Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 46D2785344 for ; Sun, 28 May 2023 22:48:32 +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 48vHf2sOPx_w for ; Sun, 28 May 2023 22:48:28 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id A553184D15 for ; Sun, 28 May 2023 22:48:28 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id C75CFFA87; Sun, 28 May 2023 22:48:27 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1685314107216150" MIME-Version: 1.0 Date: Sun, 28 May 2023 22:48:27 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/ncbi-blast+ To: pkgsrc-changes@NetBSD.org Approved: commit_and_comment Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20230528224827.C75CFFA87@cvs.NetBSD.org> This is a multi-part message in MIME format. --_----------=_1685314107216150 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Sun May 28 22:48:27 UTC 2023 Modified Files: pkgsrc/biology/ncbi-blast+: Makefile PLIST buildlink3.mk distinfo pkgsrc/biology/ncbi-blast+/patches: patch-src_build-system_cmake_cmake-cfg-xcode.sh patch-src_build-system_configure Added Files: pkgsrc/biology/ncbi-blast+/patches: patch-src_util_checksum_cityhash_city.cc patch-src_util_checksum_farmhash_farmhash.cc Log Message: biology/ncbi-blast+: Update to 2.14.0 Several minor bug fixes, a few other enhancements Also set only for 64-bit platforms (required for most bioinformatics) Changes: https://www.ncbi.nlm.nih.gov/sites/books/NBK131777/ To generate a diff of this commit: cvs rdiff -u -r1.34 -r1.35 pkgsrc/biology/ncbi-blast+/Makefile cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/ncbi-blast+/PLIST cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/ncbi-blast+/buildlink3.mk cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/ncbi-blast+/distinfo cvs rdiff -u -r1.2 -r1.3 \ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh cvs rdiff -u -r1.3 -r1.4 \ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure cvs rdiff -u -r0 -r1.1 \ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc \ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1685314107216150 Content-Disposition: inline Content-Length: 92524 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:1.34 pkgsrc/biology/ncbi-blast+/Makefile:1.35 --- pkgsrc/biology/ncbi-blast+/Makefile:1.34 Wed Apr 19 08:09:12 2023 +++ pkgsrc/biology/ncbi-blast+/Makefile Sun May 28 22:48:27 2023 @@ -1,8 +1,7 @@ -# $NetBSD: Makefile,v 1.34 2023/04/19 08:09:12 adam Exp $ +# $NetBSD: Makefile,v 1.35 2023/05/28 22:48:27 bacon Exp $ -DISTNAME= ncbi-blast-2.13.0+-src +DISTNAME= ncbi-blast-2.14.0+-src PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/} -PKGREVISION= 6 CATEGORIES= biology MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/ @@ -12,6 +11,9 @@ HOMEPAGE= http://blast.ncbi.nlm.nih.gov/ COMMENT= NCBI implementation of Basic Local Alignment Search Tool LICENSE= public-domain +# Nobody does bioinformatics on 32-bit processors anymore +ONLY_FOR_PLATFORM= ${LP64PLATFORMS} + # Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0 # Fix "unknown options" in configure SUBST_CLASSES+= configure @@ -59,7 +61,9 @@ CONFIGURE_ARGS+= --without-openmp BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts post-install: - ${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra + ${FIND} ${DESTDIR}${PREFIX} -name '\.cvs*' -exec rm -rf '{}' \; + ${FIND} ${DESTDIR}${PREFIX} -name '\.subversion*' -exec rm -rf '{}' \; + ${FIND} ${DESTDIR}${PREFIX} -name '\.git*' -exec rm -rf '{}' \; .if ${OPSYS} != Darwin ${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so .endif @@ -67,6 +71,7 @@ post-install: .include "../../devel/zlib/buildlink3.mk" .include "../../archivers/lzo/buildlink3.mk" .include "../../archivers/bzip2/buildlink3.mk" +.include "../../archivers/zstd/buildlink3.mk" .include "../../devel/pcre/buildlink3.mk" .include "../../databases/lmdb/buildlink3.mk" .include "../../security/gnutls/buildlink3.mk" Index: pkgsrc/biology/ncbi-blast+/PLIST diff -u pkgsrc/biology/ncbi-blast+/PLIST:1.4 pkgsrc/biology/ncbi-blast+/PLIST:1.5 --- pkgsrc/biology/ncbi-blast+/PLIST:1.4 Sun Apr 10 20:54:51 2022 +++ pkgsrc/biology/ncbi-blast+/PLIST Sun May 28 22:48:27 2023 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.4 2022/04/10 20:54:51 bacon Exp $ +@comment $NetBSD: PLIST,v 1.5 2023/05/28 22:48:27 bacon Exp $ bin/blast_formatter bin/blast_report bin/blastdb_aliastool @@ -21,6 +21,7 @@ bin/get_species_taxids.sh bin/legacy_blast.pl bin/lmdbxx_sample bin/makeblastdb +bin/makeclusterdb bin/makembindex bin/makeprofiledb bin/project_tree_builder @@ -288,6 +289,7 @@ include/ncbi-tools++/common/ncbi_pch_imp include/ncbi-tools++/common/ncbi_revision.h include/ncbi-tools++/common/ncbi_revision.h.in include/ncbi-tools++/common/ncbi_sanitizers.h +include/ncbi-tools++/common/ncbi_sc_version.h 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 @@ -606,14 +608,10 @@ 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 -include/ncbi-tools++/objects/access/.cvsignore -include/ncbi-tools++/objects/access/.gitignore include/ncbi-tools++/objects/access/Link_set.hpp include/ncbi-tools++/objects/access/Link_set_.hpp include/ncbi-tools++/objects/access/NCBI_Access_module.hpp include/ncbi-tools++/objects/access/access__.hpp -include/ncbi-tools++/objects/biblio/.cvsignore -include/ncbi-tools++/objects/biblio/.gitignore include/ncbi-tools++/objects/biblio/Affil.hpp include/ncbi-tools++/objects/biblio/Affil_.hpp include/ncbi-tools++/objects/biblio/ArticleId.hpp @@ -676,8 +674,6 @@ include/ncbi-tools++/objects/biblio/Titl include/ncbi-tools++/objects/biblio/biblio__.hpp include/ncbi-tools++/objects/biblio/biblio_macros.hpp include/ncbi-tools++/objects/biblio/citation_base.hpp -include/ncbi-tools++/objects/biotree/.cvsignore -include/ncbi-tools++/objects/biotree/.gitignore include/ncbi-tools++/objects/biotree/BioTreeContainer.hpp include/ncbi-tools++/objects/biotree/BioTreeContainer_.hpp include/ncbi-tools++/objects/biotree/DistanceMatrix.hpp @@ -696,8 +692,6 @@ include/ncbi-tools++/objects/biotree/Nod include/ncbi-tools++/objects/biotree/NodeSet_.hpp include/ncbi-tools++/objects/biotree/Node_.hpp include/ncbi-tools++/objects/biotree/biotree__.hpp -include/ncbi-tools++/objects/blast/.cvsignore -include/ncbi-tools++/objects/blast/.gitignore include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply.hpp include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply_.hpp include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reque.hpp @@ -827,8 +821,6 @@ include/ncbi-tools++/objects/blast/blast include/ncbi-tools++/objects/blast/blastclient.hpp include/ncbi-tools++/objects/blast/blastclient_.hpp include/ncbi-tools++/objects/blast/names.hpp -include/ncbi-tools++/objects/blastdb/.cvsignore -include/ncbi-tools++/objects/blastdb/.gitignore include/ncbi-tools++/objects/blastdb/Blast_db_mask_info.hpp include/ncbi-tools++/objects/blastdb/Blast_db_mask_info_.hpp include/ncbi-tools++/objects/blastdb/Blast_db_metadata.hpp @@ -844,8 +836,6 @@ include/ncbi-tools++/objects/blastdb/Bla include/ncbi-tools++/objects/blastdb/NCBI_BlastDL_module.hpp