diff options
3 files changed, 303 insertions, 449 deletions
diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch index 821380023..e97c77f58 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-as-needed.patch @@ -1,171 +1,170 @@ - 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(-) + .../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 ++ + .../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/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 | 11 +++++++++++ + 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 ++ + .../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 +- + .../data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib | 3 +++ + .../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 +- + .../data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib | 2 ++ + .../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 +- + 166 files changed, 315 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 @@ -208,7 +207,7 @@ index 248ee37..73143ad 100644 + +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 +index 077f111..dff1877 100644 --- a/src/algo/align/splign/Makefile.xalgoalignsplign.lib +++ b/src/algo/align/splign/Makefile.xalgoalignsplign.lib @@ -10,3 +10,5 @@ LIB = xalgoalignsplign @@ -218,28 +217,28 @@ index d67680b..3d56789 100644 + +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..c6a4c2c 100644 +index 4e424b3..8708bf0 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) - - LIB = xblast - --DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) -+DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS) seqdb xnetblast xnetblastcli xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread +@@ -81,7 +81,7 @@ LIB = xblast + DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \ + xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \ + blastdb xnetblastcli xnetblast scoremat xconnect tables \ +- $(SOBJMGR_LIBS) ++ $(SOBJMGR_LIBS) seqdb xnetblast xnetblastcli xalgoblastdbindex xalgowinmask tables composition_adjustment xobjread CFLAGS = $(FAST_CFLAGS) - # Strict gcc flags + CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS) diff --git a/src/algo/blast/blastinput/Makefile.blastinput.lib b/src/algo/blast/blastinput/Makefile.blastinput.lib -index bfb315c..2cd809a 100644 +index 372dba1..d5986c7 100644 --- a/src/algo/blast/blastinput/Makefile.blastinput.lib +++ b/src/algo/blast/blastinput/Makefile.blastinput.lib @@ -24,7 +24,7 @@ SRC = $(SRC_CXX) LIB = blastinput --DLL_LIB = xblast $(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 +-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ++DLL_LIB = seqdb ncbi_xloader_blastdb ncbi_xloader_blastdb_rmt align_format xalnmgr xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) xcgi xobjread xobjutil ncbi_xloader_genbank ncbi_xreader ncbi_xreader_id2 xalnmgr xcgi xutil # should be redundant, given the above :-/ ASN_DEP = seqset xnetblast @@ -274,15 +273,15 @@ index e64f111..475f4a1 100644 + +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 +index 3058881..7a6d07d 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) + CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(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 +-DLL_LIB = align_format blastxml xhtml xcgi ++DLL_LIB = align_format 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 @@ -314,12 +313,12 @@ index 84e2568..3632356 100644 +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 +index 2a06ee8..d73cd8f 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 + annot select_alignments_alt aligncollapser