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CVS commit: pkgsrc/biology/ncbi-blast+
Module Name: pkgsrc
Committed By: bacon
Date: Sun Apr 10 20:54:51 UTC 2022
Modified Files:
pkgsrc/biology/ncbi-blast+: Makefile PLIST buildlink3.mk distinfo
pkgsrc/biology/ncbi-blast+/patches:
patch-src_build-system_cmake_cmake-cfg-xcode.sh
patch-src_build-system_configure
Log Message:
biology/ncbi-blast+: Update to 2.13.0
Several minor bug fixes and improvements since 2.11.0
Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/?report=reader
To generate a diff of this commit:
cvs rdiff -u -r1.27 -r1.28 pkgsrc/biology/ncbi-blast+/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/ncbi-blast+/PLIST \
pkgsrc/biology/ncbi-blast+/buildlink3.mk
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/ncbi-blast+/distinfo
cvs rdiff -u -r1.1 -r1.2 \
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
cvs rdiff -u -r1.2 -r1.3 \
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:1.27 pkgsrc/biology/ncbi-blast+/Makefile:1.28
--- pkgsrc/biology/ncbi-blast+/Makefile:1.27 Wed Mar 16 00:32:01 2022
+++ pkgsrc/biology/ncbi-blast+/Makefile Sun Apr 10 20:54:51 2022
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.27 2022/03/16 00:32:01 bacon Exp $
+# $NetBSD: Makefile,v 1.28 2022/04/10 20:54:51 bacon Exp $
-DISTNAME= ncbi-blast-2.11.0+-src
+DISTNAME= ncbi-blast-2.13.0+-src
PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/}
-PKGREVISION= 2
CATEGORIES= biology
MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
@@ -48,6 +47,10 @@ WRKSRC= ${WRKDIR}/${DISTNAME}/c++
CONFIGURE_ENV+= ac_cv_func_statfs=no
.endif
+.if ${OPSYS} == Darwin
+CONFIGURE_ARGS+= --without-openmp
+.endif
+
# c++/src/objtools/edit/seq_entry_edit.cpp: In member function 'void ncbi::objects::edit::{anonymous}::CSeqdescSortMap::Init()':
# c++/src/objtools/edit/seq_entry_edit.cpp:172:44: error: array subscript has type 'char' [-Werror=char-subscripts]
# while (descr_insert_order[index] != 0)
Index: pkgsrc/biology/ncbi-blast+/PLIST
diff -u pkgsrc/biology/ncbi-blast+/PLIST:1.3 pkgsrc/biology/ncbi-blast+/PLIST:1.4
--- pkgsrc/biology/ncbi-blast+/PLIST:1.3 Fri Jun 11 13:47:39 2021
+++ pkgsrc/biology/ncbi-blast+/PLIST Sun Apr 10 20:54:51 2022
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2021/06/11 13:47:39 bacon Exp $
+@comment $NetBSD: PLIST,v 1.4 2022/04/10 20:54:51 bacon Exp $
bin/blast_formatter
bin/blast_report
bin/blastdb_aliastool
@@ -212,6 +212,12 @@ include/ncbi-tools++/algo/blast/proteink
include/ncbi-tools++/algo/blast/proteinkmer/blastkmerutils.hpp
include/ncbi-tools++/algo/blast/proteinkmer/kblastapi.hpp
include/ncbi-tools++/algo/blast/proteinkmer/mhfile.hpp
+include/ncbi-tools++/algo/blast/vdb/blastn_vdb_args.hpp
+include/ncbi-tools++/algo/blast/vdb/seqsrc_vdb.h
+include/ncbi-tools++/algo/blast/vdb/tblastn_vdb_args.hpp
+include/ncbi-tools++/algo/blast/vdb/vdb2blast_util.hpp
+include/ncbi-tools++/algo/blast/vdb/vdbalias.hpp
+include/ncbi-tools++/algo/blast/vdb/vdbblast_local.hpp
include/ncbi-tools++/algo/dustmask/sdust.tex
include/ncbi-tools++/algo/dustmask/symdust.hpp
include/ncbi-tools++/algo/segmask/segmask.hpp
@@ -258,6 +264,7 @@ include/ncbi-tools++/cgi/cgiapp.hpp
include/ncbi-tools++/cgi/cgiapp_cached.hpp
include/ncbi-tools++/cgi/cgictx.hpp
include/ncbi-tools++/cgi/error_codes.hpp
+include/ncbi-tools++/cgi/fcgiapp_mt.hpp
include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
include/ncbi-tools++/cgi/ncbicgi.hpp
include/ncbi-tools++/cgi/ncbicgir.hpp
@@ -280,6 +287,7 @@ include/ncbi-tools++/common/ncbi_package
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_sanitizers.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
@@ -290,6 +298,8 @@ include/ncbi-tools++/common/test_data_pa
