[ncbi-blast+] update to new upstream version 2.2.29

Jan Kaluža jkaluza at fedoraproject.org
Thu Jan 23 07:38:45 UTC 2014 

commit 05527893c519af2455ab7811a592e4f760db401a
Author: Jan Kaluza <jkaluza at redhat.com>
Date:   Thu Jan 23 08:39:03 2014 +0100

    update to new upstream version 2.2.29

 .gitignore                       |    1 +
 ncbi-blast+-2.2.28-libdeps.patch |  904 +++++++++++++++++++++-----------------
 ncbi-blast+.spec                 |   11 +-
 sources                          |    2 +-
 4 files changed, 514 insertions(+), 404 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index 0ee553b..49811ed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 /ncbi-blast-2.2.28+-src.tar.gz
+/ncbi-blast-2.2.29+-src.tar.gz
diff --git a/ncbi-blast+-2.2.28-libdeps.patch b/ncbi-blast+-2.2.28-libdeps.patch
index fc310ca..7f453c2 100644
--- a/ncbi-blast+-2.2.28-libdeps.patch
+++ b/ncbi-blast+-2.2.28-libdeps.patch
@@ -1,28 +1,69 @@
-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 at debian.org>
-Last-Update: 2011-08-28
+diff --git a/c++/src/algo/blast/Makefile.blast_macros.mk b/c++/src/algo/blast/Makefile.blast_macros.mk
+index c135b9b..1976029 100644
+--- 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)
+diff --git a/c++/src/algo/blast/api/Makefile.xblast.lib b/c++/src/algo/blast/api/Makefile.xblast.lib
+index 2eca751..6f9c105 100644
+--- 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)
+diff --git a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+index d245004..e7c4865 100644
+--- 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 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
+diff --git a/c++/src/algo/blast/core/Makefile.blast.lib b/c++/src/algo/blast/core/Makefile.blast.lib
+index f37a42b..70f4380 100644
 --- a/c++/src/algo/blast/core/Makefile.blast.lib
 +++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,5 +21,6 @@
- CFLAGS  = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
+@@ -21,5 +21,6 @@ LIB = blast
+ CFLAGS  = $(FAST_CFLAGS)  
+ LDFLAGS = $(FAST_LDFLAGS) 
  
 +DLL_LIB = composition_adjustment xconnect tables
  
- WATCHERS = coulouri maning madden camacho
+ WATCHERS = maning madden camacho
+diff --git a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+index fcfb9f9..1a26d31 100644
 --- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
 +++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@
+@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
  CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
  
@@ -31,27 +72,72 @@ Last-Update: 2011-08-28
  ASN_DEP = seqset
  
  WATCHERS = morgulis
+diff --git a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
+index 41a2509..d5a813c 100644
+--- 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)
+diff --git a/c++/src/algo/blast/format/Makefile.xblastformat.lib b/c++/src/algo/blast/format/Makefile.xblastformat.lib
+index 3058881..dec049f 100644
 --- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
 +++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,6 +7,7 @@
+@@ -7,6 +7,7 @@ SRC = blastfmtutil blastxml_format blast_format data4xmlformat build_archive vec
  
- CPPFLAGS = $(ORIG_CPPFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
  
 -DLL_LIB = align_format blastxml xhtml xcgi
 +DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
 +          seq general xser tables xncbi
  
  WATCHERS = jianye zaretska madden camacho fongah2
+diff --git a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+index 84e2568..395a551 100644
+--- 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)
+ 
+diff --git a/c++/src/algo/segmask/Makefile.xalgosegmask.lib b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+index bd011c1..713242a 100644
+--- 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)
+ 
+diff --git a/c++/src/algo/winmask/Makefile.xalgowinmask.lib b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+index afaf676..d18c0df 100644
 --- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
 +++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,3 +21,4 @@
+@@ -21,3 +21,4 @@ SRC = seq_masker seq_masker_score_mean seq_masker_score_mean_glob \
  CXXFLAGS = $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
  
 +DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
+diff --git a/c++/src/cgi/Makefile.cgi.lib b/c++/src/cgi/Makefile.cgi.lib
+index fb543d7..31d15b8 100644
 --- a/c++/src/cgi/Makefile.cgi.lib
 +++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@
+@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncbires ref_args cgi_run cgi_util \
        user_agent
  LIB = xcgi
  
