[med-svn] r7582 - in trunk/packages/ncbi-blast+/trunk/debian: . patches
Aaron M. Ucko
ucko at alioth.debian.org
Mon Aug 29 16:28:21 UTC 2011
Author: ucko
Date: 2011-08-29 16:28:20 +0000 (Mon, 29 Aug 2011)
New Revision: 7582
Modified:
trunk/packages/ncbi-blast+/trunk/debian/changelog
trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
Log:
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.
Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2011-08-29 16:10:10 UTC (rev 7581)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog 2011-08-29 16:28:20 UTC (rev 7582)
@@ -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 at debian.org> Mon, 29 Aug 2011 12:10:02 -0400
+ -- Aaron M. Ucko <ucko at debian.org> Mon, 29 Aug 2011 12:28:12 -0400
ncbi-blast+ (2.2.25-4) unstable; urgency=low
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2011-08-29 16:10:10 UTC (rev 7581)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2011-08-29 16:28:20 UTC (rev 7582)
@@ -3,14 +3,18 @@
* src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency
loop between libxblast and libxalgoblastdbindex by having the former
provide only the C++ BLAST API, leaving the C core only in libblast.
+ * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
+ rather than libconnect for consistency with libblast, which uses the
+ former to keep the aforementioned cycle-breaking from causing
+ inconsistency elsewhere.
Debian-Bug: 633567.
Author: Aaron M. Ucko <ucko at debian.org>
Last-Update: 2011-08-28
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 @@
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 @@
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 @@
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 @@
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/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 @@
+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 @@
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 @@
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 @@
+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 @@
# 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 @@
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/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 @@
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/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 @@
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 @@
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 @@
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 @@
+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 @@
# 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 @@
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/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 @@
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 @@
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 @@
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 @@
+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 @@
+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 @@
+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 @@
+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 @@
+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 @@
+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/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 @@
# 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 @@
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 @@
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 @@
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$(DLL)
@@ -440,8 +444,8 @@
WATCHERS = vasilche
Index: b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
===================================================================
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2011-08-27 21:57:00.000000000 -0400
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2010-05-04 11:42:43.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2011-08-29 12:15:27.000000000 -0400
@@ -12,6 +12,8 @@
# Dependencies for shared library
DLL_LIB = xconnect ncbi_xreader$(DLL)
@@ -453,8 +457,8 @@
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 @@
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 @@
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 @@
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 @@
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 @@
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 @@
+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 @@
+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 @@
+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 @@
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 @@
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 @@
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 @@
+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 @@
+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 @@
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 @@
+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 @@
+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 @@
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 @@
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 @@
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 @@
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/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 @@
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 @@
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 @@
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)
Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes 2011-08-29 16:10:10 UTC (rev 7581)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes 2011-08-29 16:28:20 UTC (rev 7582)
@@ -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 @@
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.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 @@
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/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)
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