include/ncbi-tools++/connect/connect_export.h
include/ncbi-tools++/connect/email_diag_handler.hpp
include/ncbi-tools++/connect/error_codes.hpp
+include/ncbi-tools++/connect/impl/connect_misc.hpp
+include/ncbi-tools++/connect/impl/ncbi_uv_nghttp2.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
@@ -309,6 +319,7 @@ include/ncbi-tools++/connect/ncbi_ftp_co
include/ncbi-tools++/connect/ncbi_gnutls.h
include/ncbi-tools++/connect/ncbi_heapmgr.h
include/ncbi-tools++/connect/ncbi_host_info.h
+include/ncbi-tools++/connect/ncbi_http2_session.hpp
include/ncbi-tools++/connect/ncbi_http_connector.h
include/ncbi-tools++/connect/ncbi_http_session.hpp
include/ncbi-tools++/connect/ncbi_iprange.h
@@ -427,6 +438,7 @@ include/ncbi-tools++/corelib/ncbi_messag
include/ncbi-tools++/corelib/ncbi_os_mswin.hpp
include/ncbi-tools++/corelib/ncbi_os_unix.hpp
include/ncbi-tools++/corelib/ncbi_param.hpp
+include/ncbi-tools++/corelib/ncbi_pool_balancer.hpp
include/ncbi-tools++/corelib/ncbi_process.hpp
include/ncbi-tools++/corelib/ncbi_safe_static.hpp
include/ncbi-tools++/corelib/ncbi_signal.hpp
@@ -494,7 +506,6 @@ 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
include/ncbi-tools++/dbapi/dbapi.hpp
include/ncbi-tools++/dbapi/dbapi_variant_convert.hpp
include/ncbi-tools++/dbapi/driver/dbapi_conn_factory.hpp
@@ -549,40 +560,10 @@ include/ncbi-tools++/html/page.hpp
include/ncbi-tools++/html/pager.hpp
include/ncbi-tools++/html/selection.hpp
include/ncbi-tools++/html/writer_htmlenc.hpp
+include/ncbi-tools++/misc/drmaa2.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
@@ -850,6 +831,8 @@ include/ncbi-tools++/objects/blastdb/.cv
include/ncbi-tools++/objects/blastdb/.gitignore
include/ncbi-tools++/objects/blastdb/Blast_db_mask_info.hpp
include/ncbi-tools++/objects/blastdb/Blast_db_mask_info_.hpp
+include/ncbi-tools++/objects/blastdb/Blast_db_metadata.hpp
+include/ncbi-tools++/objects/blastdb/Blast_db_metadata_.hpp
include/ncbi-tools++/objects/blastdb/Blast_def_line.hpp
include/ncbi-tools++/objects/blastdb/Blast_def_line_.hpp
include/ncbi-tools++/objects/blastdb/Blast_def_line_set.hpp
@@ -2311,6 +2294,36 @@ include/ncbi-tools++/objects/pcassay/PC_
include/ncbi-tools++/objects/pcassay/PC_ResultType.hpp
include/ncbi-tools++/objects/pcassay/PC_ResultType_.hpp
include/ncbi-tools++/objects/pcassay/pcassay__.hpp
+include/ncbi-tools++/objects/pcassay2/.cvsignore
+include/ncbi-tools++/objects/pcassay2/.gitignore
+include/ncbi-tools++/objects/pcassay2/NCBI_PCAssay2_module.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayContainer.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayContainer_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDRAttr.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDRAttr_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayData.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayData_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDescription.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayDescription_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayResults.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayResults_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssaySubmit.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssaySubmit_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayTargetInfo.hpp
+include/ncbi-tools++/objects/pcassay2/PC_AssayTargetInfo_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_CategorizedComment.hpp
+include/ncbi-tools++/objects/pcassay2/PC_CategorizedComment_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ConcentrationAttr.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ConcentrationAttr_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_IntegerMinMax.hpp
