Address ncbi-blast+'s continued failure to build on the Hurd

(accidentally broken by the fix for #633567):
* debian/patches/hurd_fixes: further patch configure(.ac) to reflect
  -Wl,rpath,... support.  (Closes: #629656.)
* debian/patches/fix_lib_deps: link makembindex and srsearch against
  libxconnect rather than libconnect for consistency with libblast,
  which uses the former for consistency with other projects.

diff --git a/debian/changelog b/debian/changelog
index 25ff3fd517c5e63d799cd7bdfbf17f4e3b5a1bd5..b4e700bf35a29ef6dc0587326cc6fc4d80aeaca3 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,13 @@
 ncbi-blast+ (2.2.25-5) UNRELEASED; urgency=low
 
   * NOT RELEASED YET
+  * debian/patches/hurd_fixes: further patch configure(.ac) to reflect
+    -Wl,rpath,... support.  (Closes: #629656.)
+  * debian/patches/fix_lib_deps: link makembindex and srsearch against
+    libxconnect rather than libconnect for consistency with libblast,
+    which uses the former for consistency with other projects.
 
- -- Aaron M. Ucko <ucko@debian.org>  Mon, 29 Aug 2011 12:10:02 -0400
+ -- Aaron M. Ucko <ucko@debian.org>  Mon, 29 Aug 2011 12:28:12 -0400
 
 ncbi-blast+ (2.2.25-4) unstable; urgency=low
 

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 5513dd103196f79625b5e54d65064104690e3053..87b209282c130b078c35f086a263f9de48c28846 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -3,14 +3,18 @@ Subject: ensure that all libraries link against all direct dependencies
  * src/**/Makefile.*.lib: set DLL_(D)LIB correctly.  Break the dependency
    loop between libxblast and libxalgoblastdbindex by having the former
    provide only the C++ BLAST API, leaving the C core only in libblast.
+ * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
+   rather than libconnect for consistency with libblast, which uses the
+   former to keep the aforementioned cycle-breaking from causing
+   inconsistency elsewhere.
 
 Debian-Bug: 633567.
 Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2011-08-28
 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
+--- 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
 @@ -21,5 +21,6 @@
  CFLAGS  = $(FAST_CFLAGS)
  LDFLAGS = $(FAST_LDFLAGS)
@@ -20,8 +24,8 @@ Index: b/c++/src/algo/blast/core/Makefile.blast.lib
  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
+--- 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
 @@ -11,6 +11,8 @@
  CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
@@ -33,8 +37,8 @@ Index: b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
  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
+--- a/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib  2010-03-18 14:56:34.000000000 -0400
++++ b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib  2011-08-29 12:15:27.000000000 -0400
 @@ -7,6 +7,8 @@
  CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
@@ -46,8 +50,8 @@ Index: b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
  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
+--- 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
 @@ -7,6 +7,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -59,8 +63,8 @@ Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib
  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
+--- a/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib       2010-03-18 14:56:34.000000000 -0400
++++ b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib       2011-08-29 12:15:27.000000000 -0400
 @@ -5,6 +5,8 @@
        njn_localmaxstat njn_localmaxstatutil njn_ioutil njn_matrix \
        njn_stringutil njn_dynprogprob njn_dynprogproblim njn_dynprogprobproto
@@ -72,8 +76,8 @@ Index: b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
  
 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
+--- 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
 @@ -21,3 +21,4 @@
  CXXFLAGS = $(FAST_CXXFLAGS)
  LDFLAGS  = $(FAST_LDFLAGS)
@@ -81,8 +85,8 @@ Index: b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
 +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
+--- 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
 @@ -8,6 +8,8 @@
        cgi_serial cgi_session cgi_exception cgiapp_cached cgi_entry_reader
  LIB = xcgi
@@ -94,8 +98,8 @@ Index: b/c++/src/cgi/Makefile.cgi.lib
  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
+--- 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
 @@ -7,4 +7,6 @@
        jsmenu commentdiag indentstream html_exception writer_htmlenc
  LIB = xhtml
@@ -105,8 +109,8 @@ Index: b/c++/src/html/Makefile.html.lib
  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
+--- 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
 @@ -2,3 +2,5 @@
  