include/ncbi-tools++/objects/blastdb/blastdb__.hpp include/ncbi-tools++/objects/blastdb/defline_extra.hpp -include/ncbi-tools++/objects/blastxml/.cvsignore -include/ncbi-tools++/objects/blastxml/.gitignore include/ncbi-tools++/objects/blastxml/BlastOutput.hpp include/ncbi-tools++/objects/blastxml/BlastOutput_.hpp include/ncbi-tools++/objects/blastxml/Hit.hpp @@ -860,8 +850,6 @@ include/ncbi-tools++/objects/blastxml/Pa include/ncbi-tools++/objects/blastxml/Statistics.hpp include/ncbi-tools++/objects/blastxml/Statistics_.hpp include/ncbi-tools++/objects/blastxml/blastxml__.hpp -include/ncbi-tools++/objects/blastxml2/.cvsignore -include/ncbi-tools++/objects/blastxml2/.gitignore include/ncbi-tools++/objects/blastxml2/BlastOutput2.hpp include/ncbi-tools++/objects/blastxml2/BlastOutput2_.hpp include/ncbi-tools++/objects/blastxml2/BlastXML2.hpp @@ -892,8 +880,6 @@ include/ncbi-tools++/objects/blastxml2/S include/ncbi-tools++/objects/blastxml2/Target.hpp include/ncbi-tools++/objects/blastxml2/Target_.hpp include/ncbi-tools++/objects/blastxml2/blastxml2__.hpp -include/ncbi-tools++/objects/cdd/.cvsignore -include/ncbi-tools++/objects/cdd/.gitignore include/ncbi-tools++/objects/cdd/Algorithm_type.hpp include/ncbi-tools++/objects/cdd/Algorithm_type_.hpp include/ncbi-tools++/objects/cdd/Align_annot.hpp @@ -962,8 +948,6 @@ include/ncbi-tools++/objects/cdd/Update_ include/ncbi-tools++/objects/cdd/Update_comment.hpp include/ncbi-tools++/objects/cdd/Update_comment_.hpp include/ncbi-tools++/objects/cdd/cdd__.hpp -include/ncbi-tools++/objects/cn3d/.cvsignore -include/ncbi-tools++/objects/cn3d/.gitignore include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix.hpp include/ncbi-tools++/objects/cn3d/Cn3d_GL_matrix_.hpp include/ncbi-tools++/objects/cn3d/Cn3d_backbone_label_style.hpp @@ -1006,8 +990,6 @@ include/ncbi-tools++/objects/cn3d/Cn3d_v include/ncbi-tools++/objects/cn3d/Cn3d_view_settings_.hpp include/ncbi-tools++/objects/cn3d/NCBI_Cn3d_module.hpp include/ncbi-tools++/objects/cn3d/cn3d__.hpp -include/ncbi-tools++/objects/coords/.cvsignore -include/ncbi-tools++/objects/coords/.gitignore include/ncbi-tools++/objects/coords/HGVS_Coordinate.hpp include/ncbi-tools++/objects/coords/HGVS_Coordinate_.hpp include/ncbi-tools++/objects/coords/HGVS_Coordinate_Set.hpp @@ -1018,8 +1000,6 @@ include/ncbi-tools++/objects/dbsnp/prima 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 include/ncbi-tools++/objects/docsum/Assay_.hpp include/ncbi-tools++/objects/docsum/Assembly.hpp @@ -1046,8 +1026,6 @@ include/ncbi-tools++/objects/docsum/Rs_. include/ncbi-tools++/objects/docsum/Ss.hpp include/ncbi-tools++/objects/docsum/Ss_.hpp include/ncbi-tools++/objects/docsum/docsum__.hpp -include/ncbi-tools++/objects/entrez2/.cvsignore -include/ncbi-tools++/objects/entrez2/.gitignore include/ncbi-tools++/objects/entrez2/E2Reply.hpp include/ncbi-tools++/objects/entrez2/E2Reply_.hpp include/ncbi-tools++/objects/entrez2/E2Request.hpp @@ -1126,8 +1104,6 @@ include/ncbi-tools++/objects/entrez2/NCB include/ncbi-tools++/objects/entrez2/entrez2__.hpp include/ncbi-tools++/objects/entrez2/entrez2_client.hpp include/ncbi-tools++/objects/entrez2/entrez2_client_.hpp -include/ncbi-tools++/objects/entrezgene/.cvsignore -include/ncbi-tools++/objects/entrezgene/.gitignore include/ncbi-tools++/objects/entrezgene/Entrezgene.hpp include/ncbi-tools++/objects/entrezgene/Entrezgene_.hpp include/ncbi-tools++/objects/entrezgene/Entrezgene_Set.hpp @@ -1146,8 +1122,6 @@ include/ncbi-tools++/objects/entrezgene/ include/ncbi-tools++/objects/entrezgene/Xtra_Terms.hpp include/ncbi-tools++/objects/entrezgene/Xtra_Terms_.hpp include/ncbi-tools++/objects/entrezgene/entrezgene__.hpp -include/ncbi-tools++/objects/featdef/.cvsignore -include/ncbi-tools++/objects/featdef/.gitignore include/ncbi-tools++/objects/featdef/FeatDef.hpp include/ncbi-tools++/objects/featdef/FeatDefGroupSet.hpp include/ncbi-tools++/objects/featdef/FeatDefGroupSet_.hpp @@ -1162,8 +1136,6 @@ include/ncbi-tools++/objects/featdef/Fea include/ncbi-tools++/objects/featdef/FeatMolType_.hpp include/ncbi-tools++/objects/featdef/NCBI_FeatDef_module.hpp include/ncbi-tools++/objects/featdef/featdef__.hpp -include/ncbi-tools++/objects/gbproj/.cvsignore -include/ncbi-tools++/objects/gbproj/.gitignore include/ncbi-tools++/objects/gbproj/AbstractProjectItem.hpp include/ncbi-tools++/objects/gbproj/AbstractProjectItem_.hpp include/ncbi-tools++/objects/gbproj/DummyObsoleteType.hpp @@ -1194,8 +1166,6 @@ include/ncbi-tools++/objects/gbproj/View include/ncbi-tools++/objects/gbproj/gbproj__.hpp include/ncbi-tools++/objects/gbproj/gbproj_export.h include/ncbi-tools++/objects/gbproj/igbproject.hpp -include/ncbi-tools++/objects/gbseq/.cvsignore -include/ncbi-tools++/objects/gbseq/.gitignore include/ncbi-tools++/objects/gbseq/GBAltSeqData.hpp include/ncbi-tools++/objects/gbseq/GBAltSeqData_.hpp include/ncbi-tools++/objects/gbseq/GBAltSeqItem.hpp @@ -1234,8 +1204,6 @@ include/ncbi-tools++/objects/gbseq/GBXre include/ncbi-tools++/objects/gbseq/GBXref_.hpp include/ncbi-tools++/objects/gbseq/NCBI_GBSeq_module.hpp include/ncbi-tools++/objects/gbseq/gbseq__.hpp -include/ncbi-tools++/objects/general/.cvsignore -include/ncbi-tools++/objects/general/.gitignore include/ncbi-tools++/objects/general/Date.hpp include/ncbi-tools++/objects/general/Date_.hpp include/ncbi-tools++/objects/general/Date_std.hpp @@ -1259,8 +1227,6 @@ include/ncbi-tools++/objects/general/gen include/ncbi-tools++/objects/general/general_exception.hpp include/ncbi-tools++/objects/general/general_macros.hpp include/ncbi-tools++/objects/general/uoconv.hpp -include/ncbi-tools++/objects/genesbyloc/.cvsignore -include/ncbi-tools++/objects/genesbyloc/.gitignore include/ncbi-tools++/objects/genesbyloc/GBL_Data.hpp include/ncbi-tools++/objects/genesbyloc/GBL_Data_.hpp include/ncbi-tools++/objects/genesbyloc/GBL_Gene.hpp @@ -1269,8 +1235,6 @@ include/ncbi-tools++/objects/genesbyloc/ include/ncbi-tools++/objects/genesbyloc/GBL_Reply_.hpp include/ncbi-tools++/objects/genesbyloc/NCBI_GenesByLoc_module.hpp include/ncbi-tools++/objects/genesbyloc/genesbyloc__.hpp -include/ncbi-tools++/objects/genomecoll/.cvsignore -include/ncbi-tools++/objects/genomecoll/.gitignore include/ncbi-tools++/objects/genomecoll/GCClientRequest.hpp include/ncbi-tools++/objects/genomecoll/GCClientRequest_.hpp include/ncbi-tools++/objects/genomecoll/GCClientResponse.hpp @@ -1342,8 +1306,6 @@ include/ncbi-tools++/objects/genomecoll/ include/ncbi-tools++/objects/genomecoll/genome_collection__.hpp include/ncbi-tools++/objects/genomecoll/genomic_collections_cli.hpp include/ncbi-tools++/objects/genomecoll/genomic_collections_cli_.hpp -include/ncbi-tools++/objects/homologene/.cvsignore -include/ncbi-tools++/objects/homologene/.gitignore include/ncbi-tools++/objects/homologene/HG_Alignment.hpp include/ncbi-tools++/objects/homologene/HG_AlignmentSet.hpp include/ncbi-tools++/objects/homologene/HG_AlignmentSet_.hpp @@ -1372,8 +1334,6 @@ include/ncbi-tools++/objects/homologene/ include/ncbi-tools++/objects/homologene/HG_Stats_.hpp