+include/ncbi-tools++/objects/pcassay2/PC_IntegerMinMax_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_RealMinMax.hpp
+include/ncbi-tools++/objects/pcassay2/PC_RealMinMax_.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ResultType.hpp
+include/ncbi-tools++/objects/pcassay2/PC_ResultType_.hpp
+include/ncbi-tools++/objects/pcassay2/pcassay2__.hpp
include/ncbi-tools++/objects/pcsubstance/.cvsignore
include/ncbi-tools++/objects/pcsubstance/.gitignore
include/ncbi-tools++/objects/pcsubstance/NCBI_PCSubstance_module.hpp
@@ -2330,6 +2343,8 @@ include/ncbi-tools++/objects/pcsubstance
include/ncbi-tools++/objects/pcsubstance/PC_BondType_.hpp
include/ncbi-tools++/objects/pcsubstance/PC_Bonds.hpp
include/ncbi-tools++/objects/pcsubstance/PC_Bonds_.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Bracket.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Bracket_.hpp
include/ncbi-tools++/objects/pcsubstance/PC_Compound.hpp
include/ncbi-tools++/objects/pcsubstance/PC_CompoundType.hpp
include/ncbi-tools++/objects/pcsubstance/PC_CompoundType_.hpp
@@ -2352,6 +2367,8 @@ include/ncbi-tools++/objects/pcsubstance
include/ncbi-tools++/objects/pcsubstance/PC_DrawAnnotations_.hpp
include/ncbi-tools++/objects/pcsubstance/PC_Element.hpp
include/ncbi-tools++/objects/pcsubstance/PC_Element_.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Group.hpp
+include/ncbi-tools++/objects/pcsubstance/PC_Group_.hpp
include/ncbi-tools++/objects/pcsubstance/PC_ID.hpp
include/ncbi-tools++/objects/pcsubstance/PC_ID_.hpp
include/ncbi-tools++/objects/pcsubstance/PC_InfoData.hpp
@@ -2573,7 +2590,6 @@ include/ncbi-tools++/objects/seq/seq_mac
include/ncbi-tools++/objects/seq/seqlocinfo.hpp
include/ncbi-tools++/objects/seq/seqport_util.hpp
include/ncbi-tools++/objects/seq/so_map.hpp
-include/ncbi-tools++/objects/seq/sofa_map.hpp
include/ncbi-tools++/objects/seq/sofa_type.hpp
include/ncbi-tools++/objects/seqalign/.cvsignore
include/ncbi-tools++/objects/seqalign/.gitignore
@@ -3552,7 +3568,6 @@ include/ncbi-tools++/objtools/blast/seqd
include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_isam.hpp
include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_lmdb.hpp
include/ncbi-tools++/objtools/blast/services/blast_services.hpp
-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
@@ -3594,6 +3609,7 @@ include/ncbi-tools++/objtools/data_loade
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/impl/wgsmaster.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
@@ -3634,6 +3650,7 @@ include/ncbi-tools++/objtools/edit/loc_e
include/ncbi-tools++/objtools/edit/mail_report.hpp
include/ncbi-tools++/objtools/edit/parse_text_options.hpp
include/ncbi-tools++/objtools/edit/promote.hpp
+include/ncbi-tools++/objtools/edit/pub_fix.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
@@ -3646,6 +3663,142 @@ include/ncbi-tools++/objtools/edit/struc
include/ncbi-tools++/objtools/edit/text_desc_field.hpp
include/ncbi-tools++/objtools/edit/text_object_description.hpp
include/ncbi-tools++/objtools/error_codes.hpp
+include/ncbi-tools++/objtools/eutils/api/efetch.hpp
+include/ncbi-tools++/objtools/eutils/api/egquery.hpp
+include/ncbi-tools++/objtools/eutils/api/ehistory.hpp
+include/ncbi-tools++/objtools/eutils/api/einfo.hpp
+include/ncbi-tools++/objtools/eutils/api/elink.hpp
+include/ncbi-tools++/objtools/eutils/api/epost.hpp
+include/ncbi-tools++/objtools/eutils/api/esearch.hpp
+include/ncbi-tools++/objtools/eutils/api/espell.hpp
+include/ncbi-tools++/objtools/eutils/api/esummary.hpp
+include/ncbi-tools++/objtools/eutils/api/eutils.hpp
+include/ncbi-tools++/objtools/eutils/egquery/.cvsignore
+include/ncbi-tools++/objtools/eutils/egquery/.gitignore
