From ae3711aa18cf7201d46b4d25d83b64ce427fc3b2 Mon Sep 17 00:00:00 2001
From: Olivier Sallou <osallou@debian.org>
Date: Wed, 7 Mar 2012 11:59:34 +0000
Subject: [PATCH] fix offset/fuzz errors in patch after upstream release update

---
 debian/patches/fix_lib_deps       | 394 +++++++++++-------------------
 debian/patches/no_multiarch_rpath |  16 +-
 2 files changed, 143 insertions(+), 267 deletions(-)

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 217071b3..b93d7ccb 100644
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -11,21 +11,17 @@ Subject: ensure that all libraries link against all direct dependencies
 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	2010-03-18 14:56:34.000000000 -0400
-+++ b/c++/src/algo/blast/core/Makefile.blast.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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)
  
 +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	2010-03-18 14:56:34.000000000 -0400
-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib	2011-08-29 12:15:27.000000000 -0400
+ WATCHERS = coulouri maning madden camacho
+--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
 @@ -11,6 +11,8 @@
  CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
@@ -35,10 +31,8 @@ Index: b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
  ASN_DEP = seqset
  
  WATCHERS = morgulis
-Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-===================================================================
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib	2010-04-26 09:36:34.000000000 -0400
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
++++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
 @@ -7,6 +7,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -47,20 +41,16 @@ Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib
 +DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
 +          seq general xser tables xncbi
  
- WATCHERS = blastsoft
-Index: b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-===================================================================
---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib	2011-02-10 12:14:32.000000000 -0500
-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib	2011-08-29 12:15:27.000000000 -0400
+ WATCHERS = jianye zaretska madden camacho fongah2
+--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
++++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
 @@ -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	2010-02-26 12:16:17.000000000 -0500
-+++ b/c++/src/cgi/Makefile.cgi.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/cgi/Makefile.cgi.lib
++++ b/c++/src/cgi/Makefile.cgi.lib
 @@ -8,6 +8,8 @@
        cgi_serial cgi_session cgi_exception cgiapp_cached cgi_entry_reader
  LIB = xcgi
@@ -70,10 +60,8 @@ Index: b/c++/src/cgi/Makefile.cgi.lib
  CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
  
  WATCHERS = vakatov
-Index: b/c++/src/html/Makefile.html.lib
-===================================================================
---- a/c++/src/html/Makefile.html.lib	2010-02-26 12:16:17.000000000 -0500
-+++ b/c++/src/html/Makefile.html.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -81,20 +69,16 @@ Index: b/c++/src/html/Makefile.html.lib
 +DLL_LIB = xncbi
 +
  WATCHERS = ivanov
-Index: b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-===================================================================
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib	2004-02-25 12:11:43.000000000 -0500
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/objtools/align_format/Makefile.align_format.lib
-===================================================================
---- a/c++/src/objtools/align_format/Makefile.align_format.lib	2010-08-03 09:56:32.000000000 -0400
-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objtools/align_format/Makefile.align_format.lib
++++ b/c++/src/objtools/align_format/Makefile.align_format.lib
 @@ -10,6 +10,10 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -106,31 +90,25 @@ Index: b/c++/src/objtools/align_format/Makefile.align_format.lib
  ###  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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
 +
-Index: b/c++/src/objtools/readers/Makefile.xobjread.lib
-===================================================================
---- a/c++/src/objtools/readers/Makefile.xobjread.lib	2011-02-02 10:48:12.000000000 -0500
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -12,5 +12,5 @@
-       wiggle_data wiggle_reader gff3_sofa gff3_reader gtf_reader \
-       gff2_data gff2_reader source_mod_parser
+--- 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
  
-Index: b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-===================================================================
---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib	2010-08-06 12:57:00.000000000 -0400
-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
 @@ -11,6 +11,6 @@
  mask_writer_blastdb_maskinfo
  
@@ -139,10 +117,8 @@ Index: b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
 +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	2010-10-15 14:36:58.000000000 -0400
-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
++++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
 @@ -7,6 +7,8 @@
  
  ASN_DEP = seqset
@@ -152,11 +128,9 @@ Index: b/c++/src/objtools/simple/Makefile.xobjsimple.lib
  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	2010-08-17 11:38:17.000000000 -0400
-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -25,6 +25,8 @@
+--- 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
  
@@ -165,10 +139,8 @@ Index: b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
  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	2010-06-16 12:03:59.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -176,10 +148,8 @@ Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
 +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	2010-06-16 12:03:59.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -189,23 +159,19 @@ Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt
  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	2010-10-15 14:36:58.000000000 -0400
-+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/algo/blast/api/Makefile.xblast.lib
-===================================================================
---- a/c++/src/algo/blast/api/Makefile.xblast.lib	2010-03-18 14:56:34.000000000 -0400
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -69,11 +69,14 @@
- winmask_filter \
- subj_ranges_set
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib
+@@ -74,11 +74,14 @@
+ deltablast_options \
+ deltablast
  
