Received: by mail.netbsd.org (Postfix, from userid 605) id 9A7EC84DD6; Mon, 7 Jan 2019 15:00:13 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 176EA84DC7 for ; Mon, 7 Jan 2019 15:00:13 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id 22WR83MooYkb for ; Mon, 7 Jan 2019 15:00:11 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 3981884CD8 for ; Mon, 7 Jan 2019 15:00:11 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 33D2CFB16; Mon, 7 Jan 2019 15:00:11 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1546873211180170" MIME-Version: 1.0 Date: Mon, 7 Jan 2019 15:00:11 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/ncbi-blast+ To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20190107150011.33D2CFB16@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1546873211180170 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Mon Jan 7 15:00:11 UTC 2019 Modified Files: pkgsrc/biology/ncbi-blast+: Makefile PLIST distinfo pkgsrc/biology/ncbi-blast+/patches: patch-src_algo_blast_core_blast__kappa.c Added Files: pkgsrc/biology/ncbi-blast+/patches: patch-src_build-system_cmake_cmake-cfg-unix.sh patch-src_util_checksum_farmhash_farmhash.h Log Message: ncbi-blast+: Upgrade to 2.8.1 Support for new BLAST database format Increased makeblastdb output file size limit to 4GB Other minor bug fixes and enhancements OK wiz@ To generate a diff of this commit: cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/ncbi-blast+/Makefile cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/ncbi-blast+/PLIST cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/ncbi-blast+/distinfo cvs rdiff -u -r1.1 -r1.2 \ pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c cvs rdiff -u -r0 -r1.1 \ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh \ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1546873211180170 Content-Disposition: inline Content-Length: 29056 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/ncbi-blast+/Makefile diff -u pkgsrc/biology/ncbi-blast+/Makefile:1.5 pkgsrc/biology/ncbi-blast+/Makefile:1.6 --- pkgsrc/biology/ncbi-blast+/Makefile:1.5 Sun Dec 9 18:52:17 2018 +++ pkgsrc/biology/ncbi-blast+/Makefile Mon Jan 7 15:00:10 2019 @@ -1,11 +1,10 @@ -# $NetBSD: Makefile,v 1.5 2018/12/09 18:52:17 adam Exp $ +# $NetBSD: Makefile,v 1.6 2019/01/07 15:00:10 bacon Exp $ -DISTNAME= ncbi-blast-${PV}+-src -PKGNAME= ncbi-blast+-${PV} -PKGREVISION= 3 +DISTNAME= ncbi-blast-2.8.1+-src +PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/} CATEGORIES= biology MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ - https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/ + https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/ MAINTAINER= bacon@NetBSD.org HOMEPAGE= http://blast.ncbi.nlm.nih.gov/ @@ -21,10 +20,11 @@ SUBST_SED.configure+= -e '/--infodir=DIR SUBST_SED.configure+= -e '/--mandir=DIR/d' SUBST_FILES.configure+= ${WRKSRC}/src/build-system/configure -USE_TOOLS+= gmake +USE_TOOLS+= bash gmake USE_LANGUAGES= c c++ GNU_CONFIGURE= yes -# REPLACE_BASH= compilers/xcode30_prj/configure +REPLACE_BASH= scripts/common/impl/define_random_macros.sh +REPLACE_BASH+= src/app/blast/get_species_taxids.sh REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py @@ -34,7 +34,6 @@ REPLACE_PYTHON= src/app/winmasker/window CONFIGURE_ENV= ncbi_cv_prog_amq_w=no CONFIGURE_ARGS+= AR="ar cr" --without-boost CONFIGURE_ARGS+= --libdir=${PREFIX}/lib/ncbi-tools++ -# MAKE_JOBS_SAFE= no # Intermittent issues WRKSRC= ${WRKDIR}/${DISTNAME}/c++ .include "../../mk/bsd.prefs.mk" @@ -45,8 +44,6 @@ WRKSRC= ${WRKDIR}/${DISTNAME}/c++ CONFIGURE_ENV+= ac_cv_func_statfs=no .endif -PV= 2.7.1 - post-install: ${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra ${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so