-Subject: ensure that all libraries link against all direct dependencies
-
- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency
- loop between libxblast and libxalgoblastdbindex by having the former
- provide only the C++ BLAST API, leaving the C core only in libblast.
- * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
- rather than libconnect for consistency with libblast, which uses the
- former to keep the aforementioned cycle-breaking from causing
- inconsistency elsewhere.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko@debian.org>
-Last-Update: 2011-08-28
---- a/c++/src/algo/blast/core/Makefile.blast.lib
-+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,6 +21,7 @@
- CFLAGS = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = composition_adjustment xconnect tables
-
- WATCHERS = madden camacho
-
---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
-+
- ASN_DEP = seqset
-
- WATCHERS = morgulis
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,7 +7,8 @@
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
--DLL_LIB = align_format blastxml blastxml2 xhtml xcgi
-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi blastxml2
-
- WATCHERS = jianye zaretska madden camacho fongah2
-
---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,7 +21,7 @@
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
--
-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
-
- USES_LIBRARIES = \
- seqmasks_io
---- a/c++/src/cgi/Makefile.cgi.lib
-+++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@
- user_agent
- LIB = xcgi
-
-+DLL_LIB = xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
-
- WATCHERS = vakatov
---- a/c++/src/html/Makefile.html.lib
-+++ b/c++/src/html/Makefile.html.lib
-@@ -7,6 +7,8 @@
- commentdiag indentstream html_exception writer_htmlenc
- LIB = xhtml
-
-+DLL_LIB = xncbi
-+
- WATCHERS = ivanov
-
-
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -3,6 +3,7 @@
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
-
- USES_LIBRARIES = \
- xconnect xnetblast
---- a/c++/src/objtools/align_format/Makefile.align_format.lib
-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -13,6 +13,10 @@
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
-+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
-+ xcgi xhtml tables xncbi
-+
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
- # CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -12,7 +12,7 @@
-
- WATCHERS = todorov dicuccio grichenk
-
--
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-
- USES_LIBRARIES = \
- tables xobjutil
---- a/c++/src/objtools/readers/Makefile.xobjread.lib
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -21,7 +21,7 @@
- message_listener line_error
-
-
--DLL_LIB = creaders
-+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi
-
-
-
---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -12,7 +12,7 @@
- mask_writer_blastdb_maskinfo
-
- ASN_DEP = seqset
--DLL_LIB = seqdb blastdb
-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
-
- WATCHERS = morgulis camacho
-
---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@
-
- ASN_DEP = seqset
-
-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
-+
- LIB = xobjsimple
- SRC = simple_om
-
---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -24,6 +24,8 @@
-
- LIB = seqdb
-
-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -7,6 +7,8 @@
-
- ASN_DEP = blastdb seqset
-
-+DLL_LIB = seqdb xobjmgr seqset seq xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -5,6 +5,8 @@
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
-+
- ASN_DEP = blastdb xnetblast
-
- WATCHERS = camacho
---- a/c++/src/algo/blast/api/Makefile.xblast.lib
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,14 +74,15 @@
- deltablast_options \
- deltablast
-
--SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
-+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
-
- 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) blast seqdb seqset seq general \
-+ xser xconnect sequtil tables xutil xncbi
-
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -24,7 +24,9 @@
-
- LIB = blastinput
-
--DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil
-+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
-+ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
-+ scoremat seqset seq xser xutil xncbi
-
- # should be redundant, given the above :-/
- ASN_DEP = seqset xnetblast
---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@
-
- SRC = symdust
-
-+DLL_LIB = xobjmgr seq xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/connect/Makefile.xconnect.lib
-+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@
- LIB = xconnect
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
-+
- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
-
- WATCHERS = lavr
---- a/c++/src/connect/ext/Makefile.xconnext.lib
-+++ b/c++/src/connect/ext/Makefile.xconnext.lib
-@@ -6,6 +6,8 @@
-
- LIB = xconnext
-
-+DLL_LIB = xconnect xncbi
-+
- WATCHERS = lavr
-
-
---- a/c++/src/objects/blast/Makefile.blast.lib
-+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -1,6 +1,8 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
-
-+DLL_LIB = scoremat seqset seq xser xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objects/blastxml/Makefile.blastxml.lib
-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
-@@ -1,6 +1,8 @@
- LIB = blastxml
- SRC = blastxml__ blastxml___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,6 +1,8 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-
-+DLL_LIB = seqset seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
-@@ -1,6 +1,7 @@
- LIB = seqedit
- SRC = seqedit__ seqedit___
--
-+
-+DLL_LIB = seqset seq general xser xncbi
-
-
- USES_LIBRARIES = \
---- a/c++/src/objects/submit/Makefile.submit.lib
-+++ b/c++/src/objects/submit/Makefile.submit.lib
-@@ -1,6 +1,8 @@
- LIB = submit
- SRC = submit__ submit___
-
-+DLL_LIB = seqset seq biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objmgr/util/Makefile.util.lib
-+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,6 +8,8 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
- LIB = xobjutil
-
-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = ucko vasilche kornbluh
-
-
---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-@@ -11,6 +11,7 @@
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
-
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-@@ -8,6 +8,8 @@
-
- LIB = blast_services
-
-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = id2 id1 ncbi_xreader \
-+ xobjmgr seq xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -15,6 +15,9 @@
- DLL_LIB =
- DLL_DLIB = $(GENBANK_READER_LDEP)
-
-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
-+ xser xconnect xcompress xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-@@ -12,6 +12,8 @@
- # Dependencies for shared library
- DLL_LIB = xconnect ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-@@ -12,7 +12,10 @@
- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
-
- # Dependencies for shared library (disabled due to problems on Darwin)
--# DLL_LIB = xconnect ncbi_xreader$(DLL)
-+DLL_LIB = xconnect ncbi_xreader$(DLL)
-+
-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
-+
-
- WATCHERS = vasilche
-
---- a/c++/src/util/compress/api/Makefile.compress.lib
-+++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -7,7 +7,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
-+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
- LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/util/sequtil/Makefile.sequtil.lib
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
-@@ -3,6 +3,8 @@
- LIB = sequtil
- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
-
-+DLL_LIB = xncbi
-+
- WATCHERS = shomrat
-
-
---- a/c++/src/corelib/Makefile.test_boost.lib
-+++ b/c++/src/corelib/Makefile.test_boost.lib
-@@ -3,6 +3,8 @@
- SRC = test_boost teamcity_messages
- LIB = test_boost
-
-+DLL_LIB = xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
-
- REQUIRES = Boost.Test.Included
---- a/c++/src/corelib/Makefile.test_mt.lib
-+++ b/c++/src/corelib/Makefile.test_mt.lib
-@@ -3,6 +3,8 @@
- SRC = test_mt
- LIB = test_mt
-
-+DLL_LIB = xncbi
-+
- # REQUIRES = MT
-
- USE_PCH = no
---- a/c++/src/objects/biblio/Makefile.biblio.lib