+include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult.hpp
+include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult_.hpp
+include/ncbi-tools++/objtools/eutils/egquery/Result.hpp
+include/ncbi-tools++/objtools/eutils/egquery/ResultItem.hpp
+include/ncbi-tools++/objtools/eutils/egquery/ResultItem_.hpp
+include/ncbi-tools++/objtools/eutils/egquery/Result_.hpp
+include/ncbi-tools++/objtools/eutils/egquery/egquery__.hpp
+include/ncbi-tools++/objtools/eutils/egquery/egquery_module.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/.cvsignore
+include/ncbi-tools++/objtools/eutils/ehistory/.gitignore
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem_.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult_.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/ehistory__.hpp
+include/ncbi-tools++/objtools/eutils/ehistory/ehistory_module.hpp
+include/ncbi-tools++/objtools/eutils/einfo/.cvsignore
+include/ncbi-tools++/objtools/eutils/einfo/.gitignore
+include/ncbi-tools++/objtools/eutils/einfo/DbInfo.hpp
+include/ncbi-tools++/objtools/eutils/einfo/DbInfo_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/DbList.hpp
+include/ncbi-tools++/objtools/eutils/einfo/DbList_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/EInfoResult.hpp
+include/ncbi-tools++/objtools/eutils/einfo/EInfoResult_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Field.hpp
+include/ncbi-tools++/objtools/eutils/einfo/FieldList.hpp
+include/ncbi-tools++/objtools/eutils/einfo/FieldList_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Field_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Link.hpp
+include/ncbi-tools++/objtools/eutils/einfo/LinkList.hpp
+include/ncbi-tools++/objtools/eutils/einfo/LinkList_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/Link_.hpp
+include/ncbi-tools++/objtools/eutils/einfo/einfo__.hpp
+include/ncbi-tools++/objtools/eutils/einfo/einfo_module.hpp
+include/ncbi-tools++/objtools/eutils/elink/.cvsignore
+include/ncbi-tools++/objtools/eutils/elink/.gitignore
+include/ncbi-tools++/objtools/eutils/elink/ELinkResult.hpp
+include/ncbi-tools++/objtools/eutils/elink/ELinkResult_.hpp
+include/ncbi-tools++/objtools/eutils/elink/FirstChars.hpp
+include/ncbi-tools++/objtools/eutils/elink/FirstChars_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IconUrl.hpp
+include/ncbi-tools++/objtools/eutils/elink/IconUrl_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Id.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdCheckList.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdCheckList_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdLinkSet.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdLinkSet_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdList.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdList_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlList.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlList_.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlSet.hpp
+include/ncbi-tools++/objtools/eutils/elink/IdUrlSet_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Id_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Link.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkInfo.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkInfo_.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSet.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDb.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDbHistory.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDbHistory_.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSetDb_.hpp
+include/ncbi-tools++/objtools/eutils/elink/LinkSet_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Link_.hpp