Index: pkgsrc/biology/ncbi-blast+/PLIST diff -u pkgsrc/biology/ncbi-blast+/PLIST:1.1 pkgsrc/biology/ncbi-blast+/PLIST:1.2 --- pkgsrc/biology/ncbi-blast+/PLIST:1.1 Fri Apr 27 20:28:28 2018 +++ pkgsrc/biology/ncbi-blast+/PLIST Mon Jan 7 15:00:10 2019 @@ -1,6 +1,7 @@ -@comment $NetBSD: PLIST,v 1.1 2018/04/27 20:28:28 bacon Exp $ +@comment $NetBSD: PLIST,v 1.2 2019/01/07 15:00:10 bacon Exp $ bin/blast_formatter bin/blastdb_aliastool +bin/blastdb_convert bin/blastdbcheck bin/blastdbcmd bin/blastdbcp @@ -13,7 +14,9 @@ bin/deltablast bin/dustmasker bin/gc_cli bin/gene_info_reader +bin/get_species_taxids.sh bin/legacy_blast.pl +bin/lmdbxx_sample bin/makeblastdb bin/makembindex bin/makeprofiledb @@ -258,10 +261,12 @@ include/ncbi-tools++/cgi/ref_args.hpp include/ncbi-tools++/cgi/user_agent.hpp include/ncbi-tools++/common/boost_skew_guard.hpp include/ncbi-tools++/common/config/ncbiconf_msvc.h +include/ncbi-tools++/common/config/ncbiconf_msvc_site.h.in include/ncbi-tools++/common/config/ncbiconf_universal.h include/ncbi-tools++/common/config/ncbiconf_xcode.h include/ncbi-tools++/common/header_template.hpp include/ncbi-tools++/common/metamodules_doxygen.h +include/ncbi-tools++/common/ncbi_build_info.h include/ncbi-tools++/common/ncbi_build_ver.h include/ncbi-tools++/common/ncbi_build_ver.h.in include/ncbi-tools++/common/ncbi_build_ver.h.last @@ -269,6 +274,7 @@ include/ncbi-tools++/common/ncbi_export. include/ncbi-tools++/common/ncbi_package_ver.h include/ncbi-tools++/common/ncbi_pch_impl.hpp include/ncbi-tools++/common/ncbi_skew_guard.h +include/ncbi-tools++/common/ncbi_source_ver.cmake_nodep include/ncbi-tools++/common/ncbi_source_ver.h include/ncbi-tools++/common/ncbiconf_impl.h include/ncbi-tools++/common/test_assert.h @@ -313,6 +319,7 @@ include/ncbi-tools++/connect/ncbi_sendma include/ncbi-tools++/connect/ncbi_server_info.h include/ncbi-tools++/connect/ncbi_service.h include/ncbi-tools++/connect/ncbi_service_connector.h +include/ncbi-tools++/connect/ncbi_service_cxx.hpp include/ncbi-tools++/connect/ncbi_socket.h include/ncbi-tools++/connect/ncbi_socket.hpp include/ncbi-tools++/connect/ncbi_socket_connector.h @@ -335,6 +342,7 @@ include/ncbi-tools++/connect/services/gr include/ncbi-tools++/connect/services/grid_rw_impl.hpp include/ncbi-tools++/connect/services/grid_worker.hpp include/ncbi-tools++/connect/services/grid_worker_app.hpp +include/ncbi-tools++/connect/services/impl/netcache_api_int.hpp include/ncbi-tools++/connect/services/impl/neticache_client_int.hpp include/ncbi-tools++/connect/services/impl/netschedule_api_int.hpp include/ncbi-tools++/connect/services/impl/netstorage_impl.hpp @@ -400,6 +408,7 @@ include/ncbi-tools++/corelib/ncbi_base64 include/ncbi-tools++/corelib/ncbi_bswap.hpp include/ncbi-tools++/corelib/ncbi_config.hpp include/ncbi-tools++/corelib/ncbi_cookies.hpp +include/ncbi-tools++/corelib/ncbi_fast.hpp include/ncbi-tools++/corelib/ncbi_limits.h include/ncbi-tools++/corelib/ncbi_limits.hpp include/ncbi-tools++/corelib/ncbi_mask.hpp @@ -1200,28 +1209,20 @@ include/ncbi-tools++/objects/genomecoll/ include/ncbi-tools++/objects/genomecoll/GCClient_AssemblyInfo_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI.hpp include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl.hpp include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_Error.hpp include/ncbi-tools++/objects/genomecoll/GCClient_Error_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyF.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyF_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ_.