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib
-@@ -1,6 +1,8 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-
-+DLL_LIB = general xser xncbi
-+
-
- USES_LIBRARIES = \
- general
---- a/c++/src/objects/blastdb/Makefile.blastdb.lib
-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -1,5 +1,7 @@
- # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $
-
-+
-+DLL_LIB = seq xser xncbi
- LIB = blastdb
- SRC = blastdb__ blastdb___
-
---- a/c++/src/objects/general/Makefile.general.lib
-+++ b/c++/src/objects/general/Makefile.general.lib
-@@ -1,6 +1,8 @@
- LIB = general
- SRC = general__ general___ uoconv
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-@@ -3,6 +3,8 @@
- LIB = genome_collection
- SRC = genome_collection__ genome_collection___
-
-+DLL_LIB = seq general xser xncbi
-+
- WATCHERS = dicuccio
-
-
---- a/c++/src/objects/id1/Makefile.id1.lib
-+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,6 +3,8 @@
- LIB = id1
- SRC = id1__ id1___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/id2/Makefile.id2.lib
-+++ b/c++/src/objects/id2/Makefile.id2.lib
-@@ -1,6 +1,8 @@
- LIB = id2
- SRC = id2__ id2___
-
-+DLL_LIB = seqsplit seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/medline/Makefile.medline.lib
-+++ b/c++/src/objects/medline/Makefile.medline.lib
-@@ -1,6 +1,8 @@
- LIB = medline
- SRC = medline__ medline___
-
-+DLL_LIB = biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- biblio
---- a/c++/src/objects/pub/Makefile.pub.lib
-+++ b/c++/src/objects/pub/Makefile.pub.lib
-@@ -1,6 +1,8 @@
- LIB = pub
- SRC = pub__ pub___
-
-+DLL_LIB = medline biblio xser xncbi
-+
-
- USES_LIBRARIES = \
- medline
---- a/c++/src/objects/seq/Makefile.seq.lib
-+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,6 +12,8 @@
- seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
- seq_loc_from_string seq_loc_reverse_complementer
-
-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = vasilche grichenk
-
-
---- a/c++/src/objects/seqcode/Makefile.seqcode.lib
-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
-@@ -1,6 +1,8 @@
- LIB = seqcode
- SRC = seqcode__ seqcode___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/seqset/Makefile.seqset.lib
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib
-@@ -1,6 +1,8 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-
-+DLL_LIB = seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- $(SEQ_LIBS) pub
---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-@@ -1,6 +1,8 @@
- LIB = seqsplit
- SRC = seqsplit__ seqsplit___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/serial/Makefile.serial.lib
-+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,6 +18,8 @@
-
- LIB = xser
-
-+DLL_LIB = xutil xncbi
-+
- WATCHERS = gouriano
-
-
---- a/c++/src/util/Makefile.util.lib
-+++ b/c++/src/util/Makefile.util.lib
-@@ -12,6 +12,7 @@
- LIB = xutil
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
- LIBS = $(ORIG_LIBS)
-
- WATCHERS = vakatov kornbluh
---- a/c++/src/util/xregexp/Makefile.xregexp.lib
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -6,7 +6,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
-
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS = $(PCRE_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@
-
- SRC = segmask
-
-+DLL_LIB = blast xobjmgr xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/objmgr/split/Makefile.id2_split.lib
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,7 +17,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(SOBJMGR_LIBS)
-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
-
- WATCHERS = vasilche
-
---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@
-
- LIB = writedb
-
-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
-+ xser sequtil xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/algo/blast/Makefile.blast_macros.mk
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@
- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
-
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
- xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-@@ -2,7 +2,7 @@
- SRC = main mkindex_app
-
- LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
-- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)
-+ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
-
- CXXFLAGS = $(FAST_CXXFLAGS)
+Subject: ensure that all libraries link against all direct dependencies\r
+\r
+ * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency\r
+ loop between libxblast and libxalgoblastdbindex by having the former\r
+ provide only the C++ BLAST API, leaving the C core only in libblast.\r
+ * src/build-system/library_relations.txt: Change xblast's\r
+ relationship to blast from includes to needs, accordingly.\r
+ * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect\r
+ rather than libconnect for consistency with libblast, which uses the\r
+ former to keep the aforementioned cycle-breaking from causing\r
+ inconsistency elsewhere.\r
+\r
+Debian-Bug: 633567.\r
+Author: Aaron M. Ucko <ucko@debian.org>\r
+Last-Update: 2014-12-02\r
+--- a/c++/src/algo/blast/core/Makefile.blast.lib\r
++++ b/c++/src/algo/blast/core/Makefile.blast.lib\r
+@@ -21,6 +21,7 @@ LIB = blast\r
+ CFLAGS = $(FAST_CFLAGS) \r
+ LDFLAGS = $(FAST_LDFLAGS) \r
+ \r
++DLL_LIB = composition_adjustment xconnect tables\r
+ \r
+ WATCHERS = madden camacho\r
+ \r
+--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib\r
++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib\r
+@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \\r
+ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)\r
+ LDFLAGS = $(FAST_LDFLAGS)\r
+ \r
++DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi\r
++\r
+ ASN_DEP = seqset\r
+ \r
+ WATCHERS = morgulis\r
+--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib\r
++++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib\r
+@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast\r
+ \r
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)\r
+ \r
+-DLL_LIB = align_format blastxml blastxml2 xhtml xcgi\r
++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \\r
++ seq general xser tables xncbi blastxml2\r
+ \r
+ WATCHERS = jianye zaretska madden camacho fongah2\r
+ \r
+--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib\r
++++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib\r
+@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s\r
+ CXXFLAGS = $(FAST_CXXFLAGS)\r
+ LDFLAGS = $(FAST_LDFLAGS)\r
+ \r
+-\r
++DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi\r
+ \r
+ USES_LIBRARIES = \\r
+ seqmasks_io\r
+--- a/c++/src/cgi/Makefile.cgi.lib\r
++++ b/c++/src/cgi/Makefile.cgi.lib\r
+@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb\r
+ user_agent\r
+ LIB = xcgi\r
+ \r
++DLL_LIB = xutil xncbi\r
++\r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)\r
+ \r
+ WATCHERS = vakatov\r
+--- a/c++/src/html/Makefile.html.lib\r
++++ b/c++/src/html/Makefile.html.lib\r
+@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se\r
+ commentdiag indentstream html_exception writer_htmlenc\r
+ LIB = xhtml\r
+ \r
++DLL_LIB = xncbi\r
++\r
+ WATCHERS = ivanov\r
+ \r
+ \r
+--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib\r
++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib\r
+@@ -3,6 +3,7 @@ ASN_DEP = xnetblast\r
+ LIB = xnetblastcli\r
+ SRC = blastclient blastclient_\r
+ \r
++DLL_LIB = xnetblast xser xconnect xutil xncbi\r
+ \r
+ USES_LIBRARIES = \\r
+ xconnect xnetblast\r
+--- a/c++/src/objtools/align_format/Makefile.align_format.lib\r
++++ b/c++/src/objtools/align_format/Makefile.align_format.lib\r
+@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho\r
+ \r
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)\r
+ \r
++DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \\r
++ xobjmgr xnetblast blastdb gene_info seqset seq general xser \\r
++ xcgi xhtml tables xncbi\r
++\r
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST\r
+ # CFLAGS = $(FAST_CFLAGS)\r
+ # CXXFLAGS = $(FAST_CXXFLAGS)\r
+--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib\r
++++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib\r
+@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge\r
+ \r
+ WATCHERS = todorov dicuccio grichenk\r
+ \r
+-\r
++DLL_LIB = xobjmgr seqset seq xser tables xncbi\r
+ \r
+ USES_LIBRARIES = \\r
