Attachment 190787 Details for Bug 226037 – update to 2.7.1

[patch] update to 2.7.1

blast-2.7.1.diff.txt (text/plain), 15.41 KB, created by Wen Heping on 2018-02-19 10:53:11 UTC

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Creator: Wen Heping

Created: 2018-02-19 10:53:11 UTC

Size: 15.41 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 462150)
>+++ Makefile	(working copy)
>@@ -1,8 +1,7 @@
> # $FreeBSD$
> 
> PORTNAME=	blast+
>-PORTVERSION=	2.5.0
>-PORTREVISION=	2
>+PORTVERSION=	2.7.1
> CATEGORIES=	biology
> MASTER_SITES=	http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \
> 		http://acadix.biz/Ports/distfiles/
>@@ -15,7 +14,8 @@
> LICENSE=	PD
> LICENSE_FILE=	${WRKSRC}/scripts/projects/blast/LICENSE
> 
>-LIB_DEPENDS=	libpcre.so:devel/pcre
>+LIB_DEPENDS=	libpcre.so:devel/pcre \
>+		liblmdb.so:databases/lmdb
> RUN_DEPENDS=	p5-List-MoreUtils>=0:lang/p5-List-MoreUtils
> 
> WRKSRC=		${WRKDIR}/${DISTNAME}/c++
>Index: distinfo
>===================================================================
>--- distinfo	(revision 462150)
>+++ distinfo	(working copy)
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1480648908
>-SHA256 (ncbi-blast-2.5.0+-src.tar.gz) = cce122a29d309127a478353856b351914232e78a9546941781ff0a4c18ec9c54
>-SIZE (ncbi-blast-2.5.0+-src.tar.gz) = 19938544
>+TIMESTAMP = 1518995346
>+SHA256 (ncbi-blast-2.7.1+-src.tar.gz) = 10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca
>+SIZE (ncbi-blast-2.7.1+-src.tar.gz) = 23254824
>Index: files/patch-src_build-system_Makefile.in.top
>===================================================================
>--- files/patch-src_build-system_Makefile.in.top	(revision 462150)
>+++ files/patch-src_build-system_Makefile.in.top	(nonexistent)
>@@ -1,11 +0,0 @@
>---- src/build-system/Makefile.in.top.orig	2014-11-13 01:41:55.000000000 +0900
>-+++ src/build-system/Makefile.in.top	2016-12-02 16:39:58.415910000 +0900
>-@@ -51,7 +51,7 @@
>- 	    done
>- 	cd $(includedir0) && find * -name CVS -prune -o -print |\
>-             cpio -pd $(pincludedir)
>--	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)
>-+	cd $(incdir) && find * | cpio -pd $(pincludedir)
>- ## set up appropriate build and status directories somewhere under $(libdir)?
>- 
>- install-gbench:
>
>Property changes on: files/patch-src_build-system_Makefile.in.top
>___________________________________________________________________
>Deleted: fbsd:nokeywords
>## -1 +0,0 ##
>-yes
>\ No newline at end of property
>Deleted: svn:eol-style
>## -1 +0,0 ##
>-native
>\ No newline at end of property
>Deleted: svn:mime-type
>## -1 +0,0 ##
>-text/plain
>\ No newline at end of property
>Index: files/patch-src_build-system_configure
>===================================================================
>--- files/patch-src_build-system_configure	(revision 462150)
>+++ files/patch-src_build-system_configure	(working copy)
>@@ -1,9 +1,9 @@
>---- src/build-system/configure.orig	2016-09-09 21:04:16.000000000 +0900
>-+++ src/build-system/configure	2016-12-02 15:04:04.258800000 +0900
>-@@ -1715,7 +1715,7 @@
>-       | --silent | --cache-file=* | -C | --config-cache | -n | --no-create \
>-       | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \
>+--- src/build-system/configure.orig	2018-02-19 01:32:40 UTC
>++++ src/build-system/configure
>+@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do
>        | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
>+       | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
>+       | --datadir=* | --sysconfdir=* | --localstatedir=* \
> -      | --with-runpath=* | --with-relative-runpath=* \
> +      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
>        | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 462150)
>+++ pkg-plist	(working copy)