@@ -60,160 +146,11 @@ Last-Update: 2011-08-28
  CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
  
  WATCHERS = vakatov
---- a/c++/src/html/Makefile.html.lib
-+++ b/c++/src/html/Makefile.html.lib
-@@ -7,4 +7,6 @@
-       jsmenu 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
-@@ -2,3 +2,5 @@
- 
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-+
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
---- 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 = $(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
-@@ -12,3 +12,5 @@
- 
- WATCHERS = todorov dicuccio grichenk
- 
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-+
---- a/c++/src/objtools/readers/Makefile.xobjread.lib
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -19,5 +19,5 @@
-       best_feat_finder source_mod_parser fasta_exception
- 
- 
--DLL_LIB = creaders
-+DLL_LIB = 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
-@@ -12,6 +12,6 @@
- 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)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -5,4 +5,6 @@
- 
- 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
-@@ -3,6 +3,8 @@
- LIB = ncbi_xloader_blastdb_rmt
- SRC = bdbloader_rmt remote_blastdb_adapter
- 
-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
-+
- ASN_DEP = blastdb xnetblast
- 
- WATCHERS = camacho
---- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-@@ -4,3 +4,5 @@
- 
- LIB = gene_info
- SRC = gene_info gene_info_reader file_utils
-+
-+DLL_LIB = xncbi
---- 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)
- # Strict gcc flags
---- 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 xobjread $(OBJMGR_LIBS) xutil
-+    DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
-+              $(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)
- 
+diff --git a/c++/src/connect/Makefile.xconnect.lib b/c++/src/connect/Makefile.xconnect.lib
+index 473bb0b..08c7014 100644
 --- a/c++/src/connect/Makefile.xconnect.lib
 +++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@
+@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
  LIB  = xconnect
  PROJ_TAG = core
  
@@ -222,175 +159,19 @@ Last-Update: 2011-08-28
  LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
  
  WATCHERS = lavr
+diff --git a/c++/src/connect/ext/Makefile.xconnext.lib b/c++/src/connect/ext/Makefile.xconnext.lib
+index 3c4875d..8cc5a9f 100644
 --- a/c++/src/connect/ext/Makefile.xconnext.lib
 +++ b/c++/src/connect/ext/Makefile.xconnext.lib
-@@ -6,4 +6,6 @@
+@@ -6,4 +6,6 @@ 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
-@@ -1,4 +1,6 @@
- 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
-@@ -1,2 +1,4 @@
- LIB = blastxml
- SRC = blastxml__ blastxml___
-+
-+DLL_LIB = xser xncbi
---- a/c++/src/objects/entrez2/Makefile.entrez2.lib
-+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
-@@ -2,3 +2,5 @@
- 
- LIB = entrez2
- SRC = entrez2__ entrez2___
-+
-+DLL_LIB = xser xncbi
---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-@@ -4,3 +4,5 @@
- 
- LIB = entrez2cli
- SRC = entrez2_client entrez2_client_
-+
-+DLL_LIB = entrez2 xser xconnect xutil xncbi
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,2 +1,4 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-+
-+DLL_LIB = seqset seq general xser xncbi
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
-@@ -1,3 +1,4 @@
- LIB = seqedit
- SRC = seqedit__ seqedit___
-- 
-+
-+DLL_LIB = seqset seq general xser xncbi
---- a/c++/src/objects/submit/Makefile.submit.lib
-+++ b/c++/src/objects/submit/Makefile.submit.lib
-@@ -1,2 +1,4 @@
- LIB = submit
- SRC = submit__ submit___
-+
-+DLL_LIB = seqset seq biblio general xser xncbi
---- a/c++/src/objmgr/util/Makefile.util.lib
-+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,5 +8,7 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
- LIB = xobjutil
- 
-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = ucko vasilche
- 
---- 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 = $(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)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,4 +12,7 @@
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
- 
-+DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache 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
-@@ -15,4 +15,7 @@
- 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
-@@ -12,6 +12,9 @@
- 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
-@@ -6,7 +6,7 @@
- 
- 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)
- 
- WATCHERS = ivanov
---- a/c++/src/util/sequtil/Makefile.sequtil.lib
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
-@@ -3,4 +3,6 @@
- LIB = sequtil
- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
- 
-+DLL_LIB = xncbi
-+
- WATCHERS = shomrat
+diff --git a/c++/src/corelib/Makefile.test_boost.lib b/c++/src/corelib/Makefile.test_boost.lib
+index 9d34c45..f978a60 100644
 --- a/c++/src/corelib/Makefile.test_boost.lib
 +++ b/c++/src/corelib/Makefile.test_boost.lib
 @@ -3,6 +3,8 @@
@@ -402,6 +183,8 @@ Last-Update: 2011-08-28
  CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
  