  LIB = xnetblastcli
@@ -115,8 +119,8 @@ Index: b/c++/src/objects/blast/Makefile.xnetblastcli.lib
 +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
+--- 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
 @@ -10,6 +10,10 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -130,8 +134,8 @@ Index: b/c++/src/objtools/align_format/Makefile.align_format.lib
  # 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
+--- 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
 @@ -10,6 +10,6 @@
        alnsegments alnseq alnvec alnvec_iterator alnvecprint           \
        pairwise_aln sparse_aln sparse_ci
@@ -142,8 +146,8 @@ Index: b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
  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
+--- 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
@@ -153,8 +157,8 @@ Index: b/c++/src/objtools/readers/Makefile.xobjread.lib
  
 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
+--- 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
 @@ -11,6 +11,6 @@
  mask_writer_blastdb_maskinfo
  
@@ -165,8 +169,8 @@ Index: b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
  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
+--- 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
 @@ -7,6 +7,8 @@
  
  ASN_DEP = seqset
@@ -178,8 +182,8 @@ Index: b/c++/src/objtools/simple/Makefile.xobjsimple.lib
  
 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
+--- 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 @@
  
  LIB = seqdb
@@ -191,8 +195,8 @@ Index: b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
  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
+--- 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
 @@ -5,4 +5,6 @@
  
  ASN_DEP = blastdb seqset
@@ -202,8 +206,8 @@ Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
  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
+--- 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
 @@ -3,6 +3,8 @@
  LIB = ncbi_xloader_blastdb_rmt
  SRC = bdbloader_rmt remote_blastdb_adapter
@@ -215,8 +219,8 @@ Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt
  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
+--- 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
 @@ -4,3 +4,5 @@
  
  LIB = gene_info
@@ -225,8 +229,8 @@ Index: b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
 +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
+--- 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
@@ -246,8 +250,8 @@ Index: b/c++/src/algo/blast/api/Makefile.xblast.lib
  # 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
+--- 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 @@
  
  LIB = blastinput
@@ -261,8 +265,8 @@ Index: b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
  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
+--- 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
 @@ -8,6 +8,8 @@
  
  SRC = symdust
@@ -274,8 +278,8 @@ Index: b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
  
 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
+--- 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
 @@ -14,6 +14,8 @@
  LIB  = xconnect
  PROJ_TAG = core
@@ -287,8 +291,8 @@ Index: b/c++/src/connect/Makefile.xconnect.lib
  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
+--- 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
 @@ -6,4 +6,6 @@
  
  LIB      = xconnext
@@ -298,8 +302,8 @@ Index: b/c++/src/connect/ext/Makefile.xconnext.lib
  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
+--- 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
 @@ -1,4 +1,6 @@
  LIB = xnetblast
  SRC = blast__ blast___ names
@@ -309,8 +313,8 @@ Index: b/c++/src/objects/blast/Makefile.blast.lib
  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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = blastxml
  SRC = blastxml__ blastxml___
@@ -318,8 +322,8 @@ Index: b/c++/src/objects/blastxml/Makefile.blastxml.lib
 +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
+--- 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
 @@ -2,3 +2,5 @@
  
  LIB = entrez2
@@ -328,8 +332,8 @@ Index: b/c++/src/objects/entrez2/Makefile.entrez2.lib
 +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
+--- 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
 @@ -4,3 +4,5 @@
  
