diff options
author | bacon <bacon@pkgsrc.org> | 2021-06-11 13:47:39 +0000 |
---|---|---|
committer | bacon <bacon@pkgsrc.org> | 2021-06-11 13:47:39 +0000 |
commit | 6f9b71eb2bd7242756c187f6c4019de4d04d32a7 (patch) | |
tree | 6a32b3877960098615de20cac789dfde18132c92 /biology | |
parent | d041d31e46656d8f8149e44db433ca4a000a5960 (diff) | |
download | pkgsrc-6f9b71eb2bd7242756c187f6c4019de4d04d32a7.tar.gz |
biology/ncbi-blast+: Update to 2.11.0
Release notes: https://www.ncbi.nlm.nih.gov/books/NBK131777/
Diffstat (limited to 'biology')
-rw-r--r-- | biology/ncbi-blast+/Makefile | 10 | ||||
-rw-r--r-- | biology/ncbi-blast+/PLIST | 141 | ||||
-rw-r--r-- | biology/ncbi-blast+/buildlink3.mk | 4 | ||||
-rw-r--r-- | biology/ncbi-blast+/distinfo | 15 | ||||
-rw-r--r-- | biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh | 15 | ||||
-rw-r--r-- | biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh | 15 | ||||
-rw-r--r-- | biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure | 15 | ||||
-rw-r--r-- | biology/ncbi-blast+/patches/patch-src_build-system_configure | 10 |
8 files changed, 171 insertions, 54 deletions
diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index fda4ac829e3..5dc30266155 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -1,8 +1,7 @@ -# $NetBSD: Makefile,v 1.23 2021/05/24 19:49:11 wiz Exp $ +# $NetBSD: Makefile,v 1.24 2021/06/11 13:47:39 bacon Exp $ -DISTNAME= ncbi-blast-2.8.1+-src +DISTNAME= ncbi-blast-2.11.0+-src PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/} -PKGREVISION= 15 CATEGORIES= biology MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/ @@ -19,7 +18,7 @@ SUBST_STAGE.configure= pre-configure SUBST_SED.configure+= -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' SUBST_SED.configure+= -e '/--infodir=DIR/d' SUBST_SED.configure+= -e '/--mandir=DIR/d' -SUBST_FILES.configure+= ${WRKSRC}/src/build-system/configure +SUBST_FILES.configure+= src/build-system/configure USE_TOOLS+= bash gmake perl USE_LANGUAGES= c c++ @@ -29,6 +28,7 @@ REPLACE_BASH= scripts/common/impl/define_random_macros.sh REPLACE_BASH+= src/app/blast/get_species_taxids.sh REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py +REPLACE_PYTHON+= src/app/blast/cleanup-blastdb-volumes.py # The test for amq can hang, but amq is not needed so just avoid the test # configure chooses /usr/local/bin/ar with no flags @@ -54,7 +54,9 @@ BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts post-install: ${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra +.if ${OPSYS} != Darwin ${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so +.endif .include "../../devel/zlib/buildlink3.mk" .include "../../archivers/lzo/buildlink3.mk" diff --git a/biology/ncbi-blast+/PLIST b/biology/ncbi-blast+/PLIST index 4169608ac79..c2f07ec0ecc 100644 --- a/biology/ncbi-blast+/PLIST +++ b/biology/ncbi-blast+/PLIST @@ -1,13 +1,16 @@ -@comment $NetBSD: PLIST,v 1.2 2019/01/07 15:00:10 bacon Exp $ +@comment $NetBSD: PLIST,v 1.3 2021/06/11 13:47:39 bacon Exp $ bin/blast_formatter +bin/blast_report bin/blastdb_aliastool bin/blastdb_convert +bin/blastdb_path bin/blastdbcheck bin/blastdbcmd bin/blastdbcp bin/blastn bin/blastp bin/blastx +bin/cleanup-blastdb-volumes.py bin/convert2blastmask bin/datatool bin/deltablast @@ -40,6 +43,7 @@ include/ncbi-tools++/algo/blast/api/blast_aux.hpp include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp include/ncbi-tools++/algo/blast/api/blast_exception.hpp include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp +include/ncbi-tools++/algo/blast/api/blast_node.hpp include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp include/ncbi-tools++/algo/blast/api/blast_options.hpp include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp @@ -50,6 +54,7 @@ include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp include/ncbi-tools++/algo/blast/api/blast_types.hpp +include/ncbi-tools++/algo/blast/api/blast_usage_report.hpp include/ncbi-tools++/algo/blast/api/blastp_kmer_options.hpp include/ncbi-tools++/algo/blast/api/blastx_options.hpp include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp @@ -273,6 +278,8 @@ 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_revision.h.in 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 @@ -286,6 +293,7 @@ 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 @@ -307,6 +315,7 @@ include/ncbi-tools++/connect/ncbi_iprange.h include/ncbi-tools++/connect/ncbi_ipv6.h include/ncbi-tools++/connect/ncbi_lbos.hpp include/ncbi-tools++/connect/ncbi_localip.h +include/ncbi-tools++/connect/ncbi_localip.hpp include/ncbi-tools++/connect/ncbi_mbedtls.h include/ncbi-tools++/connect/ncbi_memory_connector.h include/ncbi-tools++/connect/ncbi_misc.hpp @@ -318,6 +327,7 @@ 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 @@ -327,6 +337,7 @@ include/ncbi-tools++/connect/ncbi_socket_unix.h include/ncbi-tools++/connect/ncbi_socket_unix.hpp include/ncbi-tools++/connect/ncbi_tls.h include/ncbi-tools++/connect/ncbi_types.h +include/ncbi-tools++/connect/ncbi_usage_report.hpp include/ncbi-tools++/connect/ncbi_userhost.hpp include/ncbi-tools++/connect/ncbi_util.h include/ncbi-tools++/connect/server.hpp @@ -427,6 +438,7 @@ 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 @@ -454,6 +466,7 @@ 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 @@ -478,6 +491,7 @@ 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 @@ -497,6 +511,7 @@ include/ncbi-tools++/dbapi/driver/impl/dbapi_impl_cmd.hpp include/ncbi-tools++/dbapi/driver/impl/dbapi_impl_connection.hpp include/ncbi-tools++/dbapi/driver/impl/dbapi_impl_context.hpp include/ncbi-tools++/dbapi/driver/impl/dbapi_impl_result.hpp +include/ncbi-tools++/dbapi/driver/impl/dbapi_pool_balancer.hpp include/ncbi-tools++/dbapi/driver/impl/handle_stack.hpp include/ncbi-tools++/dbapi/driver/interfaces.hpp include/ncbi-tools++/dbapi/driver/odbc/interfaces.hpp @@ -535,6 +550,76 @@ include/ncbi-tools++/html/pager.hpp include/ncbi-tools++/html/selection.hpp include/ncbi-tools++/html/writer_htmlenc.hpp include/ncbi-tools++/misc/error_codes.hpp +include/ncbi-tools++/misc/jsonwrapp/jsonwrapp.hpp +include/ncbi-tools++/misc/jsonwrapp/jsonwrapp10.hpp +include/ncbi-tools++/misc/jsonwrapp/jsonwrapp11.hpp +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/__NCBI_read_me.txt +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/allocators.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/document.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/encodedstream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/encodings.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/error/en.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/error/error.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/filereadstream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/filewritestream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/biginteger.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/diyfp.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/dtoa.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/ieee754.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/itoa.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/meta.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/pow10.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/stack.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/strfunc.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/internal/strtod.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/license.txt +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/memorybuffer.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/memorystream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/msinttypes/inttypes.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/msinttypes/stdint.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/pointer.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/prettywriter.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/rapidjson.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/reader.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/stringbuffer.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson10/writer.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/__NCBI_read_me.txt +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/allocators.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/document.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/encodedstream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/encodings.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/error/en.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/error/error.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/filereadstream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/filewritestream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/fwd.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/biginteger.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/diyfp.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/dtoa.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/ieee754.