  REQUIRES = Boost.Test.Included
+diff --git a/c++/src/corelib/Makefile.test_mt.lib b/c++/src/corelib/Makefile.test_mt.lib
+index 6153eab..2f1d737 100644
 --- a/c++/src/corelib/Makefile.test_mt.lib
 +++ b/c++/src/corelib/Makefile.test_mt.lib
 @@ -3,6 +3,8 @@
@@ -413,6 +196,19 @@ Last-Update: 2011-08-28
  # REQUIRES = MT
  
  USE_PCH = no
+diff --git a/c++/src/html/Makefile.html.lib b/c++/src/html/Makefile.html.lib
+index 6d08b9e..e7377bd 100644
+--- a/c++/src/html/Makefile.html.lib
++++ b/c++/src/html/Makefile.html.lib
+@@ -7,4 +7,6 @@ SRC = node html htmlhelper page pager selection components \
+       commentdiag indentstream html_exception writer_htmlenc
+ LIB = xhtml
+ 
++DLL_LIB = xncbi
++
+ WATCHERS = ivanov
+diff --git a/c++/src/objects/biblio/Makefile.biblio.lib b/c++/src/objects/biblio/Makefile.biblio.lib
+index 2c7d491..31125ad 100644
 --- a/c++/src/objects/biblio/Makefile.biblio.lib
 +++ b/c++/src/objects/biblio/Makefile.biblio.lib
 @@ -1,2 +1,4 @@
@@ -420,13 +216,70 @@ Last-Update: 2011-08-28
  SRC = biblio__ biblio___ citation_base
 +
 +DLL_LIB = general xser xncbi
+diff --git a/c++/src/objects/blast/Makefile.blast.lib b/c++/src/objects/blast/Makefile.blast.lib
+index 0dd0fa3..9d68feb 100644
+--- a/c++/src/objects/blast/Makefile.blast.lib
++++ b/c++/src/objects/blast/Makefile.blast.lib
+@@ -1,4 +1,6 @@
+ LIB = xnetblast
+ SRC = blast__ blast___ names
+ 
++DLL_LIB = scoremat seqset seq xser xncbi
++
+ WATCHERS = camacho
+diff --git a/c++/src/objects/blast/Makefile.xnetblastcli.lib b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+index 96325c4..6bd755e 100644
+--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+@@ -2,3 +2,5 @@ ASN_DEP = xnetblast
+ 
+ LIB = xnetblastcli
+ SRC = blastclient blastclient_
++
++DLL_LIB = xnetblast xser xconnect xutil xncbi
+diff --git a/c++/src/objects/blastdb/Makefile.blastdb.lib b/c++/src/objects/blastdb/Makefile.blastdb.lib
+index 5f0ecc7..a028153 100644
 --- a/c++/src/objects/blastdb/Makefile.blastdb.lib
 +++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -1,2 +1,4 @@
+@@ -1,5 +1,7 @@
+ # $Id: Makefile.blastdb.lib 395653 2013-04-12 14:33:22Z vakatov $
+ 
++
++DLL_LIB = seq xser xncbi
  LIB = blastdb
  SRC = blastdb__ blastdb___
+ 
+diff --git a/c++/src/objects/blastxml/Makefile.blastxml.lib b/c++/src/objects/blastxml/Makefile.blastxml.lib
+index d18eb78..0e98c29 100644
+--- a/c++/src/objects/blastxml/Makefile.blastxml.lib
++++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
+@@ -1,2 +1,4 @@
+ LIB = blastxml
+ SRC = blastxml__ blastxml___
 +
-+DLL_LIB = seq xser xncbi
++DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/entrez2/Makefile.entrez2.lib b/c++/src/objects/entrez2/Makefile.entrez2.lib
+index 4507f72..0bff536 100644
+--- a/c++/src/objects/entrez2/Makefile.entrez2.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
+@@ -2,3 +2,5 @@ WATCHERS = lavr
+ 
+ LIB = entrez2
+ SRC = entrez2__ entrez2___
++
++DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/entrez2/Makefile.entrez2cli.lib b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+index 42a4649..dc01ad5 100644
+--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+@@ -4,3 +4,5 @@ ASN_DEP = entrez2
+ 
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
++
++DLL_LIB = entrez2 xser xconnect xutil xncbi
+diff --git a/c++/src/objects/general/Makefile.general.lib b/c++/src/objects/general/Makefile.general.lib
+index 951304f..417d1ed 100644
 --- a/c++/src/objects/general/Makefile.general.lib
 +++ b/c++/src/objects/general/Makefile.general.lib
 @@ -1,2 +1,4 @@
@@ -434,6 +287,8 @@ Last-Update: 2011-08-28
  SRC = general__ general___ uoconv
 +
 +DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/genomecoll/Makefile.genome_collection.lib b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+index f039af6..9f733a0 100644
 --- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
 +++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
 @@ -3,4 +3,6 @@
@@ -443,15 +298,19 @@ Last-Update: 2011-08-28
 +DLL_LIB = seq general xser xncbi
 +
  WATCHERS = dicuccio
+diff --git a/c++/src/objects/id1/Makefile.id1.lib b/c++/src/objects/id1/Makefile.id1.lib
+index d60c728..3ac9022 100644
 --- a/c++/src/objects/id1/Makefile.id1.lib
 +++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,4 +3,6 @@
+@@ -3,4 +3,6 @@ ASN_DEP = seq
  LIB = id1
  SRC = id1__ id1___
  