  LIB = entrez2cli
@@ -338,8 +342,8 @@ Index: b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
 +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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = scoremat
  SRC = scoremat__ scoremat___
@@ -347,8 +351,8 @@ Index: b/c++/src/objects/scoremat/Makefile.scoremat.lib
 +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
+--- 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
 @@ -1,3 +1,4 @@
  LIB = seqedit
  SRC = seqedit__ seqedit___
@@ -357,8 +361,8 @@ Index: b/c++/src/objects/seqedit/Makefile.seqedit.lib
 +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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = submit
  SRC = submit__ submit___
@@ -366,8 +370,8 @@ Index: b/c++/src/objects/submit/Makefile.submit.lib
 +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
+--- 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
 @@ -8,5 +8,7 @@
  SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
  LIB = xobjutil
@@ -378,8 +382,8 @@ Index: b/c++/src/objmgr/util/Makefile.util.lib
  
 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
+--- 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
 @@ -11,6 +11,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
@@ -390,8 +394,8 @@ Index: b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
  # 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
+--- 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
 @@ -8,6 +8,8 @@
  
  LIB = blast_services
@@ -403,8 +407,8 @@ Index: b/c++/src/objtools/blast/services/Makefile.blast_services.lib
  LDFLAGS  = $(FAST_LDFLAGS)
 Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
 ===================================================================
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib  2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib  2011-08-27 21:54:20.000000000 -0400
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib  2010-05-04 11:42:43.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib  2011-08-29 12:15:27.000000000 -0400
 @@ -12,4 +12,7 @@
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL)
@@ -415,8 +419,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
  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
+--- 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
 @@ -14,4 +14,7 @@
  # Dependencies for shared library
  DLL_LIB = 
@@ -427,8 +431,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
  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
+--- 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
 @@ -12,6 +12,8 @@
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL)
@@ -440,8 +444,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache
  WATCHERS = vasilche
 Index: b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
 ===================================================================
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib  2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib  2011-08-27 21:57:00.000000000 -0400
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib  2010-05-04 11:42:43.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib  2011-08-29 12:15:27.000000000 -0400
 @@ -12,6 +12,8 @@
  # Dependencies for shared library
  DLL_LIB = xconnect ncbi_xreader$(DLL)
@@ -453,8 +457,8 @@ Index: b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
  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
+--- 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
 @@ -12,6 +12,9 @@
  CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
  
@@ -468,8 +472,8 @@ 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  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
+--- 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
 @@ -6,7 +6,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -481,8 +485,8 @@ Index: b/c++/src/util/compress/api/Makefile.compress.lib
  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
+--- 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
 @@ -3,4 +3,6 @@
  LIB = sequtil
  SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
@@ -492,8 +496,8 @@ Index: b/c++/src/util/sequtil/Makefile.sequtil.lib
  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
+--- 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
 @@ -3,6 +3,8 @@
  SRC = test_boost
  LIB = test_boost
@@ -505,8 +509,8 @@ Index: b/c++/src/corelib/Makefile.test_boost.lib
  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
+--- 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
 @@ -3,6 +3,8 @@
  SRC = test_mt
  LIB    = test_mt
@@ -518,8 +522,8 @@ Index: b/c++/src/corelib/Makefile.test_mt.lib
  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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = biblio
  SRC = biblio__ biblio___ label_util
@@ -527,8 +531,8 @@ Index: b/c++/src/objects/biblio/Makefile.biblio.lib
 +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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = blastdb
  SRC = blastdb__ blastdb___
@@ -536,8 +540,8 @@ Index: b/c++/src/objects/blastdb/Makefile.blastdb.lib
 +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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = general
  SRC = general__ general___ uoconv
@@ -545,8 +549,8 @@ Index: b/c++/src/objects/general/Makefile.general.lib
 +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
+--- 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
 @@ -3,4 +3,6 @@
  LIB = genome_collection
  SRC = genome_collection__ genome_collection___
@@ -556,8 +560,8 @@ Index: b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
  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
+--- 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
 @@ -3,4 +3,6 @@
  LIB = id1
  SRC = id1__ id1___
@@ -567,8 +571,8 @@ Index: b/c++/src/objects/id1/Makefile.id1.lib
  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
+--- 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
 @@ -1,4 +1,6 @@
  LIB = id2
  SRC = id2__ id2___
@@ -578,8 +582,8 @@ Index: b/c++/src/objects/id2/Makefile.id2.lib
  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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = medline
  SRC = medline__ medline___
@@ -587,8 +591,8 @@ Index: b/c++/src/objects/medline/Makefile.medline.lib
 +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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = pub
  SRC = pub__ pub___
@@ -596,8 +600,8 @@ Index: b/c++/src/objects/pub/Makefile.pub.lib
 +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
+--- 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
@@ -607,8 +611,8 @@ Index: b/c++/src/objects/seq/Makefile.seq.lib
  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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = seqcode
  SRC = seqcode__ seqcode___
@@ -616,8 +620,8 @@ Index: b/c++/src/objects/seqcode/Makefile.seqcode.lib
 +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
+--- 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
 @@ -1,2 +1,4 @@
  LIB = seqset
  SRC = seqset__ seqset___ gb_release_file
@@ -625,8 +629,8 @@ Index: b/c++/src/objects/seqset/Makefile.seqset.lib
 +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
+--- 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
 @@ -1,4 +1,6 @@
  LIB = seqsplit
  SRC = seqsplit__ seqsplit___
@@ -636,8 +640,8 @@ Index: b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
  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
+--- 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
 @@ -18,4 +18,6 @@
  
