sci-biology/ncbi-blast+: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

1 files changed, 0 insertions, 668 deletions

diff --git a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
deleted file mode 100644
index 13dffeee7..000000000
--- a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch
+++ /dev/null
@@ -1,668 +0,0 @@
-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/build-system/library_relations.txt: Change xblast's

-   relationship to blast from includes to needs, accordingly.

- * 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: 2014-12-02

---- a/c++/src/algo/blast/core/Makefile.blast.lib

-+++ b/c++/src/algo/blast/core/Makefile.blast.lib

-@@ -21,6 +21,7 @@ LIB = blast

- 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 @@ SRC = sequence_istream_fasta \

- 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 @@ SRC = blastfmtutil blastxml_format blast

- 

- 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 @@ SRC = seq_masker seq_masker_score_mean s

- 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 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb

-       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 @@ SRC = node html htmlhelper page pager se

-       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 @@ ASN_DEP = xnetblast

- 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 @@ SRC = format_flags align_format_util sho

- 

- 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 @@ SRC = aln_builders aln_converters aln_ge

- 

- 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 @@ SRC = read_util format_guess_ex \

-       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_seqloc \

- 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 @@ WATCHERS =  jcherry

- 

- 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 @@ seqdbobj

- 

- 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 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_

- 

- 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 @@ SRC = bdbloader_rmt remote_blastdb_adapt

- 

- 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 @@ cdd_pssm_input \

- 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 @@ SRC  = $(SRC_CXX)

- 

- 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 @@ LIB = xalgodustmask

- 

- 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 @@ UNIX_SRC = $(LOCAL_LBSM)

- 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 @@ SRC      = $(SRC_C) ncbi_dblb_svcmapper

- 

- 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 @@ ASN_DEP = submit

- 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 @@ SRC = seq_writer blastdb_dataextract bla

- 

- 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 @@ SRC = blast_services

- 

- 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 @@ LIB_OR_DLL = both

- # Dependencies for shared library

- DLL_LIB = ncbi_xreader$(DLL)

- 

-+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \

-+           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 @@ LIB_OR_DLL = both

- 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 @@ LIB_OR_DLL = both

- # 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 @@ LIB_OR_DLL = both

- # 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 @@ LIB_OR_DLL = both

- 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 @@ LIB = xcompress

- 

- 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 @@ ASN_DEP = seq

- 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 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport

-       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 @@ SRC = \

- 

- 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 @@ SRC = random_gen utf8 checksum bytesrc s

- 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 @@ LIB = xregexp

- 

- 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 @@ LIB = xalgosegmask

- 

- 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 @@ LIB = id2_split

- 

- 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 @@ SRC = writedb writedb_impl writedb_volum

- 

- 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_INPUT_LIBS = blastinput \

- 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 @@ APP = makembindex

- 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)

---- a/c++/src/build-system/library_relations.txt

-+++ b/c++/src/build-system/library_relations.txt

-@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS)

- xasmcompare needs pub

- xasn needs xhtml

- xasn needs3party $(NCBI_C_ncbi)

--xblast includes blast

-+xblast needs blast

- xblast needs xalgoblastdbindex

- xblast needs xalgodustmask

- xblast needs xalgowinmask