 +DLL_LIB = seqset seq xser xncbi
 +
  WATCHERS = vasilche
+diff --git a/c++/src/objects/id2/Makefile.id2.lib b/c++/src/objects/id2/Makefile.id2.lib
+index 09d8b36..ea8b07f 100644
 --- a/c++/src/objects/id2/Makefile.id2.lib
 +++ b/c++/src/objects/id2/Makefile.id2.lib
 @@ -1,4 +1,6 @@
@@ -461,6 +320,8 @@ Last-Update: 2011-08-28
 +DLL_LIB = seqsplit seq xser xncbi
 +
  WATCHERS = vasilche
+diff --git a/c++/src/objects/medline/Makefile.medline.lib b/c++/src/objects/medline/Makefile.medline.lib
+index ea28066..0b9b02a 100644
 --- a/c++/src/objects/medline/Makefile.medline.lib
 +++ b/c++/src/objects/medline/Makefile.medline.lib
 @@ -1,2 +1,4 @@
@@ -468,6 +329,8 @@ Last-Update: 2011-08-28
  SRC = medline__ medline___
 +
 +DLL_LIB = biblio general xser xncbi
+diff --git a/c++/src/objects/pub/Makefile.pub.lib b/c++/src/objects/pub/Makefile.pub.lib
+index 78c12e1..d873e1c 100644
 --- a/c++/src/objects/pub/Makefile.pub.lib
 +++ b/c++/src/objects/pub/Makefile.pub.lib
 @@ -1,2 +1,4 @@
@@ -475,15 +338,28 @@ Last-Update: 2011-08-28
  SRC = pub__ pub___
 +
 +DLL_LIB = medline biblio xser xncbi
+diff --git a/c++/src/objects/scoremat/Makefile.scoremat.lib b/c++/src/objects/scoremat/Makefile.scoremat.lib
+index 62e01f5..7664a1b 100644
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
+@@ -1,2 +1,4 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
++
++DLL_LIB = seqset seq general xser xncbi
+diff --git a/c++/src/objects/seq/Makefile.seq.lib b/c++/src/objects/seq/Makefile.seq.lib
+index 1b5edc5..dcc8b58 100644
 --- a/c++/src/objects/seq/Makefile.seq.lib
 +++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,4 +12,6 @@
+@@ -12,4 +12,6 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport_util \
        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
+diff --git a/c++/src/objects/seqcode/Makefile.seqcode.lib b/c++/src/objects/seqcode/Makefile.seqcode.lib
+index dc9d60e..9a7e296 100644
 --- a/c++/src/objects/seqcode/Makefile.seqcode.lib
 +++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
 @@ -1,2 +1,4 @@
@@ -491,6 +367,18 @@ Last-Update: 2011-08-28
  SRC = seqcode__ seqcode___
 +
 +DLL_LIB = xser xncbi
+diff --git a/c++/src/objects/seqedit/Makefile.seqedit.lib b/c++/src/objects/seqedit/Makefile.seqedit.lib
+index 283a9b7..fdc7574 100644
+--- a/c++/src/objects/seqedit/Makefile.seqedit.lib
++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
+@@ -1,3 +1,4 @@
+ LIB = seqedit
+ SRC = seqedit__ seqedit___
+- 
++
++DLL_LIB = seqset seq general xser xncbi
+diff --git a/c++/src/objects/seqset/Makefile.seqset.lib b/c++/src/objects/seqset/Makefile.seqset.lib
+index 87f16d0..bcd250d 100644
 --- a/c++/src/objects/seqset/Makefile.seqset.lib
 +++ b/c++/src/objects/seqset/Makefile.seqset.lib
 @@ -1,2 +1,4 @@
@@ -498,6 +386,8 @@ Last-Update: 2011-08-28
  SRC = seqset__ seqset___ gb_release_file
 +
 +DLL_LIB = seq general xser xncbi
+diff --git a/c++/src/objects/seqsplit/Makefile.seqsplit.lib b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+index 87ae869..7ac4405 100644
 --- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
 +++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
 @@ -1,4 +1,6 @@
@@ -507,60 +397,104 @@ Last-Update: 2011-08-28
 +DLL_LIB = seqset seq xser xncbi
 +
  WATCHERS = vasilche
---- a/c++/src/serial/Makefile.serial.lib
-+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,4 +18,6 @@
+diff --git a/c++/src/objects/submit/Makefile.submit.lib b/c++/src/objects/submit/Makefile.submit.lib
+index 74798f8..b034f64 100644
+--- a/c++/src/objects/submit/Makefile.submit.lib
++++ b/c++/src/objects/submit/Makefile.submit.lib
+@@ -1,2 +1,4 @@
+ LIB = submit
+ SRC = submit__ submit___
++
++DLL_LIB = seqset seq biblio general xser xncbi
+diff --git a/c++/src/objmgr/split/Makefile.id2_split.lib b/c++/src/objmgr/split/Makefile.id2_split.lib
+index fafa70a..4ef60c7 100644
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib
++++ b/c++/src/objmgr/split/Makefile.id2_split.lib
+@@ -17,6 +17,6 @@ LIB = id2_split
  
