hpp
include/ncbi-tools++/objtools/data_loaders/genbank/writer_interface.hpp
include/ncbi-tools++/objtools/data_loaders/loaders.hpp
include/ncbi-tools++/objtools/edit/apply_mods.hpp
include/ncbi-tools++/objtools/edit/apply_object.hpp
include/ncbi-tools++/objtools/edit/autodef.hpp
include/ncbi-tools++/objtools/edit/autodef_options.hpp
@ -3613,6 +3622,7 @@ include/ncbi-tools++/objtools/edit/promote.hpp
include/ncbi-tools++/objtools/edit/publication_edit.hpp
include/ncbi-tools++/objtools/edit/remote_updater.hpp
include/ncbi-tools++/objtools/edit/rna_edit.hpp
include/ncbi-tools++/objtools/edit/seq_edit.hpp
include/ncbi-tools++/objtools/edit/seq_entry_edit.hpp
include/ncbi-tools++/objtools/edit/seqid_guesser.hpp
include/ncbi-tools++/objtools/edit/source_edit.hpp
@ -3676,12 +3686,16 @@ include/ncbi-tools++/objtools/format/sam_formatter.hpp
include/ncbi-tools++/objtools/format/text_ostream.hpp
include/ncbi-tools++/objtools/logging/listener.hpp
include/ncbi-tools++/objtools/logging/message.hpp
include/ncbi-tools++/objtools/pubseq_gateway/client/psg_client.hpp
include/ncbi-tools++/objtools/readers/agp_converter.hpp
include/ncbi-tools++/objtools/readers/agp_read.hpp
include/ncbi-tools++/objtools/readers/agp_seq_entry.hpp
include/ncbi-tools++/objtools/readers/agp_util.hpp
include/ncbi-tools++/objtools/readers/agp_validate_reader.hpp
include/ncbi-tools++/objtools/readers/aln_error_reporter.hpp
include/ncbi-tools++/objtools/readers/aln_formats.hpp
include/ncbi-tools++/objtools/readers/aln_reader.hpp
include/ncbi-tools++/objtools/readers/alnread.hpp
include/ncbi-tools++/objtools/readers/bed_reader.hpp
include/ncbi-tools++/objtools/readers/cigar.hpp
include/ncbi-tools++/objtools/readers/error_container.hpp
@ -3695,6 +3709,7 @@ include/ncbi-tools++/objtools/readers/gff2_data.hpp
include/ncbi-tools++/objtools/readers/gff2_reader.hpp
include/ncbi-tools++/objtools/readers/gff3_reader.hpp
include/ncbi-tools++/objtools/readers/gff3_sofa.hpp
include/ncbi-tools++/objtools/readers/gff_base_columns.hpp
include/ncbi-tools++/objtools/readers/gff_reader.hpp
include/ncbi-tools++/objtools/readers/glimmer_reader.hpp
include/ncbi-tools++/objtools/readers/gtf_reader.hpp
@ -3704,9 +3719,12 @@ include/ncbi-tools++/objtools/readers/iidmapper.hpp
include/ncbi-tools++/objtools/readers/line_error.hpp
include/ncbi-tools++/objtools/readers/message_listener.hpp
include/ncbi-tools++/objtools/readers/microarray_reader.hpp
include/ncbi-tools++/objtools/readers/mod_error.hpp
include/ncbi-tools++/objtools/readers/mod_reader.hpp
include/ncbi-tools++/objtools/readers/phrap.hpp
include/ncbi-tools++/objtools/readers/read_util.hpp
include/ncbi-tools++/objtools/readers/reader_base.hpp
include/ncbi-tools++/objtools/readers/reader_error_codes.hpp
include/ncbi-tools++/objtools/readers/reader_exception.hpp
include/ncbi-tools++/objtools/readers/reader_idgen.hpp
include/ncbi-tools++/objtools/readers/readfeat.hpp
@ -3831,12 +3849,18 @@ include/ncbi-tools++/util/ascii85.hpp
include/ncbi-tools++/util/bitset/bitset_debug.hpp
include/ncbi-tools++/util/bitset/bitset_pool.hpp
include/ncbi-tools++/util/bitset/bm.h
include/ncbi-tools++/util/bitset/bm64.h
