From 933bd4be1950dd6c920c27c6776101ad8828fa5e Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Mon, 29 Aug 2011 16:28:20 +0000 Subject: [PATCH] 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. --- debian/changelog | 7 +- debian/patches/fix_lib_deps | 274 ++++++++++++++++++++---------------- debian/patches/hurd_fixes | 40 ++++-- 3 files changed, 188 insertions(+), 133 deletions(-) diff --git a/debian/changelog b/debian/changelog index 25ff3fd5..b4e700bf 100644 --- 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 Mon, 29 Aug 2011 12:10:02 -0400 + -- Aaron M. Ucko 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 5513dd10..87b20928 100644 --- 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 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 84c70fc3..4c5d18b0 100644 --- 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 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 @@ -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 @@ -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 #include @@ -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) -- 2.30.2