+ tables xobjutil\r
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib\r
++++ b/c++/src/objtools/readers/Makefile.xobjread.lib\r
+@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \\r
+ message_listener line_error\r
+ \r
+ \r
+-DLL_LIB = creaders\r
++DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi\r
+ \r
+ \r
+ \r
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib\r
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib\r
+@@ -12,7 +12,7 @@ mask_writer_seqloc \\r
+ mask_writer_blastdb_maskinfo\r
+ \r
+ ASN_DEP = seqset\r
+-DLL_LIB = seqdb blastdb\r
++DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi\r
+ \r
+ WATCHERS = morgulis camacho\r
+ \r
+--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib\r
++++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib\r
+@@ -7,6 +7,8 @@ WATCHERS = jcherry\r
+ \r
+ ASN_DEP = seqset\r
+ \r
++DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi\r
++\r
+ LIB = xobjsimple\r
+ SRC = simple_om\r
+ \r
+--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib\r
++++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib\r
+@@ -24,6 +24,8 @@ seqdbobj\r
+ \r
+ LIB = seqdb\r
+ \r
++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi\r
++\r
+ CFLAGS = $(FAST_CFLAGS)\r
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)\r
+ CXXFLAGS = $(FAST_CXXFLAGS)\r
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib\r
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib\r
+@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_\r
+ \r
+ ASN_DEP = blastdb seqset\r
+ \r
++DLL_LIB = seqdb xobjmgr seqset seq xncbi\r
++\r
+ WATCHERS = camacho\r
+ \r
+ \r
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib\r
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib\r
+@@ -5,6 +5,8 @@ SRC = bdbloader_rmt remote_blastdb_adapt\r
+ \r
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)\r
+ \r
++DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi\r
++\r
+ ASN_DEP = blastdb xnetblast\r
+ \r
+ WATCHERS = camacho\r
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib\r
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib\r
+@@ -74,14 +74,15 @@ cdd_pssm_input \\r
+ deltablast_options \\r
+ deltablast\r
+ \r
+-SRC = $(SRC_C:%=.core_%) $(SRC_CXX)\r
++SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)\r
+ \r
+ LIB = xblast\r
+ \r
+ DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \\r
+ xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \\r
+ blastdb xnetblastcli xnetblast scoremat xconnect tables \\r
+- $(SOBJMGR_LIBS)\r
++ $(SOBJMGR_LIBS) blast seqdb seqset seq general \\r
++ xser xconnect sequtil tables xutil xncbi\r
+ \r
+ CFLAGS = $(FAST_CFLAGS) \r
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)\r
+--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib\r
++++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib\r
+@@ -24,7 +24,9 @@ SRC = $(SRC_CXX)\r
+ \r
+ LIB = blastinput\r
+ \r
+-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil\r
++ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \\r
++ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \\r
++ scoremat seqset seq xser xutil xncbi\r
+ \r
+ # should be redundant, given the above :-/\r
+ ASN_DEP = seqset xnetblast\r
+--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib\r
++++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib\r
+@@ -8,6 +8,8 @@ LIB = xalgodustmask\r
+ \r
+ SRC = symdust\r
+ \r
++DLL_LIB = xobjmgr seq xncbi\r
++\r
+ CXXFLAGS = $(FAST_CXXFLAGS)\r
+ LDFLAGS = $(FAST_LDFLAGS)\r
+ \r
+--- a/c++/src/connect/Makefile.xconnect.lib\r
++++ b/c++/src/connect/Makefile.xconnect.lib\r
+@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)\r
+ LIB = xconnect\r
+ PROJ_TAG = core\r
+ \r
++DLL_LIB = xncbi\r
++\r
+ LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)\r
+ \r
+ WATCHERS = lavr\r
+--- a/c++/src/connect/ext/Makefile.xconnext.lib\r
++++ b/c++/src/connect/ext/Makefile.xconnext.lib\r
+@@ -6,6 +6,8 @@ SRC = $(SRC_C) ncbi_dblb_svcmapper\r
+ \r
+ LIB = xconnext\r
+ \r
++DLL_LIB = xconnect xncbi\r
++\r
+ WATCHERS = lavr\r
+ \r
+ \r
+--- a/c++/src/objects/blast/Makefile.blast.lib\r
