Date: Thu, 26 Dec 2019 16:21:18 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r520932 - in head/biology/ncbi-blast+: . files Message-ID: <201912261621.xBQGLIxm036078@repo.freebsd.org>
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Author: jwb Date: Thu Dec 26 16:21:17 2019 New Revision: 520932 URL: https://svnweb.freebsd.org/changeset/ports/520932 Log: biology/ncbi-blast+: Upgrade to 2.10.0 Numerous minor bug fixes, enhancements and dependency upgrades Minor port clean-up 1 patch from previous version upstreamed Reported by: portscout Deleted: head/biology/ncbi-blast+/files/patch-src_objtools_blast_seqdb__reader_test_seqdb__perf.cpp Modified: head/biology/ncbi-blast+/Makefile head/biology/ncbi-blast+/distinfo head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top head/biology/ncbi-blast+/pkg-plist Modified: head/biology/ncbi-blast+/Makefile ============================================================================== --- head/biology/ncbi-blast+/Makefile Thu Dec 26 16:11:32 2019 (r520931) +++ head/biology/ncbi-blast+/Makefile Thu Dec 26 16:21:17 2019 (r520932) @@ -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 Modified: head/biology/ncbi-blast+/distinfo ============================================================================== --- head/biology/ncbi-blast+/distinfo Thu Dec 26 16:11:32 2019 (r520931) +++ head/biology/ncbi-blast+/distinfo Thu Dec 26 16:21:17 2019 (r520932) @@ -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 Modified: head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top ============================================================================== --- head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top Thu Dec 26 16:11:32 2019 (r520931) +++ head/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top Thu Dec 26 16:21:17 2019 (r520932) @@ -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 Modified: head/biology/ncbi-blast+/pkg-plist ============================================================================== --- head/biology/ncbi-blast+/pkg-plist Thu Dec 26 16:11:32 2019 (r520931) +++ head/biology/ncbi-blast+/pkg-plist Thu Dec 26 16:21:17 2019 (r520932) @@ -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_GetAs 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/cac 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/imp 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/seq 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
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