From: Aaron M. Ucko <ucko@debian.org>
Date: Sun, 28 Aug 2011 22:29:43 +0000 (+0000)
Subject: debian/patches/fix_lib_deps: new; ensure that all libraries link against
X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~319
X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=f08342d211319a939b1d473cee4ade2a1370c3d3;p=ncbi-blast%2B.git

debian/patches/fix_lib_deps: new; ensure that all libraries link against
all direct dependencies.  (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.)  (Closes: #633567.)
---

diff --git a/debian/changelog b/debian/changelog
index 9780df06..0eef87b6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,11 +8,15 @@ ncbi-blast+ (2.2.25-4) UNRELEASED; urgency=low
     (In conjunction with the following change, finally closes: #629656.)
   * debian/control:
     - Build-Depends += libc0.3-dev (>= 2.13-9~) [hurd-i386] to avoid #630180.
+  * debian/patches/fix_lib_deps: new; ensure that all libraries link against
+    all direct dependencies.  (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.)  (Closes: #633567.)
 
   [ Andreas Tille ]
   * Enhances: t-coffee (as stated in tasks file)
 
- -- Andreas Tille <tille@debian.org>  Sat, 06 Aug 2011 23:31:49 +0200
+ -- Aaron M. Ucko <ucko@debian.org>  Sun, 28 Aug 2011 18:29:39 -0400
 
 ncbi-blast+ (2.2.25-3) unstable; urgency=low
 
diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
new file mode 100644
index 00000000..5513dd10
--- /dev/null
+++ b/debian/patches/fix_lib_deps
@@ -0,0 +1,724 @@
+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.
+
+Debian-Bug: 633567.
+Author: Aaron M. Ucko <ucko@debian.org>
+Last-Update: 2011-08-28
+Index: b/c++/src/algo/blast/core/Makefile.blast.lib
+===================================================================
+--- a/c++/src/algo/blast/core/Makefile.blast.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/core/Makefile.blast.lib	2011-08-28 18:03:03.000000000 -0400
+@@ -21,5 +21,6 @@
+ CFLAGS  = $(FAST_CFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+ 
++DLL_LIB = composition_adjustment xconnect tables
+ 
+ WATCHERS = blastsoft
+Index: b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+===================================================================
+--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib	2011-08-27 22:03:28.000000000 -0400
+@@ -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
+Index: b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+===================================================================
+--- a/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib	2011-08-27 21:41:17.000000000 -0400
+@@ -7,6 +7,8 @@
+ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++DLL_LIB = xobjmgr xncbi
++
+ ASN_DEP = seqset
+ 
+ WATCHERS = morgulis
+Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib
+===================================================================
+--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib	2011-08-27 21:43:34.000000000 -0400
+@@ -7,6 +7,7 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+ 
+-DLL_LIB = blastxml xhtml xcgi
++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
++          seq general xser tables xncbi
+ 
+ WATCHERS = blastsoft
+Index: b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+===================================================================
+--- a/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -5,6 +5,8 @@
+       njn_localmaxstat njn_localmaxstatutil njn_ioutil njn_matrix \
+       njn_stringutil njn_dynprogprob njn_dynprogproblim njn_dynprogprobproto
+ 
++DLL_LIB = tables xutil xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+Index: b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+===================================================================
+--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib	2011-08-27 22:03:07.000000000 -0400
+@@ -21,3 +21,4 @@
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
+Index: b/c++/src/cgi/Makefile.cgi.lib
+===================================================================
+--- a/c++/src/cgi/Makefile.cgi.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/cgi/Makefile.cgi.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -8,6 +8,8 @@
+       cgi_serial cgi_session cgi_exception cgiapp_cached cgi_entry_reader
+ LIB = xcgi
+ 
++DLL_LIB = xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+ 
+ WATCHERS = vakatov
+Index: b/c++/src/html/Makefile.html.lib
+===================================================================
+--- a/c++/src/html/Makefile.html.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/html/Makefile.html.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -7,4 +7,6 @@
+       jsmenu commentdiag indentstream html_exception writer_htmlenc
+ LIB = xhtml
+ 
++DLL_LIB = xncbi
++
+ WATCHERS = ivanov
