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Bacon" Date: Mon, 16 Nov 2020 18:25:03 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r555505 - in head/biology/ncbi-blast+: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/ncbi-blast+: . files X-SVN-Commit-Revision: 555505 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 16 Nov 2020 18:25:05 -0000 Author: jwb Date: Mon Nov 16 18:25:03 2020 New Revision: 555505 URL: https://svnweb.freebsd.org/changeset/ports/555505 Log: 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 Modified: head/biology/ncbi-blast+/Makefile head/biology/ncbi-blast+/distinfo head/biology/ncbi-blast+/files/patch-src_build-system_configure head/biology/ncbi-blast+/pkg-plist Modified: head/biology/ncbi-blast+/Makefile ============================================================================== --- head/biology/ncbi-blast+/Makefile Mon Nov 16 18:18:02 2020 (r555504) +++ head/biology/ncbi-blast+/Makefile Mon Nov 16 18:25:03 2020 (r555505) @@ -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=${PREFIX}/lib/ncbi-tools++ +LDFLAGS+= -latomic WRKSRC_SUBDIR= c++ Modified: head/biology/ncbi-blast+/distinfo ============================================================================== --- head/biology/ncbi-blast+/distinfo Mon Nov 16 18:18:02 2020 (r555504) +++ head/biology/ncbi-blast+/distinfo Mon Nov 16 18:25:03 2020 (r555505) @@ -1,3 +1,3 @@ -TIMESTAMP = 1577200099 -SHA256 (ncbi-blast-2.10.0+-src.tar.gz) = 3acdd9cec01c4f43e56aeaf89049cb8f8013d60b9c1705eced10166967f1d926 -SIZE (ncbi-blast-2.10.0+-src.tar.gz) = 25547460 +TIMESTAMP = 1605480828 +SHA256 (ncbi-blast-2.11.0+-src.tar.gz) = d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954 +SIZE (ncbi-blast-2.11.0+-src.tar.gz) = 58493096 Modified: head/biology/ncbi-blast+/files/patch-src_build-system_configure ============================================================================== --- head/biology/ncbi-blast+/files/patch-src_build-system_configure Mon Nov 16 18:18:02 2020 (r555504) +++ head/biology/ncbi-blast+/files/patch-src_build-system_configure Mon Nov 16 18:25:03 2020 (r555505) @@ -1,6 +1,6 @@ ---- src/build-system/configure.orig 2017-10-18 15:21:39 UTC +--- src/build-system/configure.orig 2020-11-15 22:30:27 UTC +++ src/build-system/configure -@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; 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*) Modified: head/biology/ncbi-blast+/pkg-plist ============================================================================== --- head/biology/ncbi-blast+/pkg-plist Mon Nov 16 18:18:02 2020 (r555504) +++ head/biology/ncbi-blast+/pkg-plist Mon Nov 16 18:25:03 2020 (r555505) @@ -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. 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. 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_Se 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_cl 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_reade 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