 -SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)
 +SRC  = $(SRC_CXX) # $(SRC_C:%=.core_%)
@@ -220,11 +186,9 @@ Index: b/c++/src/algo/blast/api/Makefile.xblast.lib
  
  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	2010-03-18 14:56:34.000000000 -0400
-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -20,7 +20,9 @@
+--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
++++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+@@ -24,7 +24,9 @@
  
  LIB = blastinput
  
@@ -235,10 +199,8 @@ Index: b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
  
  # 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	2010-10-15 14:36:18.000000000 -0400
-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
++++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
 @@ -8,6 +8,8 @@
  
  SRC = symdust
@@ -248,10 +210,8 @@ Index: b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
  CXXFLAGS = $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
  
-Index: b/c++/src/connect/Makefile.xconnect.lib
-===================================================================
---- a/c++/src/connect/Makefile.xconnect.lib	2010-02-26 11:33:57.000000000 -0500
-+++ b/c++/src/connect/Makefile.xconnect.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/connect/Makefile.xconnect.lib
++++ b/c++/src/connect/Makefile.xconnect.lib
 @@ -14,6 +14,8 @@
  LIB  = xconnect
  PROJ_TAG = core
@@ -261,10 +221,8 @@ Index: b/c++/src/connect/Makefile.xconnect.lib
  LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
  
  WATCHERS = lavr
-Index: b/c++/src/connect/ext/Makefile.xconnext.lib
-===================================================================
---- a/c++/src/connect/ext/Makefile.xconnext.lib	2010-02-26 11:33:57.000000000 -0500
-+++ b/c++/src/connect/ext/Makefile.xconnext.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/connect/ext/Makefile.xconnext.lib
++++ b/c++/src/connect/ext/Makefile.xconnext.lib
 @@ -6,4 +6,6 @@
  
  LIB      = xconnext
@@ -272,10 +230,8 @@ Index: b/c++/src/connect/ext/Makefile.xconnext.lib
 +DLL_LIB = xconnect xncbi
 +
  WATCHERS = lavr
-Index: b/c++/src/objects/blast/Makefile.blast.lib
-===================================================================
---- a/c++/src/objects/blast/Makefile.blast.lib	2010-05-12 15:03:57.000000000 -0400
-+++ b/c++/src/objects/blast/Makefile.blast.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -283,67 +239,53 @@ Index: b/c++/src/objects/blast/Makefile.blast.lib
 +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	2005-06-13 12:21:41.000000000 -0400
-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/objects/entrez2/Makefile.entrez2.lib
-===================================================================
---- a/c++/src/objects/entrez2/Makefile.entrez2.lib	2010-10-15 14:36:49.000000000 -0400
-+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-===================================================================
---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib	2010-10-15 14:36:49.000000000 -0400
-+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/objects/scoremat/Makefile.scoremat.lib
-===================================================================
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib	2003-06-05 16:20:42.000000000 -0400
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/objects/seqedit/Makefile.seqedit.lib
-===================================================================
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib	2006-01-25 12:11:00.000000000 -0500
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/objects/submit/Makefile.submit.lib
-===================================================================
---- a/c++/src/objects/submit/Makefile.submit.lib	2003-06-05 16:21:46.000000000 -0400
-+++ b/c++/src/objects/submit/Makefile.submit.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
-Index: b/c++/src/objmgr/util/Makefile.util.lib
-===================================================================
---- a/c++/src/objmgr/util/Makefile.util.lib	2010-02-26 11:33:57.000000000 -0500
-+++ b/c++/src/objmgr/util/Makefile.util.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -352,10 +294,8 @@ Index: b/c++/src/objmgr/util/Makefile.util.lib
 +
  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	2010-10-15 14:36:58.000000000 -0400
-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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)
@@ -364,10 +304,8 @@ Index: b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
  
  ###  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	2010-10-15 14:36:58.000000000 -0400
-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -377,10 +315,8 @@ Index: b/c++/src/objtools/blast/services/Makefile.blast_services.lib
  CFLAGS   = $(FAST_CFLAGS)
  CXXFLAGS = $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
-Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
 @@ -12,4 +12,7 @@
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL)
@@ -389,10 +325,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
 +           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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
 @@ -14,4 +14,7 @@
  # Dependencies for shared library
  DLL_LIB = 
@@ -401,10 +335,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
 +           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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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)
@@ -414,10 +346,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache
  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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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)
@@ -427,10 +357,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
  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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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)
  
