Index: src/algo/blast/format/Makefile.xblastformat.lib =================================================================== --- src/algo/blast/format/Makefile.xblastformat.lib (revision 439078) +++ src/algo/blast/format/Makefile.xblastformat.lib (working copy) @@ -7,6 +7,6 @@ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) -DLL_LIB = align_format blastxml xhtml xcgi +DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi WATCHERS = jianye zaretska madden camacho fongah2 Index: src/app/compart/Makefile.compart.app =================================================================== --- src/app/compart/Makefile.compart.app (revision 439078) +++ src/app/compart/Makefile.compart.app (working copy) @@ -5,11 +5,11 @@ APP = compart SRC = compart -LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \ - $(BLAST_LIBS:%=%$(STATIC)) \ - $(OBJMGR_LIBS:%=%$(STATIC)) +LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ + taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ + $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) -LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) +LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) Index: src/app/compart/Makefile.compartp.app =================================================================== --- src/app/compart/Makefile.compartp.app (revision 439078) +++ src/app/compart/Makefile.compartp.app (working copy) @@ -5,7 +5,8 @@ APP = compartp SRC = compartp -LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) +LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ + xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) Index: src/app/grid/util/Makefile.ncfetch.app =================================================================== --- src/app/grid/util/Makefile.ncfetch.app (revision 439078) +++ src/app/grid/util/Makefile.ncfetch.app (working copy) @@ -5,7 +5,7 @@ APP = ncfetch.cgi SRC = ncfetch -LIB = xcgi xconnserv xconnect xutil xncbi +LIB = xcgi xconnserv xthrserv xconnect xutil xncbi LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) WATCHERS = kazimird Index: src/app/hfilter/Makefile.hfilter.app =================================================================== --- src/app/hfilter/Makefile.hfilter.app (revision 439078) +++ src/app/hfilter/Makefile.hfilter.app (working copy) @@ -5,9 +5,10 @@ APP = hfilter SRC = hitfilter_app -LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) +LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ + xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) +LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) Index: src/app/speedtest/Makefile.speedtest.app =================================================================== --- src/app/speedtest/Makefile.speedtest.app (revision 439078) +++ src/app/speedtest/Makefile.speedtest.app (working copy) @@ -8,7 +8,7 @@ APP = speedtest SRC = speedtest -LIB = prosplign xalgoalignutil xcleanup submit $(BLAST_LIBS) \ +LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) Index: src/app/splign/Makefile.splign.app =================================================================== --- src/app/splign/Makefile.splign.app (revision 439078) +++ src/app/splign/Makefile.splign.app (working copy) @@ -12,7 +12,7 @@ LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ $(BLAST_DB_DATA_LOADER_LIBS) \ ncbi_xloader_lds2 lds2 sqlitewrapp \ - xqueryparse xalgoseq $(PCRE_LIB) \ + xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ $(BLAST_LIBS:%=%$(STATIC)) submit \ $(OBJMGR_LIBS:%=%$(STATIC)) Index: src/connect/services/test/Makefile.test_nsstorage.app =================================================================== --- src/connect/services/test/Makefile.test_nsstorage.app (revision 439078) +++ src/connect/services/test/Makefile.test_nsstorage.app (working copy) @@ -2,7 +2,7 @@ APP = test_nsstorage SRC = test_nsstorage -LIB = xconnserv xconnect xutil xncbi +LIB = xconnserv xthrserv xconnect xutil xncbi LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) Index: src/misc/hgvs/test/Makefile.hgvs2variation.app =================================================================== --- src/misc/hgvs/test/Makefile.hgvs2variation.app (revision 439078) +++ src/misc/hgvs/test/Makefile.hgvs2variation.app (working copy) @@ -6,7 +6,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) -LIB_ = hgvs variation \ +LIB_ = hgvs objcoords variation \ entrez2cli entrez2 xregexp $(PCRE_LIB) xobjutil $(OBJMGR_LIBS) LIB = $(LIB_:%=%$(STATIC)) Index: src/misc/hgvs/test/Makefile.test_hgvs_parser.app =================================================================== --- src/misc/hgvs/test/Makefile.test_hgvs_parser.app (revision 439078) +++ src/misc/hgvs/test/Makefile.test_hgvs_parser.app (working copy) @@ -5,7 +5,7 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) -LIB_ = hgvs variation test_boost xregexp $(PCRE_LIB) xobjutil \ +LIB_ = hgvs objcoords variation test_boost xregexp $(PCRE_LIB) xobjutil \ entrez2cli entrez2 $(OBJMGR_LIBS) LIB = $(LIB_:%=%$(STATIC)) Index: