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Code Issues Releases Activity

biology/ncbi-blast+: Upgrade to 2.11.0

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

PR:             ports/246700
Reported by:    linimon
This commit is contained in:
Jason W. Bacon 2020-11-16 18:25:03 +00:00
parent 1bd23b5eb3
commit 2394925fbc
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=555505
4 changed files with 34 additions and 21 deletions
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4
biology/ncbi-blast+/Makefile
View File

@ -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++

6
biology/ncbi-blast+/distinfo
View File

@ -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

18
biology/ncbi-blast+/files/patch-src_build-system_configure
View File

@ -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*)

27
biology/ncbi-blast+/pkg-plist
View File

@ -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