- LIB    = xser
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
  
-+DLL_LIB = xutil xncbi
-+
- WATCHERS = gouriano
---- a/c++/src/util/Makefile.util.lib
-+++ b/c++/src/util/Makefile.util.lib
-@@ -11,6 +11,7 @@
- LIB = xutil
- PROJ_TAG = core
+-DLL_LIB = $(SOBJMGR_LIBS)
++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
  
-+DLL_LIB = xncbi
- LIBS = $(ORIG_LIBS)
+ WATCHERS = vasilche
+diff --git a/c++/src/objmgr/util/Makefile.util.lib b/c++/src/objmgr/util/Makefile.util.lib
+index 4001243..bacc47c 100644
+--- a/c++/src/objmgr/util/Makefile.util.lib
++++ b/c++/src/objmgr/util/Makefile.util.lib
+@@ -7,6 +7,7 @@ ASN_DEP = submit
  
- WATCHERS = vakatov
---- a/c++/src/util/xregexp/Makefile.xregexp.lib
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -6,7 +6,7 @@
+ 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
  
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+ WATCHERS = ucko vasilche kornbluh
  
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS    = $(PCRE_LIBS)
+diff --git a/c++/src/objtools/align_format/Makefile.align_format.lib b/c++/src/objtools/align_format/Makefile.align_format.lib
+index 1ec5bf0..b0d70c7 100644
+--- 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 showdefline showalign tabular vectorscreen
  
- WATCHERS = ivanov
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
  
- SRC = segmask
++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)
+diff --git a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+index e32c351..3f44394 100644
+--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
++++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+@@ -12,3 +12,5 @@ SRC = aln_builders aln_converters aln_generators aln_seqid aln_serial	\
  
-+DLL_LIB = blast xobjmgr xncbi
+ WATCHERS = todorov dicuccio grichenk
+ 
++DLL_LIB = xobjmgr seqset seq xser tables xncbi
 +
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
+diff --git a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+index 62f01fd..b877f98 100644
+--- 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 blastdb_formatter
  
---- a/c++/src/objmgr/split/Makefile.id2_split.lib
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,6 +17,6 @@
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
++DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
  
--DLL_LIB = $(SOBJMGR_LIBS)
-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
+ ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
+ # CFLAGS   = $(FAST_CFLAGS)
+diff --git a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+index 3a92e3e..79a75b9 100644
+--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
++++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+@@ -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/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+index 9c13307..ed8c4ae 100644
+--- 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
  
- WATCHERS = vasilche
+ LIB = seqdb
+ 
++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+diff --git a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+index 8929b72..31b9ce7 100644
 --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
 +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@
+@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volume writedb_files writedb_isam writedb_gim
  
  LIB = writedb
  
@@ -568,27 +502,203 @@ Last-Update: 2011-08-28
 +          xser sequtil xutil xncbi
 +
  CFLAGS   = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
---- 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 \
- 		xobjread creaders 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
+diff --git a/c++/src/objtools/blast/services/Makefile.blast_services.lib b/c++/src/objtools/blast/services/Makefile.blast_services.lib
+index ceba356..cd3b1ba 100644
+--- 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_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
--      xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS)
-+      xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
+ LIB = blast_services
  