+Index: b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+===================================================================
+--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -2,3 +2,5 @@
+ 
+ LIB = xnetblastcli
+ SRC = blastclient blastclient_
++
++DLL_LIB = xnetblast xser xconnect xutil xncbi
+Index: b/c++/src/objtools/align_format/Makefile.align_format.lib
+===================================================================
+--- a/c++/src/objtools/align_format/Makefile.align_format.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/align_format/Makefile.align_format.lib	2011-08-27 21:52:19.000000000 -0400
+@@ -10,6 +10,10 @@
+ 
+ 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
+ # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
+ # CFLAGS   = $(FAST_CFLAGS)
+Index: b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+===================================================================
+--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib	2011-08-27 21:53:39.000000000 -0400
+@@ -10,6 +10,6 @@
+       alnsegments alnseq alnvec alnvec_iterator alnvecprint		\
+       pairwise_aln sparse_aln sparse_ci
+ 
+-
++DLL_LIB = xobjmgr seqset seq xser tables xncbi
+ 
+ WATCHERS = todorov
+Index: b/c++/src/objtools/readers/Makefile.xobjread.lib
+===================================================================
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/objtools/readers/Makefile.xobjread.lib	2011-08-27 22:05:51.000000000 -0400
+@@ -12,5 +12,5 @@
+       wiggle_data wiggle_reader gff3_sofa gff3_reader gtf_reader \
+       gff2_data gff2_reader source_mod_parser
+ 
+-DLL_LIB = creaders
++DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi
+ 
+Index: b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+===================================================================
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib	2011-08-27 22:04:25.000000000 -0400
+@@ -11,6 +11,6 @@
+ 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
+Index: b/c++/src/objtools/simple/Makefile.xobjsimple.lib
+===================================================================
+--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib	2011-08-27 21:40:31.000000000 -0400
+@@ -7,6 +7,8 @@
+ 
+ ASN_DEP = seqset
+ 
++DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
++
+ LIB = xobjsimple
+ SRC = simple_om
+ 
+Index: b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+===================================================================
+--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib	2011-08-27 22:08:11.000000000 -0400
+@@ -25,6 +25,8 @@
+ 
+ LIB = seqdb
+ 
++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib	2011-08-27 21:50:24.000000000 -0400
+@@ -5,4 +5,6 @@
+ 
+ ASN_DEP = blastdb seqset
+ 
++DLL_LIB = seqdb xobjmgr seqset seq xncbi
++
+ WATCHERS = camacho
+Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib	2011-08-27 21:50:02.000000000 -0400
+@@ -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
+Index: b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+===================================================================
+--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -4,3 +4,5 @@
+ 
+ LIB = gene_info
+ SRC = gene_info gene_info_reader file_utils
++
++DLL_LIB = xncbi
+Index: b/c++/src/algo/blast/api/Makefile.xblast.lib
+===================================================================
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib	2011-08-27 22:01:29.000000000 -0400
+@@ -69,11 +69,14 @@
+ winmask_filter \
+ subj_ranges_set
+ 
+-SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)
++SRC  = $(SRC_CXX) # $(SRC_C:%=.core_%)
+ 
+ LIB = xblast
+ 
+-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
++DLL_LIB = xalgoblastdbindex blast composition_adjustment xalgowinmask \
++          xalgodustmask seqdb xobjread xobjutil xobjmgr \
++          xnetblastcli xnetblast scoremat seqset seq general \
++          xser xconnect sequtil tables xutil xncbi
+ 
+ CFLAGS   = $(FAST_CFLAGS)
+ # Strict gcc flags
+Index: b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+===================================================================
+--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib	2011-08-27 21:48:16.000000000 -0400
+@@ -20,7 +20,9 @@
+ 
+ LIB = blastinput
+ 
+-DLL_LIB = xblast $(OBJMGR_LIBS)
++DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \
++          ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader seqdb xobjread \
++          xobjmgr scoremat seqset seq xser xutil xncbi
+ 
+ # should be redundant, given the above :-/
+ ASN_DEP = seqset xnetblast
+Index: b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+===================================================================
+--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib	2011-08-27 22:03:50.000000000 -0400
+@@ -8,6 +8,8 @@
+ 
+ SRC = symdust
+ 