>@@ -10,6 +10,7 @@
> bin/datatool
> bin/deltablast
> bin/dustmasker
>+bin/gc_cli
> bin/gene_info_reader
> bin/legacy_blast.pl
> bin/makeblastdb
>@@ -45,6 +46,7 @@
> 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/blastp_kmer_options.hpp
> include/ncbi-tools++/algo/blast/api/blastx_options.hpp
> include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
> include/ncbi-tools++/algo/blast/api/deltablast.hpp
>@@ -105,6 +107,7 @@
> include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
> include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
> include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
>+include/ncbi-tools++/algo/blast/blastinput/kblastp_args.hpp
> include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp
> include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
> include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
>@@ -175,6 +178,7 @@
> include/ncbi-tools++/algo/blast/core/phi_extend.h
> include/ncbi-tools++/algo/blast/core/phi_gapalign.h
> include/ncbi-tools++/algo/blast/core/phi_lookup.h
>+include/ncbi-tools++/algo/blast/core/spliced_hits.h
> include/ncbi-tools++/algo/blast/core/split_query.h
> include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
> include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
>@@ -181,6 +185,7 @@
> include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
> include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
> include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
>+include/ncbi-tools++/algo/blast/format/blast_async_format.hpp
> include/ncbi-tools++/algo/blast/format/blast_format.hpp
> include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp
> include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
>@@ -191,6 +196,13 @@
> include/ncbi-tools++/algo/blast/format/sam.hpp
> include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
> include/ncbi-tools++/algo/blast/igblast/igblast.hpp
>+include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp
>+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp
>+include/ncbi-tools++/algo/blast/proteinkmer/blastkmeroptions.hpp
>+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp
>+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/dustmask/sdust.tex
> include/ncbi-tools++/algo/dustmask/symdust.hpp
> include/ncbi-tools++/algo/segmask/segmask.hpp
>@@ -284,7 +296,11 @@
> include/ncbi-tools++/connect/ncbi_host_info.h
> include/ncbi-tools++/connect/ncbi_http_connector.h
> include/ncbi-tools++/connect/ncbi_http_session.hpp
>+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_mbedtls.h
> include/ncbi-tools++/connect/ncbi_memory_connector.h
> include/ncbi-tools++/connect/ncbi_misc.hpp
> include/ncbi-tools++/connect/ncbi_monkey.hpp
>@@ -301,6 +317,7 @@
> include/ncbi-tools++/connect/ncbi_socket_connector.h
> 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_userhost.hpp
> include/ncbi-tools++/connect/ncbi_util.h
>@@ -327,6 +344,7 @@
> include/ncbi-tools++/connect/services/netcache_api.hpp
> include/ncbi-tools++/connect/services/netcache_api_expt.hpp
> include/ncbi-tools++/connect/services/netcache_key.hpp
>+include/ncbi-tools++/connect/services/netcache_search.hpp
> include/ncbi-tools++/connect/services/netcomponent.hpp
> include/ncbi-tools++/connect/services/neticache_client.hpp
> include/ncbi-tools++/connect/services/netschedule_api.hpp
>@@ -337,7 +355,6 @@
> include/ncbi-tools++/connect/services/netservice_protocol_parser.hpp
> include/ncbi-tools++/connect/services/netstorage.hpp
> include/ncbi-tools++/connect/services/netstorage_ft.hpp
>-include/ncbi-tools++/connect/services/netstorage_impl.hpp
> include/ncbi-tools++/connect/services/ns_client_factory.hpp
> include/ncbi-tools++/connect/services/ns_job_serializer.hpp