src/objects/biblio/Makefile.biblio.lib =================================================================== --- src/objects/biblio/Makefile.biblio.lib (revision 439078) +++ src/objects/biblio/Makefile.biblio.lib (working copy) @@ -1,2 +1,4 @@ LIB = biblio SRC = biblio__ biblio___ citation_base + +DLL_LIB = general Index: src/objects/blast/Makefile.blast.lib =================================================================== --- src/objects/blast/Makefile.blast.lib (revision 439078) +++ src/objects/blast/Makefile.blast.lib (working copy) @@ -1,4 +1,6 @@ LIB = xnetblast SRC = blast__ blast___ names +DLL_LIB = scoremat seqset + WATCHERS = camacho Index: src/objects/blast/Makefile.xnetblastcli.lib =================================================================== --- src/objects/blast/Makefile.xnetblastcli.lib (revision 439078) +++ src/objects/blast/Makefile.xnetblastcli.lib (working copy) @@ -2,3 +2,5 @@ LIB = xnetblastcli SRC = blastclient blastclient_ + +DLL_LIB = xnetblast xconnect Index: src/objects/blastdb/Makefile.blastdb.lib =================================================================== --- src/objects/blastdb/Makefile.blastdb.lib (revision 439078) +++ src/objects/blastdb/Makefile.blastdb.lib (working copy) @@ -1,2 +1,4 @@ LIB = blastdb SRC = blastdb__ blastdb___ + +DLL_LIB = seq Index: src/objects/general/Makefile.general.lib =================================================================== --- src/objects/general/Makefile.general.lib (revision 439078) +++ src/objects/general/Makefile.general.lib (working copy) @@ -1,2 +1,4 @@ LIB = general SRC = general__ general___ uoconv + +DLL_LIB = xser Index: src/objects/medline/Makefile.medline.lib =================================================================== --- src/objects/medline/Makefile.medline.lib (revision 439078) +++ src/objects/medline/Makefile.medline.lib (working copy) @@ -1,2 +1,4 @@ LIB = medline SRC = medline__ medline___ + +DLL_LIB = biblio general Index: src/objects/pub/Makefile.pub.lib =================================================================== --- src/objects/pub/Makefile.pub.lib (revision 439078) +++ src/objects/pub/Makefile.pub.lib (working copy) @@ -1,2 +1,4 @@ LIB = pub SRC = pub__ pub___ + +DLL_LIB = medline biblio Index: src/objects/scoremat/Makefile.scoremat.lib =================================================================== --- src/objects/scoremat/Makefile.scoremat.lib (revision 439078) +++ src/objects/scoremat/Makefile.scoremat.lib (working copy) @@ -1,2 +1,4 @@ LIB = scoremat SRC = scoremat__ scoremat___ + +DLL_LIB = seqset Index: src/objects/seq/Makefile.seq.lib =================================================================== --- src/objects/seq/Makefile.seq.lib (revision 439078) +++ src/objects/seq/Makefile.seq.lib (working copy) @@ -13,3 +13,5 @@ seq_loc_from_string seq_loc_reverse_complementer WATCHERS = vasilche grichenk + +DLL_LIB = seqcode pub biblio general xser sequtil Index: src/objects/seqset/Makefile.seqset.lib =================================================================== --- src/objects/seqset/Makefile.seqset.lib (revision 439078) +++ src/objects/seqset/Makefile.seqset.lib (working copy) @@ -1,2 +1,4 @@ LIB = seqset SRC = seqset__ seqset___ gb_release_file + +DLL_LIB = xser Index: src/objects/taxon1/Makefile.taxon1.lib =================================================================== --- src/objects/taxon1/Makefile.taxon1.lib (revision 439078) +++ src/objects/taxon1/Makefile.taxon1.lib (working copy) @@ -3,4 +3,6 @@ LIB = taxon1 SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont +DLL_LIB = xconnect + WATCHERS = domrach Index: src/objmgr/util/Makefile.util.lib =================================================================== --- src/objmgr/util/Makefile.util.lib (revision 439078) +++ src/objmgr/util/Makefile.util.lib (working copy) @@ -8,5 +8,7 @@ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util LIB = xobjutil +DLL_LIB = xobjmgr + WATCHERS = ucko vasilche Index: src/objtools/blast/seqdb_reader/Makefile.seqdb.lib =================================================================== --- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (revision 439078) +++ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (working copy) @@ -29,4 +29,6 @@ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) +DLL_LIB = xobjmgr blastdb + WATCHERS = maning camacho Index: src/objtools/blast/services/Makefile.blast_services.lib =================================================================== --- src/objtools/blast/services/Makefile.blast_services.lib (revision 439078) +++ src/objtools/blast/services/Makefile.blast_services.lib (working copy) @@ -13,3 +13,4 @@ CXXFLAGS = $(FAST_CXXFLAGS) LDFLAGS = $(FAST_LDFLAGS) +DLL_LIB = xnetblastcli xconnect Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib =================================================================== --- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (revision 