++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
  CXXFLAGS = $(FAST_CXXFLAGS)
+diff --git a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+index 4fb6117..837108e 100644
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+@@ -7,4 +7,6 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+ 
+ ASN_DEP = blastdb seqset
+ 
++DLL_LIB = seqdb xobjmgr seqset seq xncbi
++
+ WATCHERS = camacho
+diff --git 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
+index 243467f..e20368e 100644
+--- 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_adapter
+ 
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
+ 
++DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
++
+ ASN_DEP = blastdb xnetblast
+ 
+ WATCHERS = camacho
+diff --git a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+index 9ae861b..7a3a9c1 100644
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+@@ -12,4 +12,7 @@ LIB_OR_DLL = both
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++           xobjmgr seq xutil xncbi
++
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+index f3bb947..eccf6d1 100644
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+@@ -15,4 +15,7 @@ LIB_OR_DLL = both
+ DLL_LIB = 
+ DLL_DLIB = $(GENBANK_READER_LDEP)
+ 
++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
++           xser xconnect xcompress xutil xncbi
++
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+index f3164f5..98a627c 100644
+--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
++++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+ WATCHERS = vasilche
+diff --git a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+index c6f8076..0bcc0c5 100644
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+@@ -12,6 +12,8 @@ LIB_OR_DLL = both
+ # Dependencies for shared library
+ DLL_LIB = xconnect ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+ WATCHERS = vasilche
+diff --git 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
+index 0a29cbf..c5c4b6a 100644
+--- 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
+@@ -12,6 +12,9 @@ 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
+diff --git a/c++/src/objtools/readers/Makefile.xobjread.lib b/c++/src/objtools/readers/Makefile.xobjread.lib
+index eae8a72..15f2cec 100644
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib
++++ b/c++/src/objtools/readers/Makefile.xobjread.lib
+@@ -20,5 +20,5 @@ SRC = read_util format_guess_ex \
+       message_listener line_error
+ 
+ 
+-DLL_LIB = creaders
++DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi
+ 
+diff --git a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+index 8115a7f..88bfd38 100644
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+@@ -12,6 +12,6 @@ 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
+diff --git a/c++/src/objtools/simple/Makefile.xobjsimple.lib b/c++/src/objtools/simple/Makefile.xobjsimple.lib
+index dab25d6..1dc389d 100644
+--- 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
+ 
+diff --git a/c++/src/serial/Makefile.serial.lib b/c++/src/serial/Makefile.serial.lib