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/itoa.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/meta.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/pow10.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/regex.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/stack.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/strfunc.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/strtod.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/internal/swap.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/istreamwrapper.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/license.txt +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/memorybuffer.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/memorystream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/msinttypes/inttypes.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/msinttypes/stdint.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/ostreamwrapper.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/pointer.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/prettywriter.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/rapidjson.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/reader.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/schema.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/stream.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/stringbuffer.h +include/ncbi-tools++/misc/jsonwrapp/rapidjson11/writer.h include/ncbi-tools++/ncbi_pch.hpp include/ncbi-tools++/ncbi_random_macro.h include/ncbi-tools++/ncbi_source_ver.h @@ -946,6 +1031,10 @@ include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set.hpp include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set_.hpp include/ncbi-tools++/objects/coords/NCBI_HGVSCoordinate_module.hpp include/ncbi-tools++/objects/coords/objcoords__.hpp +include/ncbi-tools++/objects/dbsnp/primary_track/dbsnp.grpc.pb.h +include/ncbi-tools++/objects/dbsnp/primary_track/dbsnp.pb.h +include/ncbi-tools++/objects/dbsnp/primary_track/impl/snpptis_impl.hpp +include/ncbi-tools++/objects/dbsnp/primary_track/snpptis.hpp include/ncbi-tools++/objects/docsum/.cvsignore include/ncbi-tools++/objects/docsum/.gitignore include/ncbi-tools++/objects/docsum/Assay.hpp @@ -1219,6 +1308,8 @@ 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 @@ -3398,6 +3489,7 @@ include/ncbi-tools++/objtools/alnmgr/aln_container.hpp include/ncbi-tools++/objtools/alnmgr/aln_converters.hpp include/ncbi-tools++/objtools/alnmgr/aln_explorer.hpp include/ncbi-tools++/objtools/alnmgr/aln_generators.hpp +include/ncbi-tools++/objtools/alnmgr/aln_rng_coll_list_oper.hpp include/ncbi-tools++/objtools/alnmgr/aln_rng_coll_oper.hpp include/ncbi-tools++/objtools/alnmgr/aln_seqid.hpp include/ncbi-tools++/objtools/alnmgr/aln_serial.hpp @@ -3464,7 +3556,9 @@ include/ncbi-tools++/objtools/cleanup/autogenerated_cleanup.hpp include/ncbi-tools++/objtools/cleanup/capitalization_string.hpp include/ncbi-tools++/objtools/cleanup/cleanup.hpp include/ncbi-tools++/objtools/cleanup/cleanup_change.hpp -include/ncbi-tools++/objtools/cleanup/newcleanup.hpp +include/ncbi-tools++/objtools/cleanup/cleanup_message.hpp +include/ncbi-tools++/objtools/cleanup/cleanup_pub.hpp +include/ncbi-tools++/objtools/cleanup/fix_feature_id.hpp include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader.hpp include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader_rmt.hpp include/ncbi-tools++/objtools/data_loaders/blastdb/blastdb_adapter.hpp @@ -3476,6 +3570,7 @@ 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 @@ -3492,12 +3587,14 @@ 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 @@ -3514,7 +3611,6 @@ 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 @@ -3541,6 +3637,7 @@ 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 @@ -3604,12 +3701,17 @@ 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/impl/misc.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 @@ -3623,6 +3725,7 @@ 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 @@ -3632,13 +3735,20 @@ 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/psl_reader.