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[pkgsrc/trunk]: pkgsrc/biology/ncbi-blast+ biology/ncbi-blast+: Update to 2.13.0
details: https://anonhg.NetBSD.org/pkgsrc/rev/082d6f8db012
branches: trunk
changeset: 376653:082d6f8db012
user: bacon <bacon%pkgsrc.org@localhost>
date: Sun Apr 10 20:54:51 2022 +0000
description:
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
diffstat:
biology/ncbi-blast+/Makefile | 9 +-
biology/ncbi-blast+/PLIST | 302 ++++++++-
biology/ncbi-blast+/buildlink3.mk | 4 +-
biology/ncbi-blast+/distinfo | 8 +-
biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh | 2 +-
biology/ncbi-blast+/patches/patch-src_build-system_configure | 2 +-
6 files changed, 276 insertions(+), 51 deletions(-)
diffs (truncated from 613 to 300 lines):
diff -r 6007b60f47d0 -r 082d6f8db012 biology/ncbi-blast+/Makefile
--- a/biology/ncbi-blast+/Makefile Sun Apr 10 20:35:26 2022 +0000
+++ b/biology/ncbi-blast+/Makefile Sun Apr 10 20:54:51 2022 +0000
@@ -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 @@
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)
diff -r 6007b60f47d0 -r 082d6f8db012 biology/ncbi-blast+/PLIST
--- a/biology/ncbi-blast+/PLIST Sun Apr 10 20:35:26 2022 +0000
+++ b/biology/ncbi-blast+/PLIST Sun Apr 10 20:54:51 2022 +0000
@@ -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/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_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_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++/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_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_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_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/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/.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_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/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/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/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/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_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/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/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
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