++++ b/c++/src/objects/blast/Makefile.blast.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = xnetblast\r
+ SRC = blast__ blast___ names\r
+ \r
++DLL_LIB = scoremat seqset seq xser xncbi\r
++\r
+ WATCHERS = camacho\r
+ \r
+ \r
+--- a/c++/src/objects/blastxml/Makefile.blastxml.lib\r
++++ b/c++/src/objects/blastxml/Makefile.blastxml.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = blastxml\r
+ SRC = blastxml__ blastxml___\r
+ \r
++DLL_LIB = xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ xser\r
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib\r
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = scoremat\r
+ SRC = scoremat__ scoremat___\r
+ \r
++DLL_LIB = seqset seq general xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ seqset\r
+--- a/c++/src/objects/seqedit/Makefile.seqedit.lib\r
++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib\r
+@@ -1,6 +1,7 @@\r
+ LIB = seqedit\r
+ SRC = seqedit__ seqedit___\r
+- \r
++\r
++DLL_LIB = seqset seq general xser xncbi\r
+ \r
+ \r
+ USES_LIBRARIES = \\r
+--- a/c++/src/objects/submit/Makefile.submit.lib\r
++++ b/c++/src/objects/submit/Makefile.submit.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = submit\r
+ SRC = submit__ submit___\r
+ \r
++DLL_LIB = seqset seq biblio general xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ seqset\r
+--- a/c++/src/objmgr/util/Makefile.util.lib\r
++++ b/c++/src/objmgr/util/Makefile.util.lib\r
+@@ -8,6 +8,8 @@ ASN_DEP = submit\r
+ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci\r
+ LIB = xobjutil\r
+ \r
++DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi\r
++\r
+ WATCHERS = ucko vasilche kornbluh\r
+ \r
+ \r
+--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib\r
++++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib\r
+@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla\r
+ \r
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)\r
+ \r
++DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi\r
+ \r
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST\r
+ # CFLAGS = $(FAST_CFLAGS)\r
+--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib\r
++++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib\r
+@@ -8,6 +8,8 @@ SRC = blast_services\r
+ \r
+ LIB = blast_services\r
+ \r
++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi\r
++\r
+ CFLAGS = $(FAST_CFLAGS)\r
+ CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)\r
+ CXXFLAGS = $(FAST_CXXFLAGS)\r
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib\r
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib\r
+@@ -12,6 +12,9 @@ LIB_OR_DLL = both\r
+ # Dependencies for shared library\r
+ DLL_LIB = ncbi_xreader$(DLL)\r
+ \r
++DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \\r
++ id2 id1 ncbi_xreader xobjmgr seq xutil xncbi\r
++\r
+ WATCHERS = vasilche\r
+ \r
+ \r
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib\r
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib\r
+@@ -15,6 +15,9 @@ LIB_OR_DLL = both\r
+ DLL_LIB = \r
+ DLL_DLIB = $(GENBANK_READER_LDEP)\r
+ \r
++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \\r
++ xser xconnect xcompress xutil xncbi\r
++\r
+ WATCHERS = vasilche\r
+ \r
+ \r
+--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib\r
++++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib\r
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both\r
+ # Dependencies for shared library\r
+ DLL_LIB = ncbi_xreader$(DLL)\r
+ \r
++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi\r
++\r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)\r
+ \r
+ WATCHERS = vasilche\r
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib\r
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib\r
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both\r
+ # Dependencies for shared library\r
+ DLL_LIB = xconnect ncbi_xreader$(DLL)\r
+ \r
++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi\r
++\r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)\r
+ \r
+ WATCHERS = vasilche\r
+--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib\r
++++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib\r