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/reader_listener.hpp +include/ncbi-tools++/objtools/readers/reader_message.hpp include/ncbi-tools++/objtools/readers/readfeat.hpp include/ncbi-tools++/objtools/readers/rm_reader.hpp +include/ncbi-tools++/objtools/readers/seqid_validate.hpp include/ncbi-tools++/objtools/readers/source_mod_parser.hpp include/ncbi-tools++/objtools/readers/source_mod_parser_wrapper.hpp include/ncbi-tools++/objtools/readers/struct_cmt_reader.hpp @@ -3662,6 +3772,8 @@ include/ncbi-tools++/serial/delaybuf.hpp include/ncbi-tools++/serial/enumvalues.hpp include/ncbi-tools++/serial/error_codes.hpp include/ncbi-tools++/serial/exception.hpp +include/ncbi-tools++/serial/grpc_integration/grpc_integration.hpp +include/ncbi-tools++/serial/grpc_integration/impl/grpc_support.hpp include/ncbi-tools++/serial/impl/aliasinfo.hpp include/ncbi-tools++/serial/impl/asntypes.hpp include/ncbi-tools++/serial/impl/autoptrinfo.hpp @@ -3759,12 +3871,18 @@ 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 @@ -3772,7 +3890,9 @@ include/ncbi-tools++/util/bitset/bmdef.h 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/bmintervals.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 @@ -3783,11 +3903,13 @@ 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 include/ncbi-tools++/util/bitset/bmutil.h include/ncbi-tools++/util/bitset/bmvmin.h +include/ncbi-tools++/util/bitset/bmxor.h include/ncbi-tools++/util/bitset/encoding.h include/ncbi-tools++/util/bitset/license.txt include/ncbi-tools++/util/bitset/ncbi_bitset.hpp @@ -3802,6 +3924,7 @@ 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 @@ -3818,6 +3941,7 @@ 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 @@ -3830,6 +3954,8 @@ 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 @@ -3857,6 +3983,7 @@ include/ncbi-tools++/util/ncbi_url.hpp include/ncbi-tools++/util/random_gen.hpp include/ncbi-tools++/util/range.hpp include/ncbi-tools++/util/range_coll.hpp +include/ncbi-tools++/util/range_set.hpp include/ncbi-tools++/util/rangelist.hpp include/ncbi-tools++/util/rangemap.hpp include/ncbi-tools++/util/rangemap.inl @@ -3951,13 +4078,13 @@ lib/ncbi-tools++/libconnect-static.a lib/ncbi-tools++/libconnect.a lib/ncbi-tools++/libconnssl-static.a lib/ncbi-tools++/libconnssl.a -lib/ncbi-tools++/libcreaders-static.a -lib/ncbi-tools++/libcreaders.a lib/ncbi-tools++/libdbapi-static.a lib/ncbi-tools++/libdbapi.a lib/ncbi-tools++/libdbapi_driver-dll.so lib/ncbi-tools++/libdbapi_driver-static.a lib/ncbi-tools++/libdbapi_driver.a +lib/ncbi-tools++/libdbsnp_ptis-static.a +lib/ncbi-tools++/libdbsnp_ptis.a lib/ncbi-tools++/libdbsnp_tooltip_service-static.a lib/ncbi-tools++/libdbsnp_tooltip_service.a lib/ncbi-tools++/libdocsum-static.a @@ -3984,6 +4111,8 @@ lib/ncbi-tools++/libgenesbyloc-static.a lib/ncbi-tools++/libgenesbyloc.a lib/ncbi-tools++/libgenome_collection-static.a lib/ncbi-tools++/libgenome_collection.a +lib/ncbi-tools++/libgrpc_integration-static.a +lib/ncbi-tools++/libgrpc_integration.a lib/ncbi-tools++/libhomologene-static.a lib/ncbi-tools++/libhomologene.a lib/ncbi-tools++/libid1-static.a @@ -4062,6 +4191,8 @@ 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 diff --git a/biology/ncbi-blast+/buildlink3.mk b/biology/ncbi-blast+/buildlink3.mk index acbe65a0343..96fea5afd0e 100644 --- a/biology/ncbi-blast+/buildlink3.mk +++ b/biology/ncbi-blast+/buildlink3.mk @@ -1,11 +1,11 @@ -# $NetBSD: buildlink3.mk,v 1.2 2018/04/29 21:00:04 adam Exp $ +# $NetBSD: buildlink3.mk,v 1.3 2021/06/11 13:47:40 bacon Exp $ BUILDLINK_TREE+= ncbi-blast+ .if !defined(NCBI_BLAST+_BUILDLINK3_MK) NCBI_BLAST+_BUILDLINK3_MK:= -BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.7.1 +BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.11.0 BUILDLINK_PKGSRCDIR.ncbi-blast+?= ../../biology/ncbi-blast+ .endif # NCBI_BLAST+_BUILDLINK3_MK diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo index 6fb935f0072..f9fcfe557cc 100644 --- a/biology/ncbi-blast+/distinfo +++ b/biology/ncbi-blast+/distinfo @@ -1,14 +1,13 @@ -$NetBSD: distinfo,v 1.3 2019/01/07 15:00:10 bacon Exp $ +$NetBSD: distinfo,v 1.4 2021/06/11 13:47:40 bacon Exp $ -SHA1 (ncbi-blast-2.8.1+-src.tar.gz) = 16573b642d7861d0bed67f3eb1174fc646819eec -RMD160 (ncbi-blast-2.8.1+-src.tar.gz) = ef8df6c4b3cae18b2ab4509af15554ee8d8f9bfd -SHA512 (ncbi-blast-2.8.1+-src.tar.gz) = 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f -Size (ncbi-blast-2.8.1+-src.tar.gz) = 24973554 bytes +SHA1 (ncbi-blast-2.11.0+-src.tar.gz) = af9bdc82ec01959fb2ab8367636face8a0ef3e91 +RMD160 (ncbi-blast-2.11.0+-src.tar.gz) = a8036dca9cc85b589bbb7f7f24e47c7e0053ead6 +SHA512 (ncbi-blast-2.11.0+-src.tar.gz) = 617994a0e3a4675a5f7048f165ac405bbd6a715ece9aba115d7c26b6be446b889b817dd496a2e15673545e5b594684c83fc4edb22cb5ecca2fd6d342c3bd642e +Size (ncbi-blast-2.11.0+-src.tar.gz) = 58493096 bytes SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5 SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de62ebf6927f SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01 -SHA1 (patch-src_build-system_cmake_cmake-cfg-unix.sh) = 90468f3109800e01fc7351926adb331919a12fb2 -SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97 -SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6 +SHA1 (patch-src_build-system_cmake_cmake-cfg-xcode.sh) = 9167a5092d30da46a06b0be05199afa3b08680c6 +SHA1 (patch-src_build-system_configure) = 95185d53179a69a1b1cfa6870aca36dd962d2c43 SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd SHA1 (patch-src_util_checksum_farmhash_farmhash.h) = c3ff60de9a9020d3b706c2bff37f6f4cde4e6b6b diff --git a/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh b/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh deleted file mode 100644 index 0e184ea4aff..00000000000 --- a/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh +++ /dev/null @@ -1,15 +0,0 @@ -$NetBSD: patch-src_build-system_cmake_cmake-cfg-unix.sh,v 1.1 2019/01/07 15:00:10 bacon Exp $ - -# Portability - ---- src/build-system/cmake/cmake-cfg-unix.sh.orig 2019-01-02 01:22:44.549100012 +0000 -+++ src/build-system/cmake/cmake-cfg-unix.sh -@@ -166,7 +166,7 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L - CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_CCACHE=$USE_CCACHE" - CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_DISTCC=$USE_DISTCC" - build_root=CMake-${CC_NAME}${CC_VERSION}-${BUILD_TYPE} --if [ "$BUILD_SHARED_LIBS" == "ON" ]; then -+if [ "$BUILD_SHARED_LIBS" = "ON" ]; then - build_root="$build_root"DLL - fi - #build_root="$build_root"64 diff --git a/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh b/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh new file mode 100644 index 00000000000..d4f072e5e2f --- /dev/null +++ b/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh @@ -0,0 +1,15 @@ +$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.1 2021/06/11 13:47:40 bacon Exp $ + +# Portability + +--- src/build-system/cmake/cmake-cfg-xcode.sh.orig 2021-06-10 11:54:05.800996703 +0000 ++++ src/build-system/cmake/cmake-cfg-xcode.sh +@@ -218,7 +218,7 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L + + if [ -z "$BUILD_ROOT" ]; then + BUILD_ROOT=CMake-${CC_NAME}${CC_VERSION} +- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then ++ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then + BUILD_ROOT="$BUILD_ROOT"-DLL + fi + fi diff --git a/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure b/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure deleted file mode 100644 index afa61932c70..00000000000 --- a/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure +++ /dev/null @@ -1,15 +0,0 @@ -$NetBSD: patch-src_build-system_cmake_cmake-configure,v 1.1 2018/04/27 20:28:28 bacon Exp $ - -# Fix portability issue - ---- src/build-system/cmake/cmake-configure.orig 2018-03-26 14:13:44.229849356 +0000 -+++ src/build-system/cmake/cmake-configure -@@ -468,7 +468,7 @@ fi - if [ -z "$ROOT" ]; then - if [ -z "$GPIPEROOT" ]; then - ROOT="CMake-$BUILD_TYPE" -- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then -+ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then - ROOT="$ROOT"DLL - fi - else diff --git a/biology/ncbi-blast+/patches/patch-src_build-system_configure b/biology/ncbi-blast+/patches/patch-src_build-system_configure index 466f7b69c59..563c661e65c 100644 --- a/biology/ncbi-blast+/patches/patch-src_build-system_configure +++ b/biology/ncbi-blast+/patches/patch-src_build-system_configure @@ -1,15 +1,15 @@ -$NetBSD: patch-src_build-system_configure,v 1.1 2018/04/27 20:28:28 bacon Exp $ +$NetBSD: patch-src_build-system_configure,v 1.2 2021/06/11 13:47:40 bacon Exp $ -# Fix support for localstatedir +# Avert missing --with-libiconv-prefix option ---- src/build-system/configure.orig 2018-02-19 01:32:40 UTC +--- src/build-system/configure.orig 2021-06-10 19:44:11.069762486 +0000 +++ src/build-system/configure -@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do +@@ -2015,7 +2015,7 @@ for x_arg in "$@" ; do | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \ | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \ | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | --with-runpath=* | --with-relative-runpath=* \ -+ | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \ ++ | --with-runpath=* | --with-relative-runpath=* | --with-libiconv-prefix=* \ | --with-experimental=* | --with-extra-action=* | --with-build-root=* \ | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \ | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \ |