[med-svn] r7584 - in trunk/packages/ncbi-blast+/tags: . 2.2.25-5/debian 2.2.25-5/debian/patches
Aaron M. Ucko
ucko at alioth.debian.org
Mon Aug 29 17:21:20 UTC 2011
Author: ucko
Date: 2011-08-29 17:21:20 +0000 (Mon, 29 Aug 2011)
New Revision: 7584
Added:
trunk/packages/ncbi-blast+/tags/2.2.25-5/
trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/hurd_fixes
Removed:
trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/hurd_fixes
Log:
[svn-buildpackage] Tagging ncbi-blast+ 2.2.25-5
Deleted: trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2011-08-29 13:23:07 UTC (rev 7579)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/changelog 2011-08-29 17:21:20 UTC (rev 7584)
@@ -1,62 +0,0 @@
-ncbi-blast+ (2.2.25-4) unstable; urgency=low
-
- [ Aaron M. Ucko ]
- * Team upload.
- * debian/patches/support_other_cpus: belatedly add a descriptive header.
- * debian/patches/hurd_fixes: new; fix hurd-specific issues.
- (In conjunction with the following change, finally closes: #629656.)
- * debian/control:
- - Build-Depends += libc0.3-dev (>= 2.13-9~) [hurd-i386] to avoid #630180.
- - Declare both binary packages as Multi-Arch: foreign.
- * debian/patches/fix_lib_deps: new; ensure that all libraries link against
- all direct dependencies. (Break the dependency loop between libxblast
- and libxalgoblastdbindex by having the former provide only the C++ BLAST
- API, leaving the C core only in libblast.) (Closes: #633567.)
- * debian/rules: tweak LDFLAGS, supplying -Wl,--as-needed across the
- board (as it is now safe to do so) and adding -Wl,--enable-new-dtags
- to allow LD_LIBRARY_PATH to override the private rpath.
- * debian/patches/no_multiarch_rpath: new; avoid redundant rpath entries
- on multiarch systems (courtesy of overzealous logic to ensure
- executables will be able to find libstdc++.)
-
- [ Andreas Tille ]
- * Enhances: t-coffee (as stated in tasks file)
-
- -- Aaron M. Ucko <ucko at debian.org> Sun, 28 Aug 2011 18:45:19 -0400
-
-ncbi-blast+ (2.2.25-3) unstable; urgency=low
-
- * Team upload.
- * debian/rules:
- - Export MAKE to override an internal upstream build script that
- otherwise incorrectly defaults to gmake on non-Linux
- architectures. (Really closes: #629656, with any luck.)
- - Force CONFIG_SHELL=/bin/bash to avoid lossage that can occur with zsh4
- masquerading as ksh, which configure otherwise favors (due to complaints
- from users with broken BASH_ENV scripts that change directories).
-
- -- Aaron M. Ucko <ucko at debian.org> Thu, 09 Jun 2011 19:25:45 -0400
-
-ncbi-blast+ (2.2.25-2) unstable; urgency=low
-
- * Team upload.
- * Fix several sources of build failures (closes: #629656):
- - debian/rules (override_dh_install): Correctly support building only
- architecture-dependent packages.
- (DEB_CONFIGURE_EXTRA_FLAGS): Add --without-caution to override the
- upstream build system's reluctance to build shared libraries on the
- Hurd or kFreeBSD, which it doesn't specifically recognize. Limit C++
- optimization level to -O (rather than the default -O2) on mips(el),
- on which g++ otherwise crashes. :-/
- - debian/patches/support_other_cpus (new; committed upstream too):
- build correctly on architectures that wound up defining
- NCBI_SLOW_ATOMIC_SWAP (spuriously in the case of powerpc,
- whose detection the patch fixes as well).
-
- -- Aaron M. Ucko <ucko at debian.org> Wed, 08 Jun 2011 21:42:52 -0400
-
-ncbi-blast+ (2.2.25-1) unstable; urgency=low
-
- * Initial release (Closes: #624394)
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 08 Jun 2011 00:15:15 +0200
Copied: trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/changelog (from rev 7583, trunk/packages/ncbi-blast+/trunk/debian/changelog)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/changelog (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/changelog 2011-08-29 17:21:20 UTC (rev 7584)
@@ -0,0 +1,73 @@
+ncbi-blast+ (2.2.25-5) unstable; urgency=low
+
+ * Team upload.
+ * 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 12:31:05 -0400
+
+ncbi-blast+ (2.2.25-4) unstable; urgency=low
+
+ [ Aaron M. Ucko ]
+ * Team upload.
+ * debian/patches/support_other_cpus: belatedly add a descriptive header.
+ * debian/patches/hurd_fixes: new; fix hurd-specific issues.
+ (In conjunction with the following change, finally closes: #629656.)
+ * debian/control:
+ - Build-Depends += libc0.3-dev (>= 2.13-9~) [hurd-i386] to avoid #630180.
+ - Declare both binary packages as Multi-Arch: foreign.
+ * debian/patches/fix_lib_deps: new; ensure that all libraries link against
+ all direct dependencies. (Break the dependency loop between libxblast
+ and libxalgoblastdbindex by having the former provide only the C++ BLAST
+ API, leaving the C core only in libblast.) (Closes: #633567.)
+ * debian/rules: tweak LDFLAGS, supplying -Wl,--as-needed across the
+ board (as it is now safe to do so) and adding -Wl,--enable-new-dtags
+ to allow LD_LIBRARY_PATH to override the private rpath.
+ * debian/patches/no_multiarch_rpath: new; avoid redundant rpath entries
+ on multiarch systems (courtesy of overzealous logic to ensure
+ executables will be able to find libstdc++.)
+
+ [ Andreas Tille ]
+ * Enhances: t-coffee (as stated in tasks file)
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 28 Aug 2011 18:45:19 -0400
+
+ncbi-blast+ (2.2.25-3) unstable; urgency=low
+
+ * Team upload.
+ * debian/rules:
+ - Export MAKE to override an internal upstream build script that
+ otherwise incorrectly defaults to gmake on non-Linux
+ architectures. (Really closes: #629656, with any luck.)
+ - Force CONFIG_SHELL=/bin/bash to avoid lossage that can occur with zsh4
+ masquerading as ksh, which configure otherwise favors (due to complaints
+ from users with broken BASH_ENV scripts that change directories).
+
+ -- Aaron M. Ucko <ucko at debian.org> Thu, 09 Jun 2011 19:25:45 -0400
+
+ncbi-blast+ (2.2.25-2) unstable; urgency=low
+
+ * Team upload.
+ * Fix several sources of build failures (closes: #629656):
+ - debian/rules (override_dh_install): Correctly support building only
+ architecture-dependent packages.
+ (DEB_CONFIGURE_EXTRA_FLAGS): Add --without-caution to override the
+ upstream build system's reluctance to build shared libraries on the
+ Hurd or kFreeBSD, which it doesn't specifically recognize. Limit C++
+ optimization level to -O (rather than the default -O2) on mips(el),
+ on which g++ otherwise crashes. :-/
+ - debian/patches/support_other_cpus (new; committed upstream too):
+ build correctly on architectures that wound up defining
+ NCBI_SLOW_ATOMIC_SWAP (spuriously in the case of powerpc,
+ whose detection the patch fixes as well).
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 08 Jun 2011 21:42:52 -0400
+
+ncbi-blast+ (2.2.25-1) unstable; urgency=low
+
+ * Initial release (Closes: #624394)
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Wed, 08 Jun 2011 00:15:15 +0200
Deleted: trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps 2011-08-29 13:23:07 UTC (rev 7579)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/fix_lib_deps 2011-08-29 17:21:20 UTC (rev 7584)
@@ -1,724 +0,0 @@
-Subject: ensure that all libraries link against all direct dependencies
-
- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency
- loop between libxblast and libxalgoblastdbindex by having the former
- provide only the C++ BLAST API, leaving the C core only in libblast.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko 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
-@@ -21,5 +21,6 @@
- CFLAGS = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = composition_adjustment xconnect tables
-
- WATCHERS = blastsoft
-Index: b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-===================================================================
---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib 2011-08-27 22:03:28.000000000 -0400
-@@ -11,6 +11,8 @@
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
-+
- ASN_DEP = seqset
-
- WATCHERS = morgulis
-Index: b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
-===================================================================
---- a/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib 2011-08-27 21:41:17.000000000 -0400
-@@ -7,6 +7,8 @@
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = xobjmgr xncbi
-+
- ASN_DEP = seqset
-
- WATCHERS = morgulis
-Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-===================================================================
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib 2011-08-27 21:43:34.000000000 -0400
-@@ -7,6 +7,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS)
-
--DLL_LIB = blastxml xhtml xcgi
-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi
-
- WATCHERS = blastsoft
-Index: b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
-===================================================================
---- a/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -5,6 +5,8 @@
- njn_localmaxstat njn_localmaxstatutil njn_ioutil njn_matrix \
- njn_stringutil njn_dynprogprob njn_dynprogproblim njn_dynprogprobproto
-
-+DLL_LIB = tables xutil xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-Index: b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-===================================================================
---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib 2011-08-27 22:03:07.000000000 -0400
-@@ -21,3 +21,4 @@
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
-Index: b/c++/src/cgi/Makefile.cgi.lib
-===================================================================
---- a/c++/src/cgi/Makefile.cgi.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/cgi/Makefile.cgi.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -8,6 +8,8 @@
- cgi_serial cgi_session cgi_exception cgiapp_cached cgi_entry_reader
- LIB = xcgi
-