+@@ -12,7 +12,10 @@ LIB_OR_DLL = both\r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)\r
+ \r
+ # Dependencies for shared library (disabled due to problems on Darwin)\r
+-# DLL_LIB = xconnect ncbi_xreader$(DLL)\r
++DLL_LIB = xconnect ncbi_xreader$(DLL)\r
++\r
++DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi\r
++\r
+ \r
+ WATCHERS = vasilche\r
+ \r
+--- a/c++/src/util/compress/api/Makefile.compress.lib\r
++++ b/c++/src/util/compress/api/Makefile.compress.lib\r
+@@ -7,7 +7,7 @@ LIB = xcompress\r
+ \r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)\r
+ \r
+-DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)\r
++DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi\r
+ LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)\r
+ \r
+ WATCHERS = ivanov\r
+--- a/c++/src/util/sequtil/Makefile.sequtil.lib\r
++++ b/c++/src/util/sequtil/Makefile.sequtil.lib\r
+@@ -3,6 +3,8 @@\r
+ LIB = sequtil\r
+ SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared\r
+ \r
++DLL_LIB = xncbi\r
++\r
+ WATCHERS = shomrat\r
+ \r
+ \r
+--- a/c++/src/corelib/Makefile.test_boost.lib\r
++++ b/c++/src/corelib/Makefile.test_boost.lib\r
+@@ -3,6 +3,8 @@\r
+ SRC = test_boost teamcity_messages\r
+ LIB = test_boost\r
+ \r
++DLL_LIB = xncbi\r
++\r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)\r
+ \r
+ REQUIRES = Boost.Test.Included\r
+--- a/c++/src/corelib/Makefile.test_mt.lib\r
++++ b/c++/src/corelib/Makefile.test_mt.lib\r
+@@ -3,6 +3,8 @@\r
+ SRC = test_mt\r
+ LIB = test_mt\r
+ \r
++DLL_LIB = xncbi\r
++\r
+ # REQUIRES = MT\r
+ \r
+ USE_PCH = no\r
+--- a/c++/src/objects/biblio/Makefile.biblio.lib\r
++++ b/c++/src/objects/biblio/Makefile.biblio.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = biblio\r
+ SRC = biblio__ biblio___ citation_base\r
+ \r
++DLL_LIB = general xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ general\r
+--- a/c++/src/objects/blastdb/Makefile.blastdb.lib\r
++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib\r
+@@ -1,5 +1,7 @@\r
+ # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $\r
+ \r
++\r
++DLL_LIB = seq xser xncbi\r
+ LIB = blastdb\r
+ SRC = blastdb__ blastdb___\r
+ \r
+--- a/c++/src/objects/general/Makefile.general.lib\r
++++ b/c++/src/objects/general/Makefile.general.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = general\r
+ SRC = general__ general___ uoconv\r
+ \r
++DLL_LIB = xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ xser\r
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib\r
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib\r
+@@ -3,6 +3,8 @@\r
+ LIB = genome_collection\r
+ SRC = genome_collection__ genome_collection___\r
+ \r
++DLL_LIB = seq general xser xncbi\r
++\r
+ WATCHERS = dicuccio\r
+ \r
+ \r
+--- a/c++/src/objects/id1/Makefile.id1.lib\r
++++ b/c++/src/objects/id1/Makefile.id1.lib\r
+@@ -3,6 +3,8 @@ ASN_DEP = seq\r
+ LIB = id1\r
+ SRC = id1__ id1___\r
+ \r
++DLL_LIB = seqset seq xser xncbi\r
++\r
+ WATCHERS = vasilche\r
+ \r
+ \r
+--- a/c++/src/objects/id2/Makefile.id2.lib\r
++++ b/c++/src/objects/id2/Makefile.id2.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = id2\r
+ SRC = id2__ id2___\r
+ \r
++DLL_LIB = seqsplit seq xser xncbi\r
++\r
+ WATCHERS = vasilche\r
+ \r
+ \r
+--- a/c++/src/objects/medline/Makefile.medline.lib\r
++++ b/c++/src/objects/medline/Makefile.medline.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = medline\r
+ SRC = medline__ medline___\r
+ \r
++DLL_LIB = biblio general xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ biblio\r
+--- a/c++/src/objects/pub/Makefile.pub.lib\r
++++ b/c++/src/objects/pub/Makefile.pub.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = pub\r
+ SRC = pub__ pub___\r
+ \r
++DLL_LIB = medline biblio xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ medline\r
+--- a/c++/src/objects/seq/Makefile.seq.lib\r
++++ b/c++/src/objects/seq/Makefile.seq.lib\r
+@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport\r
+ seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \\r
+ seq_loc_from_string seq_loc_reverse_complementer\r
+ \r
++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi\r
++\r
+ WATCHERS = vasilche grichenk\r
+ \r
+ \r