++DLL_LIB = xobjmgr seq xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+Index: b/c++/src/connect/Makefile.xconnect.lib
+===================================================================
+--- a/c++/src/connect/Makefile.xconnect.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/connect/Makefile.xconnect.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -14,6 +14,8 @@
+ LIB  = xconnect
+ PROJ_TAG = core
+ 
++DLL_LIB = xncbi
++
+ LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
+ 
+ WATCHERS = lavr
+Index: b/c++/src/connect/ext/Makefile.xconnext.lib
+===================================================================
+--- a/c++/src/connect/ext/Makefile.xconnext.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/connect/ext/Makefile.xconnext.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -6,4 +6,6 @@
+ 
+ LIB      = xconnext
+ 
++DLL_LIB = xconnect xncbi
++
+ WATCHERS = lavr
+Index: b/c++/src/objects/blast/Makefile.blast.lib
+===================================================================
+--- a/c++/src/objects/blast/Makefile.blast.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/blast/Makefile.blast.lib	2011-08-27 22:02:07.000000000 -0400
+@@ -1,4 +1,6 @@
+ LIB = xnetblast
+ SRC = blast__ blast___ names
+ 
++DLL_LIB = scoremat seqset seq xser xncbi
++
+ WATCHERS = camacho
+Index: b/c++/src/objects/blastxml/Makefile.blastxml.lib
+===================================================================
+--- a/c++/src/objects/blastxml/Makefile.blastxml.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/blastxml/Makefile.blastxml.lib	2011-08-27 21:44:06.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = blastxml
+ SRC = blastxml__ blastxml___
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/entrez2/Makefile.entrez2.lib
+===================================================================
+--- a/c++/src/objects/entrez2/Makefile.entrez2.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/entrez2/Makefile.entrez2.lib	2011-08-27 21:44:25.000000000 -0400
+@@ -2,3 +2,5 @@
+ 
+ LIB = entrez2
+ SRC = entrez2__ entrez2___
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+===================================================================
+--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -4,3 +4,5 @@
+ 
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
++
++DLL_LIB = entrez2 xser xconnect xutil xncbi
+Index: b/c++/src/objects/scoremat/Makefile.scoremat.lib
+===================================================================
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib	2011-08-27 22:10:12.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
++
++DLL_LIB = seqset seq general xser xncbi
+Index: b/c++/src/objects/seqedit/Makefile.seqedit.lib
+===================================================================
+--- a/c++/src/objects/seqedit/Makefile.seqedit.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib	2011-08-27 22:10:26.000000000 -0400
+@@ -1,3 +1,4 @@
+ LIB = seqedit
+ SRC = seqedit__ seqedit___
+- 
++
++DLL_LIB = seqset seq general xser xncbi
+Index: b/c++/src/objects/submit/Makefile.submit.lib
+===================================================================
+--- a/c++/src/objects/submit/Makefile.submit.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/submit/Makefile.submit.lib	2011-08-27 22:10:36.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = submit
+ SRC = submit__ submit___
++
++DLL_LIB = seqset seq biblio general xser xncbi
+Index: b/c++/src/objmgr/util/Makefile.util.lib
+===================================================================
+--- a/c++/src/objmgr/util/Makefile.util.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objmgr/util/Makefile.util.lib	2011-08-27 22:05:46.000000000 -0400
+@@ -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
+ 
+Index: b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+===================================================================
+--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib	2011-08-27 22:06:49.000000000 -0400
+@@ -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
+ # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
+Index: b/c++/src/objtools/blast/services/Makefile.blast_services.lib
+===================================================================
+--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -8,6 +8,8 @@
+ 
+ LIB = blast_services
+ 
++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib	2011-08-27 21:54:20.000000000 -0400
+@@ -12,4 +12,7 @@
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++           xobjmgr seq xutil xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib	2011-08-27 21:58:18.000000000 -0400
+@@ -14,4 +14,7 @@
+ # Dependencies for shared library
+ DLL_LIB = 
+ 
++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
++           xser xconnect xcompress xutil xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib	2011-08-27 21:56:19.000000000 -0400