include/ncbi-tools++/objects/homologene/HomoloGene_module.hpp include/ncbi-tools++/objects/homologene/homologene__.hpp -include/ncbi-tools++/objects/id1/.cvsignore -include/ncbi-tools++/objects/id1/.gitignore include/ncbi-tools++/objects/id1/Entry_complexities.hpp include/ncbi-tools++/objects/id1/Entry_complexities_.hpp include/ncbi-tools++/objects/id1/ID1SeqEntry_info.hpp @@ -1394,8 +1354,6 @@ include/ncbi-tools++/objects/id1/NCBI_ID include/ncbi-tools++/objects/id1/id1__.hpp include/ncbi-tools++/objects/id1/id1_client.hpp include/ncbi-tools++/objects/id1/id1_client_.hpp -include/ncbi-tools++/objects/id2/.cvsignore -include/ncbi-tools++/objects/id2/.gitignore include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Chunk.hpp include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Chunk_.hpp include/ncbi-tools++/objects/id2/ID2S_Reply_Get_Split_Info.hpp @@ -1456,8 +1414,6 @@ include/ncbi-tools++/objects/id2/id2_cli include/ncbi-tools++/objects/id2/id2_client_.hpp include/ncbi-tools++/objects/id2/id2processor.hpp include/ncbi-tools++/objects/id2/id2processor_interface.hpp -include/ncbi-tools++/objects/insdseq/.cvsignore -include/ncbi-tools++/objects/insdseq/.gitignore include/ncbi-tools++/objects/insdseq/INSDAltSeqData.hpp include/ncbi-tools++/objects/insdseq/INSDAltSeqData_.hpp include/ncbi-tools++/objects/insdseq/INSDAltSeqItem.hpp @@ -1496,8 +1452,6 @@ include/ncbi-tools++/objects/insdseq/INS include/ncbi-tools++/objects/insdseq/INSDXref_.hpp include/ncbi-tools++/objects/insdseq/INSD_INSDSeq_module.hpp include/ncbi-tools++/objects/insdseq/insdseq__.hpp -include/ncbi-tools++/objects/macro/.cvsignore -include/ncbi-tools++/objects/macro/.gitignore include/ncbi-tools++/objects/macro/AECRParse_action.hpp include/ncbi-tools++/objects/macro/AECRParse_action_.hpp include/ncbi-tools++/objects/macro/AECR_action.hpp @@ -1858,16 +1812,12 @@ include/ncbi-tools++/objects/macro/Word_ include/ncbi-tools++/objects/macro/Xref_type.hpp include/ncbi-tools++/objects/macro/Xref_type_.hpp include/ncbi-tools++/objects/macro/macro__.hpp -include/ncbi-tools++/objects/medlars/.cvsignore -include/ncbi-tools++/objects/medlars/.gitignore include/ncbi-tools++/objects/medlars/Medlars_entry.hpp include/ncbi-tools++/objects/medlars/Medlars_entry_.hpp include/ncbi-tools++/objects/medlars/Medlars_record.hpp include/ncbi-tools++/objects/medlars/Medlars_record_.hpp include/ncbi-tools++/objects/medlars/NCBI_Medlars_module.hpp include/ncbi-tools++/objects/medlars/medlars__.hpp -include/ncbi-tools++/objects/medline/.cvsignore -include/ncbi-tools++/objects/medline/.gitignore include/ncbi-tools++/objects/medline/DocRef.hpp include/ncbi-tools++/objects/medline/DocRef_.hpp include/ncbi-tools++/objects/medline/Medline_entry.hpp @@ -1884,8 +1834,6 @@ include/ncbi-tools++/objects/medline/Med include/ncbi-tools++/objects/medline/Medline_si_.hpp include/ncbi-tools++/objects/medline/NCBI_Medline_module.hpp include/ncbi-tools++/objects/medline/medline__.hpp -include/ncbi-tools++/objects/mim/.cvsignore -include/ncbi-tools++/objects/mim/.gitignore include/ncbi-tools++/objects/mim/Mim_allelic_variant.hpp include/ncbi-tools++/objects/mim/Mim_allelic_variant_.hpp include/ncbi-tools++/objects/mim/Mim_author.hpp @@ -1917,8 +1865,6 @@ include/ncbi-tools++/objects/mim/mim__.h include/ncbi-tools++/objects/misc/error_codes.hpp include/ncbi-tools++/objects/misc/sequence_macros.hpp include/ncbi-tools++/objects/misc/sequence_util_macros.hpp -include/ncbi-tools++/objects/mla/.cvsignore -include/ncbi-tools++/objects/mla/.gitignore include/ncbi-tools++/objects/mla/Error_val.hpp include/ncbi-tools++/objects/mla/Error_val_.hpp include/ncbi-tools++/objects/mla/Mla_back.hpp @@ -1935,8 +1881,6 @@ include/ncbi-tools++/objects/mla/Title_t include/ncbi-tools++/objects/mla/mla__.hpp include/ncbi-tools++/objects/mla/mla_client.hpp include/ncbi-tools++/objects/mla/mla_client_.hpp -include/ncbi-tools++/objects/mmdb1/.cvsignore -include/ncbi-tools++/objects/mmdb1/.gitignore include/ncbi-tools++/objects/mmdb1/Atom.hpp include/ncbi-tools++/objects/mmdb1/Atom_.hpp include/ncbi-tools++/objects/mmdb1/Atom_id.hpp @@ -1998,8 +1942,6 @@ include/ncbi-tools++/objects/mmdb1/Resid include/ncbi-tools++/objects/mmdb1/Residue_id.hpp include/ncbi-tools++/objects/mmdb1/Residue_id_.hpp include/ncbi-tools++/objects/mmdb1/mmdb1__.hpp -include/ncbi-tools++/objects/mmdb2/.cvsignore -include/ncbi-tools++/objects/mmdb2/.gitignore include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id.hpp include/ncbi-tools++/objects/mmdb2/Alternate_conformation_id_.hpp include/ncbi-tools++/objects/mmdb2/Alternate_conformation_ids.hpp @@ -2046,8 +1988,6 @@ include/ncbi-tools++/objects/mmdb2/T_mes include/ncbi-tools++/objects/mmdb2/Triangles.hpp include/ncbi-tools++/objects/mmdb2/Triangles_.hpp include/ncbi-tools++/objects/mmdb2/mmdb2__.hpp -include/ncbi-tools++/objects/mmdb3/.cvsignore -include/ncbi-tools++/objects/mmdb3/.gitignore include/ncbi-tools++/objects/mmdb3/Align_stats.hpp include/ncbi-tools++/objects/mmdb3/Align_stats_.hpp include/ncbi-tools++/objects/mmdb3/Atom_pntrs.hpp @@ -2124,8 +2064,6 @@ include/ncbi-tools++/objects/mmdb3/Trans include/ncbi-tools++/objects/mmdb3/Transform.hpp include/ncbi-tools++/objects/mmdb3/Transform_.hpp include/ncbi-tools++/objects/mmdb3/mmdb3__.hpp -include/ncbi-tools++/objects/ncbimime/.cvsignore -include/ncbi-tools++/objects/ncbimime/.gitignore include/ncbi-tools++/objects/ncbimime/Biostruc_align.hpp include/ncbi-tools++/objects/ncbimime/Biostruc_align_.hpp include/ncbi-tools++/objects/ncbimime/Biostruc_align_seq.hpp @@ -2146,8 +2084,6 @@ include/ncbi-tools++/objects/ncbimime/NC include/ncbi-tools++/objects/ncbimime/Ncbi_mime_asn1.hpp include/ncbi-tools++/objects/ncbimime/Ncbi_mime_asn1_.hpp include/ncbi-tools++/objects/ncbimime/ncbimime__.hpp -include/ncbi-tools++/objects/objprt/.cvsignore -include/ncbi-tools++/objects/objprt/.gitignore include/ncbi-tools++/objects/objprt/NCBI_ObjPrt_module.hpp include/ncbi-tools++/objects/objprt/PrintForm.hpp include/ncbi-tools++/objects/objprt/PrintFormBlock.hpp @@ -2170,8 +2106,6 @@ include/ncbi-tools++/objects/objprt/Temp include/ncbi-tools++/objects/objprt/UserFormat.hpp include/ncbi-tools++/objects/objprt/UserFormat_.hpp include/ncbi-tools++/objects/objprt/objprt__.hpp -include/ncbi-tools++/objects/omssa/.cvsignore -include/ncbi-tools++/objects/omssa/.gitignore include/ncbi-tools++/objects/omssa/MSBioseq.hpp include/ncbi-tools++/objects/omssa/MSBioseqSet.hpp include/ncbi-tools++/objects/omssa/MSBioseqSet_.hpp @@ -2258,8 +2192,6 @@ include/ncbi-tools++/objects/omssa/NameV include/ncbi-tools++/objects/omssa/NameValue_.hpp include/ncbi-tools++/objects/omssa/OMSSA_module.hpp include/ncbi-tools++/objects/omssa/omssa__.hpp -include/ncbi-tools++/objects/pcassay/.cvsignore -include/ncbi-tools++/objects/pcassay/.gitignore include/ncbi-tools++/objects/pcassay/NCBI_PCAssay_module.hpp include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef.hpp include/ncbi-tools++/objects/pcassay/PC_AnnotatedXRef_.hpp @@ -2294,8 +2226,6 @@ include/ncbi-tools++/objects/pcassay/PC_ include/ncbi-tools++/objects/pcassay/PC_ResultType.hpp include/ncbi-tools++/objects/pcassay/PC_ResultType_.hpp include/ncbi-tools++/objects/pcassay/pcassay__.hpp -include/ncbi-tools++/objects/pcassay2/.cvsignore -include/ncbi-tools++/objects/pcassay2/.gitignore include/ncbi-tools++/objects/pcassay2/NCBI_PCAssay2_module.hpp include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef.hpp include/ncbi-tools++/objects/pcassay2/PC_AnnotatedXRef_.hpp @@ -2324,8 +2254,6 @@ include/ncbi-tools++/objects/pcassay2/PC include/ncbi-tools++/objects/pcassay2/PC_ResultType.hpp include/ncbi-tools++/objects/pcassay2/PC_ResultType_.hpp include/ncbi-tools++/objects/pcassay2/pcassay2__.hpp -include/ncbi-tools++/objects/pcsubstance/.cvsignore -include/ncbi-tools++/objects/pcsubstance/.gitignore include/ncbi-tools++/objects/pcsubstance/NCBI_PCSubstance_module.hpp include/ncbi-tools++/objects/pcsubstance/PC_AtomInt.hpp include/ncbi-tools++/objects/pcsubstance/PC_AtomInt_.hpp @@ -2406,8 +2334,6 @@ include/ncbi-tools++/objects/pcsubstance include/ncbi-tools++/objects/pcsubstance/PC_XRefData.hpp include/ncbi-tools++/objects/pcsubstance/PC_XRefData_.hpp include/ncbi-tools++/objects/pcsubstance/pcsubstance__.hpp -include/ncbi-tools++/objects/proj/.cvsignore -include/ncbi-tools++/objects/proj/.gitignore include/ncbi-tools++/objects/proj/NCBI_Project_module.hpp include/ncbi-tools++/objects/proj/Projdesc.hpp include/ncbi-tools++/objects/proj/Projdesc_.hpp @@ -2420,8 +2346,6 @@ include/ncbi-tools++/objects/proj/Projec include/ncbi-tools++/objects/proj/Project_item.hpp include/ncbi-tools++/objects/proj/Project_item_.hpp include/ncbi-tools++/objects/proj/proj__.hpp -include/ncbi-tools++/objects/pub/.cvsignore -include/ncbi-tools++/objects/pub/.gitignore include/ncbi-tools++/objects/pub/NCBI_Pub_module.hpp include/ncbi-tools++/objects/pub/Pub.hpp include/ncbi-tools++/objects/pub/Pub_.hpp @@ -2431,16 +2355,12 @@ include/ncbi-tools++/objects/pub/Pub_set include/ncbi-tools++/objects/pub/Pub_set_.hpp include/ncbi-tools++/objects/pub/pub__.hpp include/ncbi-tools++/objects/pub/pub_macros.hpp -include/ncbi-tools++/objects/pubmed/.cvsignore -include/ncbi-tools++/objects/pubmed/.gitignore include/ncbi-tools++/objects/pubmed/NCBI_PubMed_module.hpp include/ncbi-tools++/objects/pubmed/Pubmed_entry.hpp include/ncbi-tools++/objects/pubmed/Pubmed_entry_.hpp include/ncbi-tools++/objects/pubmed/Pubmed_url.hpp include/ncbi-tools++/objects/pubmed/Pubmed_url_.hpp include/ncbi-tools++/objects/pubmed/pubmed__.hpp -include/ncbi-tools++/objects/remap/.cvsignore -include/ncbi-tools++/objects/remap/.gitignore include/ncbi-tools++/objects/remap/NCBI_Remap_module.hpp include/ncbi-tools++/objects/remap/RMReply.hpp include/ncbi-tools++/objects/remap/RMReply_.hpp @@ -2461,8 +2381,6 @@ include/ncbi-tools++/objects/remap/Remap include/ncbi-tools++/objects/remap/remap__.hpp include/ncbi-tools++/objects/remap/remap_client.hpp include/ncbi-tools++/objects/remap/remap_client_.hpp -include/ncbi-tools++/objects/scoremat/.cvsignore -include/ncbi-tools++/objects/scoremat/.gitignore include/ncbi-tools++/objects/scoremat/BlockProperty.hpp include/ncbi-tools++/objects/scoremat/BlockProperty_.hpp include/ncbi-tools++/objects/scoremat/CoreBlock.hpp @@ -2489,8 +2407,6 @@ include/ncbi-tools++/objects/scoremat/Si include/ncbi-tools++/objects/scoremat/Site_annot_set.hpp include/ncbi-tools++/objects/scoremat/Site_annot_set_.hpp include/ncbi-tools++/objects/scoremat/scoremat__.hpp -include/ncbi-tools++/objects/seq/.cvsignore -include/ncbi-tools++/objects/seq/.gitignore include/ncbi-tools++/objects/seq/Align_def.hpp include/ncbi-tools++/objects/seq/Align_def_.hpp include/ncbi-tools++/objects/seq/Annot_descr.hpp @@ -2591,8 +2507,6 @@ include/ncbi-tools++/objects/seq/seqloci include/ncbi-tools++/objects/seq/seqport_util.hpp include/ncbi-tools++/objects/seq/so_map.hpp include/ncbi-tools++/objects/seq/sofa_type.hpp -include/ncbi-tools++/objects/seqalign/.cvsignore -include/ncbi-tools++/objects/seqalign/.gitignore include/ncbi-tools++/objects/seqalign/Dense_diag.hpp include/ncbi-tools++/objects/seqalign/Dense_diag_.hpp include/ncbi-tools++/objects/seqalign/Dense_seg.hpp @@ -2633,8 +2547,6 @@ include/ncbi-tools++/objects/seqalign/St include/ncbi-tools++/objects/seqalign/seqalign__.hpp include/ncbi-tools++/objects/seqalign/seqalign_exception.hpp include/ncbi-tools++/objects/seqalign/seqalign_macros.hpp -include/ncbi-tools++/objects/seqblock/.cvsignore -include/ncbi-tools++/objects/seqblock/.gitignore include/ncbi-tools++/objects/seqblock/EMBL_General_module.hpp include/ncbi-tools++/objects/seqblock/EMBL_block.hpp include/ncbi-tools++/objects/seqblock/EMBL_block_.hpp @@ -2663,8 +2575,6 @@ include/ncbi-tools++/objects/seqblock/SP include/ncbi-tools++/objects/seqblock/SP_block_.hpp include/ncbi-tools++/objects/seqblock/seqblock__.hpp include/ncbi-tools++/objects/seqblock/seqblock_macros.hpp -include/ncbi-tools++/objects/seqcode/.cvsignore -include/ncbi-tools++/objects/seqcode/.gitignore include/ncbi-tools++/objects/seqcode/NCBI_SeqCode_module.hpp include/ncbi-tools++/objects/seqcode/Seq_code_set.hpp include/ncbi-tools++/objects/seqcode/Seq_code_set_.hpp @@ -2675,8 +2585,6 @@ include/ncbi-tools++/objects/seqcode/Seq include/ncbi-tools++/objects/seqcode/Seq_map_table.hpp include/ncbi-tools++/objects/seqcode/Seq_map_table_.hpp include/ncbi-tools++/objects/seqcode/seqcode__.hpp -include/ncbi-tools++/objects/seqedit/.cvsignore -include/ncbi-tools++/objects/seqedit/.gitignore include/ncbi-tools++/objects/seqedit/NCBI_SeqEdit_module.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Cmd_.hpp @@ -2725,8 +2633,6 @@ include/ncbi-tools++/objects/seqedit/Seq include/ncbi-tools++/objects/seqedit/SeqEdit_Id.hpp include/ncbi-tools++/objects/seqedit/SeqEdit_Id_.hpp include/ncbi-tools++/objects/seqedit/seqedit__.hpp -include/ncbi-tools++/objects/seqfeat/.cvsignore -include/ncbi-tools++/objects/seqfeat/.gitignore include/ncbi-tools++/objects/seqfeat/BinomialOrgName.hpp include/ncbi-tools++/objects/seqfeat/BinomialOrgName_.hpp include/ncbi-tools++/objects/seqfeat/BioSource.hpp @@ -2847,8 +2753,6 @@ include/ncbi-tools++/objects/seqfeat/Var include/ncbi-tools++/objects/seqfeat/Variation_ref_.hpp include/ncbi-tools++/objects/seqfeat/seqfeat__.hpp include/ncbi-tools++/objects/seqfeat/seqfeat_macros.hpp -include/ncbi-tools++/objects/seqloc/.cvsignore -include/ncbi-tools++/objects/seqloc/.gitignore include/ncbi-tools++/objects/seqloc/Giimport_id.hpp include/ncbi-tools++/objects/seqloc/Giimport_id_.hpp include/ncbi-tools++/objects/seqloc/NCBI_Seqloc_module.hpp @@ -2884,8 +2788,6 @@ include/ncbi-tools++/objects/seqloc/Text include/ncbi-tools++/objects/seqloc/Textseq_id_.hpp include/ncbi-tools++/objects/seqloc/seqloc__.hpp include/ncbi-tools++/objects/seqloc/seqloc_macros.hpp -include/ncbi-tools++/objects/seqres/.cvsignore -include/ncbi-tools++/objects/seqres/.gitignore include/ncbi-tools++/objects/seqres/Byte_graph.hpp include/ncbi-tools++/objects/seqres/Byte_graph_.hpp include/ncbi-tools++/objects/seqres/Int_graph.hpp @@ -2896,8 +2798,6 @@ include/ncbi-tools++/objects/seqres/Real include/ncbi-tools++/objects/seqres/Seq_graph.hpp include/ncbi-tools++/objects/seqres/Seq_graph_.hpp include/ncbi-tools++/objects/seqres/seqres__.hpp -include/ncbi-tools++/objects/seqset/.cvsignore -include/ncbi-tools++/objects/seqset/.gitignore include/ncbi-tools++/objects/seqset/Bioseq_set.hpp include/ncbi-tools++/objects/seqset/Bioseq_set_.hpp include/ncbi-tools++/objects/seqset/NCBI_Seqset_module.hpp @@ -2907,8 +2807,6 @@ include/ncbi-tools++/objects/seqset/gb_r include/ncbi-tools++/objects/seqset/seqset__.hpp include/ncbi-tools++/objects/seqset/seqset_exception.hpp include/ncbi-tools++/objects/seqset/seqset_macros.hpp -include/ncbi-tools++/objects/seqsplit/.cvsignore -include/ncbi-tools++/objects/seqsplit/.gitignore include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids.hpp include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Ids_.hpp include/ncbi-tools++/objects/seqsplit/ID2S_Bioseq_Info.hpp @@ -2965,8 +2863,6 @@ include/ncbi-tools++/objects/seqsplit/ID include/ncbi-tools++/objects/seqsplit/ID2S_Split_Info_.hpp include/ncbi-tools++/objects/seqsplit/NCBI_Seq_split_module.hpp include/ncbi-tools++/objects/seqsplit/seqsplit__.hpp -include/ncbi-tools++/objects/seqtable/.cvsignore -include/ncbi-tools++/objects/seqtable/.gitignore include/ncbi-tools++/objects/seqtable/BVector_data.hpp include/ncbi-tools++/objects/seqtable/BVector_data_.hpp include/ncbi-tools++/objects/seqtable/CommonBytes_table.hpp @@ -2993,8 +2889,6 @@ include/ncbi-tools++/objects/seqtable/Se include/ncbi-tools++/objects/seqtable/impl/delta_cache.hpp include/ncbi-tools++/objects/seqtable/seq_table_exception.hpp include/ncbi-tools++/objects/seqtable/seqtable__.hpp -include/ncbi-tools++/objects/seqtest/.cvsignore -include/ncbi-tools++/objects/seqtest/.gitignore include/ncbi-tools++/objects/seqtest/NCBI_SeqTest_module.hpp include/ncbi-tools++/objects/seqtest/SeqTestResults.hpp include/ncbi-tools++/objects/seqtest/SeqTestResults_.hpp @@ -3003,8 +2897,6 @@ include/ncbi-tools++/objects/seqtest/Seq include/ncbi-tools++/objects/seqtest/Seq_test_result_set.hpp include/ncbi-tools++/objects/seqtest/Seq_test_result_set_.hpp include/ncbi-tools++/objects/seqtest/seqtest__.hpp -include/ncbi-tools++/objects/submit/.cvsignore -include/ncbi-tools++/objects/submit/.gitignore include/ncbi-tools++/objects/submit/Contact_info.hpp include/ncbi-tools++/objects/submit/Contact_info_.hpp include/ncbi-tools++/objects/submit/NCBI_Submit_module.hpp @@ -3014,8 +2906,6 @@ include/ncbi-tools++/objects/submit/Subm include/ncbi-tools++/objects/submit/Submit_block_.hpp include/ncbi-tools++/objects/submit/submit__.hpp include/ncbi-tools++/objects/submit/submit_macros.hpp -include/ncbi-tools++/objects/taxon1/.cvsignore -include/ncbi-tools++/objects/taxon1/.gitignore include/ncbi-tools++/objects/taxon1/NCBI_Taxon1_module.hpp include/ncbi-tools++/objects/taxon1/Taxon1_data.hpp include/ncbi-tools++/objects/taxon1/Taxon1_data_.hpp @@ -3034,8 +2924,6 @@ include/ncbi-tools++/objects/taxon1/Taxo 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 -include/ncbi-tools++/objects/taxon3/.gitignore include/ncbi-tools++/objects/taxon3/NCBI_Taxon3_module.hpp include/ncbi-tools++/objects/taxon3/SequenceOfInt.hpp include/ncbi-tools++/objects/taxon3/SequenceOfInt_.hpp @@ -3059,16 +2947,12 @@ include/ncbi-tools++/objects/taxon3/cach include/ncbi-tools++/objects/taxon3/itaxon3.hpp include/ncbi-tools++/objects/taxon3/taxon3.hpp include/ncbi-tools++/objects/taxon3/taxon3__.hpp -include/ncbi-tools++/objects/tinyseq/.cvsignore -include/ncbi-tools++/objects/tinyseq/.gitignore include/ncbi-tools++/objects/tinyseq/NCBI_TSeq_module.hpp include/ncbi-tools++/objects/tinyseq/TSeq.hpp include/ncbi-tools++/objects/tinyseq/TSeqSet.hpp include/ncbi-tools++/objects/tinyseq/TSeqSet_.hpp include/ncbi-tools++/objects/tinyseq/TSeq_.hpp include/ncbi-tools++/objects/tinyseq/tinyseq__.hpp -include/ncbi-tools++/objects/trackmgr/.cvsignore -include/ncbi-tools++/objects/trackmgr/.gitignore include/ncbi-tools++/objects/trackmgr/NCBI_TrackManager_module.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel.hpp include/ncbi-tools++/objects/trackmgr/TMgr_ACL_AccessLevel_.hpp @@ -3227,16 +3111,12 @@ include/ncbi-tools++/objects/trackmgr/tr include/ncbi-tools++/objects/trackmgr/trackmgr_client_.hpp include/ncbi-tools++/objects/trackmgr/trackmgr_export.h include/ncbi-tools++/objects/trackmgr/trackset_client.hpp -include/ncbi-tools++/objects/valerr/.cvsignore -include/ncbi-tools++/objects/valerr/.gitignore include/ncbi-tools++/objects/valerr/NCBI_ValErrors_module.hpp include/ncbi-tools++/objects/valerr/ValidErrItem.hpp include/ncbi-tools++/objects/valerr/ValidErrItem_.hpp include/ncbi-tools++/objects/valerr/ValidError.hpp include/ncbi-tools++/objects/valerr/ValidError_.hpp include/ncbi-tools++/objects/valerr/valerr__.hpp -include/ncbi-tools++/objects/valid/.cvsignore -include/ncbi-tools++/objects/valid/.gitignore include/ncbi-tools++/objects/valid/Comment_rule.hpp include/ncbi-tools++/objects/valid/Comment_rule_.hpp include/ncbi-tools++/objects/valid/Comment_set.hpp @@ -3255,8 +3135,6 @@ include/ncbi-tools++/objects/valid/Phras include/ncbi-tools++/objects/valid/Severity_level.hpp include/ncbi-tools++/objects/valid/Severity_level_.hpp include/ncbi-tools++/objects/valid/valid__.hpp -include/ncbi-tools++/objects/variation/.cvsignore -include/ncbi-tools++/objects/variation/.gitignore include/ncbi-tools++/objects/variation/NCBI_VariationPackage_module.hpp include/ncbi-tools++/objects/variation/VariantPlacement.hpp include/ncbi-tools++/objects/variation/VariantPlacement_.hpp @@ -3267,8 +3145,6 @@ 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 @@ -3277,8 +3153,6 @@ include/ncbi-tools++/objects/variation_l 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 @@ -3291,8 +3165,6 @@ include/ncbi-tools++/objects/variation_l 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 include/ncbi-tools++/objects/varrep/AaInterval_.hpp include/ncbi-tools++/objects/varrep/AaLocation.hpp @@ -3574,6 +3446,7 @@ include/ncbi-tools++/objtools/cleanup/cl 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/cleanup/huge_file_cleanup.hpp include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader.hpp include/ncbi-tools++/objtools/data_loaders/blastdb/bdbloader_rmt.hpp include/ncbi-tools++/objtools/data_loaders/blastdb/blastdb_adapter.hpp @@ -3637,6 +3510,7 @@ include/ncbi-tools++/objtools/edit/cds_f 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/eutils_updater.