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques.hpp -include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse.hpp include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse_.hpp include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo.hpp include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo_.hpp +include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLx.hpp +include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLx_.hpp include/ncbi-tools++/objects/genomecoll/GC_Assemblies.hpp include/ncbi-tools++/objects/genomecoll/GC_Assemblies_.hpp include/ncbi-tools++/objects/genomecoll/GC_Assembly.hpp @@ -2923,6 +2924,7 @@ include/ncbi-tools++/objects/taxon1/Taxo include/ncbi-tools++/objects/taxon1/Taxon1_resp_.hpp include/ncbi-tools++/objects/taxon1/Taxon2_data.hpp include/ncbi-tools++/objects/taxon1/Taxon2_data_.hpp +include/ncbi-tools++/objects/taxon1/local_taxon.hpp include/ncbi-tools++/objects/taxon1/taxon1.hpp include/ncbi-tools++/objects/taxon1/taxon1__.hpp include/ncbi-tools++/objects/taxon3/.cvsignore @@ -2991,6 +2993,10 @@ include/ncbi-tools++/objects/trackmgr/TM include/ncbi-tools++/objects/trackmgr/TMgr_BlastRIDRequest_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRepl.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRepl_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRequ.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_CreateRemoteTrackRequ_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetRequest.hpp @@ -3001,6 +3007,8 @@ include/ncbi-tools++/objects/trackmgr/TM include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReply_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReques.hpp include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReques_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_DHubId.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_DHubId_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_DTrackId.hpp include/ncbi-tools++/objects/trackmgr/TMgr_DTrackId_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_DatasetItem.hpp @@ -3017,6 +3025,10 @@ include/ncbi-tools++/objects/trackmgr/TM include/ncbi-tools++/objects/trackmgr/TMgr_DisplayTrack_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_GenomeContext.hpp include/ncbi-tools++/objects/trackmgr/TMgr_GenomeContext_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_Hub.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_HubTrack.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_HubTrack_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_Hub_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Identity.hpp include/ncbi-tools++/objects/trackmgr/TMgr_IdentityId.hpp include/ncbi-tools++/objects/trackmgr/TMgr_IdentityIdType.hpp @@ -3041,6 +3053,8 @@ include/ncbi-tools++/objects/trackmgr/TM include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserTrackReques_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio.hpp include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectix.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectix_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Reply.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Reply_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_Request.hpp @@ -3057,6 +3071,8 @@ include/ncbi-tools++/objects/trackmgr/TM include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRx.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRx_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextReq.hpp @@ -3083,9 +3099,12 @@ include/ncbi-tools++/objects/trackmgr/TM include/ncbi-tools++/objects/trackmgr/TMgr_TrackSet_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat.hpp include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat_.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_TypeTrackType.hpp +include/ncbi-tools++/objects/trackmgr/TMgr_TypeTrackType_.