> include/ncbi-tools++/connect/services/ns_output_parser.hpp
>@@ -446,10 +463,13 @@
> include/ncbi-tools++/corelib/rwstream.hpp
> include/ncbi-tools++/corelib/stream_utils.hpp
> include/ncbi-tools++/corelib/syslog.hpp
>+include/ncbi-tools++/corelib/teamcity_messages.h
> include/ncbi-tools++/corelib/tempstr.hpp
> include/ncbi-tools++/corelib/test_boost.hpp
> include/ncbi-tools++/corelib/test_mt.hpp
> include/ncbi-tools++/corelib/version.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
>@@ -506,6 +526,7 @@
> include/ncbi-tools++/html/writer_htmlenc.hpp
> include/ncbi-tools++/misc/error_codes.hpp
> include/ncbi-tools++/ncbi_pch.hpp
>+include/ncbi-tools++/ncbi_random_macro.h
> include/ncbi-tools++/ncbi_source_ver.h
> include/ncbi-tools++/ncbiconf.h
> include/ncbi-tools++/ncbiconf_unix.h
>@@ -2422,6 +2443,7 @@
> include/ncbi-tools++/objects/seq/seq_macros.hpp
> 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
>@@ -2974,6 +2996,10 @@
> include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply_.hpp
> include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque.hpp
> include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque_.hpp
>+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply.hpp
>+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdReply_.hpp
>+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest.hpp
>+include/ncbi-tools++/objects/trackmgr/TMgr_SeqTrackIdRequest_.hpp
> include/ncbi-tools++/objects/trackmgr/TMgr_Status.hpp
> include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp
> include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp
>@@ -3012,6 +3038,7 @@
> include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp
> include/ncbi-tools++/objects/trackmgr/gridrpcclient.hpp
> include/ncbi-tools++/objects/trackmgr/item_resolver_client.hpp
>+include/ncbi-tools++/objects/trackmgr/primary_snp.hpp
> include/ncbi-tools++/objects/trackmgr/removeusertrack_client.hpp
> include/ncbi-tools++/objects/trackmgr/supported_assemblies_client.hpp
> include/ncbi-tools++/objects/trackmgr/switch_context_client.hpp
>@@ -3237,8 +3264,18 @@
> include/ncbi-tools++/objmgr/table_field.hpp
> include/ncbi-tools++/objmgr/tse_handle.hpp
> include/ncbi-tools++/objmgr/unsupp_editsaver.hpp
>+include/ncbi-tools++/objmgr/util/autodef.hpp
>+include/ncbi-tools++/objmgr/util/autodef_available_modifier.hpp
>+include/ncbi-tools++/objmgr/util/autodef_feature_clause.hpp
>+include/ncbi-tools++/objmgr/util/autodef_feature_clause_base.hpp
>+include/ncbi-tools++/objmgr/util/autodef_mod_combo.hpp
>+include/ncbi-tools++/objmgr/util/autodef_options.hpp
>+include/ncbi-tools++/objmgr/util/autodef_source_desc.hpp
>+include/ncbi-tools++/objmgr/util/autodef_source_group.hpp
> include/ncbi-tools++/objmgr/util/create_defline.hpp
> include/ncbi-tools++/objmgr/util/feature.hpp
>+include/ncbi-tools++/objmgr/util/feature_edit.hpp
>+include/ncbi-tools++/objmgr/util/indexer.hpp
> include/ncbi-tools++/objmgr/util/obj_sniff.hpp
> include/ncbi-tools++/objmgr/util/objutil.hpp
> include/ncbi-tools++/objmgr/util/seq_align_util.hpp
>@@ -3290,6 +3327,7 @@
> include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_formatter.hpp
> include/ncbi-tools++/objtools/blast/blastdb_format/blastdb_seqid.hpp
> include/ncbi-tools++/objtools/blast/blastdb_format/invalid_data_exception.hpp
>+include/ncbi-tools++/objtools/blast/blastdb_format/seq_formatter.hpp
> include/ncbi-tools++/objtools/blast/blastdb_format/seq_writer.hpp
> include/ncbi-tools++/objtools/blast/gene_info_reader/file_utils.hpp
> include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp
>@@ -3372,13 +3410,9 @@
> include/ncbi-tools++/objtools/data_loaders/loaders.hpp
> include/ncbi-tools++/objtools/edit/apply_object.hpp
> include/ncbi-tools++/objtools/edit/autodef.hpp