include/ncbi-tools++/util/bitset/bmaggregator.h
include/ncbi-tools++/util/bitset/bmalgo.h
include/ncbi-tools++/util/bitset/bmalgo_impl.h
include/ncbi-tools++/util/bitset/bmalgo_similarity.h
include/ncbi-tools++/util/bitset/bmalloc.h
include/ncbi-tools++/util/bitset/bmavx2.h
include/ncbi-tools++/util/bitset/bmavx512.h
include/ncbi-tools++/util/bitset/bmblocks.h
include/ncbi-tools++/util/bitset/bmbmatrix.h
include/ncbi-tools++/util/bitset/bmbmi1.h
include/ncbi-tools++/util/bitset/bmbmi2.h
include/ncbi-tools++/util/bitset/bmbuffer.h
include/ncbi-tools++/util/bitset/bmconst.h
include/ncbi-tools++/util/bitset/bmdbg.h
@ -3845,6 +3869,7 @@ include/ncbi-tools++/util/bitset/bmfunc.h
include/ncbi-tools++/util/bitset/bmfwd.h
include/ncbi-tools++/util/bitset/bmgamma.h
include/ncbi-tools++/util/bitset/bmrandom.h
include/ncbi-tools++/util/bitset/bmrs.h
include/ncbi-tools++/util/bitset/bmserial.h
include/ncbi-tools++/util/bitset/bmsimd.h
include/ncbi-tools++/util/bitset/bmsparsevec.h
@ -3855,6 +3880,7 @@ include/ncbi-tools++/util/bitset/bmsparsevec_util.h
include/ncbi-tools++/util/bitset/bmsse2.h
include/ncbi-tools++/util/bitset/bmsse4.h
include/ncbi-tools++/util/bitset/bmsse_util.h
include/ncbi-tools++/util/bitset/bmstrsparsevec.h
include/ncbi-tools++/util/bitset/bmtimer.h
include/ncbi-tools++/util/bitset/bmtrans.h
include/ncbi-tools++/util/bitset/bmundef.h
@ -3874,6 +3900,7 @@ include/ncbi-tools++/util/cache/icache.hpp
include/ncbi-tools++/util/cache/icache_cf.hpp
include/ncbi-tools++/util/cache/icache_clean_thread.hpp
include/ncbi-tools++/util/checksum.hpp
include/ncbi-tools++/util/compile_time.hpp
include/ncbi-tools++/util/compress/archive.hpp
include/ncbi-tools++/util/compress/archive_.hpp
include/ncbi-tools++/util/compress/bzip2.hpp
@ -3890,6 +3917,7 @@ include/ncbi-tools++/util/compress/zlib/zlib.h
include/ncbi-tools++/util/compress/zlib/zutil.h
include/ncbi-tools++/util/creaders/alnread.h
include/ncbi-tools++/util/creaders/creaders_export.h
include/ncbi-tools++/util/data_histogram.hpp
include/ncbi-tools++/util/ddump_viewer.hpp
include/ncbi-tools++/util/dictionary.hpp
include/ncbi-tools++/util/dictionary_util.hpp
@ -3902,6 +3930,8 @@ include/ncbi-tools++/util/format_guess.hpp
include/ncbi-tools++/util/histogram_binning.hpp
include/ncbi-tools++/util/icanceled.hpp
include/ncbi-tools++/util/id_mux.hpp
include/ncbi-tools++/util/impl/compile_time_bits.hpp
include/ncbi-tools++/util/impl/ct_crc32.hpp
include/ncbi-tools++/util/impl/floating_point_comparison.hpp
include/ncbi-tools++/util/itransaction.hpp
include/ncbi-tools++/util/itree.hpp
@ -4134,6 +4164,8 @@ lib/ncbi-tools++/libproj-static.a
lib/ncbi-tools++/libproj.a
lib/ncbi-tools++/libproteinkmer-static.a
lib/ncbi-tools++/libproteinkmer.a
lib/ncbi-tools++/libpsg_client-static.a
lib/ncbi-tools++/libpsg_client.a
lib/ncbi-tools++/libpub-static.a
lib/ncbi-tools++/libpub.a
lib/ncbi-tools++/libpubmed-static.a
@ -4258,4 +4290,3 @@ lib/ncbi-tools++/libxutil-static.a
lib/ncbi-tools++/libxutil.a
lib/ncbi-tools++/libxxconnect-static.a
lib/ncbi-tools++/libxxconnect.a
@dir include/ncbi-tools++/objtools/data_loaders/genbank/psg