+include/ncbi-tools++/objtools/eutils/elink/ObjUrl.hpp
+include/ncbi-tools++/objtools/eutils/elink/ObjUrl_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Provider.hpp
+include/ncbi-tools++/objtools/eutils/elink/Provider_.hpp
+include/ncbi-tools++/objtools/eutils/elink/Url.hpp
+include/ncbi-tools++/objtools/eutils/elink/Url_.hpp
+include/ncbi-tools++/objtools/eutils/elink/elink__.hpp
+include/ncbi-tools++/objtools/eutils/elink/elink_module.hpp
+include/ncbi-tools++/objtools/eutils/epost/.cvsignore
+include/ncbi-tools++/objtools/eutils/epost/.gitignore
+include/ncbi-tools++/objtools/eutils/epost/EPostResult.hpp
+include/ncbi-tools++/objtools/eutils/epost/EPostResult_.hpp
+include/ncbi-tools++/objtools/eutils/epost/InvalidIdList.hpp
+include/ncbi-tools++/objtools/eutils/epost/InvalidIdList_.hpp
+include/ncbi-tools++/objtools/eutils/epost/epost__.hpp
+include/ncbi-tools++/objtools/eutils/epost/epost_module.hpp
+include/ncbi-tools++/objtools/eutils/esearch/.cvsignore
+include/ncbi-tools++/objtools/eutils/esearch/.gitignore
+include/ncbi-tools++/objtools/eutils/esearch/ESearchResult.hpp
+include/ncbi-tools++/objtools/eutils/esearch/ESearchResult_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/ErrorList.hpp
+include/ncbi-tools++/objtools/eutils/esearch/ErrorList_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/IdList.hpp
+include/ncbi-tools++/objtools/eutils/esearch/IdList_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TermSet.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TermSet_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/Translation.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationSet.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationSet_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationStack.hpp
+include/ncbi-tools++/objtools/eutils/esearch/TranslationStack_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/Translation_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/WarningList.hpp
+include/ncbi-tools++/objtools/eutils/esearch/WarningList_.hpp
+include/ncbi-tools++/objtools/eutils/esearch/esearch__.hpp
+include/ncbi-tools++/objtools/eutils/esearch/esearch_module.hpp
+include/ncbi-tools++/objtools/eutils/espell/.cvsignore
+include/ncbi-tools++/objtools/eutils/espell/.gitignore
+include/ncbi-tools++/objtools/eutils/espell/ESpellResult.hpp
+include/ncbi-tools++/objtools/eutils/espell/ESpellResult_.hpp
+include/ncbi-tools++/objtools/eutils/espell/SpelledQuery.hpp
+include/ncbi-tools++/objtools/eutils/espell/SpelledQuery_.hpp
+include/ncbi-tools++/objtools/eutils/espell/espell__.hpp
+include/ncbi-tools++/objtools/eutils/espell/espell_module.hpp
+include/ncbi-tools++/objtools/eutils/esummary/.cvsignore
+include/ncbi-tools++/objtools/eutils/esummary/.gitignore
+include/ncbi-tools++/objtools/eutils/esummary/DocSum.hpp
+include/ncbi-tools++/objtools/eutils/esummary/DocSum_.hpp
+include/ncbi-tools++/objtools/eutils/esummary/ESummaryResult.hpp
+include/ncbi-tools++/objtools/eutils/esummary/ESummaryResult_.hpp
+include/ncbi-tools++/objtools/eutils/esummary/Item.hpp
+include/ncbi-tools++/objtools/eutils/esummary/Item_.hpp
+include/ncbi-tools++/objtools/eutils/esummary/esummary__.hpp
+include/ncbi-tools++/objtools/eutils/esummary/esummary_module.hpp
+include/ncbi-tools++/objtools/eutils/uilist/.cvsignore
+include/ncbi-tools++/objtools/eutils/uilist/.gitignore
+include/ncbi-tools++/objtools/eutils/uilist/IdList.hpp
+include/ncbi-tools++/objtools/eutils/uilist/IdList_.hpp
+include/ncbi-tools++/objtools/eutils/uilist/uilist__.hpp
+include/ncbi-tools++/objtools/eutils/uilist/uilist_module.hpp
include/ncbi-tools++/objtools/format/cigar_formatter.hpp
include/ncbi-tools++/objtools/format/context.hpp