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest_.hpp include/ncbi-tools++/objects/trackmgr/blast_client.hpp +include/ncbi-tools++/objects/trackmgr/createremotetrack_client.hpp include/ncbi-tools++/objects/trackmgr/createtrackset_client.hpp include/ncbi-tools++/objects/trackmgr/createusertrack_client.hpp include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp @@ -3141,6 +3160,30 @@ include/ncbi-tools++/objects/variation/V include/ncbi-tools++/objects/variation/VariationMethod_.hpp include/ncbi-tools++/objects/variation/Variation_.hpp include/ncbi-tools++/objects/variation/variation__.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.cvsignore +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/.gitignore +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Error_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/NCBI_search_by_rsid_module.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Placement.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/Placement_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/SearchByRsIdReply_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/search_by_rsid/search_by_rsid__.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.cvsignore +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/.gitignore +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipData_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSection.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSectionValue.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSectionValue_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipSection_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceError.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceError_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceReply.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/DbsnpTooltipServiceReply_.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/NCBI_dbsnp_tooltips_module.hpp +include/ncbi-tools++/objects/variation_libs/dbsnp/tooltip_service/dbsnp_tooltip_service__.hpp include/ncbi-tools++/objects/varrep/.cvsignore include/ncbi-tools++/objects/varrep/.gitignore include/ncbi-tools++/objects/varrep/AaInterval.hpp @@ -3390,6 +3433,8 @@ include/ncbi-tools++/objtools/blast/gene include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info.hpp include/ncbi-tools++/objtools/blast/gene_info_reader/gene_info_reader.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/column_reader.hpp +include/ncbi-tools++/objtools/blast/seqdb_reader/impl/lmdb++.h +include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbatlas.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbcol.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/impl/seqdbfile.hpp @@ -3401,9 +3446,11 @@ include/ncbi-tools++/objtools/blast/seqd include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbblob.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbcommon.hpp include/ncbi-tools++/objtools/blast/seqdb_reader/seqdbexpert.hpp +include/ncbi-tools++/objtools/blast/seqdb_reader/seqidlist_reader.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/build_db.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/impl/criteria.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/multisource_util.hpp +include/ncbi-tools++/objtools/blast/seqdb_writer/seqidlist_writer.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/taxid_set.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_convert.hpp @@ -3411,8 +3458,10 @@ include/ncbi-tools++/objtools/blast/seqd include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_files.