+@@ -12,6 +12,8 @@
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib	2011-08-27 21:57:00.000000000 -0400
+@@ -12,6 +12,8 @@
+ # Dependencies for shared library
+ DLL_LIB = xconnect ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib	2011-08-27 21:55:08.000000000 -0400
+@@ -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
+Index: b/c++/src/util/compress/api/Makefile.compress.lib
+===================================================================
+--- a/c++/src/util/compress/api/Makefile.compress.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/util/compress/api/Makefile.compress.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -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
+Index: b/c++/src/util/sequtil/Makefile.sequtil.lib
+===================================================================
+--- a/c++/src/util/sequtil/Makefile.sequtil.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/util/sequtil/Makefile.sequtil.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -3,4 +3,6 @@
+ LIB = sequtil
+ SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
+ 
++DLL_LIB = xncbi
++
+ WATCHERS = shomrat
+Index: b/c++/src/corelib/Makefile.test_boost.lib
+===================================================================
+--- a/c++/src/corelib/Makefile.test_boost.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/corelib/Makefile.test_boost.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -3,6 +3,8 @@
+ SRC = test_boost
+ LIB = test_boost
+ 
++DLL_LIB = xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
+ 
+ REQUIRES = Boost.Test.Included
+Index: b/c++/src/corelib/Makefile.test_mt.lib
+===================================================================
+--- a/c++/src/corelib/Makefile.test_mt.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/corelib/Makefile.test_mt.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -3,6 +3,8 @@
+ SRC = test_mt
+ LIB    = test_mt
+ 
++DLL_LIB = xncbi
++
+ # REQUIRES = MT
+ 
+ USE_PCH = no
+Index: b/c++/src/objects/biblio/Makefile.biblio.lib
+===================================================================
+--- a/c++/src/objects/biblio/Makefile.biblio.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/biblio/Makefile.biblio.lib	2011-08-27 22:13:52.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = biblio
+ SRC = biblio__ biblio___ label_util
++
++DLL_LIB = general xser xncbi
+Index: b/c++/src/objects/blastdb/Makefile.blastdb.lib
+===================================================================
+--- a/c++/src/objects/blastdb/Makefile.blastdb.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib	2011-08-27 22:11:45.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = blastdb
+ SRC = blastdb__ blastdb___
++
++DLL_LIB = seq xser xncbi
+Index: b/c++/src/objects/general/Makefile.general.lib
+===================================================================
+--- a/c++/src/objects/general/Makefile.general.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/general/Makefile.general.lib	2011-08-27 22:14:06.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = general
+ SRC = general__ general___ uoconv
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+===================================================================
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib	2011-08-27 22:11:30.000000000 -0400
+@@ -3,4 +3,6 @@
+ LIB = genome_collection
+ SRC = genome_collection__ genome_collection___
+ 
++DLL_LIB = seq general xser xncbi
++
+ WATCHERS = dicuccio
+Index: b/c++/src/objects/id1/Makefile.id1.lib
+===================================================================
+--- a/c++/src/objects/id1/Makefile.id1.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/id1/Makefile.id1.lib	2011-08-27 21:59:44.000000000 -0400
+@@ -3,4 +3,6 @@
+ LIB = id1
+ SRC = id1__ id1___
+ 
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objects/id2/Makefile.id2.lib
+===================================================================
+--- a/c++/src/objects/id2/Makefile.id2.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/id2/Makefile.id2.lib	2011-08-27 21:59:51.000000000 -0400
+@@ -1,4 +1,6 @@
+ LIB = id2
+ SRC = id2__ id2___
+ 
++DLL_LIB = seqsplit seq xser xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objects/medline/Makefile.medline.lib
+===================================================================
+--- a/c++/src/objects/medline/Makefile.medline.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/medline/Makefile.medline.lib	2011-08-27 22:13:36.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = medline
+ SRC = medline__ medline___
++
++DLL_LIB = biblio general xser xncbi
+Index: b/c++/src/objects/pub/Makefile.pub.lib
+===================================================================