+--- a/c++/src/objects/seqcode/Makefile.seqcode.lib\r
++++ b/c++/src/objects/seqcode/Makefile.seqcode.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = seqcode\r
+ SRC = seqcode__ seqcode___\r
+ \r
++DLL_LIB = xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ xser\r
+--- a/c++/src/objects/seqset/Makefile.seqset.lib\r
++++ b/c++/src/objects/seqset/Makefile.seqset.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = seqset\r
+ SRC = seqset__ seqset___ gb_release_file\r
+ \r
++DLL_LIB = seq general xser xncbi\r
++\r
+ \r
+ USES_LIBRARIES = \\r
+ $(SEQ_LIBS) pub\r
+--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib\r
++++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib\r
+@@ -1,6 +1,8 @@\r
+ LIB = seqsplit\r
+ SRC = seqsplit__ seqsplit___\r
+ \r
++DLL_LIB = seqset seq xser xncbi\r
++\r
+ WATCHERS = vasilche\r
+ \r
+ \r
+--- a/c++/src/serial/Makefile.serial.lib\r
++++ b/c++/src/serial/Makefile.serial.lib\r
+@@ -18,6 +18,8 @@ SRC = \\r
+ \r
+ LIB = xser\r
+ \r
++DLL_LIB = xutil xncbi\r
++\r
+ WATCHERS = gouriano\r
+ \r
+ \r
+--- a/c++/src/util/Makefile.util.lib\r
++++ b/c++/src/util/Makefile.util.lib\r
+@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s\r
+ LIB = xutil\r
+ PROJ_TAG = core\r
+ \r
++DLL_LIB = xncbi\r
+ LIBS = $(ORIG_LIBS)\r
+ \r
+ WATCHERS = vakatov kornbluh\r
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib\r
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib\r
+@@ -6,7 +6,7 @@ LIB = xregexp\r
+ \r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)\r
+ \r
+-DLL_LIB = $(PCRE_LIB)\r
++DLL_LIB = $(PCRE_LIB) xncbi\r
+ LIBS = $(PCRE_LIBS)\r
+ \r
+ WATCHERS = ivanov\r
+--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib\r
++++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib\r
+@@ -8,6 +8,8 @@ LIB = xalgosegmask\r
+ \r
+ SRC = segmask\r
+ \r
++DLL_LIB = blast xobjmgr xncbi\r
++\r
+ CXXFLAGS = $(FAST_CXXFLAGS)\r
+ LDFLAGS = $(FAST_LDFLAGS)\r
+ \r
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib\r
++++ b/c++/src/objmgr/split/Makefile.id2_split.lib\r
+@@ -17,7 +17,7 @@ LIB = id2_split\r
+ \r
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)\r
+ \r
+-DLL_LIB = $(SOBJMGR_LIBS)\r
++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi\r
+ \r
+ WATCHERS = vasilche\r
+ \r
+--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib\r
++++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib\r
+@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum\r
+ \r
+ LIB = writedb\r
+ \r
++DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \\r
++ xser sequtil xutil xncbi\r
++\r
+ CFLAGS = $(FAST_CFLAGS)\r
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)\r
+ CXXFLAGS = $(FAST_CXXFLAGS)\r
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk\r
++++ b/c++/src/algo/blast/Makefile.blast_macros.mk\r
+@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \\r
+ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)\r
+ \r
+ # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS\r
+-BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \\r
++BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \\r
+ xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \\r
+ $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr\r
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)\r
+--- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app\r
++++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app\r
+@@ -2,7 +2,7 @@ APP = makembindex\r
+ SRC = main mkindex_app\r
+ \r
+ LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \\r
+- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)\r
++ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)\r
+ LIB = $(LIB_:%=%$(STATIC))\r
+ \r
+ CXXFLAGS = $(FAST_CXXFLAGS)\r
+--- a/c++/src/build-system/library_relations.txt\r
++++ b/c++/src/build-system/library_relations.txt\r
+@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS)\r
+ xasmcompare needs pub\r
+ xasn needs xhtml\r
+ xasn needs3party $(NCBI_C_ncbi)\r
+-xblast includes blast\r
++xblast needs blast\r
+ xblast needs xalgoblastdbindex\r
+ xblast needs xalgodustmask\r
+ xblast needs xalgowinmask\r
projects / ncbi-blast+.git / commitdiff