path: root/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch

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