+index 2563b5f..116ad11 100644
+--- a/c++/src/serial/Makefile.serial.lib
++++ b/c++/src/serial/Makefile.serial.lib
+@@ -18,4 +18,6 @@ SRC = \
+ 
+ LIB    = xser
+ 
++DLL_LIB = xutil xncbi
++
+ WATCHERS = gouriano
+diff --git a/c++/src/util/Makefile.util.lib b/c++/src/util/Makefile.util.lib
+index 25654a5..3613b12 100644
+--- a/c++/src/util/Makefile.util.lib
++++ b/c++/src/util/Makefile.util.lib
+@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc strbuffer itree smalldns \
+ LIB = xutil
+ PROJ_TAG = core
+ 
++DLL_LIB = xncbi
+ LIBS = $(ORIG_LIBS)
+ 
+ WATCHERS = vakatov kornbluh
+diff --git a/c++/src/util/compress/api/Makefile.compress.lib b/c++/src/util/compress/api/Makefile.compress.lib
+index 5e5d3d6..baeab24 100644
+--- 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
+diff --git a/c++/src/util/sequtil/Makefile.sequtil.lib b/c++/src/util/sequtil/Makefile.sequtil.lib
+index c068a32..003d3d3 100644
+--- a/c++/src/util/sequtil/Makefile.sequtil.lib
++++ b/c++/src/util/sequtil/Makefile.sequtil.lib
+@@ -3,4 +3,6 @@
+ LIB = sequtil
+ SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
+ 
++DLL_LIB = xncbi
++
+ WATCHERS = shomrat
+diff --git a/c++/src/util/xregexp/Makefile.xregexp.lib b/c++/src/util/xregexp/Makefile.xregexp.lib
+index 965fac4..508a058 100644
+--- 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
diff --git a/ncbi-blast+.spec b/ncbi-blast+.spec
index d2c58a2..db66a0e 100644
--- a/ncbi-blast+.spec
+++ b/ncbi-blast+.spec
@@ -68,14 +68,11 @@
 %global __requires_exclude %__requires_exclude|^libxutil.so
 
 Name:        ncbi-blast+
-Version:     2.2.28
-Release:     2%{?dist}
+Version:     2.2.29
+Release:     1%{?dist}
 License:     Public Domain and MIT
 Url:         http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
 Source0:     ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-%{version}+-src.tar.gz
-# Backported upstream patch to fix build with newer gnutls
-# http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B/src/connect/ncbi_gnutls.c?r1=57856&r2=57915&view=patch
-Patch0:      ncbi-blast+-2.2.28-gnutls.patch
 # Debian patch to fix shared libraries dependencies
 Patch1:      ncbi-blast+-2.2.28-libdeps.patch
 # Ignore unknown ./configure options to be able to use configure rpm macro
@@ -101,7 +98,6 @@ members of gene families.
 
 %prep 
 %setup -q -n ncbi-blast-%{version}+-src
-%patch0 -p1 -b .gnutls
 %patch1 -p1 -b .libdeps
 %patch2 -p1 -b .configure
 
@@ -158,6 +154,9 @@ popd
 %{_libdir}/ncbi-blast+
 
 %changelog
+* Thu Jan 23 2014 Jan Kaluza <jkaluza at redhat.com> - 2.2.29-1
+- update to new upstream version 2.2.29
+
 * Thu Oct 03 2013 Jan Kaluza <jkaluza at redhat.com> - 2.2.28-2
 - use RPM configure macro instead of ./configure (#1007956)
 
diff --git a/sources b/sources
index be7a6e6..98d62e9 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-41b87107894d5714eca4217b4739e241  ncbi-blast-2.2.28+-src.tar.gz
+1290360b24448dd79840a6800482b597  ncbi-blast-2.2.29+-src.tar.gz

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