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 @@ -3645,13 +3519,20 @@ include/ncbi-tools++/objtools/edit/gap_t 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 +include/ncbi-tools++/objtools/edit/huge_asn_loader.hpp +include/ncbi-tools++/objtools/edit/huge_asn_macro_reader.hpp +include/ncbi-tools++/objtools/edit/huge_asn_reader.hpp +include/ncbi-tools++/objtools/edit/huge_file.hpp +include/ncbi-tools++/objtools/edit/huge_file_process.hpp include/ncbi-tools++/objtools/edit/link_cds_mrna.hpp include/ncbi-tools++/objtools/edit/loc_edit.hpp include/ncbi-tools++/objtools/edit/mail_report.hpp +include/ncbi-tools++/objtools/edit/mla_updater.hpp include/ncbi-tools++/objtools/edit/parse_text_options.hpp include/ncbi-tools++/objtools/edit/promote.hpp include/ncbi-tools++/objtools/edit/pub_fix.hpp include/ncbi-tools++/objtools/edit/publication_edit.hpp +include/ncbi-tools++/objtools/edit/pubmed_updater.hpp include/ncbi-tools++/objtools/edit/remote_updater.hpp include/ncbi-tools++/objtools/edit/rna_edit.hpp include/ncbi-tools++/objtools/edit/seq_edit.hpp @@ -3673,8 +3554,704 @@ include/ncbi-tools++/objtools/eutils/api include/ncbi-tools++/objtools/eutils/api/espell.hpp include/ncbi-tools++/objtools/eutils/api/esummary.hpp include/ncbi-tools++/objtools/eutils/api/eutils.hpp -include/ncbi-tools++/objtools/eutils/egquery/.cvsignore -include/ncbi-tools++/objtools/eutils/egquery/.gitignore +include/ncbi-tools++/objtools/eutils/efetch/Abs.hpp +include/ncbi-tools++/objtools/eutils/efetch/Abs_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Abstract.hpp +include/ncbi-tools++/objtools/eutils/efetch/AbstractText.hpp +include/ncbi-tools++/objtools/eutils/efetch/AbstractText_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Abstract_.hpp +include/ncbi-tools++/objtools/eutils/efetch/AccessionNumber.hpp +include/ncbi-tools++/objtools/eutils/efetch/AccessionNumberList.hpp +include/ncbi-tools++/objtools/eutils/efetch/AccessionNumberList_.hpp +include/ncbi-tools++/objtools/eutils/efetch/AccessionNumber_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Acronym.hpp +include/ncbi-tools++/objtools/eutils/efetch/Acronym_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Affiliation.hpp +include/ncbi-tools++/objtools/eutils/efetch/AffiliationInfo.hpp +include/ncbi-tools++/objtools/eutils/efetch/AffiliationInfo_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Affiliation_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Agency.hpp +include/ncbi-tools++/objtools/eutils/efetch/Agency_.hpp +include/ncbi-tools++/objtools/eutils/efetch/And.hpp +include/ncbi-tools++/objtools/eutils/efetch/And_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Annotation.hpp +include/ncbi-tools++/objtools/eutils/efetch/Annotation_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Annotation_xml.hpp +include/ncbi-tools++/objtools/eutils/efetch/Annotation_xml_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Apply.hpp +include/ncbi-tools++/objtools/eutils/efetch/Apply_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Apply_content.hpp +include/ncbi-tools++/objtools/eutils/efetch/Apply_content_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Approx.hpp +include/ncbi-tools++/objtools/eutils/efetch/Approx_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccos.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccos_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccosh.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccosh_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccot.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccot_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccoth.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccoth_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccsc.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccsc_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccsch.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arccsch_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsec.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsec_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsech.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsech_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsin.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsin_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsinh.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arcsinh_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arctan.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arctan_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arctanh.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arctanh_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arg.hpp +include/ncbi-tools++/objtools/eutils/efetch/Arg_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Article.hpp +include/ncbi-tools++/objtools/eutils/efetch/ArticleDate.hpp +include/ncbi-tools++/objtools/eutils/efetch/ArticleDate_.hpp 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+include/ncbi-tools++/objtools/eutils/efetch/Suffix.hpp +include/ncbi-tools++/objtools/eutils/efetch/Suffix_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Sum.hpp +include/ncbi-tools++/objtools/eutils/efetch/Sum_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Sup.hpp +include/ncbi-tools++/objtools/eutils/efetch/Sup_.hpp +include/ncbi-tools++/objtools/eutils/efetch/SupplMeshList.hpp +include/ncbi-tools++/objtools/eutils/efetch/SupplMeshList_.hpp +include/ncbi-tools++/objtools/eutils/efetch/SupplMeshName.hpp +include/ncbi-tools++/objtools/eutils/efetch/SupplMeshName_.hpp +include/ncbi-tools++/objtools/eutils/efetch/TableCellExpression.hpp +include/ncbi-tools++/objtools/eutils/efetch/TableCellExpression_.hpp +include/ncbi-tools++/objtools/eutils/efetch/TableRowExpression.hpp +include/ncbi-tools++/objtools/eutils/efetch/TableRowExpression_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Tan.hpp +include/ncbi-tools++/objtools/eutils/efetch/Tan_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Tanh.hpp +include/ncbi-tools++/objtools/eutils/efetch/Tanh_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Tendsto.hpp +include/ncbi-tools++/objtools/eutils/efetch/Tendsto_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Text.hpp +include/ncbi-tools++/objtools/eutils/efetch/Text_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Times.hpp +include/ncbi-tools++/objtools/eutils/efetch/Times_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Title.hpp +include/ncbi-tools++/objtools/eutils/efetch/Title_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Token_content.hpp +include/ncbi-tools++/objtools/eutils/efetch/Token_content_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Transpose.hpp +include/ncbi-tools++/objtools/eutils/efetch/Transpose_.hpp +include/ncbi-tools++/objtools/eutils/efetch/True.hpp +include/ncbi-tools++/objtools/eutils/efetch/True_.hpp +include/ncbi-tools++/objtools/eutils/efetch/U.hpp +include/ncbi-tools++/objtools/eutils/efetch/URL.hpp +include/ncbi-tools++/objtools/eutils/efetch/URL_.hpp +include/ncbi-tools++/objtools/eutils/efetch/U_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Union.hpp +include/ncbi-tools++/objtools/eutils/efetch/Union_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Uplimit.hpp +include/ncbi-tools++/objtools/eutils/efetch/Uplimit_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Variance.hpp +include/ncbi-tools++/objtools/eutils/efetch/Variance_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Vector.hpp +include/ncbi-tools++/objtools/eutils/efetch/Vector_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Vectorproduct.hpp +include/ncbi-tools++/objtools/eutils/efetch/Vectorproduct_.hpp +include/ncbi-tools++/objtools/eutils/efetch/VernacularTitle.hpp +include/ncbi-tools++/objtools/eutils/efetch/VernacularTitle_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Volume.hpp +include/ncbi-tools++/objtools/eutils/efetch/VolumeTitle.hpp +include/ncbi-tools++/objtools/eutils/efetch/VolumeTitle_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Volume_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Xor.hpp +include/ncbi-tools++/objtools/eutils/efetch/Xor_.hpp +include/ncbi-tools++/objtools/eutils/efetch/Year.hpp +include/ncbi-tools++/objtools/eutils/efetch/Year_.hpp +include/ncbi-tools++/objtools/eutils/efetch/efetch__.hpp +include/ncbi-tools++/objtools/eutils/efetch/efetch_module.hpp include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult.hpp include/ncbi-tools++/objtools/eutils/egquery/EGQueryResult_.hpp include/ncbi-tools++/objtools/eutils/egquery/Result.hpp @@ -3683,16 +4260,12 @@ include/ncbi-tools++/objtools/eutils/egq include/ncbi-tools++/objtools/eutils/egquery/Result_.hpp include/ncbi-tools++/objtools/eutils/egquery/egquery__.hpp include/ncbi-tools++/objtools/eutils/egquery/egquery_module.hpp -include/ncbi-tools++/objtools/eutils/ehistory/.cvsignore -include/ncbi-tools++/objtools/eutils/ehistory/.gitignore include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem.hpp include/ncbi-tools++/objtools/eutils/ehistory/EHistoryItem_.hpp include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult.hpp include/ncbi-tools++/objtools/eutils/ehistory/EHistoryResult_.hpp include/ncbi-tools++/objtools/eutils/ehistory/ehistory__.hpp include/ncbi-tools++/objtools/eutils/ehistory/ehistory_module.hpp -include/ncbi-tools++/objtools/eutils/einfo/.cvsignore -include/ncbi-tools++/objtools/eutils/einfo/.gitignore include/ncbi-tools++/objtools/eutils/einfo/DbInfo.hpp include/ncbi-tools++/objtools/eutils/einfo/DbInfo_.hpp include/ncbi-tools++/objtools/eutils/einfo/DbList.hpp @@ -3709,8 +4282,6 @@ include/ncbi-tools++/objtools/eutils/ein include/ncbi-tools++/objtools/eutils/einfo/Link_.hpp include/ncbi-tools++/objtools/eutils/einfo/einfo__.hpp include/ncbi-tools++/objtools/eutils/einfo/einfo_module.hpp -include/ncbi-tools++/objtools/eutils/elink/.cvsignore -include/ncbi-tools++/objtools/eutils/elink/.gitignore include/ncbi-tools++/objtools/eutils/elink/ELinkResult.hpp include/ncbi-tools++/objtools/eutils/elink/ELinkResult_.hpp include/ncbi-tools++/objtools/eutils/elink/FirstChars.hpp @@ -3747,16 +4318,12 @@ include/ncbi-tools++/objtools/eutils/eli include/ncbi-tools++/objtools/eutils/elink/Url_.hpp include/ncbi-tools++/objtools/eutils/elink/elink__.hpp include/ncbi-tools++/objtools/eutils/elink/elink_module.hpp -include/ncbi-tools++/objtools/eutils/epost/.cvsignore -include/ncbi-tools++/objtools/eutils/epost/.gitignore include/ncbi-tools++/objtools/eutils/epost/EPostResult.hpp include/ncbi-tools++/objtools/eutils/epost/EPostResult_.hpp include/ncbi-tools++/objtools/eutils/epost/InvalidIdList.hpp include/ncbi-tools++/objtools/eutils/epost/InvalidIdList_.hpp include/ncbi-tools++/objtools/eutils/epost/epost__.hpp include/ncbi-tools++/objtools/eutils/epost/epost_module.hpp -include/ncbi-tools++/objtools/eutils/esearch/.cvsignore -include/ncbi-tools++/objtools/eutils/esearch/.gitignore include/ncbi-tools++/objtools/eutils/esearch/ESearchResult.hpp include/ncbi-tools++/objtools/eutils/esearch/ESearchResult_.hpp include/ncbi-tools++/objtools/eutils/esearch/ErrorList.hpp @@ -3775,16 +4342,12 @@ include/ncbi-tools++/objtools/eutils/ese include/ncbi-tools++/objtools/eutils/esearch/WarningList_.hpp include/ncbi-tools++/objtools/eutils/esearch/esearch__.hpp include/ncbi-tools++/objtools/eutils/esearch/esearch_module.hpp -include/ncbi-tools++/objtools/eutils/espell/.cvsignore -include/ncbi-tools++/objtools/eutils/espell/.gitignore include/ncbi-tools++/objtools/eutils/espell/ESpellResult.hpp include/ncbi-tools++/objtools/eutils/espell/ESpellResult_.hpp include/ncbi-tools++/objtools/eutils/espell/SpelledQuery.hpp include/ncbi-tools++/objtools/eutils/espell/SpelledQuery_.hpp include/ncbi-tools++/objtools/eutils/espell/espell__.hpp include/ncbi-tools++/objtools/eutils/espell/espell_module.hpp -include/ncbi-tools++/objtools/eutils/esummary/.cvsignore -include/ncbi-tools++/objtools/eutils/esummary/.gitignore include/ncbi-tools++/objtools/eutils/esummary/DocSum.hpp include/ncbi-tools++/objtools/eutils/esummary/DocSum_.hpp include/ncbi-tools++/objtools/eutils/esummary/ESummaryResult.hpp @@ -3793,8 +4356,6 @@ include/ncbi-tools++/objtools/eutils/esu include/ncbi-tools++/objtools/eutils/esummary/Item_.hpp include/ncbi-tools++/objtools/eutils/esummary/esummary__.hpp include/ncbi-tools++/objtools/eutils/esummary/esummary_module.hpp -include/ncbi-tools++/objtools/eutils/uilist/.cvsignore -include/ncbi-tools++/objtools/eutils/uilist/.gitignore include/ncbi-tools++/objtools/eutils/uilist/IdList.hpp include/ncbi-tools++/objtools/eutils/uilist/IdList_.hpp include/ncbi-tools++/objtools/eutils/uilist/uilist__.hpp @@ -4044,9 +4605,11 @@ include/ncbi-tools++/sra/readers/ncbi_tr include/ncbi-tools++/sra/readers/sra/csraread.hpp include/ncbi-tools++/sra/readers/sra/exception.hpp include/ncbi-tools++/sra/readers/sra/graphread.hpp +include/ncbi-tools++/sra/readers/sra/impl/snpread_packed.hpp include/ncbi-tools++/sra/readers/sra/impl/wgs-contig.h include/ncbi-tools++/sra/readers/sra/impl/wgsresolver_impl.hpp include/ncbi-tools++/sra/readers/sra/kdbread.hpp +include/ncbi-tools++/sra/readers/sra/limited_resource_map.hpp include/ncbi-tools++/sra/readers/sra/sdk.hpp include/ncbi-tools++/sra/readers/sra/snpread.hpp include/ncbi-tools++/sra/readers/sra/sraread.hpp @@ -4111,6 +4674,7 @@ include/ncbi-tools++/util/bitset/ncbi_bi include/ncbi-tools++/util/bitset/ncbi_bitset_alloc.hpp include/ncbi-tools++/util/bitset/ncbi_bitset_util.hpp include/ncbi-tools++/util/bitset/readme +include/ncbi-tools++/util/bitset/sse2neon.h include/ncbi-tools++/util/buffer_writer.hpp include/ncbi-tools++/util/bytesrc.hpp include/ncbi-tools++/util/cache/cache_async.hpp @@ -4134,6 +4698,7 @@ include/ncbi-tools++/util/compress/zlib. include/ncbi-tools++/util/compress/zlib/zconf.h include/ncbi-tools++/util/compress/zlib/zlib.h include/ncbi-tools++/util/compress/zlib/zutil.h +include/ncbi-tools++/util/compress/zstd.hpp include/ncbi-tools++/util/creaders/alnread.h include/ncbi-tools++/util/creaders/creaders_export.h include/ncbi-tools++/util/data_histogram.hpp @@ -4151,11 +4716,14 @@ include/ncbi-tools++/util/icanceled.hpp include/ncbi-tools++/util/id_mux.hpp include/ncbi-tools++/util/impl/compile_time_bits.hpp include/ncbi-tools++/util/impl/const_tuple.hpp +include/ncbi-tools++/util/impl/ct_bitset_cxx14.hpp +include/ncbi-tools++/util/impl/ct_bitset_cxx17.hpp include/ncbi-tools++/util/impl/ct_crc32.hpp include/ncbi-tools++/util/impl/ct_string_cxx14.hpp include/ncbi-tools++/util/impl/ct_string_cxx17.hpp