>-include/ncbi-tools++/objtools/edit/autodef_available_modifier.hpp
>-include/ncbi-tools++/objtools/edit/autodef_feature_clause.hpp
>-include/ncbi-tools++/objtools/edit/autodef_feature_clause_base.hpp
>-include/ncbi-tools++/objtools/edit/autodef_mod_combo.hpp
> include/ncbi-tools++/objtools/edit/autodef_options.hpp
> include/ncbi-tools++/objtools/edit/autodef_source_desc.hpp
>-include/ncbi-tools++/objtools/edit/autodef_source_group.hpp
>+include/ncbi-tools++/objtools/edit/autodef_with_tax.hpp
> include/ncbi-tools++/objtools/edit/capitalization_string.hpp
> include/ncbi-tools++/objtools/edit/cds_fix.hpp
> include/ncbi-tools++/objtools/edit/dblink_field.hpp
>@@ -3385,6 +3419,7 @@
> include/ncbi-tools++/objtools/edit/edit_exception.hpp
> include/ncbi-tools++/objtools/edit/feattable_edit.hpp
> include/ncbi-tools++/objtools/edit/field_handler.hpp
>+include/ncbi-tools++/objtools/edit/gap_trim.hpp
> include/ncbi-tools++/objtools/edit/gaps_edit.hpp
> include/ncbi-tools++/objtools/edit/gb_block_field.hpp
> include/ncbi-tools++/objtools/edit/gene_utils.hpp
>@@ -3420,9 +3455,6 @@
> include/ncbi-tools++/objtools/format/gbseq_formatter.hpp
> include/ncbi-tools++/objtools/format/genbank_formatter.hpp
> include/ncbi-tools++/objtools/format/genbank_gather.hpp
>-include/ncbi-tools++/objtools/format/gff3_formatter.hpp
>-include/ncbi-tools++/objtools/format/gff_formatter.hpp
>-include/ncbi-tools++/objtools/format/gff_gather.hpp
> include/ncbi-tools++/objtools/format/item_formatter.hpp
> include/ncbi-tools++/objtools/format/item_ostream.hpp
> include/ncbi-tools++/objtools/format/items/accession_item.hpp
>@@ -3470,6 +3502,7 @@
> include/ncbi-tools++/objtools/readers/error_container.hpp
> include/ncbi-tools++/objtools/readers/fasta.hpp
> include/ncbi-tools++/objtools/readers/fasta_exception.hpp
>+include/ncbi-tools++/objtools/readers/fasta_reader_utils.hpp
> include/ncbi-tools++/objtools/readers/featuredump.hpp
> include/ncbi-tools++/objtools/readers/format_guess_ex.hpp
> include/ncbi-tools++/objtools/readers/getfeature.hpp
>@@ -3495,6 +3528,7 @@
> include/ncbi-tools++/objtools/readers/rm_reader.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
> include/ncbi-tools++/objtools/readers/table_filter.hpp
> include/ncbi-tools++/objtools/readers/track_data.hpp
> include/ncbi-tools++/objtools/readers/ucscregion_reader.hpp
>@@ -3624,6 +3658,9 @@
> include/ncbi-tools++/util/bitset/bmgamma.h
> include/ncbi-tools++/util/bitset/bmrandom.h
> include/ncbi-tools++/util/bitset/bmserial.h
>+include/ncbi-tools++/util/bitset/bmsparsevec.h
>+include/ncbi-tools++/util/bitset/bmsparsevec_algo.h
>+include/ncbi-tools++/util/bitset/bmsparsevec_serial.h
> include/ncbi-tools++/util/bitset/bmsse2.h
> include/ncbi-tools++/util/bitset/bmsse4.h
> include/ncbi-tools++/util/bitset/bmsse_util.h
>@@ -3709,6 +3746,14 @@
> include/ncbi-tools++/util/resize_iter.hpp
> include/ncbi-tools++/util/resource_pool.hpp
> include/ncbi-tools++/util/retry_ctx.hpp
>+include/ncbi-tools++/util/row_reader.hpp
>+include/ncbi-tools++/util/row_reader.inl
>+include/ncbi-tools++/util/row_reader_base.hpp
>+include/ncbi-tools++/util/row_reader_char_delimited.hpp
>+include/ncbi-tools++/util/row_reader_excel_csv.hpp
>+include/ncbi-tools++/util/row_reader_iana_csv.hpp
>+include/ncbi-tools++/util/row_reader_iana_tsv.hpp
>+include/ncbi-tools++/util/row_reader_ncbi_tsv.hpp
> include/ncbi-tools++/util/scheduler.hpp
> include/ncbi-tools++/util/sequtil/sequtil.hpp
> include/ncbi-tools++/util/sequtil/sequtil_convert.hpp
>@@ -3887,6 +3932,8 @@
> lib/libpcsubstance.a
> lib/libproj-static.a
> lib/libproj.a
>+lib/libproteinkmer-static.a
>+lib/libproteinkmer.a
> lib/libpub-static.a
> lib/libpub.a
> lib/libpubmed-static.a

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Attachments on bug 226037: 190787