-+DLL_LIB = xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
-
- WATCHERS = vakatov
-Index: b/c++/src/html/Makefile.html.lib
-===================================================================
---- a/c++/src/html/Makefile.html.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/html/Makefile.html.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -7,4 +7,6 @@
- jsmenu commentdiag indentstream html_exception writer_htmlenc
- LIB = xhtml
-
-+DLL_LIB = xncbi
-+
- WATCHERS = ivanov
-Index: b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-===================================================================
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -2,3 +2,5 @@
-
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-+
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
-Index: b/c++/src/objtools/align_format/Makefile.align_format.lib
-===================================================================
---- a/c++/src/objtools/align_format/Makefile.align_format.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib 2011-08-27 21:52:19.000000000 -0400
-@@ -10,6 +10,10 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS)
-
-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
-+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
-+ xcgi xhtml tables xncbi
-+
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
- # CFLAGS = $(FAST_CFLAGS)
-Index: b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-===================================================================
---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib 2011-08-27 21:53:39.000000000 -0400
-@@ -10,6 +10,6 @@
- alnsegments alnseq alnvec alnvec_iterator alnvecprint \
- pairwise_aln sparse_aln sparse_ci
-
--
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-
- WATCHERS = todorov
-Index: b/c++/src/objtools/readers/Makefile.xobjread.lib
-===================================================================
---- a/c++/src/objtools/readers/Makefile.xobjread.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib 2011-08-27 22:05:51.000000000 -0400
-@@ -12,5 +12,5 @@
- wiggle_data wiggle_reader gff3_sofa gff3_reader gtf_reader \
- gff2_data gff2_reader source_mod_parser
-
--DLL_LIB = creaders
-+DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi
-
-Index: b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-===================================================================
---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib 2011-08-27 22:04:25.000000000 -0400
-@@ -11,6 +11,6 @@
- mask_writer_blastdb_maskinfo
-
- ASN_DEP = seqset
--DLL_LIB = seqdb blastdb
-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
-
- WATCHERS = morgulis camacho
-Index: b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-===================================================================
---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib 2011-08-27 21:40:31.000000000 -0400
-@@ -7,6 +7,8 @@
-
- ASN_DEP = seqset
-
-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
-+
- LIB = xobjsimple
- SRC = simple_om
-
-Index: b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-===================================================================
---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib 2011-08-27 22:08:11.000000000 -0400
-@@ -25,6 +25,8 @@
-
- LIB = seqdb
-
-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib 2011-08-27 21:50:24.000000000 -0400
-@@ -5,4 +5,6 @@
-
- ASN_DEP = blastdb seqset
-
-+DLL_LIB = seqdb xobjmgr seqset seq xncbi
-+
- WATCHERS = camacho
-Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib 2011-08-27 21:50:02.000000000 -0400
-@@ -3,6 +3,8 @@
- LIB = ncbi_xloader_blastdb_rmt
- SRC = bdbloader_rmt remote_blastdb_adapter
-
-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
-+
- ASN_DEP = blastdb xnetblast
-
- WATCHERS = camacho
-Index: b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-===================================================================
---- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -4,3 +4,5 @@
-
- LIB = gene_info
- SRC = gene_info gene_info_reader file_utils
-+
-+DLL_LIB = xncbi
-Index: b/c++/src/algo/blast/api/Makefile.xblast.lib
-===================================================================
---- a/c++/src/algo/blast/api/Makefile.xblast.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib 2011-08-27 22:01:29.000000000 -0400
-@@ -69,11 +69,14 @@
- winmask_filter \
- subj_ranges_set
-
--SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
-+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
-
- LIB = xblast
-
--DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgoblastdbindex blast composition_adjustment xalgowinmask \
-+ xalgodustmask seqdb xobjread xobjutil xobjmgr \
-+ xnetblastcli xnetblast scoremat seqset seq general \
-+ xser xconnect sequtil tables xutil xncbi
-
- CFLAGS = $(FAST_CFLAGS)
- # Strict gcc flags
-Index: b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-===================================================================
---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib 2011-08-27 21:48:16.000000000 -0400
-@@ -20,7 +20,9 @@
-
- LIB = blastinput
-
--DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \
-+ ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader seqdb xobjread \
-+ xobjmgr scoremat seqset seq xser xutil xncbi
-
- # should be redundant, given the above :-/
- ASN_DEP = seqset xnetblast
-Index: b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-===================================================================
---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib 2011-08-27 22:03:50.000000000 -0400
-@@ -8,6 +8,8 @@