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_general.hpp include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_isam.hpp +include/ncbi-tools++/objtools/blast/seqdb_writer/writedb_lmdb.hpp include/ncbi-tools++/objtools/blast/services/blast_services.hpp 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 @@ -3465,6 +3514,7 @@ include/ncbi-tools++/objtools/data_loade include/ncbi-tools++/objtools/data_loaders/genbank/writer.hpp include/ncbi-tools++/objtools/data_loaders/genbank/writer_interface.hpp include/ncbi-tools++/objtools/data_loaders/loaders.hpp +include/ncbi-tools++/objtools/edit/apply_mods.hpp include/ncbi-tools++/objtools/edit/apply_object.hpp include/ncbi-tools++/objtools/edit/autodef.hpp include/ncbi-tools++/objtools/edit/autodef_options.hpp @@ -3473,8 +3523,11 @@ include/ncbi-tools++/objtools/edit/autod include/ncbi-tools++/objtools/edit/capitalization_string.hpp include/ncbi-tools++/objtools/edit/cds_fix.hpp include/ncbi-tools++/objtools/edit/dblink_field.hpp +include/ncbi-tools++/objtools/edit/edit_error.hpp include/ncbi-tools++/objtools/edit/edit_exception.hpp +include/ncbi-tools++/objtools/edit/external_annots.hpp include/ncbi-tools++/objtools/edit/feattable_edit.hpp +include/ncbi-tools++/objtools/edit/feature_propagate.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 @@ -3494,6 +3547,7 @@ include/ncbi-tools++/objtools/edit/sourc include/ncbi-tools++/objtools/edit/string_constraint.hpp include/ncbi-tools++/objtools/edit/struc_comm_field.hpp include/ncbi-tools++/objtools/edit/text_desc_field.hpp +include/ncbi-tools++/objtools/edit/text_object_description.hpp include/ncbi-tools++/objtools/error_codes.hpp include/ncbi-tools++/objtools/format/cigar_formatter.hpp include/ncbi-tools++/objtools/format/context.hpp @@ -3548,6 +3602,8 @@ include/ncbi-tools++/objtools/format/ite include/ncbi-tools++/objtools/format/ostream_text_ostream.hpp 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/readers/agp_converter.hpp include/ncbi-tools++/objtools/readers/agp_read.hpp include/ncbi-tools++/objtools/readers/agp_seq_entry.hpp @@ -3705,8 +3761,11 @@ include/ncbi-tools++/util/bitset/bitset_ include/ncbi-tools++/util/bitset/bm.h include/ncbi-tools++/util/bitset/bmalgo.h include/ncbi-tools++/util/bitset/bmalgo_impl.h +include/ncbi-tools++/util/bitset/bmalgo_similarity.h include/ncbi-tools++/util/bitset/bmalloc.h +include/ncbi-tools++/util/bitset/bmavx2.h include/ncbi-tools++/util/bitset/bmblocks.h +include/ncbi-tools++/util/bitset/bmbuffer.h include/ncbi-tools++/util/bitset/bmconst.h include/ncbi-tools++/util/bitset/bmdbg.h include/ncbi-tools++/util/bitset/bmdef.h @@ -3715,12 +3774,16 @@ include/ncbi-tools++/util/bitset/bmfwd.h 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/bmsimd.h include/ncbi-tools++/util/bitset/bmsparsevec.h include/ncbi-tools++/util/bitset/bmsparsevec_algo.h +include/ncbi-tools++/util/bitset/bmsparsevec_compr.h include/ncbi-tools++/util/bitset/bmsparsevec_serial.h +include/ncbi-tools++/util/bitset/bmsparsevec_util.h include/ncbi-tools++/util/bitset/bmsse2.h include/ncbi-tools++/util/bitset/bmsse4.h include/ncbi-tools++/util/bitset/bmsse_util.h +include/ncbi-tools++/util/bitset/bmtimer.h include/ncbi-tools++/util/bitset/bmtrans.h include/ncbi-tools++/util/bitset/bmundef.h include/ncbi-tools++/util/bitset/bmutil.h @@ -3733,6 +3796,7 @@ include/ncbi-tools++/util/bitset/ncbi_bi include/ncbi-tools++/util/bitset/readme include/ncbi-tools++/util/buffer_writer.hpp include/ncbi-tools++/util/bytesrc.hpp +include/ncbi-tools++/util/cache/cache_async.hpp include/ncbi-tools++/util/cache/cache_ref.hpp include/ncbi-tools++/util/cache/icache.hpp include/ncbi-tools++/util/cache/icache_cf.hpp @@ -3774,6 +3838,8 @@ include/ncbi-tools++/util/lightstr.hpp include/ncbi-tools++/util/limited_size_map.hpp include/ncbi-tools++/util/line_reader.hpp include/ncbi-tools++/util/linkedset.hpp +include/ncbi-tools++/util/lmdb/lmdb.h +include/ncbi-tools++/util/lmdbxx/lmdb++.h include/ncbi-tools++/util/lock_vector.hpp include/ncbi-tools++/util/logrotate.hpp