biology/ncbi-blast+: Upgrade to 2.9.0

Fixes build issue with gcc9

PR:             238471
Reported by:    gerald

3 files changed, 78 insertions, 6 deletions

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index 365a726a6aa9..d2a451c39ea9 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	ncbi-blast+
-DISTVERSION=	2.8.1
-PORTREVISION=	2
+DISTVERSION=	2.9.0
 CATEGORIES=	biology perl5 python
 MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
 		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/
diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
index 49f31441580a..1722d26f693d 100644
--- a/biology/ncbi-blast+/distinfo
+++ b/biology/ncbi-blast+/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1545573763
-SHA256 (ncbi-blast-2.8.1+-src.tar.gz) = e03dd1a30e37cb8a859d3788a452c5d70ee1f9102d1ee0f93b2fbd145925118f
-SIZE (ncbi-blast-2.8.1+-src.tar.gz) = 24973554
+TIMESTAMP = 1560352108
+SHA256 (ncbi-blast-2.9.0+-src.tar.gz) = a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257
+SIZE (ncbi-blast-2.9.0+-src.tar.gz) = 25411110
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index e1b555036e92..5ff2fc12148d 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -1,6 +1,8 @@
 bin/blast_formatter
+bin/blast_report
 bin/blastdb_aliastool
 bin/blastdb_convert
+bin/blastdb_path
 bin/blastdbcheck
 bin/blastdbcmd
 bin/blastdbcp
@@ -534,6 +536,76 @@ 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
@@ -3463,7 +3535,8 @@ 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_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