include/ncbi-tools++/objtools/format/embl_formatter.hpp
@@ -3723,10 +3876,9 @@ include/ncbi-tools++/objtools/readers/fo
include/ncbi-tools++/objtools/readers/getfeature.hpp
include/ncbi-tools++/objtools/readers/gff2_data.hpp
include/ncbi-tools++/objtools/readers/gff2_reader.hpp
+include/ncbi-tools++/objtools/readers/gff3_location_merger.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
include/ncbi-tools++/objtools/readers/gvf_reader.hpp
@@ -3737,6 +3889,7 @@ include/ncbi-tools++/objtools/readers/me
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/objhook_lambdas.hpp
include/ncbi-tools++/objtools/readers/phrap.hpp
include/ncbi-tools++/objtools/readers/psl_reader.hpp
include/ncbi-tools++/objtools/readers/read_util.hpp
@@ -3863,6 +4016,43 @@ include/ncbi-tools++/serial/serializable
include/ncbi-tools++/serial/serialutil.hpp
include/ncbi-tools++/serial/streamiter.hpp
include/ncbi-tools++/serial/typeinfo.hpp
+include/ncbi-tools++/sra/data_loaders/bam/bamloader.hpp
+include/ncbi-tools++/sra/data_loaders/bam/impl/bamloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/csra/csraloader.hpp
+include/ncbi-tools++/sra/data_loaders/csra/impl/csraloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/snp/id2snp.hpp
+include/ncbi-tools++/sra/data_loaders/snp/id2snp_entry.hpp
+include/ncbi-tools++/sra/data_loaders/snp/id2snp_params.h
+include/ncbi-tools++/sra/data_loaders/snp/impl/id2snp_impl.hpp
+include/ncbi-tools++/sra/data_loaders/snp/impl/snploader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/snp/snploader.hpp
+include/ncbi-tools++/sra/data_loaders/sra/impl/sraloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/sra/sraloader.hpp
+include/ncbi-tools++/sra/data_loaders/vdbgraph/impl/vdbgraphloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/vdbgraph/vdbgraphloader.hpp
+include/ncbi-tools++/sra/data_loaders/wgs/impl/wgsloader_impl.hpp
+include/ncbi-tools++/sra/data_loaders/wgs/wgsloader.hpp
+include/ncbi-tools++/sra/error_codes.hpp
+include/ncbi-tools++/sra/readers/bam/bamgraph.hpp
+include/ncbi-tools++/sra/readers/bam/bamindex.hpp
+include/ncbi-tools++/sra/readers/bam/bamread.hpp
+include/ncbi-tools++/sra/readers/bam/bamread_base.hpp
+include/ncbi-tools++/sra/readers/bam/bgzf.hpp
+include/ncbi-tools++/sra/readers/bam/cache_with_lock.hpp
+include/ncbi-tools++/sra/readers/bam/vdbfile.hpp
+include/ncbi-tools++/sra/readers/ncbi_traces_path.hpp
+include/ncbi-tools++/sra/readers/sra/csraread.hpp
+include/ncbi-tools++/sra/readers/sra/exception.hpp
+include/ncbi-tools++/sra/readers/sra/graphread.hpp
+include/ncbi-tools++/sra/readers/sra/impl/wgs-contig.h
+include/ncbi-tools++/sra/readers/sra/impl/wgsresolver_impl.hpp
+include/ncbi-tools++/sra/readers/sra/kdbread.hpp
+include/ncbi-tools++/sra/readers/sra/sdk.hpp
+include/ncbi-tools++/sra/readers/sra/snpread.hpp
+include/ncbi-tools++/sra/readers/sra/sraread.hpp
+include/ncbi-tools++/sra/readers/sra/vdbread.hpp
+include/ncbi-tools++/sra/readers/sra/wgsread.hpp
+include/ncbi-tools++/sra/readers/sra/wgsresolver.hpp
include/ncbi-tools++/util/align_range.hpp
include/ncbi-tools++/util/align_range_coll.hpp
include/ncbi-tools++/util/align_range_oper.hpp
@@ -3871,6 +4061,7 @@ 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/bm3vl.h
include/ncbi-tools++/util/bitset/bm64.h
include/ncbi-tools++/util/bitset/bmaggregator.h
include/ncbi-tools++/util/bitset/bmalgo.h
@@ -3884,6 +4075,7 @@ include/ncbi-tools++/util/bitset/bmbmatr
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/bmbvimport.h
include/ncbi-tools++/util/bitset/bmconst.h
include/ncbi-tools++/util/bitset/bmdbg.h
include/ncbi-tools++/util/bitset/bmdef.h
@@ -3898,12 +4090,15 @@ include/ncbi-tools++/util/bitset/bmsimd.