  LIB    = xser
@@ -647,8 +651,8 @@ Index: b/c++/src/serial/Makefile.serial.lib
  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
+--- 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
 @@ -11,6 +11,7 @@
  LIB = xutil
  PROJ_TAG = core
@@ -659,8 +663,8 @@ Index: b/c++/src/util/Makefile.util.lib
  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
+--- 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
 @@ -6,7 +6,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
@@ -672,8 +676,8 @@ Index: b/c++/src/util/xregexp/Makefile.xregexp.lib
  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
+--- 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
 @@ -8,6 +8,8 @@
  
  SRC = segmask
@@ -685,8 +689,8 @@ Index: b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
  
 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
+--- 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
 @@ -17,6 +17,6 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
@@ -697,8 +701,8 @@ Index: b/c++/src/objmgr/split/Makefile.id2_split.lib
  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
+--- 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
 @@ -8,6 +8,9 @@
  
  LIB = writedb
@@ -711,8 +715,8 @@ Index: b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
  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
+--- 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)
  
@@ -722,3 +726,29 @@ Index: b/c++/src/algo/blast/Makefile.blast_macros.mk
                xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
                xobjread creaders xnetblastcli xnetblast blastdb scoremat tables
  # 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
+@@ -2,7 +2,7 @@
+ SRC = main mkindex_app
+ 
+ LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
+-      xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS)
++      xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+ 
+ CXXFLAGS = $(FAST_CXXFLAGS)
+Index: b/c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app
+===================================================================
+--- a/c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app 2011-08-29 12:18:27.000000000 -0400
++++ b/c++/src/algo/blast/dbindex_search/srsearch/Makefile.srsearch.app 2011-08-29 12:18:31.000000000 -0400
+@@ -2,7 +2,7 @@
+ SRC = main srsearch_app
+ 
+ LIB_ = xalgoblastdbindex xalgoblastdbindex_search blast composition_adjustment seqdb blastdb \
+-      xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS)
++      xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS)
+ LIB = $(LIB_:%=%$(STATIC))
+ 
+ CXXFLAGS = $(FAST_CXXFLAGS)

diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes
index 84c70fc313a42cf4f623434023f936ad78630d3d..4c5d18b0dedf7c64e70c2f496605c56c7dc7d94a 100644 (file)
--- a/debian/patches/hurd_fixes
+++ b/debian/patches/hurd_fixes
@@ -1,7 +1,9 @@
 Subject: fix portability issues that led to Hurd build failures
 
-* src/build-system/configure(.ac): when checking how select works, reset
-  the alarm from the signal handler to avoid spinning forever.
+* src/build-system/configure(.ac):
+  - Reflect the Hurd's support for -Wl,rpath,... .
+  - When checking how select works, reset the alarm from the signal handler
+    to avoid spinning forever.
 * src/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c:
   cope with missing PATH_MAX everywhere, not just under Windows.
 