LIB = xalgognomon -DLL_LIB = xobjutil $(SOBJMGR_LIBS) +DLL_LIB = xobjutil $(SOBJMGR_LIBS) xalgoseq @@ -347,10 +346,10 @@ index 872b92e..78261eb 100644 + +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 +index c7e2778..51ebe9d 100644 --- a/src/algo/phy_tree/Makefile.xalgophytree.lib +++ b/src/algo/phy_tree/Makefile.xalgophytree.lib -@@ -6,7 +6,7 @@ ASN_DEP = biotree +@@ -6,7 +6,7 @@ ASN_DEP = biotree seqset SRC = bio_tree phy_node dist_methods lex.newick newick.tab tree_to_dist_mat phytree_calc LIB = xalgophytree @@ -389,7 +388,7 @@ index b1bea47..a0e5b1b 100644 + +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..724e939 100644 +index 70d42a1..ab7b80f 100644 --- a/src/algo/sequence/Makefile.xalgoseq.lib +++ b/src/algo/sequence/Makefile.xalgoseq.lib @@ -13,3 +13,5 @@ LDFLAGS = $(FAST_LDFLAGS) @@ -452,13 +451,13 @@ index c06a2c0..9f1ff25 100644 + +DLL_LIB = xutil diff --git a/src/algo/text/Makefile.xalgotext.lib b/src/algo/text/Makefile.xalgotext.lib -index 81ba0e6..f25073e 100644 +index 7c0b48a..ba055ad 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) +@@ -8,3 +8,5 @@ SRC = text_util vector_serial - ASN_DEP = general + CXXFLAGS = $(FAST_CXXFLAGS) + LDFLAGS = $(FAST_LDFLAGS) + +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 @@ -482,17 +481,17 @@ index afaf676..ad2c1fe 100644 +DLL_LIB = seqmasks_io xobjread xobjutil + diff --git a/src/cgi/Makefile.cgi.lib b/src/cgi/Makefile.cgi.lib -index a990390..edf40aa 100644 +index fb543d7..10762e4 100644 --- a/src/cgi/Makefile.cgi.lib +++ b/src/cgi/Makefile.cgi.lib -@@ -11,3 +11,5 @@ LIB = xcgi +@@ -12,3 +12,5 @@ LIB = xcgi CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE) WATCHERS = vakatov + +DLL_LIB = xncbi xutil diff --git a/src/cgi/Makefile.fcgi.lib b/src/cgi/Makefile.fcgi.lib -index 2569b41..6b85780 100644 +index f68060b..c87d8e9 100644 --- a/src/cgi/Makefile.fcgi.lib +++ b/src/cgi/Makefile.fcgi.lib @@ -12,3 +12,5 @@ LIB = xfcgi @@ -530,7 +529,7 @@ index 473bb0b..88dae10 100644 + +DLL_LIB = xncbi xutil diff --git a/src/connect/Makefile.xthrserv.lib b/src/connect/Makefile.xthrserv.lib -index 1e5b857..0833a78 100644 +index c7060d2..0dd00a0 100644 --- a/src/connect/Makefile.xthrserv.lib +++ b/src/connect/Makefile.xthrserv.lib @@ -4,6 +4,6 @@ SRC = threaded_server server server_monitor connection_pool @@ -540,7 +539,7 @@ index 1e5b857..0833a78 100644 -DLL_LIB = xutil xconnect +DLL_LIB = xncbi xutil xconnect - WATCHERS = ivanovp + WATCHERS = vakatov diff --git a/src/connect/Makefile.xxconnect.lib b/src/connect/Makefile.xxconnect.lib index d7ba751..8e27819 100644 --- a/src/connect/Makefile.xxconnect.lib @@ -565,7 +564,7 @@ index 606f4f1..e6cfdac 100644 CPPFLAGS = $(ORIG_CPPFLAGS) LIBS = $(ORIG_LIBS) diff --git a/src/connect/services/Makefile.xconnserv.lib b/src/connect/services/Makefile.xconnserv.lib -index 4b8f21f..04fcbf8 100644 +index 77382f2..5d124f2 100644 --- a/src/connect/services/Makefile.xconnserv.lib +++ b/src/connect/services/Makefile.xconnserv.lib @@ -15,6 +15,6 @@ LIB = xconnserv @@ -576,23 +575,13 @@ index 4b8f21f..04fcbf8 100644 +DLL_LIB = xthrserv xconnect xutil xncbi WATCHERS = kazimird -diff --git a/src/connect/test/Makefile.conntest.lib b/src/connect/test/Makefile.conntest.lib -index 58a2fa5..3d9876c 100644 ---- a/src/connect/test/Makefile.conntest.lib -+++ b/src/connect/test/Makefile.conntest.lib -@@ -4,3 +4,5 @@ SRC = ncbi_conntest - LIB = xconntest - - WATCHERS = lavr -+ -+DLL_LIB = xncbi xutil connect diff --git a/src/corelib/Makefile.test_boost.lib b/src/corelib/Makefile.test_boost.lib -index