From ae3e6180c230a13dc94e8d8599316d55ceab3d39 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Thu, 21 Feb 2013 23:56:39 +0100 Subject: First working patch Signed-off-by: Justin Lecher --- .../files/ncbi-tools++-9.0.0-as-needed.patch | 758 ++++++++++++++++----- 1 file changed, 602 insertions(+), 156 deletions(-) (limited to 'sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch') diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch index 610ee24ab..f5d6a3d67 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-9.0.0-as-needed.patch @@ -1,135 +1,184 @@ - src/algo/align/ngalign/Makefile.xngalign.lib | 2 ++ - src/algo/blast/api/Makefile.xblast.lib | 2 +- - src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +- - src/algo/blast/core/Makefile.blast.lib | 2 ++ - src/algo/cobalt/Makefile.cobalt.lib | 2 ++ - src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++ - src/algo/sequence/Makefile.xalgoseq.lib | 2 ++ - src/algo/structure/struct_dp/Makefile.xstruct_dp.lib | 2 ++ - src/algo/structure/struct_util/Makefile.xstruct_util.lib | 2 ++ - src/algo/structure/threader/Makefile.xstruct_thread.lib | 2 ++ - src/algo/winmask/Makefile.xalgowinmask.lib | 1 + - src/cgi/Makefile.cgi.lib | 2 ++ - src/cgi/Makefile.fcgi.lib | 2 ++ - src/connect/Makefile.connssl.lib | 2 ++ - src/connect/Makefile.xconnect.lib | 4 ++++ - src/connect/Makefile.xthrserv.lib | 2 +- - src/connect/Makefile.xxconnect.lib | 2 ++ - src/connect/services/Makefile.ncbi_xcache_netcache.lib | 2 +- - src/connect/services/Makefile.xconnserv.lib | 2 +- - src/connect/test/Makefile.conntest.lib | 2 ++ - src/corelib/Makefile.test_boost.lib | 2 ++ - src/corelib/Makefile.test_mt.lib | 2 ++ - src/corelib/test/Makefile.pbacktest.lib | 2 ++ - src/db/bdb/Makefile.bdb.lib | 4 ++++ - src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +- - src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++ - src/dbapi/Makefile.dbapi.lib | 5 +++++ - src/dbapi/driver/Makefile.dbapi_driver.lib | 2 ++ - src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib | 2 ++ - src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib | 2 +- - src/dbapi/simple/Makefile.sdbapi.lib | 1 + - src/html/Makefile.html.lib | 2 ++ - src/objects/access/Makefile.access.lib | 1 + - src/objects/biblio/Makefile.biblio.lib | 2 ++ - src/objects/biotree/Makefile.biotree.lib | 2 ++ - src/objects/blast/Makefile.blast.lib | 2 ++ - src/objects/blast/Makefile.xnetblastcli.lib | 2 ++ - src/objects/blastdb/Makefile.blastdb.lib | 2 ++ - src/objects/blastxml/Makefile.blastxml.lib | 2 ++ - src/objects/cdd/Makefile.cdd.lib | 2 ++ - src/objects/cn3d/Makefile.cn3d.lib | 2 ++ - src/objects/docsum/Makefile.docsum.lib | 2 ++ - src/objects/entrez2/Makefile.entrez2.lib | 2 ++ - src/objects/entrez2/Makefile.entrez2cli.lib | 2 ++ - src/objects/entrezgene/Makefile.entrezgene.lib | 2 ++ - src/objects/featdef/Makefile.featdef.lib | 2 ++ - src/objects/gbseq/Makefile.gbseq.lib | 2 ++ - src/objects/general/Makefile.general.lib | 2 ++ - src/objects/genomecoll/Makefile.genome_collection.lib | 2 ++ - src/objects/homologene/Makefile.homologene.lib | 2 ++ - src/objects/id1/Makefile.id1.lib | 2 ++ - src/objects/id1/Makefile.id1cli.lib | 2 ++ - src/objects/id2/Makefile.id2.lib | 2 ++ - src/objects/id2/Makefile.id2cli.lib | 2 ++ - src/objects/insdseq/Makefile.insdseq.lib | 2 ++ - src/objects/macro/Makefile.macro.lib | 2 ++ - src/objects/medlars/Makefile.medlars.lib | 2 ++ - src/objects/medline/Makefile.medline.lib | 2 ++ - src/objects/mim/Makefile.mim.lib | 2 ++ - src/objects/mla/Makefile.mla.lib | 2 ++ - src/objects/mla/Makefile.mlacli.lib | 2 ++ - src/objects/mmdb/Makefile.mmdb.lib | 2 ++ - src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++ - src/objects/objprt/Makefile.objprt.lib | 2 ++ - src/objects/omssa/Makefile.omssa.lib | 2 ++ - src/objects/pcassay/Makefile.pcassay.lib | 2 ++ - src/objects/pcsubstance/Makefile.pcsubstance.lib | 2 ++ - src/objects/proj/Makefile.proj.lib | 2 ++ - src/objects/pub/Makefile.pub.lib | 2 ++ - src/objects/pubmed/Makefile.pubmed.lib | 2 ++ - src/objects/remap/Makefile.remap.lib | 2 ++ - src/objects/remap/Makefile.remapcli.lib | 2 ++ - src/objects/scoremat/Makefile.scoremat.lib | 2 ++ - src/objects/seq/Makefile.seq.lib | 2 ++ - src/objects/seqcode/Makefile.seqcode.lib | 2 ++ - src/objects/seqedit/Makefile.seqedit.lib | 1 + - src/objects/seqset/Makefile.seqset.lib | 1 + - src/objects/seqsplit/Makefile.seqsplit.lib | 2 ++ - src/objects/seqtest/Makefile.seqtest.lib | 2 ++ - src/objects/submit/Makefile.submit.lib | 1 + - src/objects/taxon1/Makefile.taxon1.lib | 2 ++ - src/objects/taxon3/Makefile.taxon3.lib | 2 ++ - src/objects/tinyseq/Makefile.tinyseq.lib | 2 ++ - src/objects/valerr/Makefile.valerr.lib | 2 ++ - src/objects/valid/Makefile.valid.lib | 2 ++ - src/objects/variation/Makefile.variation.lib | 1 + - src/objmgr/split/Makefile.id2_split.lib | 2 +- - src/objmgr/util/Makefile.util.lib | 1 + - src/objtools/align_format/Makefile.align_format.lib | 2 ++ - src/objtools/alnmgr/Makefile.alnmgr.lib | 1 + - src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++ - src/objtools/blast/gene_info_reader/Makefile.gene_info.lib | 2 ++ - src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib | 2 ++ - src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++ - src/objtools/blast/seqdb_writer/Makefile.writedb.lib | 2 ++ - src/objtools/blast/services/Makefile.blast_services.lib | 1 + - src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++ - src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- - src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++ - src/objtools/edit/Makefile.edit.lib | 2 ++ - src/objtools/eutils/egquery/Makefile.egquery.lib | 2 ++ - src/objtools/eutils/ehistory/Makefile.ehistory.lib | 2 ++ - src/objtools/eutils/einfo/Makefile.einfo.lib | 2 ++ - src/objtools/eutils/elink/Makefile.elink.lib | 2 ++ - src/objtools/eutils/epost/Makefile.epost.lib | 2 ++ - src/objtools/eutils/esearch/Makefile.esearch.lib | 2 ++ - src/objtools/eutils/espell/Makefile.espell.lib | 2 ++ - src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++ - src/objtools/eutils/linkout/Makefile.linkout.lib | 2 ++ - src/objtools/format/Makefile.xformat.lib | 2 ++ - src/objtools/lds/Makefile.lds.lib | 2 +- - src/objtools/manip/Makefile.xobjmanip.lib | 2 ++ - src/objtools/readers/Makefile.xobjread.lib | 3 +-- - src/objtools/readers/Makefile.xobjreadex.lib | 2 +- - src/objtools/simple/Makefile.xobjsimple.lib | 1 + - src/objtools/validator/Makefile.validator.lib | 2 ++ - src/objtools/writers/Makefile.xobjwrite.lib | 1 + - src/serial/Makefile.serial.lib | 2 ++ - src/serial/soap/Makefile.soap.lib | 2 ++ - src/serial/soap/Makefile.soap_server.lib | 2 ++ - src/serial/test/Makefile.we_cpp.lib | 1 + - src/sra/sdk/libs/align/Makefile.align-writer.lib | 2 +- - src/util/Makefile.util.lib | 2 ++ - src/util/compress/api/Makefile.compress.lib | 2 +- - src/util/qparse/Makefile.xqueryparse.lib | 2 ++ - src/util/regexp/Makefile.regexp.lib | 2 ++ - src/util/sequtil/Makefile.sequtil.lib | 2 ++ - src/util/xregexp/Makefile.xregexp.lib | 2 +- - 128 files changed, 237 insertions(+), 16 deletions(-) + src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib | 2 ++ + src/algo/align/ngalign/Makefile.xngalign.lib | 2 ++ + src/algo/align/nw/Makefile.xalgoalignnw.lib | 2 ++ + src/algo/align/prosplign/Makefile.prosplign.lib | 2 ++ + src/algo/align/splign/Makefile.xalgoalignsplign.lib | 2 ++ + src/algo/blast/api/Makefile.xblast.lib | 2 +- + src/algo/blast/blastinput/Makefile.blastinput.lib | 2 +- + src/algo/blast/core/Makefile.blast.lib | 2 ++ + src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib | 2 ++ + src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib | 2 ++ + src/algo/blast/format/Makefile.xblastformat.lib | 2 +- + src/algo/blast/gumbel_params/Makefile.gumbelparams.lib | 1 + + src/algo/cobalt/Makefile.cobalt.lib | 2 ++ + src/algo/dustmask/Makefile.xalgodustmask.lib | 1 + + src/algo/gnomon/Makefile.gnomon.lib | 2 +- + src/algo/ms/formats/pepxml/Makefile.pepXML.lib | 2 ++ + src/algo/ms/omssa/Makefile.xomssa.lib | 2 ++ + src/algo/phy_tree/Makefile.xalgophytree.lib | 2 +- + src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib | 2 ++ + src/algo/segmask/Makefile.xalgosegmask.lib | 1 + + src/algo/seqqa/Makefile.xalgoseqqa.lib | 2 ++ + src/algo/sequence/Makefile.xalgoseq.lib | 2 ++ + src/algo/structure/bma_refine/Makefile.xbma_refiner.lib | 3 +++ + src/algo/structure/cd_utils/Makefile.xcd_utils.lib | 2 +- + src/algo/structure/struct_dp/Makefile.xstruct_dp.lib | 2 ++ + src/algo/structure/struct_util/Makefile.xstruct_util.lib | 2 ++ + src/algo/structure/threader/Makefile.xstruct_thread.lib | 2 ++ + src/algo/text/Makefile.xalgotext.lib | 2 ++ + src/algo/volume_merge/Makefile.xalgovmerge.lib | 2 ++ + src/algo/winmask/Makefile.xalgowinmask.lib | 2 ++ + src/cgi/Makefile.cgi.lib | 2 ++ + src/cgi/Makefile.fcgi.lib | 2 ++ + src/connect/Makefile.connssl.lib | 2 ++ + src/connect/Makefile.xconnect.lib | 4 ++++ + src/connect/Makefile.xthrserv.lib | 2 +- + src/connect/Makefile.xxconnect.lib | 2 ++ + src/connect/services/Makefile.ncbi_xcache_netcache.lib | 2 +- + src/connect/services/Makefile.xconnserv.lib | 2 +- + src/connect/test/Makefile.conntest.lib | 2 ++ + src/corelib/Makefile.test_boost.lib | 2 ++ + src/corelib/Makefile.test_mt.lib | 2 ++ + src/corelib/test/Makefile.pbacktest.lib | 2 ++ + src/db/bdb/Makefile.bdb.lib | 4 ++++ + src/db/bdb/Makefile.ncbi_xcache_bdb.lib | 2 +- + src/db/sqlite/Makefile.sqlitewrapp.lib | 3 +++ + src/dbapi/Makefile.dbapi.lib | 5 +++++ + src/dbapi/driver/Makefile.dbapi_driver.lib | 2 ++ + src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib | 2 ++ + src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib | 2 +- + src/dbapi/simple/Makefile.sdbapi.lib | 1 + + src/html/Makefile.html.lib | 2 ++ + src/misc/cgi_redirect/Makefile.cgi_redirect.lib | 2 ++ + src/misc/grid_cgi/Makefile.xgridcgi.lib | 2 ++ + src/objects/access/Makefile.access.lib | 1 + + src/objects/biblio/Makefile.biblio.lib | 2 ++ + src/objects/biotree/Makefile.biotree.lib | 2 ++ + src/objects/blast/Makefile.blast.lib | 2 ++ + src/objects/blast/Makefile.xnetblastcli.lib | 2 ++ + src/objects/blastdb/Makefile.blastdb.lib | 2 ++ + src/objects/blastxml/Makefile.blastxml.lib | 2 ++ + src/objects/cdd/Makefile.cdd.lib | 2 ++ + src/objects/cn3d/Makefile.cn3d.lib | 2 ++ + src/objects/docsum/Makefile.docsum.lib | 2 ++ + src/objects/entrez2/Makefile.entrez2.lib | 2 ++ + src/objects/entrez2/Makefile.entrez2cli.lib | 2 ++ + src/objects/entrezgene/Makefile.entrezgene.lib | 2 ++ + src/objects/featdef/Makefile.featdef.lib | 2 ++ + src/objects/gbseq/Makefile.gbseq.lib | 2 ++ + src/objects/general/Makefile.general.lib | 2 ++ + src/objects/genomecoll/Makefile.genome_collection.lib | 2 ++ + src/objects/homologene/Makefile.homologene.lib | 2 ++ + src/objects/id1/Makefile.id1.lib | 2 ++ + src/objects/id1/Makefile.id1cli.lib | 2 ++ + src/objects/id2/Makefile.id2.lib | 2 ++ + src/objects/id2/Makefile.id2cli.lib | 2 ++ + src/objects/insdseq/Makefile.insdseq.lib | 2 ++ + src/objects/macro/Makefile.macro.lib | 2 ++ + src/objects/medlars/Makefile.medlars.lib | 2 ++ + src/objects/medline/Makefile.medline.lib | 2 ++ + src/objects/mim/Makefile.mim.lib | 2 ++ + src/objects/mla/Makefile.mla.lib | 2 ++ + src/objects/mla/Makefile.mlacli.lib | 2 ++ + src/objects/mmdb/Makefile.mmdb.lib | 2 ++ + src/objects/ncbimime/Makefile.ncbimime.lib | 2 ++ + src/objects/objprt/Makefile.objprt.lib | 2 ++ + src/objects/omssa/Makefile.omssa.lib | 2 ++ + src/objects/pcassay/Makefile.pcassay.lib | 2 ++ + src/objects/pcsubstance/Makefile.pcsubstance.lib | 2 ++ + src/objects/proj/Makefile.proj.lib | 2 ++ + src/objects/pub/Makefile.pub.lib | 2 ++ + src/objects/pubmed/Makefile.pubmed.lib | 2 ++ + src/objects/remap/Makefile.remap.lib | 2 ++ + src/objects/remap/Makefile.remapcli.lib | 2 ++ + src/objects/scoremat/Makefile.scoremat.lib | 2 ++ + src/objects/seq/Makefile.seq.lib | 2 ++ + src/objects/seqcode/Makefile.seqcode.lib | 2 ++ + src/objects/seqedit/Makefile.seqedit.lib | 1 + + src/objects/seqset/Makefile.seqset.lib | 1 + + src/objects/seqsplit/Makefile.seqsplit.lib | 2 ++ + src/objects/seqtest/Makefile.seqtest.lib | 2 ++ + src/objects/submit/Makefile.submit.lib | 1 + + src/objects/taxon1/Makefile.taxon1.lib | 2 ++ + src/objects/taxon3/Makefile.taxon3.lib | 2 ++ + src/objects/tinyseq/Makefile.tinyseq.lib | 2 ++ + src/objects/valerr/Makefile.valerr.lib | 2 ++ + src/objects/valid/Makefile.valid.lib | 2 ++ + src/objects/variation/Makefile.variation.lib | 1 + + src/objmgr/split/Makefile.id2_split.lib | 2 +- + src/objmgr/util/Makefile.util.lib | 1 + + src/objtools/align/Makefile.xalntool.lib | 2 ++ + src/objtools/align_format/Makefile.align_format.lib | 2 ++ + src/objtools/alnmgr/Makefile.alnmgr.lib | 1 + + src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib | 2 ++ + src/objtools/blast/gene_info_reader/Makefile.gene_info.lib | 2 ++ + src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib | 2 ++ + src/objtools/blast/seqdb_reader/Makefile.seqdb.lib | 2 ++ + src/objtools/blast/seqdb_writer/Makefile.writedb.lib | 2 ++ + src/objtools/blast/services/Makefile.blast_services.lib | 1 + + src/objtools/cddalignview/Makefile.cddalignview.lib | 2 ++ + src/objtools/cleanup/Makefile.cleanup.lib | 2 +- + src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++ + .../data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib | 2 ++ + src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib | 2 ++ + src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib | 2 +- + src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++ + src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib | 2 ++ + src/objtools/data_loaders/trace/Makefile.xloader_trace.lib | 2 ++ + src/objtools/edit/Makefile.edit.lib | 2 ++ + src/objtools/eutils/api/Makefile.eutils.lib | 2 ++ + src/objtools/eutils/egquery/Makefile.egquery.lib | 2 ++ + src/objtools/eutils/ehistory/Makefile.ehistory.lib | 2 ++ + src/objtools/eutils/einfo/Makefile.einfo.lib | 2 ++ + src/objtools/eutils/elink/Makefile.elink.lib | 2 ++ + src/objtools/eutils/epost/Makefile.epost.lib | 2 ++ + src/objtools/eutils/esearch/Makefile.esearch.lib | 2 ++ + src/objtools/eutils/espell/Makefile.espell.lib | 2 ++ + src/objtools/eutils/esummary/Makefile.esummary.lib | 2 ++ + src/objtools/eutils/linkout/Makefile.linkout.lib | 2 ++ + src/objtools/eutils/uilist/Makefile.uilist.lib | 2 ++ + src/objtools/format/Makefile.xformat.lib | 2 ++ + src/objtools/lds/Makefile.lds.lib | 2 +- + src/objtools/manip/Makefile.xobjmanip.lib | 2 ++ + src/objtools/readers/Makefile.xobjread.lib | 3 +-- + src/objtools/readers/Makefile.xobjreadex.lib | 2 +- + src/objtools/seqmasks_io/Makefile.seqmasks_io.lib | 2 +- + src/objtools/simple/Makefile.xobjsimple.lib | 1 + + src/objtools/snputil/Makefile.snputil.lib | 2 ++ + src/objtools/validator/Makefile.validator.lib | 2 ++ + src/objtools/writers/Makefile.xobjwrite.lib | 1 + + src/sample/app/asn/Makefile.sample_asn.lib | 2 ++ + src/sample/app/soap/Makefile.soap_dataobj.lib | 2 ++ + src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib | 2 ++ + src/sample/lib/basic/Makefile.basic_sample_lib.lib | 2 ++ + src/sample/lib/dtd/Makefile.dtd_sample_lib.lib | 2 ++ + src/sample/lib/xsd/Makefile.xsd_sample_lib.lib | 2 ++ + src/serial/Makefile.serial.lib | 2 ++ + src/serial/soap/Makefile.soap.lib | 2 ++ + src/serial/soap/Makefile.soap_server.lib | 2 ++ + src/serial/test/Makefile.we_cpp.lib | 1 + + src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib | 2 +- + src/sra/sdk/libs/align/Makefile.align-writer.lib | 2 +- + src/util/Makefile.util.lib | 2 ++ + src/util/compress/api/Makefile.compress.lib | 2 +- + src/util/qparse/Makefile.xqueryparse.lib | 2 ++ + src/util/regexp/Makefile.regexp.lib | 2 ++ + src/util/sequtil/Makefile.sequtil.lib | 2 ++ + src/util/xregexp/Makefile.xregexp.lib | 2 +- + 167 files changed, 307 insertions(+), 23 deletions(-) +diff --git a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib +index c8851d8..35ae629 100644 +--- a/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib ++++ b/src/algo/align/contig_assembly/Makefile.xalgocontig_assembly.lib +@@ -10,3 +10,5 @@ LIB = xalgocontig_assembly + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = align_format blastinput dbapi_driver seq xalgoalignnw xalgodustmask xalnmgr xblast xncbi xobjmgr xobjutil xser # axf diff --git a/src/algo/align/ngalign/Makefile.xngalign.lib b/src/algo/align/ngalign/Makefile.xngalign.lib -index d163f7c..f9c79ba 100644 +index d163f7c..ade88ce 100644 --- a/src/algo/align/ngalign/Makefile.xngalign.lib +++ b/src/algo/align/ngalign/Makefile.xngalign.lib @@ -15,3 +15,5 @@ LIB = xngalign @@ -137,9 +186,39 @@ index d163f7c..f9c79ba 100644 CXXFLAGS = $(FAST_CXXFLAGS) -I./. LDFLAGS = $(FAST_LDFLAGS) + -+DLL_LIB = seq xalgoalignutil xncbi blastinput ++DLL_LIB = seq xalgoalignutil xncbi blastinput xalgoalignnw align_format xcgi ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 +diff --git a/src/algo/align/nw/Makefile.xalgoalignnw.lib b/src/algo/align/nw/Makefile.xalgoalignnw.lib +index acc1ddf..acba81c 100644 +--- a/src/algo/align/nw/Makefile.xalgoalignnw.lib ++++ b/src/algo/align/nw/Makefile.xalgoalignnw.lib +@@ -15,3 +15,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + + WATCHERS = kiryutin ++ ++DLL_LIB = access align_format dbapi_driver general seq writedb xncbi xser # axf +diff --git a/src/algo/align/prosplign/Makefile.prosplign.lib b/src/algo/align/prosplign/Makefile.prosplign.lib +index 248ee37..73143ad 100644 +--- a/src/algo/align/prosplign/Makefile.prosplign.lib ++++ b/src/algo/align/prosplign/Makefile.prosplign.lib +@@ -10,3 +10,5 @@ LIB = prosplign + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = align_format blastinput dbapi_driver general igblast seq xalgoalignutil xalnmgr xncbi xobjmgr xobjutil xser # axf +diff --git a/src/algo/align/splign/Makefile.xalgoalignsplign.lib b/src/algo/align/splign/Makefile.xalgoalignsplign.lib +index d67680b..3d56789 100644 +--- a/src/algo/align/splign/Makefile.xalgoalignsplign.lib ++++ b/src/algo/align/splign/Makefile.xalgoalignsplign.lib +@@ -10,3 +10,5 @@ LIB = xalgoalignsplign + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) ++ ++DLL_LIB = access align_format blastinput dbapi_driver gene_info general seq seqdb xalgoalignnw xalgoalignutil xalgoseq xblast xncbi xobjmgr xobjutil xser xutil # axf prosplign diff --git a/src/algo/blast/api/Makefile.xblast.lib b/src/algo/blast/api/Makefile.xblast.lib -index 073973b..3be07ae 100644 +index 073973b..c6a4c2c 100644 --- a/src/algo/blast/api/Makefile.xblast.lib +++ b/src/algo/blast/api/Makefile.xblast.lib @@ -78,7 +78,7 @@ SRC = $(SRC_C:%=.core_%) $(SRC_CXX) @@ -147,12 +226,12 @@ index 073973b..3be07ae 100644 LIB = xblast -DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) -+DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread ++DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xnetblastcli xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread CFLAGS = $(FAST_CFLAGS) # Strict gcc flags diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib -index bfb315c..6f56c5a 100644 +index bfb315c..2cd809a 100644 --- a/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/src/algo/blast/blastinput/Makefile.blastinput.lib @@ -24,7 +24,7 @@ SRC = $(SRC_CXX) @@ -160,7 +239,7 @@ index bfb315c..6f56c5a 100644 LIB = blastinput -DLL_LIB = xblast $(OBJMGR_LIBS) -+DLL_LIB = seqdb ncbi_xloader_blastdb $(OBJMGR_LIBS) ++DLL_LIB = seqdb ncbi_xloader_blastdb ncbi_xloader_blastdb_rmt align_format xalnmgr xblast xcgi xobjread xobjutil ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 xalnmgr xcgi # should be redundant, given the above :-/ ASN_DEP = seqset xnetblast @@ -174,8 +253,49 @@ index 8e889a7..1326aee 100644 WATCHERS = coulouri maning madden camacho + +DLL_LIB = xutil +diff --git a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +index fcfb9f9..0e762b4 100644 +--- a/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib ++++ b/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib +@@ -14,3 +14,5 @@ LDFLAGS = $(FAST_LDFLAGS) + ASN_DEP = seqset + + WATCHERS = morgulis ++ ++DLL_LIB = dbapi_driver seq seqdb seqset xncbi xobjmgr xobjread xobjutil xser xutil # axf +diff --git a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib +index e64f111..475f4a1 100644 +--- a/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib ++++ b/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib +@@ -10,3 +10,5 @@ LDFLAGS = $(FAST_LDFLAGS) + ASN_DEP = seqset + + WATCHERS = morgulis ++ ++DLL_LIB = dbapi_driver xncbi xobjmgr # axf +diff --git a/src/algo/blast/format/Makefile.xblastformat.lib b/src/algo/blast/format/Makefile.xblastformat.lib +index f7da067..9920332 100644 +--- a/src/algo/blast/format/Makefile.xblastformat.lib ++++ b/src/algo/blast/format/Makefile.xblastformat.lib +@@ -7,6 +7,6 @@ SRC = blastfmtutil blastxml_format blast_format data4xmlformat build_archive vec + + CPPFLAGS = $(ORIG_CPPFLAGS) + +-DLL_LIB = blastxml xhtml xcgi ++DLL_LIB = blastxml xhtml xcgi align_format general scoremat seq seqdb xalnmgr xblast xnetblast xobjmgr xobjutil blast_services ncbi_xloader_genbank xcgi # cobalt + + WATCHERS = jianye zaretska madden camacho fongah2 +diff --git a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib +index 316d4fa..844de85 100644 +--- a/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib ++++ b/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib +@@ -11,3 +11,4 @@ LDFLAGS = $(FAST_LDFLAGS) + + WATCHERS = boratyng madden camacho + ++DLL_LIB = dbapi_driver xncbi xutil # axf diff --git a/src/algo/cobalt/Makefile.cobalt.lib b/src/algo/cobalt/Makefile.cobalt.lib -index e618f67..32905ca 100644 +index e618f67..b406cc5 100644 --- a/src/algo/cobalt/Makefile.cobalt.lib +++ b/src/algo/cobalt/Makefile.cobalt.lib @@ -14,3 +14,5 @@ ASN_DEP = seq seqset biotree xnetblast blastdb @@ -183,9 +303,41 @@ index e618f67..32905ca 100644 CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) + -+DLL_LIB = align_format ++DLL_LIB = align_format dbapi_driver general igblast seq seqdb seqset xalgoalignnw xalgophytree xblast xncbi xnetblast xobjmgr xobjutil xser fastme # axf +diff --git a/src/algo/dustmask/Makefile.xalgodustmask.lib b/src/algo/dustmask/Makefile.xalgodustmask.lib +index 84e2568..3632356 100644 +--- a/src/algo/dustmask/Makefile.xalgodustmask.lib ++++ b/src/algo/dustmask/Makefile.xalgodustmask.lib +@@ -11,3 +11,4 @@ SRC = symdust + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = dbapi_driver seq xncbi xobjmgr # axf +diff --git a/src/algo/gnomon/Makefile.gnomon.lib b/src/algo/gnomon/Makefile.gnomon.lib +index af363c0..3235647 100644 +--- a/src/algo/gnomon/Makefile.gnomon.lib ++++ b/src/algo/gnomon/Makefile.gnomon.lib +@@ -6,7 +6,7 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) \ + gnomon_engine gnomon_objmgr score gnomon_model parse hmm gnomon_seq asn1 chainer id_handler \ + annot select_alignments_alt + LIB = xalgognomon +-DLL_LIB = xobjutil $(SOBJMGR_LIBS) ++DLL_LIB = xobjutil $(SOBJMGR_LIBS) xalgoseq + + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) +diff --git a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib +index 686dd70..98f57b2 100644 +--- a/src/algo/ms/formats/pepxml/Makefile.pepXML.lib ++++ b/src/algo/ms/formats/pepxml/Makefile.pepXML.lib +@@ -2,3 +2,5 @@ WATCHERS = lewisg slottad + + LIB = pepXML + SRC = pepXML__ pepXML___ ++ ++DLL_LIB = access align_format dbapi_driver xncbi xser # axf diff --git a/src/algo/ms/omssa/Makefile.xomssa.lib b/src/algo/ms/omssa/Makefile.xomssa.lib -index 872b92e..24fcff3 100644 +index 872b92e..78261eb 100644 --- a/src/algo/ms/omssa/Makefile.xomssa.lib +++ b/src/algo/ms/omssa/Makefile.xomssa.lib @@ -19,3 +19,5 @@ LIB = xomssa @@ -193,9 +345,51 @@ index 872b92e..24fcff3 100644 CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) + -+DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast ++DLL_LIB = xutil omssa pepXML xcompress xconnect seqdb xblast xregexp +diff --git a/src/algo/phy_tree/Makefile.xalgophytree.lib b/src/algo/phy_tree/Makefile.xalgophytree.lib +index 5964ef4..8163366 100644 +--- a/src/algo/phy_tree/Makefile.xalgophytree.lib ++++ b/src/algo/phy_tree/Makefile.xalgophytree.lib +@@ -6,7 +6,7 @@ ASN_DEP = biotree + + SRC = bio_tree phy_node dist_methods lex.newick newick.tab tree_to_dist_mat phytree_calc + LIB = xalgophytree +-DLL_LIB = biotree ++DLL_LIB = biotree seq xalnmgr xobjutil # fastme + + # The -I flag is necessary because filenames in #line directives throw + # off some compilers (GCC 2.95 at least). :-/ +diff --git a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib +index 15d7440..fab9207 100644 +--- a/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib ++++ b/src/algo/phy_tree/phytree_format/Makefile.phytreeformat.lib +@@ -10,3 +10,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) + ASN_DEP = biotree seqset taxon1 + + WATCHERS = boratyng ++ ++DLL_LIB = access align_format biotree dbapi_driver fastme gene_info seq taxon1 xalgophytree xncbi xobjmgr xobjutil xser # axf +diff --git a/src/algo/segmask/Makefile.xalgosegmask.lib b/src/algo/segmask/Makefile.xalgosegmask.lib +index bd011c1..97281ec 100644 +--- a/src/algo/segmask/Makefile.xalgosegmask.lib ++++ b/src/algo/segmask/Makefile.xalgosegmask.lib +@@ -11,3 +11,4 @@ SRC = segmask + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++DLL_LIB = align_format xobjmgr +diff --git a/src/algo/seqqa/Makefile.xalgoseqqa.lib b/src/algo/seqqa/Makefile.xalgoseqqa.lib +index b1bea47..a0e5b1b 100644 +--- a/src/algo/seqqa/Makefile.xalgoseqqa.lib ++++ b/src/algo/seqqa/Makefile.xalgoseqqa.lib +@@ -12,3 +12,5 @@ LIB = xalgoseqqa + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE) ++ ++DLL_LIB = access align_format dbapi_driver entrez2cli gene_info general seq seqtest xalgognomon xalgoseq xalnmgr xncbi xobjmgr xobjutil xser # axf diff --git a/src/algo/sequence/Makefile.xalgoseq.lib b/src/algo/sequence/Makefile.xalgoseq.lib -index 51f4cd7..0c20790 100644 +index 51f4cd7..724e939 100644 --- a/src/algo/sequence/Makefile.xalgoseq.lib +++ b/src/algo/sequence/Makefile.xalgoseq.lib @@ -13,3 +13,5 @@ LDFLAGS = $(FAST_LDFLAGS) @@ -203,7 +397,30 @@ index 51f4cd7..0c20790 100644 WATCHERS = dicuccio + -+DLL_LIB = taxon1 xalnmgr ++DLL_LIB = taxon1 xalnmgr xregexp align_format seqset xobjmgr xobjutil +diff --git a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib +index 5562f82..68d3a87 100644 +--- a/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib ++++ b/src/algo/structure/bma_refine/Makefile.xbma_refiner.lib +@@ -24,3 +24,6 @@ SRC = RowSelector \ + RefinerTrial \ + RefinerEngine \ + Interface ++ ++DLL_LIB = blastinput cdd ncbi_xcache_bdb xcd_utils xncbi xser xutil ++ +diff --git a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib +index eda71f8..8d3a96a 100644 +--- a/src/algo/structure/cd_utils/Makefile.xcd_utils.lib ++++ b/src/algo/structure/cd_utils/Makefile.xcd_utils.lib +@@ -68,6 +68,6 @@ SRC = \ + cuTaxTree \ + cuUtils + +-DLL_LIB = xobjread ++DLL_LIB = xobjread blastdb blast_services cdd entrez2cli id1cli mmdb ncbimime scoremat taxon1 xblast xobjmgr xregexp + + CPPFLAGS = $(ORIG_CPPFLAGS) diff --git a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib b/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib index 676a8dd..3d3e4c9 100644 --- a/src/algo/structure/struct_dp/Makefile.xstruct_dp.lib @@ -234,15 +451,36 @@ index c06a2c0..9f1ff25 100644 LIB = xstruct_thread + +DLL_LIB = xutil +diff --git a/src/algo/text/Makefile.xalgotext.lib b/src/algo/text/Makefile.xalgotext.lib +index 81ba0e6..f25073e 100644 +--- a/src/algo/text/Makefile.xalgotext.lib ++++ b/src/algo/text/Makefile.xalgotext.lib +@@ -10,3 +10,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + + ASN_DEP = general ++ ++DLL_LIB = align_format blastinput ncbi_xcache_bdb xcompress xncbi xutil # axf +diff --git a/src/algo/volume_merge/Makefile.xalgovmerge.lib b/src/algo/volume_merge/Makefile.xalgovmerge.lib +index 499861a..3ffb80b 100644 +--- a/src/algo/volume_merge/Makefile.xalgovmerge.lib ++++ b/src/algo/volume_merge/Makefile.xalgovmerge.lib +@@ -10,3 +10,5 @@ SRC = volume_merge + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + ++ ++DLL_LIB = xncbi diff --git a/src/algo/winmask/Makefile.xalgowinmask.lib b/src/algo/winmask/Makefile.xalgowinmask.lib -index afaf676..7344871 100644 +index afaf676..ad2c1fe 100644 --- a/src/algo/winmask/Makefile.xalgowinmask.lib +++ b/src/algo/winmask/Makefile.xalgowinmask.lib -@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \ +@@ -21,3 +21,5 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) -+DLL_LIB = seqmasks_io ++DLL_LIB = seqmasks_io xobjread xobjutil ++ diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib index a990390..edf40aa 100644 --- a/src/cgi/Makefile.cgi.lib @@ -479,6 +717,26 @@ index a57c1e3..0005299 100644 WATCHERS = ivanov + +DLL_LIB = xncbi xutil +diff --git a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib +index 6d7a4af..332e5d0 100644 +--- a/src/misc/cgi_redirect/Makefile.cgi_redirect.lib ++++ b/src/misc/cgi_redirect/Makefile.cgi_redirect.lib +@@ -7,3 +7,5 @@ SRC = redirect + LIB = xcgi_redirect + + WATCHERS = ivanov ++ ++DLL_LIB = axf dbapi_driver xcgi xhtml xncbi +diff --git a/src/misc/grid_cgi/Makefile.xgridcgi.lib b/src/misc/grid_cgi/Makefile.xgridcgi.lib +index c9ef138..8e25cbe 100644 +--- a/src/misc/grid_cgi/Makefile.xgridcgi.lib ++++ b/src/misc/grid_cgi/Makefile.xgridcgi.lib +@@ -9,3 +9,5 @@ LIB = xgridcgi + CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) + + WATCHERS = vakatov ++ ++DLL_LIB = xncbi xcgi xconnserv xhtml diff --git a/src/objects/access/Makefile.access.lib b/src/objects/access/Makefile.access.lib index 11421d9..e7900a1 100644 --- a/src/objects/access/Makefile.access.lib @@ -545,14 +803,14 @@ index d18eb78..f90501d 100644 + +DLL_LIB = xser diff --git a/src/objects/cdd/Makefile.cdd.lib b/src/objects/cdd/Makefile.cdd.lib -index 978cae9..2365261 100644 +index 978cae9..24b726c 100644 --- a/src/objects/cdd/Makefile.cdd.lib +++ b/src/objects/cdd/Makefile.cdd.lib @@ -1,2 +1,4 @@ LIB = cdd SRC = cdd__ cdd___ + -+DLL_LIB = mmdb xser scoremat ++DLL_LIB = mmdb xser scoremat cn3d diff --git a/src/objects/cn3d/Makefile.cn3d.lib b/src/objects/cn3d/Makefile.cn3d.lib index 1af5d1d..ecd31b2 100644 --- a/src/objects/cn3d/Makefile.cn3d.lib @@ -1006,8 +1264,18 @@ index 90eeee0..138e836 100644 WATCHERS = ucko vasilche +DLL_LIB = xser xobjmgr +diff --git a/src/objtools/align/Makefile.xalntool.lib b/src/objtools/align/Makefile.xalntool.lib +index cb9846d..9c2a8f9 100644 +--- a/src/objtools/align/Makefile.xalntool.lib ++++ b/src/objtools/align/Makefile.xalntool.lib +@@ -6,3 +6,5 @@ ASN_DEP = seqset + + LIB = xalntool + SRC = alngraphic ++ ++DLL_LIB = access dbapi_driver general seq xhtml xncbi xobjmgr xobjutil xser # align_format axf blastinput diff --git a/src/objtools/align_format/Makefile.align_format.lib b/src/objtools/align_format/Makefile.align_format.lib -index 4b3e59e..d8e9345 100644 +index 4b3e59e..c67c352 100644 --- a/src/objtools/align_format/Makefile.align_format.lib +++ b/src/objtools/align_format/Makefile.align_format.lib @@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) @@ -1015,18 +1283,18 @@ index 4b3e59e..d8e9345 100644 WATCHERS = zaretska jianye madden camacho + -+DLL_LIB = seqdb blastdb xser ++DLL_LIB = seqdb blastdb xser xhtml gene_info xnetblast blast_services ncbi_xloader_genbank xalnmgr xcgi xobjread xobjutil diff --git a/src/objtools/alnmgr/Makefile.alnmgr.lib b/src/objtools/alnmgr/Makefile.alnmgr.lib -index e32c351..1702b90 100644 +index e32c351..41355ff 100644 --- a/src/objtools/alnmgr/Makefile.alnmgr.lib +++ b/src/objtools/alnmgr/Makefile.alnmgr.lib @@ -12,3 +12,4 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial \ WATCHERS = todorov dicuccio grichenk -+DLL_LIB = tables ++DLL_LIB = tables dbapi_driver ncbi_xcache_bdb seq seqset sequtil xncbi xobjmgr xobjutil xser # align_format axf diff --git a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib -index d8177ed..f7beead 100644 +index d8177ed..aa4d8e4 100644 --- a/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib +++ b/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib @@ -18,3 +18,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) @@ -1034,7 +1302,7 @@ index d8177ed..f7beead 100644 # # LIB_OR_DLL = dll + -+DLL_LIB = xncbi xser xobjutil seq ++DLL_LIB = xncbi xser xobjutil seq seqdb diff --git a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib index bf5fd1b..c32aca4 100644 --- a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib @@ -1084,6 +1352,29 @@ index 10a878c..7a70b22 100644 LDFLAGS = $(FAST_LDFLAGS) +DLL_LIB = xncbi xser xnetblast xnetblastcli +diff --git a/src/objtools/cddalignview/Makefile.cddalignview.lib b/src/objtools/cddalignview/Makefile.cddalignview.lib +index 8e39baa..f4d3a35 100644 +--- a/src/objtools/cddalignview/Makefile.cddalignview.lib ++++ b/src/objtools/cddalignview/Makefile.cddalignview.lib +@@ -11,3 +11,5 @@ SRC = \ + cav_seqset + + LIB = xcddalignview ++ ++DLL_LIB = cdd dbapi_driver general ncbimime seq seqset xncbi xser # align_format axf ncbi_xloader_bam +diff --git a/src/objtools/cleanup/Makefile.cleanup.lib b/src/objtools/cleanup/Makefile.cleanup.lib +index 663d755..ad7b3cf 100644 +--- a/src/objtools/cleanup/Makefile.cleanup.lib ++++ b/src/objtools/cleanup/Makefile.cleanup.lib +@@ -10,7 +10,7 @@ SRC = autogenerated_cleanup cleanup \ + cleanup_utils \ + newcleanupp + +-DLL_LIB = xregexp $(PCRE_LIB) ++DLL_LIB = xregexp $(PCRE_LIB) access biblio general pub seq seqset sequtil submit xobjmgr xobjutil xser + LIB = xcleanup + + LIBS = $(PCRE_LIBS) diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib index 80af69f..704ed7a 100644 --- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib @@ -1095,6 +1386,26 @@ index 80af69f..704ed7a 100644 + +DLL_LIB = seqdb + +diff --git a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib +index 80abb48..2ddec92 100644 +--- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib ++++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib +@@ -6,3 +6,5 @@ SRC = bdbloader_rmt remote_blastdb_adapter + ASN_DEP = blastdb xnetblast + + WATCHERS = camacho ++ ++DLL_LIB = blast_services ncbi_xloader_blastdb xobjmgr +diff --git a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib +index a51042b..fa92fc9 100644 +--- a/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib ++++ b/src/objtools/data_loaders/cdd/Makefile.ncbi_xloader_cdd.lib +@@ -9,3 +9,5 @@ LIB = ncbi_xloader_cdd + SRC = cdd + + ASN_DEP = seqset ++ ++DLL_LIB = dbapi_driver general seq seqset xconnect xncbi xobjmgr xser # align_format axf ncbi_xloader_bam diff --git a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib index f2b2b49..864e4b1 100644 --- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib @@ -1108,7 +1419,7 @@ index f2b2b49..864e4b1 100644 WATCHERS = vasilche diff --git a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib -index 0a29cbf..015ac93 100644 +index 0a29cbf..74c30dc 100644 --- a/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib +++ b/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib @@ -15,3 +15,5 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE) @@ -1116,7 +1427,27 @@ index 0a29cbf..015ac93 100644 WATCHERS = vasilche + -+DLL_LIB = xncbi ++DLL_LIB = xncbi gene_info id2 ncbi_xreader xconnect xser +diff --git a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib +index 8d09d8c..d6040ed 100644 +--- a/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib ++++ b/src/objtools/data_loaders/patcher/Makefile.ncbi_xloader_patcher.lib +@@ -7,3 +7,5 @@ ASN_DEP = seq seqset seqedit + + + WATCHERS = vasilche ++ ++DLL_LIB = dbapi_driver seq seqedit seqset xncbi xobjmgr xser # axf +diff --git a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib +index d2debd5..33fed34 100644 +--- a/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib ++++ b/src/objtools/data_loaders/trace/Makefile.xloader_trace.lib +@@ -9,3 +9,5 @@ LIB = ncbi_xloader_trace + SRC = trace_chgr + + ASN_DEP = id1 ++ ++DLL_LIB = dbapi_driver general id1 id1cli seq xncbi xobjmgr xser # align_format axf diff --git a/src/objtools/edit/Makefile.edit.lib b/src/objtools/edit/Makefile.edit.lib index 7ce0d11..f5458c5 100644 --- a/src/objtools/edit/Makefile.edit.lib @@ -1127,6 +1458,16 @@ index 7ce0d11..f5458c5 100644 WATCHERS = bollin + +DLL_LIB = xncbi seq xobjutil xobjmgr +diff --git a/src/objtools/eutils/api/Makefile.eutils.lib b/src/objtools/eutils/api/Makefile.eutils.lib +index da71ea9..b444e72 100644 +--- a/src/objtools/eutils/api/Makefile.eutils.lib ++++ b/src/objtools/eutils/api/Makefile.eutils.lib +@@ -10,3 +10,5 @@ ASN_DEP = einfo esearch egquery epost elink esummary espell uilist \ + ehistory + + WATCHERS = grichenk ++ ++DLL_LIB = dbapi_driver xconnect xncbi xser # align_format axf ncbi_xloader_bam diff --git a/src/objtools/eutils/egquery/Makefile.egquery.lib b/src/objtools/eutils/egquery/Makefile.egquery.lib index 82b4ed0..7030a29 100644 --- a/src/objtools/eutils/egquery/Makefile.egquery.lib @@ -1217,8 +1558,18 @@ index 19b2b8a..77dcc3c 100644 WATCHERS = grichenk + +DLL_LIB = xser +diff --git a/src/objtools/eutils/uilist/Makefile.uilist.lib b/src/objtools/eutils/uilist/Makefile.uilist.lib +index b49c3c5..2ee63f0 100644 +--- a/src/objtools/eutils/uilist/Makefile.uilist.lib ++++ b/src/objtools/eutils/uilist/Makefile.uilist.lib +@@ -4,3 +4,5 @@ SRC = uilist__ uilist___ + LIB = uilist + + WATCHERS = grichenk ++ ++DLL_LIB = access dbapi_driver xncbi xser # align_format axf diff --git a/src/objtools/format/Makefile.xformat.lib