include/ncbi-tools++/util/impl/ctsort_cxx14.hpp include/ncbi-tools++/util/impl/floating_point_comparison.hpp +include/ncbi-tools++/util/impl/generated_fsm.hpp include/ncbi-tools++/util/itransaction.hpp include/ncbi-tools++/util/itree.hpp include/ncbi-tools++/util/itree.inl @@ -4172,6 +4740,7 @@ include/ncbi-tools++/util/math/matrix.hp include/ncbi-tools++/util/math/miscmath.h include/ncbi-tools++/util/math/promote.hpp include/ncbi-tools++/util/md5.hpp +include/ncbi-tools++/util/message_queue.hpp include/ncbi-tools++/util/miscmath.h include/ncbi-tools++/util/multi_writer.hpp include/ncbi-tools++/util/multipattern_search.hpp @@ -4290,6 +4859,8 @@ lib/ncbi-tools++/libdbsnp_tooltip_servic lib/ncbi-tools++/libdbsnp_tooltip_service.a lib/ncbi-tools++/libdocsum-static.a lib/ncbi-tools++/libdocsum.a +lib/ncbi-tools++/libefetch-static.a +lib/ncbi-tools++/libefetch.a lib/ncbi-tools++/libegquery-static.a lib/ncbi-tools++/libegquery.a lib/ncbi-tools++/libehistory-static.a Index: pkgsrc/biology/ncbi-blast+/buildlink3.mk diff -u pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.5 pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.6 --- pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.5 Tue Jun 28 11:31:01 2022 +++ pkgsrc/biology/ncbi-blast+/buildlink3.mk Sun May 28 22:48:27 2023 @@ -1,12 +1,11 @@ -# $NetBSD: buildlink3.mk,v 1.5 2022/06/28 11:31:01 wiz Exp $ +# $NetBSD: buildlink3.mk,v 1.6 2023/05/28 22:48:27 bacon Exp $ BUILDLINK_TREE+= ncbi-blast+ .if !defined(NCBI_BLAST+_BUILDLINK3_MK) NCBI_BLAST+_BUILDLINK3_MK:= -BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.13.0 -BUILDLINK_ABI_DEPENDS.ncbi-blast+?= ncbi-blast+>=2.13.0nb2 +BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.14.0 BUILDLINK_PKGSRCDIR.ncbi-blast+?= ../../biology/ncbi-blast+ .endif # NCBI_BLAST+_BUILDLINK3_MK Index: pkgsrc/biology/ncbi-blast+/distinfo diff -u pkgsrc/biology/ncbi-blast+/distinfo:1.7 pkgsrc/biology/ncbi-blast+/distinfo:1.8 --- pkgsrc/biology/ncbi-blast+/distinfo:1.7 Sun Apr 10 20:54:51 2022 +++ pkgsrc/biology/ncbi-blast+/distinfo Sun May 28 22:48:27 2023 @@ -1,12 +1,14 @@ -$NetBSD: distinfo,v 1.7 2022/04/10 20:54:51 bacon Exp $ +$NetBSD: distinfo,v 1.8 2023/05/28 22:48:27 bacon Exp $ -BLAKE2s (ncbi-blast-2.13.0+-src.tar.gz) = a83651c7f2824def1c86a8541cf7060ed77e6d60e8f7bd0383464088591733f3 -SHA512 (ncbi-blast-2.13.0+-src.tar.gz) = 7842ba4dac3d046a23cb182c6289d88cb1173e8570fb6334c1aa88dd2e640aacad43efe1ef7d69b8fedbf9b8093b7d601ef8999812d5735a6789ab2752e97c2b -Size (ncbi-blast-2.13.0+-src.tar.gz) = 59995353 bytes +BLAKE2s (ncbi-blast-2.14.0+-src.tar.gz) = fbda12e9d778e0a84df0195964b397a08fba4f067c55525556e3831ecdd7b252 +SHA512 (ncbi-blast-2.14.0+-src.tar.gz) = 30f6292cacb7c2ec0a00803c697ab0255ccee1c82a40923df0f3e4f856204db8da5be212b5ec02e0acb8000396a71f600c35e63f83eaf30e1a9639e4c95c4a83 +Size (ncbi-blast-2.14.0+-src.tar.gz) = 28200227 bytes SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5 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-xcode.sh) = 9167a5092d30da46a06b0be05199afa3b08680c6 +SHA1 (patch-src_build-system_cmake_cmake-cfg-xcode.sh) = b50a53ac7f2bd191d0d85cf490ac891f2cf20bfa SHA1 (patch-src_build-system_configure) = 95185d53179a69a1b1cfa6870aca36dd962d2c43 SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd +SHA1 (patch-src_util_checksum_cityhash_city.cc) = ff8e84d90a4fc0d9d33e17abd05ed8e9f2de12fc +SHA1 (patch-src_util_checksum_farmhash_farmhash.cc) = 9b56d69ab7c0da328c35bba4dde04134dd80efc6 SHA1 (patch-src_util_checksum_farmhash_farmhash.h) = c3ff60de9a9020d3b706c2bff37f6f4cde4e6b6b Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.2 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.3 --- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh:1.2 Sun Apr 10 20:54:51 2022 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh Sun May 28 22:48:27 2023 @@ -1,15 +1,21 @@ -$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.2 2022/04/10 20:54:51 bacon Exp $ +$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.3 2023/05/28 22:48:27 bacon Exp $ -# Portability +# sh portability ---- src/build-system/cmake/cmake-cfg-xcode.sh.orig 2021-06-10 11:54:05.800996703 +0000 +--- src/build-system/cmake/cmake-cfg-xcode.sh.orig 2023-05-26 12:05:14.109542442 +0000 +++ src/build-system/cmake/cmake-cfg-xcode.sh -@@ -218,7 +218,7 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L - +@@ -249,12 +249,12 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L if [ -z "$BUILD_ROOT" ]; then - BUILD_ROOT=CMake-${CC_NAME}${CC_VERSION} -- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then -+ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then - BUILD_ROOT="$BUILD_ROOT"-DLL + if [ -z "$BUILD_TYPE" ]; then + BUILD_ROOT=CMake-${CC_NAME}${CC_VERSION} +- if [ "$BUILD_SHARED_LIBS" == "ON" ]; then ++ if [ "$BUILD_SHARED_LIBS" = "ON" ]; then + BUILD_ROOT="$BUILD_ROOT"-DLL + fi + else + 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 fi - fi Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure diff -u pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.3 pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.4 --- pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.3 Sun Apr 10 20:54:51 2022 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure Sun May 28 22:48:27 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-src_build-system_configure,v 1.3 2022/04/10 20:54:51 bacon Exp $ +$NetBSD: patch-src_build-system_configure,v 1.4 2023/05/28 22:48:27 bacon Exp $ # Avert missing --with-libiconv-prefix option Added files: Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc:1.1 --- /dev/null Sun May 28 22:48:27 2023 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc Sun May 28 22:48:27 2023 @@ -0,0 +1,17 @@ +$NetBSD: patch-src_util_checksum_cityhash_city.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $ + +Ensure bswap_32() and bswap_64() is defined on NetBSD. + +--- src/util/checksum/cityhash/city.cc.orig 2018-09-28 20:34:39.000000000 +0000 ++++ src/util/checksum/cityhash/city.cc +@@ -82,10 +82,8 @@ static uint32 UNALIGNED_LOAD32(const cha + + #include + #include +-#if defined(__BSWAP_RENAME) && !defined(__bswap_32) + #define bswap_32(x) bswap32(x) + #define bswap_64(x) bswap64(x) +-#endif + + #else + Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc:1.1 --- /dev/null Sun May 28 22:48:27 2023 +++ pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc Sun May 28 22:48:27 2023 @@ -0,0 +1,21 @@ +$NetBSD: patch-src_util_checksum_farmhash_farmhash.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $ + +Ensure bswap_32() and bswap_64() gets defined on NetBSD. + +--- src/util/checksum/farmhash/farmhash.cc.orig 2018-09-26 12:38:06.000000000 +0000 ++++ src/util/checksum/farmhash/farmhash.cc +@@ -158,12 +158,12 @@ + + #include + #include +-#if defined(__BSWAP_RENAME) && !defined(__bswap_32) ++#if defined(bswap_32) && defined(bswap_64) + #undef bswap_32 + #undef bswap_64 ++#endif + #define bswap_32(x) bswap32(x) + #define bswap_64(x) bswap64(x) +-#endif + + #elif defined(__HAIKU__) + --_----------=_1685314107216150--