biology/ncbi-blast+: Upgrade to 2.11.0

A few bug fixes and performance improvements since 2.10.0
Also overcomes GCC 10 build issues

PR:             ports/246700
Reported by:    linimon

4 files changed, 34 insertions, 21 deletions

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index 4cefc9ec1f61..4da3f9e73a4b 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	ncbi-blast+
-DISTVERSION=	2.10.0
-PORTREVISION=	2
+DISTVERSION=	2.11.0
 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+/${PORTVERSION}/
@@ -48,6 +47,7 @@ GNU_CONFIGURE=	yes
 # --libdir=${PREFIX}/lib/ncbi-tools++ doesn't respect DESTDIR, so do
 # a postinstall mv.
 CONFIGURE_ARGS=	AR="ar cr" --without-boost --libdir=${PREFIX}/lib/ncbi-tools++
+LDFLAGS+=	-latomic
 
 WRKSRC_SUBDIR=		c++
 
diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
index 2ee82eb4d945..3be1e6d567eb 100644
--- a/biology/ncbi-blast+/distinfo
+++ b/biology/ncbi-blast+/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1577200099
-SHA256 (ncbi-blast-2.10.0+-src.tar.gz) = 3acdd9cec01c4f43e56aeaf89049cb8f8013d60b9c1705eced10166967f1d926
-SIZE (ncbi-blast-2.10.0+-src.tar.gz) = 25547460
+TIMESTAMP = 1605480828
+SHA256 (ncbi-blast-2.11.0+-src.tar.gz) = d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954
+SIZE (ncbi-blast-2.11.0+-src.tar.gz) = 58493096
diff --git a/biology/ncbi-blast+/files/patch-src_build-system_configure b/biology/ncbi-blast+/files/patch-src_build-system_configure
index 03a625d3dbe6..459391967cf2 100644
--- a/biology/ncbi-blast+/files/patch-src_build-system_configure
+++ b/biology/ncbi-blast+/files/patch-src_build-system_configure
@@ -1,6 +1,6 @@
---- src/build-system/configure.orig	2017-10-18 15:21:39 UTC
+--- src/build-system/configure.orig	2020-11-15 22:30:27 UTC
 +++ 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=* \
@@ -9,22 +9,12 @@
        | --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]* \
-@@ -1828,9 +1828,7 @@ Fine tuning of the installation director
-   --oldincludedir=DIR    C header files for non-gcc [/usr/include]
-   --datarootdir=DIR      read-only arch.-independent data root [PREFIX/share]
-   --datadir=DIR          read-only architecture-independent data [DATAROOTDIR]
--  --infodir=DIR          info documentation [DATAROOTDIR/info]
-   --localedir=DIR        locale-dependent data [DATAROOTDIR/locale]
--  --mandir=DIR           man documentation [DATAROOTDIR/man]
-   --docdir=DIR           documentation root [DATAROOTDIR/doc/ncbi-tools--]
-   --htmldir=DIR          html documentation [DOCDIR]
-   --dvidir=DIR           dvi documentation [DOCDIR]
-@@ -8086,7 +8084,7 @@ case "$host_os:$compiler" in
+@@ -9092,7 +9092,7 @@ case "$host_os:$compiler" in
  esac
  
  if test "$with_mt" != "no" ; then
 -   CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE"
-+   CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -D__RUNETYPE_INTERNAL"
++   CPPFLAGS="$CPPFLAGS -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL"
     LIBS="$LIBS $THREAD_LIBS"
     case "$host_os:$compiler" in
       solaris2.??:* | solaris*:GCC | *:Compaq | irix* | aix* | darwin* | cygwin*)
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index bd0ae1ba846d..87aa37184ba1 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -42,6 +42,7 @@ 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
@@ -52,6 +53,7 @@ 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
@@ -309,6 +311,7 @@ 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
@@ -330,6 +333,7 @@ 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
@@ -503,6 +507,7 @@ 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
@@ -1022,6 +1027,10 @@ 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
@@ -3476,6 +3485,7 @@ 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
@@ -3542,6 +3552,7 @@ 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/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
@@ -3686,6 +3697,7 @@ 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
@@ -3722,13 +3734,17 @@ 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
@@ -3752,6 +3768,8 @@ 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
@@ -3868,6 +3886,7 @@ 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
@@ -3886,6 +3905,7 @@ 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
@@ -3959,6 +3979,7 @@ 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
@@ -4053,13 +4074,13 @@ 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
@@ -4086,6 +4107,8 @@ 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