b/src/objtools/format/Makefile.xformat.lib -index a4fc469..0203fea 100644 +index a4fc469..fa58b3c 100644 --- a/src/objtools/format/Makefile.xformat.lib +++ b/src/objtools/format/Makefile.xformat.lib @@ -19,3 +19,5 @@ SRC = accession_item basecount_item comment_item contig_item date_item \ @@ -1226,7 +1577,7 @@ index a4fc469..0203fea 100644 WATCHERS = ludwigf dicuccio kornbluh + -+DLL_LIB = submit connect xncbi gbseq xobjmgr ++DLL_LIB = submit connect xncbi gbseq xobjmgr xobjutil xalnmgr xconnect diff --git a/src/objtools/lds/Makefile.lds.lib b/src/objtools/lds/Makefile.lds.lib index e371035..689cfb4 100644 --- a/src/objtools/lds/Makefile.lds.lib @@ -1270,6 +1621,18 @@ index 85eefe2..9f317ae 100644 -DLL_LIB = xobjread +DLL_LIB = xobjread xncbi xutil seq xobjmgr xobjutil +diff --git a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib +index 687af1e..f48568c 100644 +--- a/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib ++++ b/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib +@@ -11,6 +11,6 @@ mask_writer_seqloc \ + mask_writer_blastdb_maskinfo + + ASN_DEP = seqset +-DLL_LIB = seqdb blastdb ++DLL_LIB = seqdb blastdb xobjread xobjutil + + WATCHERS = morgulis camacho diff --git a/src/objtools/simple/Makefile.xobjsimple.lib b/src/objtools/simple/Makefile.xobjsimple.lib index dab25d6..f676dc7 100644 --- a/src/objtools/simple/Makefile.xobjsimple.lib @@ -1279,6 +1642,16 @@ index dab25d6..f676dc7 100644 SRC = simple_om +DLL_LIB = xobjmgr ncbi_xloader_genbank +diff --git a/src/objtools/snputil/Makefile.snputil.lib b/src/objtools/snputil/Makefile.snputil.lib +index 15abef3..5ad1560 100644 +--- a/src/objtools/snputil/Makefile.snputil.lib ++++ b/src/objtools/snputil/Makefile.snputil.lib +@@ -9,3 +9,5 @@ SRC = snp_utils snp_bitfield \ + ASN_DEP = seqset + + WATCHERS = rudnev ++ ++DLL_LIB = general seq xncbi xobjmgr xser diff --git a/src/objtools/validator/Makefile.validator.lib b/src/objtools/validator/Makefile.validator.lib index 80a74d8..6eec94b 100644 --- a/src/objtools/validator/Makefile.validator.lib @@ -1298,6 +1671,66 @@ index cd6596b..a7d0c01 100644 WATCHERS = ludwigf boukn +DLL_LIB = xobjutil xalnmgr +diff --git a/src/sample/app/asn/Makefile.sample_asn.lib b/src/sample/app/asn/Makefile.sample_asn.lib +index 0db9ebd..26e6ad9 100644 +--- a/src/sample/app/asn/Makefile.sample_asn.lib ++++ b/src/sample/app/asn/Makefile.sample_asn.lib +@@ -10,3 +10,5 @@ LIB = sample_asn + ASN_DEP = general + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver general xncbi xser +diff --git a/src/sample/app/soap/Makefile.soap_dataobj.lib b/src/sample/app/soap/Makefile.soap_dataobj.lib +index 4b87f51..c398ded 100644 +--- a/src/sample/app/soap/Makefile.soap_dataobj.lib ++++ b/src/sample/app/soap/Makefile.soap_dataobj.lib +@@ -2,3 +2,5 @@ LIB = soap_dataobj + SRC = soap_dataobj__ soap_dataobj___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser +diff --git a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib +index f9d6103..4c22831 100644 +--- a/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib ++++ b/src/sample/lib/asn_lib/Makefile.asn_sample_lib.lib +@@ -2,3 +2,5 @@ LIB = asn_sample_lib + SRC = asn_sample_lib__ asn_sample_lib___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser +diff --git a/src/sample/lib/basic/Makefile.basic_sample_lib.lib b/src/sample/lib/basic/Makefile.basic_sample_lib.lib +index a6ba11a..364d9fc 100644 +--- a/src/sample/lib/basic/Makefile.basic_sample_lib.lib ++++ b/src/sample/lib/basic/Makefile.basic_sample_lib.lib +@@ -5,3 +5,5 @@ SRC = basic_sample_lib + + + WATCHERS = gouriano ++ ++DLL_LIB = xncbi +diff --git a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib +index d2a27ef..a63a7e8 100644 +--- a/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib ++++ b/src/sample/lib/dtd/Makefile.dtd_sample_lib.lib +@@ -2,3 +2,5 @@ LIB = dtd_sample_lib + SRC = dtd_sample_lib__ dtd_sample_lib___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser +diff --git a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib +index 4b7b6e2..838e8ea 100644 +--- a/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib ++++ b/src/sample/lib/xsd/Makefile.xsd_sample_lib.lib +@@ -2,3 +2,5 @@ LIB = xsd_sample_lib + SRC = xsd_sample_lib__ xsd_sample_lib___ + + WATCHERS = gouriano ++ ++DLL_LIB = access align_format axf dbapi_driver xncbi xser diff --git a/src/serial/Makefile.serial.lib b/src/serial/Makefile.serial.lib index 2563b5f..efad054 100644 --- a/src/serial/Makefile.serial.lib @@ -1337,6 +1770,19 @@ index 9877691..599ef5d 100644 WATCHERS = gouriano +DLL_LIB = xncbi xutil xser +diff --git a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib +index 4896661..8e2ad56 100644 +--- a/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib ++++ b/src/sra/data_loaders/bam/Makefile.ncbi_xloader_bam.lib +@@ -12,7 +12,7 @@ ASN_DEP = seqset seq + + LIB_OR_DLL = both + +-DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB) ++DLL_LIB = $(SOBJMGR_LIBS) bamread$(STATIC) $(BAM_LIBS) $(CMPRS_LIB) xobjreadex + LIBS = $(CMPRS_LIBS) $(ORIG_LIBS) + + CPPFLAGS = $(SRA_INCLUDE) -DNCBI_XLOADER_BAM_EXPORTS $(ORIG_CPPFLAGS) diff --git a/src/sra/sdk/libs/align/Makefile.align-writer.lib b/src/sra/sdk/libs/align/Makefile.align-writer.lib index f2a2f58..f61b25a 100644 --- a/src/sra/sdk/libs/align/Makefile.align-writer.lib -- cgit v1.2.3-18-g5258