@@ -442,10 +370,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
 +
  
  WATCHERS = vasilche
-Index: b/c++/src/util/compress/api/Makefile.compress.lib
-===================================================================
---- a/c++/src/util/compress/api/Makefile.compress.lib	2010-04-26 10:47:05.000000000 -0400
-+++ b/c++/src/util/compress/api/Makefile.compress.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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)
@@ -455,10 +381,8 @@ Index: b/c++/src/util/compress/api/Makefile.compress.lib
  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	2010-02-26 11:33:57.000000000 -0500
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -466,10 +390,8 @@ Index: b/c++/src/util/sequtil/Makefile.sequtil.lib
 +DLL_LIB = xncbi
 +
  WATCHERS = shomrat
-Index: b/c++/src/corelib/Makefile.test_boost.lib
-===================================================================
---- a/c++/src/corelib/Makefile.test_boost.lib	2010-02-26 12:16:17.000000000 -0500
-+++ b/c++/src/corelib/Makefile.test_boost.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/corelib/Makefile.test_boost.lib
++++ b/c++/src/corelib/Makefile.test_boost.lib
 @@ -3,6 +3,8 @@
  SRC = test_boost
  LIB = test_boost
@@ -479,10 +401,8 @@ Index: b/c++/src/corelib/Makefile.test_boost.lib
  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	2010-04-14 10:30:21.000000000 -0400
-+++ b/c++/src/corelib/Makefile.test_mt.lib	2011-08-29 12:15:27.000000000 -0400
+--- 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
@@ -492,37 +412,29 @@ Index: b/c++/src/corelib/Makefile.test_mt.lib
  # REQUIRES = MT
  
  USE_PCH = no
-Index: b/c++/src/objects/biblio/Makefile.biblio.lib
-===================================================================
---- a/c++/src/objects/biblio/Makefile.biblio.lib	2004-02-24 10:53:48.000000000 -0500
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/biblio/Makefile.biblio.lib
++++ b/c++/src/objects/biblio/Makefile.biblio.lib
 @@ -1,2 +1,4 @@
  LIB = biblio
- SRC = biblio__ biblio___ label_util
+ SRC = biblio__ biblio___ citation_base
 +
 +DLL_LIB = general xser xncbi
-Index: b/c++/src/objects/blastdb/Makefile.blastdb.lib
-===================================================================
---- a/c++/src/objects/blastdb/Makefile.blastdb.lib	2003-08-06 12:13:02.000000000 -0400
-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
 @@ -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	2006-03-14 16:14:34.000000000 -0500
-+++ b/c++/src/objects/general/Makefile.general.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/general/Makefile.general.lib
++++ b/c++/src/objects/general/Makefile.general.lib
 @@ -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	2010-08-20 12:43:35.000000000 -0400
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
 @@ -3,4 +3,6 @@
  LIB = genome_collection
  SRC = genome_collection__ genome_collection___
@@ -530,10 +442,8 @@ Index: b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
 +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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objects/id1/Makefile.id1.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/id1/Makefile.id1.lib
++++ b/c++/src/objects/id1/Makefile.id1.lib
 @@ -3,4 +3,6 @@
  LIB = id1
  SRC = id1__ id1___
@@ -541,10 +451,8 @@ Index: b/c++/src/objects/id1/Makefile.id1.lib
 +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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objects/id2/Makefile.id2.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/id2/Makefile.id2.lib
++++ b/c++/src/objects/id2/Makefile.id2.lib
 @@ -1,4 +1,6 @@
  LIB = id2
  SRC = id2__ id2___
@@ -552,57 +460,45 @@ Index: b/c++/src/objects/id2/Makefile.id2.lib
 +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	2003-06-05 16:21:46.000000000 -0400
-+++ b/c++/src/objects/medline/Makefile.medline.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/medline/Makefile.medline.lib
++++ b/c++/src/objects/medline/Makefile.medline.lib
 @@ -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	2003-06-05 16:21:46.000000000 -0400
-+++ b/c++/src/objects/pub/Makefile.pub.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/pub/Makefile.pub.lib
++++ b/c++/src/objects/pub/Makefile.pub.lib
 @@ -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	2010-08-05 12:25:14.000000000 -0400
-+++ b/c++/src/objects/seq/Makefile.seq.lib	2011-08-29 12:15:27.000000000 -0400
-@@ -11,4 +11,6 @@
-       seq_id_tree seq_id_handle seq_id_mapper \
-       seq_loc_mapper_base seq_align_mapper_base seqlocinfo
+--- a/c++/src/objects/seq/Makefile.seq.lib
++++ b/c++/src/objects/seq/Makefile.seq.lib
+@@ -12,4 +12,6 @@
+       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
-Index: b/c++/src/objects/seqcode/Makefile.seqcode.lib
-===================================================================
---- a/c++/src/objects/seqcode/Makefile.seqcode.lib	2003-06-05 16:21:46.000000000 -0400
-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/seqcode/Makefile.seqcode.lib
++++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
 @@ -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	2004-05-19 10:49:26.000000000 -0400
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/seqset/Makefile.seqset.lib
++++ b/c++/src/objects/seqset/Makefile.seqset.lib
 @@ -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	2010-05-04 11:42:43.000000000 -0400
-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
++++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
 @@ -1,4 +1,6 @@
  LIB = seqsplit
  SRC = seqsplit__ seqsplit___
@@ -610,10 +506,8 @@ Index: b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
 +DLL_LIB = seqset seq xser xncbi
 +
  WATCHERS = vasilche
-Index: b/c++/src/serial/Makefile.serial.lib
-===================================================================
---- a/c++/src/serial/Makefile.serial.lib	2010-02-26 12:16:17.000000000 -0500
-+++ b/c++/src/serial/Makefile.serial.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/serial/Makefile.serial.lib
++++ b/c++/src/serial/Makefile.serial.lib
 @@ -18,4 +18,6 @@
  
