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CVS commit: pkgsrc/biology/ncbi-blast+

Module Name:    pkgsrc
Committed By:   bacon
Date:           Fri Jun 11 13:47:40 UTC 2021

Modified Files:
        pkgsrc/biology/ncbi-blast+: Makefile PLIST buildlink3.mk distinfo
        pkgsrc/biology/ncbi-blast+/patches: patch-src_build-system_configure
Added Files:
        pkgsrc/biology/ncbi-blast+/patches:
            patch-src_build-system_cmake_cmake-cfg-xcode.sh
Removed Files:
        pkgsrc/biology/ncbi-blast+/patches:
            patch-src_build-system_cmake_cmake-cfg-unix.sh
            patch-src_build-system_cmake_cmake-configure

Log Message:
biology/ncbi-blast+: Update to 2.11.0

Release notes: https://www.ncbi.nlm.nih.gov/books/NBK131777/


To generate a diff of this commit:
cvs rdiff -u -r1.23 -r1.24 pkgsrc/biology/ncbi-blast+/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/ncbi-blast+/PLIST \
    pkgsrc/biology/ncbi-blast+/buildlink3.mk
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/ncbi-blast+/distinfo
cvs rdiff -u -r1.1 -r0 \
    pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh \
    pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.


Modified files:

Index: pkgsrc/biology/ncbi-blast+/Makefile
diff -u pkgsrc/biology/ncbi-blast+/Makefile:1.23 pkgsrc/biology/ncbi-blast+/Makefile:1.24
--- pkgsrc/biology/ncbi-blast+/Makefile:1.23    Mon May 24 19:49:11 2021
+++ pkgsrc/biology/ncbi-blast+/Makefile Fri Jun 11 13:47:39 2021
@@ -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/defin
 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-su
 
 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"

Index: pkgsrc/biology/ncbi-blast+/PLIST
diff -u pkgsrc/biology/ncbi-blast+/PLIST:1.2 pkgsrc/biology/ncbi-blast+/PLIST:1.3
--- pkgsrc/biology/ncbi-blast+/PLIST:1.2        Mon Jan  7 15:00:10 2019
+++ pkgsrc/biology/ncbi-blast+/PLIST    Fri Jun 11 13:47:39 2021
@@ -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/blas
 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/blas
 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_v
 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
 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_iprang
 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_c
 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
 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.h
 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/d
 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
 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/
 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
 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/au
 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_loade
 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_loade
 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_loade
 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/promo
 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
 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/gf
 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/ii
 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/bmspars
 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.h
 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/
 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.h
 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
Index: pkgsrc/biology/ncbi-blast+/buildlink3.mk
diff -u pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.2 pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.3
--- pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.2        Sun Apr 29 21:00:04 2018
+++ pkgsrc/biology/ncbi-blast+/buildlink3.mk    Fri Jun 11 13:47:40 2021
@@ -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

Index: pkgsrc/biology/ncbi-blast+/distinfo
diff -u pkgsrc/biology/ncbi-blast+/distinfo:1.3 pkgsrc/biology/ncbi-blast+/distinfo:1.4
--- pkgsrc/biology/ncbi-blast+/distinfo:1.3     Mon Jan  7 15:00:10 2019
+++ pkgsrc/biology/ncbi-blast+/distinfo Fri Jun 11 13:47:40 2021
@@ -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

Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.2
--- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.1     Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure Fri Jun 11 13:47:40 2021
@@ -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]* \

Added files:

Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.1
--- /dev/null   Fri Jun 11 13:47:40 2021
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh  Fri Jun 11 13:47:40 2021
@@ -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
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