include/ncbi-tools++/util/mask_regexp.hpp @@ -3783,6 +3849,7 @@ include/ncbi-tools++/util/math/promote.h include/ncbi-tools++/util/md5.hpp include/ncbi-tools++/util/miscmath.h include/ncbi-tools++/util/multi_writer.hpp +include/ncbi-tools++/util/multipattern_search.hpp include/ncbi-tools++/util/mutex_pool.hpp include/ncbi-tools++/util/ncbi_cache.hpp include/ncbi-tools++/util/ncbi_table.hpp @@ -3891,6 +3958,8 @@ 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_tooltip_service-static.a +lib/ncbi-tools++/libdbsnp_tooltip_service.a lib/ncbi-tools++/libdocsum-static.a lib/ncbi-tools++/libdocsum.a lib/ncbi-tools++/libentrez2-static.a @@ -3931,6 +4000,8 @@ lib/ncbi-tools++/libigblast-static.a lib/ncbi-tools++/libigblast.a lib/ncbi-tools++/libinsdseq-static.a lib/ncbi-tools++/libinsdseq.a +lib/ncbi-tools++/liblocal_taxon-static.a +lib/ncbi-tools++/liblocal_taxon.a lib/ncbi-tools++/libmacro-static.a lib/ncbi-tools++/libmacro.a lib/ncbi-tools++/libmedlars-static.a @@ -4001,6 +4072,8 @@ lib/ncbi-tools++/libremapcli-static.a lib/ncbi-tools++/libremapcli.a lib/ncbi-tools++/libscoremat-static.a lib/ncbi-tools++/libscoremat.a +lib/ncbi-tools++/libsearchbyrsid-static.a +lib/ncbi-tools++/libsearchbyrsid.a lib/ncbi-tools++/libseq-static.a lib/ncbi-tools++/libseq.a lib/ncbi-tools++/libseqcode-static.a @@ -4081,6 +4154,8 @@ lib/ncbi-tools++/libxformat-static.a lib/ncbi-tools++/libxformat.a lib/ncbi-tools++/libxhtml-static.a lib/ncbi-tools++/libxhtml.a +lib/ncbi-tools++/libxlogging-static.a +lib/ncbi-tools++/libxlogging.a lib/ncbi-tools++/libxncbi-static.a lib/ncbi-tools++/libxncbi.a lib/ncbi-tools++/libxnetblast-static.a Index: pkgsrc/biology/ncbi-blast+/distinfo diff -u pkgsrc/biology/ncbi-blast+/distinfo:1.2 pkgsrc/biology/ncbi-blast+/distinfo:1.3 --- pkgsrc/biology/ncbi-blast+/distinfo:1.2 Tue May 22 21:37:29 2018 +++ pkgsrc/biology/ncbi-blast+/distinfo Mon Jan 7 15:00:10 2019 @@ -1,12 +1,14 @@ -$NetBSD: distinfo,v 1.2 2018/05/22 21:37:29 bacon Exp $ +$NetBSD: distinfo,v 1.3 2019/01/07 15:00:10 bacon Exp $ -SHA1 (ncbi-blast-2.7.1+-src.tar.gz) = d04a25f01c386abd8515957a2ce1dabf376743f8 -RMD160 (ncbi-blast-2.7.1+-src.tar.gz) = 7277419e16fb215aae4136a16e13bec963b70cbd -SHA512 (ncbi-blast-2.7.1+-src.tar.gz) = e4b3914f51165ae4c82051068ed9d3470687a4e0f1df6274018c0ba14b241666a570d72265c7d167b8ce2a9075652744244a00e3e95c00c4252da0fbd80d17c6 -Size (ncbi-blast-2.7.1+-src.tar.gz) = 23254824 bytes +SHA1 (ncbi-blast-2.8.1+-src.tar.gz) = 16573b642d7861d0bed67f3eb1174fc646819eec +RMD160 (ncbi-blast-2.8.1+-src.tar.gz) = ef8df6c4b3cae18b2ab4509af15554ee8d8f9bfd +SHA512 (ncbi-blast-2.8.1+-src.tar.gz) = 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f +Size (ncbi-blast-2.8.1+-src.tar.gz) = 24973554 bytes SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5 -SHA1 (patch-src_algo_blast_core_blast__kappa.c) = a580a5fb2d5a3af04c27dd63a7edd349b7ae1be7 +SHA1 (patch-src_algo_blast_core_blast__kappa.c) = 6fcad996b3a8e5b6c2400608bff9de62ebf6927f SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01 +SHA1 (patch-src_build-system_cmake_cmake-cfg-unix.sh) = 90468f3109800e01fc7351926adb331919a12fb2 SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97 SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6 SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd +SHA1 (patch-src_util_checksum_farmhash_farmhash.h) = c3ff60de9a9020d3b706c2bff37f6f4cde4e6b6b Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c:1.1 pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c:1.2 --- pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c:1.1 Fri Apr 27 20:28:28 2018 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c Mon Jan 7 15:00:10 2019 @@ -1,8 +1,8 @@ -$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.1 2018/04/27 20:28:28 bacon Exp $ +$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.2 2019/01/07 15:00:10 bacon Exp $ # Work around NetBSD stderr def choking macro ---- src/algo/blast/core/blast_kappa.c.orig 2018-03-26 21:55:44.000000000 +0000 +--- src/algo/blast/core/blast_kappa.c.orig 2019-01-02 04:00:17.000000000 +0000 +++ src/algo/blast/core/blast_kappa.c @@ -32,6 +32,7 @@ * system for each match in blastpgp @@ -12,7 +12,16 @@ $NetBSD: patch-src_algo_blast_core_blast #include #include #include -@@ -3404,13 +3405,15 @@ Blast_RedoAlignmentCore_MT(EBlastProgram +@@ -57,7 +58,7 @@ + * shared(...) list. */ + # define STDERR_COMMA + # else +-# define STDERR_COMMA stderr, ++# define STDERR_COMMA my_stderr, + # endif + #endif + +@@ -3412,6 +3413,8 @@ Blast_RedoAlignmentCore_MT(EBlastProgram } Boolean interrupt = FALSE; @@ -21,11 +30,3 @@ $NetBSD: patch-src_algo_blast_core_blast #pragma omp parallel \ default(none) num_threads(actual_num_threads) \ if(actual_num_threads>1) \ - shared(interrupt, seqsrc_tld, score_params_tld, hit_params_tld, \ - gap_align_tld, results_tld, \ - redoneMatches_tld, \ -- stderr, \ -+ my_stderr, \ - numQueries, numMatches, theseMatches, \ - numFrames, program_number, subjectBlk_tld, positionBased, \ - default_db_genetic_code, localScalingFactor, queryInfo, \ Added files: Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh:1.1 --- /dev/null Mon Jan 7 15:00:11 2019 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh Mon Jan 7 15:00:10 2019 @@ -0,0 +1,15 @@ +$NetBSD: patch-src_build-system_cmake_cmake-cfg-unix.sh,v 1.1 2019/01/07 15:00:10 bacon Exp $ + +# Portability + +--- src/build-system/cmake/cmake-cfg-unix.sh.orig 2019-01-02 01:22:44.549100012 +0000 ++++ src/build-system/cmake/cmake-cfg-unix.sh +@@ -166,7 +166,7 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L + CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_CCACHE=$USE_CCACHE" + CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_DISTCC=$USE_DISTCC" + build_root=CMake-${CC_NAME}${CC_VERSION}-${BUILD_TYPE} +-if [ "$BUILD_SHARED_LIBS" == "ON" ]; then ++if [ "$BUILD_SHARED_LIBS" = "ON" ]; then + build_root="$build_root"DLL + fi + #build_root="$build_root"64 Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h:1.1 --- /dev/null Mon Jan 7 15:00:11 2019 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h Mon Jan 7 15:00:11 2019 @@ -0,0 +1,29 @@ +$NetBSD: patch-src_util_checksum_farmhash_farmhash.h,v 1.1 2019/01/07 15:00:11 bacon Exp $ + +# __GNUC__ does not imply location of endian.h. Check for BSD first. + +--- src/util/checksum/farmhash/farmhash.h.orig 2018-09-26 12:38:06.000000000 +0000 ++++ src/util/checksum/farmhash/farmhash.h +@@ -305,15 +305,18 @@ inline uint128_t Fingerprint128(const St + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN + #endif +-#elif defined(__linux__) || defined(__CYGWIN__) || defined( __GNUC__ ) || defined( __GNU_LIBRARY__ ) +- #include // libc6-dev, GLIBC ++#elif defined(__OpenBSD__) || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__s390x__) ++ #include + #if BYTE_ORDER == BIG_ENDIAN + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN + #endif + #endif +-#elif defined(__OpenBSD__) || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__DragonFly__) || defined(__s390x__) +- #include ++// __GNUC__ actually does not imply the location of endian.h. It could ++// be set on any system running GCC. I'm wondering why this was added ++// Working around breakage for BSD systems by checking for BSD first. ++#elif defined(__linux__) || defined(__CYGWIN__) || defined( __GNUC__ ) || defined( __GNU_LIBRARY__ ) ++ #include // libc6-dev, GLIBC + #if BYTE_ORDER == BIG_ENDIAN + #if !defined(FARMHASH_BIG_ENDIAN) + #define FARMHASH_BIG_ENDIAN --_----------=_1546873211180170--