+--- a/c++/src/objects/pub/Makefile.pub.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/pub/Makefile.pub.lib	2011-08-27 22:12:30.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = pub
+ SRC = pub__ pub___
++
++DLL_LIB = medline biblio xser xncbi
+Index: b/c++/src/objects/seq/Makefile.seq.lib
+===================================================================
+--- a/c++/src/objects/seq/Makefile.seq.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/seq/Makefile.seq.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -11,4 +11,6 @@
+       seq_id_tree seq_id_handle seq_id_mapper \
+       seq_loc_mapper_base seq_align_mapper_base seqlocinfo
+ 
++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = vasilche grichenk
+Index: b/c++/src/objects/seqcode/Makefile.seqcode.lib
+===================================================================
+--- a/c++/src/objects/seqcode/Makefile.seqcode.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/seqcode/Makefile.seqcode.lib	2011-08-27 22:13:01.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = seqcode
+ SRC = seqcode__ seqcode___
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/seqset/Makefile.seqset.lib
+===================================================================
+--- a/c++/src/objects/seqset/Makefile.seqset.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/seqset/Makefile.seqset.lib	2011-08-27 22:11:14.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = seqset
+ SRC = seqset__ seqset___ gb_release_file
++
++DLL_LIB = seq general xser xncbi
+Index: b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+===================================================================
+--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib	2011-08-27 22:10:19.000000000 -0400
+@@ -1,4 +1,6 @@
+ LIB = seqsplit
+ SRC = seqsplit__ seqsplit___
+ 
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/serial/Makefile.serial.lib
+===================================================================
+--- a/c++/src/serial/Makefile.serial.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/serial/Makefile.serial.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -18,4 +18,6 @@
+ 
+ LIB    = xser
+ 
++DLL_LIB = xutil xncbi
++
+ WATCHERS = gouriano
+Index: b/c++/src/util/Makefile.util.lib
+===================================================================
+--- a/c++/src/util/Makefile.util.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/util/Makefile.util.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -11,6 +11,7 @@
+ LIB = xutil
+ PROJ_TAG = core
+ 
++DLL_LIB = xncbi
+ LIBS = $(ORIG_LIBS)
+ 
+ WATCHERS = vakatov
+Index: b/c++/src/util/xregexp/Makefile.xregexp.lib
+===================================================================
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib	2011-08-27 21:03:03.000000000 -0400
+@@ -6,7 +6,7 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+ 
+-DLL_LIB = $(PCRE_LIB)
++DLL_LIB = $(PCRE_LIB) xncbi
+ LIBS    = $(PCRE_LIBS)
+ 
+ WATCHERS = ivanov
+Index: b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+===================================================================
+--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib	2011-08-27 21:38:35.000000000 -0400
+@@ -8,6 +8,8 @@
+ 
+ SRC = segmask
+ 
++DLL_LIB = blast xobjmgr xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+Index: b/c++/src/objmgr/split/Makefile.id2_split.lib
+===================================================================
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objmgr/split/Makefile.id2_split.lib	2011-08-27 21:36:26.000000000 -0400
+@@ -17,6 +17,6 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+-DLL_LIB = $(SOBJMGR_LIBS)
++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
+ 
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+===================================================================
+--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib	2011-08-27 21:03:01.000000000 -0400
++++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib	2011-08-27 21:39:32.000000000 -0400
+@@ -8,6 +8,9 @@
+ 
+ LIB = writedb
+ 
++DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
++          xser sequtil xutil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+Index: b/c++/src/algo/blast/Makefile.blast_macros.mk
+===================================================================
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk	2011-08-27 21:03:02.000000000 -0400
++++ b/c++/src/algo/blast/Makefile.blast_macros.mk	2011-08-27 21:03:03.000000000 -0400
+@@ -15,7 +15,7 @@
+     $(BLAST_DB_DATA_LOADER_LIBS) $(BLAST_FORMATTER_MINIMAL_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
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
diff --git a/debian/patches/series b/debian/patches/series
index eb1f6ac9..b0158468 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ legacy_rename_rpsblast
 fix_checks
 fix_gcc46_errors
 support_other_cpus
+fix_lib_deps