include/ncbi-tools++/util/bitset/bmsparsevec.h
include/ncbi-tools++/util/bitset/bmsparsevec_algo.h
include/ncbi-tools++/util/bitset/bmsparsevec_compr.h
+include/ncbi-tools++/util/bitset/bmsparsevec_parallel.h
include/ncbi-tools++/util/bitset/bmsparsevec_serial.h
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/bmtask.h
+include/ncbi-tools++/util/bitset/bmthreadpool.h
include/ncbi-tools++/util/bitset/bmtimer.h
include/ncbi-tools++/util/bitset/bmtrans.h
include/ncbi-tools++/util/bitset/bmundef.h
@@ -3955,7 +4150,11 @@ include/ncbi-tools++/util/histogram_binn
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/const_tuple.hpp
include/ncbi-tools++/util/impl/ct_crc32.hpp
+include/ncbi-tools++/util/impl/ct_string_cxx14.hpp
+include/ncbi-tools++/util/impl/ct_string_cxx17.hpp
+include/ncbi-tools++/util/impl/ctsort_cxx14.hpp
include/ncbi-tools++/util/impl/floating_point_comparison.hpp
include/ncbi-tools++/util/itransaction.hpp
include/ncbi-tools++/util/itree.hpp
@@ -3980,6 +4179,7 @@ include/ncbi-tools++/util/mutex_pool.hpp
include/ncbi-tools++/util/ncbi_cache.hpp
include/ncbi-tools++/util/ncbi_table.hpp
include/ncbi-tools++/util/ncbi_url.hpp
+include/ncbi-tools++/util/profile/rtprofile.hpp
include/ncbi-tools++/util/random_gen.hpp
include/ncbi-tools++/util/range.hpp
include/ncbi-tools++/util/range_coll.hpp
@@ -4041,6 +4241,7 @@ include/ncbi-tools++/util/value_convert_
include/ncbi-tools++/util/weakmap.hpp
include/ncbi-tools++/util/weakmap.inl
include/ncbi-tools++/util/xregexp/arg_regexp.hpp
+include/ncbi-tools++/util/xregexp/convert_dates_iso8601.hpp
include/ncbi-tools++/util/xregexp/mask_regexp.hpp
include/ncbi-tools++/util/xregexp/regexp.hpp
include/ncbi-tools++/util/xregexp/regexp_template_tester.hpp
@@ -4089,12 +4290,30 @@ lib/ncbi-tools++/libdbsnp_tooltip_servic
lib/ncbi-tools++/libdbsnp_tooltip_service.a
lib/ncbi-tools++/libdocsum-static.a
lib/ncbi-tools++/libdocsum.a
+lib/ncbi-tools++/libegquery-static.a
+lib/ncbi-tools++/libegquery.a
+lib/ncbi-tools++/libehistory-static.a
+lib/ncbi-tools++/libehistory.a
+lib/ncbi-tools++/libeinfo-static.a
+lib/ncbi-tools++/libeinfo.a
+lib/ncbi-tools++/libelink-static.a
+lib/ncbi-tools++/libelink.a
lib/ncbi-tools++/libentrez2-static.a
lib/ncbi-tools++/libentrez2.a
lib/ncbi-tools++/libentrez2cli-static.a
lib/ncbi-tools++/libentrez2cli.a
lib/ncbi-tools++/libentrezgene-static.a
lib/ncbi-tools++/libentrezgene.a
+lib/ncbi-tools++/libepost-static.a
+lib/ncbi-tools++/libepost.a
+lib/ncbi-tools++/libesearch-static.a
+lib/ncbi-tools++/libesearch.a
+lib/ncbi-tools++/libespell-static.a
+lib/ncbi-tools++/libespell.a
+lib/ncbi-tools++/libesummary-static.a
+lib/ncbi-tools++/libesummary.a
+lib/ncbi-tools++/libeutils-static.a
+lib/ncbi-tools++/libeutils.a
lib/ncbi-tools++/libfeatdef-static.a
lib/ncbi-tools++/libfeatdef.a
lib/ncbi-tools++/libgbproj-static.a
@@ -4147,9 +4366,6 @@ lib/ncbi-tools++/libmmdb-static.a
lib/ncbi-tools++/libmmdb.a
lib/ncbi-tools++/libncbi_xblobstorage_netcache-static.a
lib/ncbi-tools++/libncbi_xblobstorage_netcache.a
-lib/ncbi-tools++/libncbi_xcache_dbapi-dll.so
-lib/ncbi-tools++/libncbi_xcache_dbapi-static.a
-lib/ncbi-tools++/libncbi_xcache_dbapi.a
lib/ncbi-tools++/libncbi_xcache_netcache-dll.so
lib/ncbi-tools++/libncbi_xcache_netcache-static.a
lib/ncbi-tools++/libncbi_xcache_netcache.a
@@ -4185,6 +4401,8 @@ lib/ncbi-tools++/libomssa-static.a
lib/ncbi-tools++/libomssa.a
lib/ncbi-tools++/libpcassay-static.a