e8fa174..f90441d 100644 +index 9d34c45..5678a38 100644 --- a/src/corelib/Makefile.test_boost.lib +++ b/src/corelib/Makefile.test_boost.lib @@ -9,3 +9,5 @@ REQUIRES = Boost.Test.Included - WATCHERS = ivanovp + WATCHERS = vakatov PROJ_TAG = test + +DLL_LIB = xncbi @@ -642,71 +631,84 @@ index 7e97a26..8f54efc 100644 CPPFLAGS = $(ORIG_CPPFLAGS) $(BERKELEYDB_INCLUDE) LIBS = $(BERKELEYDB_LIBS) $(ORIG_LIBS) diff --git a/src/db/sqlite/Makefile.sqlitewrapp.lib b/src/db/sqlite/Makefile.sqlitewrapp.lib -index cecfd16..c01668b 100644 +index 77c9bf5..2c136d1 100644 --- a/src/db/sqlite/Makefile.sqlitewrapp.lib +++ b/src/db/sqlite/Makefile.sqlitewrapp.lib @@ -8,3 +8,6 @@ CPPFLAGS= $(ORIG_CPPFLAGS) $(SQLITE3_INCLUDE) REQUIRES = SQLITE3 - WATCHERS = ivanovp + WATCHERS = vakatov + +DLL_LIB = xncbi xutil +LIBS = $(SQLITE3_LIBS) diff --git a/src/dbapi/Makefile.dbapi.lib b/src/dbapi/Makefile.dbapi.lib -index 6e3ad4c..e3d6a49 100644 +index 9e45b7a..b3fbb74 100644 --- a/src/dbapi/Makefile.dbapi.lib +++ b/src/dbapi/Makefile.dbapi.lib @@ -10,3 +10,8 @@ LIB = dbapi CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) - WATCHERS = ivanovp + WATCHERS = ucko + +#ASN_DEP = driver dbapi_driver + +DLL_LIB = xncbi xutil # dbapi_driver$(DLL) +LIBS = $(PYTHON_LIBS) diff --git a/src/dbapi/driver/Makefile.dbapi_driver.lib b/src/dbapi/driver/Makefile.dbapi_driver.lib -index dfeac5a..bc113ed 100644 +index 779ea8f..fd6306b 100644 --- a/src/dbapi/driver/Makefile.dbapi_driver.lib +++ b/src/dbapi/driver/Makefile.dbapi_driver.lib @@ -22,3 +22,5 @@ CXXFLAGS_darwin = -fno-inline CXXFLAGS = $(ORIG_CXXFLAGS) $(CXXFLAGS_$(OSTYPE)) - WATCHERS = ivanovp + WATCHERS = ucko + +DLL_LIB = xncbi xutil diff --git a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib -index 941ccd6..f1f872c 100644 +index 672570d..817f07a 100644 --- a/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib +++ b/src/dbapi/driver/samples/Makefile.dbapi_sample_base.lib @@ -6,3 +6,5 @@ LIB = dbapi_sample_base CPPFLAGS = $(ORIG_CPPFLAGS) $(SYBASE_INCLUDE) - WATCHERS = ivanovp + WATCHERS = ucko + +DLL_LIB = xncbi xutil dbapi_driver diff --git a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib -index ebe08c4..86ecda6 100644 +index 2cfe73f..6ce8c66 100644 --- a/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib +++ b/src/dbapi/lang_bind/python/Makefile.python_ncbi_dbapi.lib -@@ -11,7 +11,7 @@ LIB_OR_DLL = dll +@@ -11,6 +11,6 @@ LIB_OR_DLL = dll # Dependencies for shared library DLL_LIB = dbapi dbapi_driver$(DLL) $(XCONNEXT) xconnect xutil xncbi -LIBS = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS) +LIBS = $(RUNPATH_ORIGIN)/python_ncbi_dbapi/$(NCBI_PACKAGE_VERSION) $(ORIG_LIBS) $(PYTHON_LIBS) - # Drop other flags to build with full dependencies under ICC. - DLL_LDFLAGS = $(DLL_UNDEF_FLAGS) + WATCHERS = ucko diff --git a/src/dbapi/simple/Makefile.sdbapi.lib b/src/dbapi/simple/Makefile.sdbapi.lib -index 603fd1e..0d06323 100644 +index 75be96d..bc87bc1 100644 --- a/src/dbapi/simple/Makefile.sdbapi.lib +++ b/src/dbapi/simple/Makefile.sdbapi.lib -@@ -5,3 +5,4 @@ LIB = sdbapi +@@ -1,3 +1,4 @@ ++<<<<<<< + # $Id: Makefile.sdbapi.lib 370257 2012-07-27 14:56:37Z ivanovp $ + + SRC = sdbapi +@@ -5,3 +6,13 @@ LIB = sdbapi - WATCHERS = ivanovp + WATCHERS = ucko ++||||||| ++ ++WATCHERS = ivanovp ++ ++======= ++ ++WATCHERS = ivanovp ++ +DLL_LIB = xncbi xutil dbapi_driver ncbi_xdbapi_ftds xconnect xser bdb xconnserv ++>>>>>>> diff --git a/src/html/Makefile.html.lib b/src/html/Makefile.html.lib index a57c1e3..0005299 100644 --- a/src/html/Makefile.html.lib @@ -755,11 +757,11 @@ index 2c7d491..cb54ba6 100644 + +DLL_LIB = general xser xncbi xutil diff --git a/src/objects/biotree/Makefile.biotree.lib b/src/objects/biotree/Makefile.biotree.lib -index 8019285..2c689ae 100644 +index 94b7e3d..e8f047a 100644 --- a/src/objects/biotree/Makefile.biotree.lib +++ b/src/objects/biotree/Makefile.biotree.lib -@@ -1,3 +1,5 @@ - ASN_DEP = seq seqset +@@ -2,3 +2,5 @@ + LIB = biotree SRC = biotree__ biotree___ + @@ -775,7 +777,7 @@ index 0dd0fa3..d50f29f 100644 + +DLL_LIB = xncbi xutil xser seq seqset scoremat diff --git a/src/objects/blast/Makefile.xnetblastcli.lib b/src/objects/blast/Makefile.xnetblastcli.lib -index 96325c4..5a72805 100644 +index 96325c4..d30f8ee 100644 --- a/src/objects/blast/Makefile.xnetblastcli.lib +++ b/src/objects/blast/Makefile.xnetblastcli.lib @@ -2,3 +2,5 @@ ASN_DEP = xnetblast @@ -1187,10 +1189,10 @@ index 74798f8..c74707c 100644 SRC = submit__ submit___ +DLL_LIB = xser xncbi seq biblio seqset diff --git a/src/objects/taxon1/Makefile.taxon1.lib b/src/objects/taxon1/Makefile.taxon1.lib -index 61658ab..f46db75 100644 +index f0f9c66..35d6a61 100644 --- a/src/objects/taxon1/Makefile.taxon1.lib +++ b/src/objects/taxon1/Makefile.taxon1.lib -@@ -3,3 +3,5 @@ LIB = taxon1 +@@ -4,3 +4,5 @@ LIB = taxon1 SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont WATCHERS = domrach @@ -1275,13 +1277,13 @@ index cb9846d..9c2a8f9 100644 + +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..c67c352 100644 +index 1ec5bf0..6da8514 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) +@@ -20,3 +20,5 @@ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) # LIB_OR_DLL = dll - WATCHERS = zaretska jianye madden camacho + WATCHERS = zaretska jianye madden camacho fongah2 + +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 @@ -1294,60 +1296,60 @@ index e32c351..41355ff 100644 +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..aa4d8e4 100644 +index 62f01fd..f7768e0 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) +@@ -17,3 +17,5 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) # CXXFLAGS = $(FAST_CXXFLAGS) # # LIB_OR_DLL = dll + +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 +index 3a92e3e..79a75b9 100644 --- a/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib +++ b/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib -@@ -4,3 +4,5 @@ WATCHERS = camacho - +@@ -5,3 +5,5 @@ WATCHERS = camacho + CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG_CPPFLAGS) LIB = gene_info SRC = gene_info gene_info_reader file_utils + +DLL_LIB = xncbi diff --git a/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib b/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib -index b0a00dc..37569f8 100644 +index a067ae2..e1a6d3e 100644 --- a/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib +++ b/src/objtools/blast/gene_info_writer/Makefile.gene_info_writer.lib -@@ -6,3 +6,5 @@ LIB = gene_info_writer +@@ -7,3 +7,5 @@ LIB = gene_info_writer SRC = gene_info_writer ASN_DEP = blastdb + +DLL_LIB = gene_info xncbi seqdb diff --git a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -index 25898aa..0b0e478 100644 +index 9c13307..65822c6 100644 --- a/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib +++ b/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -@@ -29,3 +29,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) +@@ -30,3 +30,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) WATCHERS = maning camacho + +DLL_LIB = blastdb xobjmgr diff --git a/src/objtools/blast/seqdb_writer/Makefile.writedb.lib b/src/objtools/blast/seqdb_writer/Makefile.writedb.lib -index 7b9c8e1..6dbdbaa 100644 +index 3b15ed6..77f5202 100644 --- a/src/objtools/blast/seqdb_writer/Makefile.writedb.lib +++ b/src/objtools/blast/seqdb_writer/Makefile.writedb.lib -@@ -13,3 +13,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) +@@ -14,3 +14,5 @@ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) - WATCHERS = maning camacho + WATCHERS = maning camacho fongah2 + +DLL_LIB = seq blastdb seqdb xobjmgr xobjread xutil diff --git a/src/objtools/blast/services/Makefile.blast_services.lib b/src/objtools/blast/services/Makefile.blast_services.lib -index 10a878c..7a70b22 100644 +index ceba356..d2bd900 100644 --- a/src/objtools/blast/services/Makefile.blast_services.lib +++ b/src/objtools/blast/services/Makefile.blast_services.lib -@@ -12,3 +12,4 @@ CFLAGS = $(FAST_CFLAGS) +@@ -13,3 +13,4 @@ CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS) CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) @@ -1363,10 +1365,10 @@ index 8e39baa..f4d3a35 100644 + +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 +index 291948f..adecac0 100644 --- a/src/objtools/cleanup/Makefile.cleanup.lib +++ b/src/objtools/cleanup/Makefile.cleanup.lib -@@ -10,7 +10,7 @@ SRC = autogenerated_cleanup cleanup \ +@@ -10,7 +10,7 @@ SRC = autogenerated_cleanup autogenerated_extended_cleanup cleanup \ cleanup_utils \ newcleanupp @@ -1376,10 +1378,10 @@ index 663d755..ad7b3cf 100644 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 +index 4fb6117..934a3b6 100644 --- a/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib +++ b/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib -@@ -6,3 +6,6 @@ SRC = bdbloader cached_sequence local_blastdb_adapter +@@ -8,3 +8,6 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) ASN_DEP = blastdb seqset WATCHERS = camacho @@ -1387,10 +1389,10 @@ 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 +index 243467f..3a2115c 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 +@@ -8,3 +8,5 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS) ASN_DEP = blastdb xnetblast WATCHERS = camacho @@ -1407,15 +1409,16 @@ index a51042b..fa92fc9 100644 + +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 +index f3bb947..90d3af9 100644 --- a/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib +++ b/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib -@@ -12,6 +12,6 @@ LIB = ncbi_xreader +@@ -12,7 +12,7 @@ LIB = ncbi_xreader LIB_OR_DLL = both # Dependencies for shared library -DLL_LIB = +DLL_LIB = xcompress xobjmgr seqsplit xconnect id1 id2 + DLL_DLIB = $(GENBANK_READER_LDEP) 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 @@ -1569,11 +1572,11 @@ index b49c3c5..2ee63f0 100644 + +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..fa58b3c 100644 +index 041a43a..bda6c63 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 \ - gather_iter html_anchor_item inst_info_map + gather_iter html_anchor_item inst_info_map gene_finder flat_qual_slots WATCHERS = ludwigf dicuccio kornbluh + @@ -1601,7 +1604,7 @@ index 300ceb2..4a81ac9 100644 + +DLL_LIB = xncbi general diff --git a/src/objtools/readers/Makefile.xobjread.lib b/src/objtools/readers/Makefile.xobjread.lib -index 0fbffd4..4ca9fed 100644 +index 8c9d2bf..28bbb88 100644 --- a/src/objtools/readers/Makefile.xobjread.lib +++ b/src/objtools/readers/Makefile.xobjread.lib @@ -19,5 +19,4 @@ SRC = read_util format_guess_ex \ @@ -1622,10 +1625,10 @@ 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 +index 8115a7f..f46b506 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 \ +@@ -12,6 +12,6 @@ mask_writer_seqloc \ mask_writer_blastdb_maskinfo ASN_DEP = seqset @@ -1643,27 +1646,27 @@ index dab25d6..f676dc7 100644 +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 +index a259eca..dbcc9cd 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 + ASN_DEP = seqset variation 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 +index 4b78f86..63c2386 100644 --- a/src/objtools/validator/Makefile.validator.lib +++ b/src/objtools/validator/Makefile.validator.lib -@@ -19,3 +19,5 @@ NOOPT_CXX = $(CXX_WRAPPER) $(CXX) $(CXXFLAGS_ALL:-xO%=) +@@ -12,3 +12,5 @@ LIB = xvalidate + ASN_DEP = general biblio pub seq seqset submit taxon3 valerr valid - lat_lon_country_map.o: $(srcdir)/lat_lon_country_map.cpp - $(NOOPT_CXX) $(srcdir)/lat_lon_country_map.cpp -o $@ $(CXX_FILTER) + WATCHERS = bollin + +DLL_LIB = xncbi xobjutil xalnmgr xformat taxon3 valerr valid diff --git a/src/objtools/writers/Makefile.xobjwrite.lib b/src/objtools/writers/Makefile.xobjwrite.lib -index cd6596b..a7d0c01 100644 +index d27e197..5dde419 100644 --- a/src/objtools/writers/Makefile.xobjwrite.lib +++ b/src/objtools/writers/Makefile.xobjwrite.lib @@ -15,3 +15,4 @@ SRC = agp_write \ @@ -1784,20 +1787,20 @@ index 4896661..8e2ad56 100644 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 +index a7c4e77..0f39423 100644 --- a/src/sra/sdk/libs/align/Makefile.align-writer.lib +++ b/src/sra/sdk/libs/align/Makefile.align-writer.lib -@@ -6,7 +6,7 @@ LIB = align-writer - SRC = dna-reverse-cmpl reader-cmn reader-refseq refseq-mgr writer-cmn \ - writer-refseq writer-alignment writer-sequence writer-ref writer-reference +@@ -7,7 +7,7 @@ SRC = dna-reverse-cmpl reader-cmn reference-cmn reader-refseq refseq-mgr \ + writer-cmn writer-refseq writer-alignment writer-sequence writer-ref \ + writer-reference --DLL_LIB = wvdb wkdb load kfg kfs klib $(Z_LIB) -+DLL_LIB = wvdb wkdb load kfg kfs klib kapp $(Z_LIB) +-DLL_LIB = wvdb wkdb kfg kfs klib $(Z_LIB) ++DLL_LIB = wvdb wkdb kfg kfs klib kapp $(Z_LIB) LIBS = $(Z_LIBS) $(ORIG_LIBS) CPPFLAGS = $(SRA_INCLUDE) $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY $(ORIG_CPPFLAGS) diff --git a/src/util/Makefile.util.lib b/src/util/Makefile.util.lib -index f103ff1..829a71c 100644 +index bb93ec9..d1b2737 100644 --- a/src/util/Makefile.util.lib +++ b/src/util/Makefile.util.lib @@ -14,3 +14,5 @@ PROJ_TAG = core diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch index 820960354..3ed3e7d5f 100644 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch @@ -1,117 +1,11 @@ - src/build-system/configure | 34 +++++++++++++++++++++++----------- - src/build-system/configure.ac | 33 ++++++++++++++++++++++----------- - 2 files changed, 45 insertions(+), 22 deletions(-) + src/build-system/configure.ac | 17 ++++++++++++++--- + 1 file changed, 14 insertions(+), 3 deletions(-) -diff --git a/src/build-system/configure b/src/build-system/configure -index 82fc9ef..d31a4f2 100755 ---- a/src/build-system/configure -+++ b/src/build-system/configure -@@ -924,7 +924,7 @@ Optional Packages: - --without-distcc do not automatically use distcc if available - --without-ncbi-c do not use NCBI C Toolkit - --without-sss do not use NCBI SSS libraries -- --without-utils do not use NCBI SSS UTIL library -+ --without-sssutils do not use NCBI SSS UTIL library - --without-sssdb do not use NCBI SSS DB library - --with-included-sss use the in-tree copy of SSS - --with-z=DIR use zlib installation in DIR -@@ -2835,12 +2835,12 @@ check ncbi-public strip pch caution ccache distcc \ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ --ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ - bdb python jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl 3psw \ - local-lbsm ncbi-crypt connext \ --serial objects dbapi app ctools gui algo internal gbench" -+serial objects dbapi app ctools gui algo internal gbench x" - - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` - -@@ -2864,6 +2864,7 @@ for x_arg in "$@" ; do - case "$x_arg" in - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ - | --cache-file= | --build= | --host= | --target= | --with-runpath= \ -+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ - | --with-relative-runpath= | --x-includes= | --x-libraries= ) - { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5 - echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} -@@ -2876,6 +2877,7 @@ echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [A-Z]*=* \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -3023,7 +3025,8 @@ echo "$as_me: error: --without-extra-action is not allowed" >&2;} - fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5 - echo "$as_me: using default projects file \"projects\"." >&6;} - with_projects=projects -@@ -3049,6 +3052,16 @@ echo "$as_me: WARNING: default projects file \"projects\" is a dangling link." > - ;; - esac - -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ as_fn_error $? "unable to read requested projects file \"$abs_projects\"." "$LINENO" 5 -+fi -+ - - #### Always define this - -@@ -32712,7 +32725,7 @@ else - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - { { echo "$as_me:$LINENO: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&5 - echo "$as_me: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&2;} - { (exit 1); exit 1; }; } -@@ -34949,11 +34962,9 @@ if test "$with_flat_makefile" != "no"; then - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -34997,7 +35008,8 @@ lib) - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac -index 7b733af..3b55bf5 100644 +index 03e34b4..336453d 100644 --- a/src/build-system/configure.ac +++ b/src/build-system/configure.ac -@@ -222,7 +222,7 @@ AC_ARG_WITH(ncbi-c, +@@ -224,7 +224,7 @@ AC_ARG_WITH(ncbi-c, AC_ARG_WITH(sss, [ --without-sss do not use NCBI SSS libraries]) AC_ARG_WITH(sssutils, @@ -120,22 +14,23 @@ index 7b733af..3b55bf5 100644 AC_ARG_WITH(sssdb, [ --without-sssdb do not use NCBI SSS DB library]) AC_ARG_WITH(included-sss, -@@ -462,12 +462,12 @@ check ncbi-public strip pch caution ccache distcc \ +@@ -490,13 +490,13 @@ check ncbi-public strip pch caution ccache distcc \ ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ geo included-geo \ - z bz2 lzo pcre gnutls openssl sybase sybase-local sybase-new \ --ftds mysql orbacus freetype fltk opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype fltk opengl mesa glut glew glew-mx \ - bdb python jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt xerces xalan oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl 3psw \ + z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ +-ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ ++ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ + bdb python perl jni sqlite3 icu boost boost-tag \ + sp expat sablot libxml libxslt libexslt xerces xalan zorba \ + oechem sge muparser hdf5 \ + gif jpeg tiff png xpm magic curl mimetic 3psw \ local-lbsm ncbi-crypt connext \ -serial objects dbapi app ctools gui algo internal gbench" +serial objects dbapi app ctools gui algo internal gbench x" changequote(, )dnl x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` -@@ -493,6 +493,7 @@ for x_arg in "$@" ; do +@@ -522,6 +522,7 @@ for x_arg in "$@" ; do case "$x_arg" in --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ | --cache-file= | --build= | --host= | --target= | --with-runpath= \ @@ -143,7 +38,7 @@ index 7b733af..3b55bf5 100644 | --with-relative-runpath= | --x-includes= | --x-libraries= ) AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) ;; -@@ -503,6 +504,7 @@ for x_arg in "$@" ; do +@@ -532,6 +533,7 @@ for x_arg in "$@" ; do | --with-universal=* | --with-tcheck=* \ | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ @@ -151,20 +46,10 @@ index 7b733af..3b55bf5 100644 | [[A-Z]*=*] \ | --with-z=* | --with-bz2=* | --with-lzo=* \ | --with-pcre=* \ -@@ -581,7 +583,8 @@ if test "$with_extra_action" = "no" ; then +@@ -647,6 +649,15 @@ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then + *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; + esac fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - AC_MSG_NOTICE([using default projects file "projects".]) - with_projects=projects - AC_SUBST(PROJECTS, "\$(top_srcdir)/projects") -@@ -599,6 +602,15 @@ case "$with_projects" in - * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; - esac - +if test -n "$with_projects"; then + case "$with_projects" in + /* ) abs_projects=$with_projects ;; @@ -177,37 +62,3 @@ index 7b733af..3b55bf5 100644 #### Always define this AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) -@@ -6198,7 +6210,7 @@ else - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - AC_MSG_ERROR([--with-internal: Cannot build INTERNAL projects: missing $reason]) - else - AC_MSG_WARN([--with-internal: Cannot build all INTERNAL projects: missing $reason]) -@@ -6807,11 +6819,9 @@ if test "$with_flat_makefile" != "no"; then - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -6854,7 +6864,8 @@ lib) - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index f217ab346..a839d6b81 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit eutils flag-o-matic multilib toolchain-funcs +inherit autotools eutils flag-o-matic multilib toolchain-funcs MY_TAG="Jun_15_2010" MY_Y="${MY_TAG/*_/}" @@ -105,8 +105,8 @@ src_prepare() { # The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers local PATCHES=( - #"${FILESDIR}"/${P}-conf-opts.patch - #"${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-conf-opts.patch + "${FILESDIR}"/${P}-as-needed.patch "${FILESDIR}"/${P}-fix-creaders-linking.patch "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch @@ -115,7 +115,8 @@ src_prepare() { tc-export CXX CC -# cd src/build-system || die + cd src/build-system || die + eautoreconf # eaclocal -I. # eautoconf } @@ -216,7 +217,7 @@ src_configure() { $(use_with ssl openssl "${EPREFIX}/usr") $(use_with ftds ftds "${EPREFIX}/usr") $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with fltk fltk "${EPREFIX}/usr") + $(usex fltk --with-fltk="${EPREFIX}/usr" "") $(use_with opengl opengl "${EPREFIX}/usr") $(use_with mesa mesa "${EPREFIX}/usr") $(use_with opengl glut "${EPREFIX}/usr") @@ -227,7 +228,7 @@ src_configure() { $(use_with freetype freetype "${EPREFIX}/usr") $(use_with fastcgi fastcgi "${EPREFIX}/usr") $(use_with berkdb bdb "${EPREFIX}/usr") - $(use_with odbc odbc "${EPREFIX}/usr") + $(usex odbc --with-odbc="${EPREFIX}/usr" "") $(use_with python python "${EPREFIX}/usr") $(use_with boost boost "${EPREFIX}/usr") $(use_with sqlite sqlite3 "${EPREFIX}/usr") @@ -259,7 +260,6 @@ src_configure() { # bash \ # ./src/build-system/configure \ -# cd src/build-system || die econf \ --srcdir="${S}" \ --prefix="${EPREFIX}/usr" \ |