  LIB    = xser
@@ -621,10 +515,8 @@ Index: b/c++/src/serial/Makefile.serial.lib
 +DLL_LIB = xutil xncbi
 +
  WATCHERS = gouriano
-Index: b/c++/src/util/Makefile.util.lib
-===================================================================
---- a/c++/src/util/Makefile.util.lib	2010-02-26 11:33:57.000000000 -0500
-+++ b/c++/src/util/Makefile.util.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/util/Makefile.util.lib
++++ b/c++/src/util/Makefile.util.lib
 @@ -11,6 +11,7 @@
  LIB = xutil
  PROJ_TAG = core
@@ -633,10 +525,8 @@ Index: b/c++/src/util/Makefile.util.lib
  LIBS = $(ORIG_LIBS)
  
  WATCHERS = vakatov
-Index: b/c++/src/util/xregexp/Makefile.xregexp.lib
-===================================================================
---- a/c++/src/util/xregexp/Makefile.xregexp.lib	2010-02-26 11:33:57.000000000 -0500
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib
 @@ -6,7 +6,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
@@ -646,10 +536,8 @@ Index: b/c++/src/util/xregexp/Makefile.xregexp.lib
  LIBS    = $(PCRE_LIBS)
  
  WATCHERS = ivanov
-Index: b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-===================================================================
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib	2010-10-21 15:09:21.000000000 -0400
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
++++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
 @@ -8,6 +8,8 @@
  
  SRC = segmask
@@ -659,10 +547,8 @@ Index: b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
  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	2010-02-26 11:33:57.000000000 -0500
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib
++++ b/c++/src/objmgr/split/Makefile.id2_split.lib
 @@ -17,6 +17,6 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -671,10 +557,8 @@ Index: b/c++/src/objmgr/split/Makefile.id2_split.lib
 +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	2010-08-06 12:42:59.000000000 -0400
-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib	2011-08-29 12:15:27.000000000 -0400
+--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
++++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
 @@ -8,6 +8,9 @@
  
  LIB = writedb
@@ -685,23 +569,19 @@ Index: b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
  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	2010-10-21 15:23:10.000000000 -0400
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk	2011-08-29 12:15:27.000000000 -0400
-@@ -15,7 +15,7 @@
-     $(BLAST_DB_DATA_LOADER_LIBS) $(BLAST_FORMATTER_MINIMAL_LIBS)
+--- 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
+ 		xobjread creaders xnetblastcli xnetblast blastdb scoremat tables xalnmgr
  # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
-Index: b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-===================================================================
---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app	2011-08-29 12:17:36.000000000 -0400
-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app	2011-08-29 12:17:39.000000000 -0400
+--- 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/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 52ddd623..2d5399c5 100644
--- a/debian/patches/no_multiarch_rpath
+++ b/debian/patches/no_multiarch_rpath
@@ -8,11 +8,9 @@ Subject: avoid redundant rpath entries on multiarch systems
 Debian-Bug: 633567.
 Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2011-08-28
-Index: b/c++/src/build-system/configure
-===================================================================
---- a/c++/src/build-system/configure	2011-08-28 11:41:27.000000000 -0400
-+++ b/c++/src/build-system/configure	2011-08-28 11:48:06.000000000 -0400
-@@ -5613,7 +5613,7 @@
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -5751,7 +5751,7 @@
                 break
                 ;;
              /* )
@@ -21,11 +19,9 @@ Index: b/c++/src/build-system/configure
                 break
                 ;;
          esac
-Index: b/c++/src/build-system/configure.ac
-===================================================================
---- a/c++/src/build-system/configure.ac	2011-08-28 11:41:27.000000000 -0400
-+++ b/c++/src/build-system/configure.ac	2011-08-28 11:48:11.000000000 -0400
-@@ -1494,7 +1494,7 @@
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1558,7 +1558,7 @@
                 break
                 ;;
              /* )
-- 
2.30.2