@@ -9,8 +11,17 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2011-06-10
 Index: b/c++/src/build-system/configure
 ===================================================================
---- a/c++/src/build-system/configure   2011-06-10 20:18:43.000000000 -0400
-+++ b/c++/src/build-system/configure   2011-06-10 20:19:52.000000000 -0400
+--- a/c++/src/build-system/configure   2011-03-16 14:40:24.000000000 -0400
++++ b/c++/src/build-system/configure   2011-08-29 12:12:56.000000000 -0400
+@@ -5559,7 +5559,7 @@
+     solaris* )
+       CONF_f_runpath="-R"
+       ;;
+-    linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
++    linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC )
+       CONF_f_runpath="-Wl,-rpath,"
+       ;;
+     linux*:ICC )
 @@ -11416,7 +11416,7 @@
           #ifdef HAVE_UNISTD_H
           #  include <unistd.h>
@@ -22,8 +33,17 @@ Index: b/c++/src/build-system/configure
  {
 Index: b/c++/src/build-system/configure.ac
 ===================================================================
---- a/c++/src/build-system/configure.ac        2011-06-10 20:18:43.000000000 -0400
-+++ b/c++/src/build-system/configure.ac        2011-06-10 20:19:39.000000000 -0400
+--- a/c++/src/build-system/configure.ac        2011-03-16 14:40:24.000000000 -0400
++++ b/c++/src/build-system/configure.ac        2011-08-29 12:12:41.000000000 -0400
+@@ -1441,7 +1441,7 @@
+     solaris* )
+       CONF_f_runpath="-R"
+       ;;
+-    linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC )
++    linux*:GCC | *bsd*:GCC | cygwin*:GCC | osf*:GCC | gnu*:GCC )
+       CONF_f_runpath="-Wl,-rpath,"
+       ;;
+     linux*:ICC )
 @@ -2811,7 +2811,7 @@
           #ifdef HAVE_UNISTD_H
           #  include <unistd.h>
@@ -35,8 +55,8 @@ Index: b/c++/src/build-system/configure.ac
           alarm(1);
 Index: b/c++/src/connect/ncbi_socket_cxx.cpp
 ===================================================================
---- a/c++/src/connect/ncbi_socket_cxx.cpp      2011-06-10 20:19:06.000000000 -0400
-+++ b/c++/src/connect/ncbi_socket_cxx.cpp      2011-06-10 20:20:12.000000000 -0400
+--- a/c++/src/connect/ncbi_socket_cxx.cpp      2011-03-16 10:54:49.000000000 -0400
++++ b/c++/src/connect/ncbi_socket_cxx.cpp      2011-08-29 12:11:45.000000000 -0400
 @@ -34,7 +34,7 @@
  #include <ncbi_pch.hpp>
  #include <connect/ncbi_socket_unix.hpp>
@@ -48,8 +68,8 @@ Index: b/c++/src/connect/ncbi_socket_cxx.cpp
  
 Index: b/c++/src/connect/ext/ncbi_localnet.c
 ===================================================================
---- a/c++/src/connect/ext/ncbi_localnet.c      2011-06-10 23:40:40.000000000 -0400
-+++ b/c++/src/connect/ext/ncbi_localnet.c      2011-06-10 23:40:45.000000000 -0400
+--- a/c++/src/connect/ext/ncbi_localnet.c      2010-03-22 12:11:37.000000000 -0400
++++ b/c++/src/connect/ext/ncbi_localnet.c      2011-08-29 12:11:45.000000000 -0400
 @@ -64,6 +64,8 @@
  
  #if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)