439078) +++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (working copy) @@ -7,4 +7,6 @@ ASN_DEP = blastdb seqset +DLL_LIB = seqdb + WATCHERS = camacho Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib =================================================================== --- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (revision 439078) +++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (working copy) @@ -7,4 +7,6 @@ ASN_DEP = blastdb xnetblast +DLL_LIB = blast_services + WATCHERS = camacho Index: src/objtools/lds2/Makefile.lds2.lib =================================================================== --- src/objtools/lds2/Makefile.lds2.lib (revision 439078) +++ src/objtools/lds2/Makefile.lds2.lib (working copy) @@ -8,9 +8,9 @@ SRC = lds2 lds2_db lds2_handlers # Dependencies for shared library -#DLL_LIB = sqlitewrapp +DLL_LIB = sqlitewrapp $(COMPRESS_LIBS) -LIBS = $(CMPRS_LIBS) $(ORIG_LIBS) +LIBS = $(SQLITE3_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) CPPFLAGS = $(SQLITE3_INCLUDE) $(CMPRS_INCLUDE) $(ORIG_CPPFLAGS) Index: src/objtools/readers/Makefile.xobjread.lib =================================================================== --- src/objtools/readers/Makefile.xobjread.lib (revision 439078) +++ src/objtools/readers/Makefile.xobjread.lib (working copy) @@ -19,5 +19,6 @@ best_feat_finder source_mod_parser fasta_exception -DLL_LIB = creaders +DLL_LIB = seqset $(SEQ_LIBS) pub general creaders xutil + Index: src/sample/app/cgi/Makefile.cgi_session_sample.app =================================================================== --- src/sample/app/cgi/Makefile.cgi_session_sample.app (revision 439078) +++ src/sample/app/cgi/Makefile.cgi_session_sample.app (working copy) @@ -11,7 +11,7 @@ # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. ### BEGIN COPIED SETTINGS -LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi +LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) Index: src/sample/app/netcache/Makefile.netcache_cgi_sample.app =================================================================== --- src/sample/app/netcache/Makefile.netcache_cgi_sample.app (revision 439078) +++ src/sample/app/netcache/Makefile.netcache_cgi_sample.app (working copy) @@ -4,7 +4,7 @@ SRC = netcache_cgi_sample ### BEGIN COPIED SETTINGS -LIB = xconnserv xconnect xcgi xhtml xutil xncbi +LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) ### END COPIED SETTINGS Index: src/serial/Makefile.serial.lib =================================================================== --- src/serial/Makefile.serial.lib (revision 439078) +++ src/serial/Makefile.serial.lib (working copy) @@ -19,3 +19,5 @@ LIB = xser WATCHERS = gouriano + +DLL_LIB = xutil xncbi Index: src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app =================================================================== --- src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (revision 439078) +++ src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (working copy) @@ -7,7 +7,8 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) -LIB = ncbi_xloader_bam bamread $(BAM_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) +LIB = ncbi_xloader_bam bamread $(BAM_LIBS) \ + xobjreadex $(OBJREAD_LIBS) xobjutil test_boost $(OBJMGR_LIBS) LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) Index: src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app =================================================================== --- src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (revision 439078) +++ src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (working copy) @@ -5,7 +5,8 @@ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) -LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) +LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil \ + test_boost $(OBJMGR_LIBS) LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) Index: src/sra/readers/bam/test/Makefile.bam_test.app =================================================================== --- src/sra/readers/bam/test/Makefile.bam_test.app (revision 439078) +++ src/sra/readers/bam/test/Makefile.bam_test.app (working copy) @@ -9,7 +9,8 @@ APP = bam_test SRC = bam_test -LIB = bamread xobjreadex xobjutil xobjsimple $(OBJMGR_LIBS) $(BAM_LIBS) +LIB = bamread $(BAM_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil xobjsimple \ + $(OBJMGR_LIBS) LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) REQUIRES = objects Index: src/sra/sdk/libs/vfs/Makefile.vfs.lib =================================================================== --- src/sra/sdk/libs/vfs/Makefile.vfs.lib (revision 16076) +++ src/sra/sdk/libs/vfs/Makefile.vfs.lib (working copy) @@ -8,6 +8,9 @@ CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \ $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS) -DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) +DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) \ + krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) +LIBS = $(SRA_SDK_SYSLIBS) + LIB_OR_DLL = both