lib/ncbi-tools++/libpcassay.a
+lib/ncbi-tools++/libpcassay2-static.a
+lib/ncbi-tools++/libpcassay2.a
lib/ncbi-tools++/libpcsubstance-static.a
lib/ncbi-tools++/libpcsubstance.a
lib/ncbi-tools++/libproj-static.a
@@ -4243,6 +4461,10 @@ lib/ncbi-tools++/libtrackmgrcli-static.a
lib/ncbi-tools++/libtrackmgrcli.a
lib/ncbi-tools++/libtrackmgrgridcli-static.a
lib/ncbi-tools++/libtrackmgrgridcli.a
+lib/ncbi-tools++/libuilist-static.a
+lib/ncbi-tools++/libuilist.a
+lib/ncbi-tools++/libutrtprof-static.a
+lib/ncbi-tools++/libutrtprof.a
lib/ncbi-tools++/libvalerr-static.a
lib/ncbi-tools++/libvalerr.a
lib/ncbi-tools++/libvalid-static.a
Index: pkgsrc/biology/ncbi-blast+/buildlink3.mk
diff -u pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.3 pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.4
--- pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.3 Fri Jun 11 13:47:40 2021
+++ pkgsrc/biology/ncbi-blast+/buildlink3.mk Sun Apr 10 20:54:51 2022
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.3 2021/06/11 13:47:40 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.4 2022/04/10 20:54:51 bacon Exp $
BUILDLINK_TREE+= ncbi-blast+
.if !defined(NCBI_BLAST+_BUILDLINK3_MK)
NCBI_BLAST+_BUILDLINK3_MK:=
-BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.11.0
+BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.13.0
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:1.6 pkgsrc/biology/ncbi-blast+/distinfo:1.7
--- pkgsrc/biology/ncbi-blast+/distinfo:1.6 Tue Oct 26 10:03:41 2021
+++ pkgsrc/biology/ncbi-blast+/distinfo Sun Apr 10 20:54:51 2022
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.6 2021/10/26 10:03:41 nia Exp $
+$NetBSD: distinfo,v 1.7 2022/04/10 20:54:51 bacon Exp $
-BLAKE2s (ncbi-blast-2.11.0+-src.tar.gz) = 0f6acaa372e9ded638d6ec462fccb01f28028e0d4eb0b0f3eef26eda8c3fee6d
-SHA512 (ncbi-blast-2.11.0+-src.tar.gz) = 617994a0e3a4675a5f7048f165ac405bbd6a715ece9aba115d7c26b6be446b889b817dd496a2e15673545e5b594684c83fc4edb22cb5ecca2fd6d342c3bd642e
-Size (ncbi-blast-2.11.0+-src.tar.gz) = 58493096 bytes
+BLAKE2s (ncbi-blast-2.13.0+-src.tar.gz) = a83651c7f2824def1c86a8541cf7060ed77e6d60e8f7bd0383464088591733f3
+SHA512 (ncbi-blast-2.13.0+-src.tar.gz) = 7842ba4dac3d046a23cb182c6289d88cb1173e8570fb6334c1aa88dd2e640aacad43efe1ef7d69b8fedbf9b8093b7d601ef8999812d5735a6789ab2752e97c2b
+Size (ncbi-blast-2.13.0+-src.tar.gz) = 59995353 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
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.2
--- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.1 Fri Jun 11 13:47:40 2021
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh Sun Apr 10 20:54:51 2022
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.1 2021/06/11 13:47:40 bacon Exp $
+$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.2 2022/04/10 20:54:51 bacon Exp $
# Portability
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.2 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.3
--- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.2 Fri Jun 11 13:47:40 2021
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure Sun Apr 10 20:54:51 2022
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_build-system_configure,v 1.2 2021/06/11 13:47:40 bacon Exp $
+$NetBSD: patch-src_build-system_configure,v 1.3 2022/04/10 20:54:51 bacon Exp $
# Avert missing --with-libiconv-prefix option
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