-
- SRC = symdust
-
-+DLL_LIB = xobjmgr seq xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-Index: b/c++/src/connect/Makefile.xconnect.lib
-===================================================================
---- a/c++/src/connect/Makefile.xconnect.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/connect/Makefile.xconnect.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -14,6 +14,8 @@
- LIB = xconnect
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
-+
- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
-
- WATCHERS = lavr
-Index: b/c++/src/connect/ext/Makefile.xconnext.lib
-===================================================================
---- a/c++/src/connect/ext/Makefile.xconnext.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/connect/ext/Makefile.xconnext.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -6,4 +6,6 @@
-
- LIB = xconnext
-
-+DLL_LIB = xconnect xncbi
-+
- WATCHERS = lavr
-Index: b/c++/src/objects/blast/Makefile.blast.lib
-===================================================================
---- a/c++/src/objects/blast/Makefile.blast.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/blast/Makefile.blast.lib 2011-08-27 22:02:07.000000000 -0400
-@@ -1,4 +1,6 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
-
-+DLL_LIB = scoremat seqset seq xser xncbi
-+
- WATCHERS = camacho
-Index: b/c++/src/objects/blastxml/Makefile.blastxml.lib
-===================================================================
---- a/c++/src/objects/blastxml/Makefile.blastxml.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib 2011-08-27 21:44:06.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = blastxml
- SRC = blastxml__ blastxml___
-+
-+DLL_LIB = xser xncbi
-Index: b/c++/src/objects/entrez2/Makefile.entrez2.lib
-===================================================================
---- a/c++/src/objects/entrez2/Makefile.entrez2.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/entrez2/Makefile.entrez2.lib 2011-08-27 21:44:25.000000000 -0400
-@@ -2,3 +2,5 @@
-
- LIB = entrez2
- SRC = entrez2__ entrez2___
-+
-+DLL_LIB = xser xncbi
-Index: b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-===================================================================
---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -4,3 +4,5 @@
-
- LIB = entrez2cli
- SRC = entrez2_client entrez2_client_
-+
-+DLL_LIB = entrez2 xser xconnect xutil xncbi
-Index: b/c++/src/objects/scoremat/Makefile.scoremat.lib
-===================================================================
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib 2011-08-27 22:10:12.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-+
-+DLL_LIB = seqset seq general xser xncbi
-Index: b/c++/src/objects/seqedit/Makefile.seqedit.lib
-===================================================================
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib 2011-08-27 22:10:26.000000000 -0400
-@@ -1,3 +1,4 @@
- LIB = seqedit
- SRC = seqedit__ seqedit___
--
-+
-+DLL_LIB = seqset seq general xser xncbi
-Index: b/c++/src/objects/submit/Makefile.submit.lib
-===================================================================
---- a/c++/src/objects/submit/Makefile.submit.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/submit/Makefile.submit.lib 2011-08-27 22:10:36.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = submit
- SRC = submit__ submit___
-+
-+DLL_LIB = seqset seq biblio general xser xncbi
-Index: b/c++/src/objmgr/util/Makefile.util.lib
-===================================================================
---- a/c++/src/objmgr/util/Makefile.util.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objmgr/util/Makefile.util.lib 2011-08-27 22:05:46.000000000 -0400
-@@ -8,5 +8,7 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
- LIB = xobjutil
-
-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = ucko vasilche
-
-Index: b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-===================================================================
---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib 2011-08-27 22:06:49.000000000 -0400
-@@ -11,6 +11,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS)
-
-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
-
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
-Index: b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-===================================================================
---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -8,6 +8,8 @@
-
- LIB = blast_services
-
-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2011-08-27 21:54:20.000000000 -0400
-@@ -12,4 +12,7 @@
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
-+ xobjmgr seq xutil xncbi
-+
- WATCHERS = vasilche
-Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib 2011-08-27 21:58:18.000000000 -0400
-@@ -14,4 +14,7 @@
- # Dependencies for shared library
- DLL_LIB =
-
-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
-+ xser xconnect xcompress xutil xncbi
-+
- WATCHERS = vasilche
-Index: b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib 2011-08-27 21:56:19.000000000 -0400
-@@ -12,6 +12,8 @@
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
-Index: b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2011-08-27 21:57:00.000000000 -0400
-@@ -12,6 +12,8 @@
- # Dependencies for shared library
- DLL_LIB = xconnect ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
-Index: b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-===================================================================
---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib 2011-08-27 21:55:08.000000000 -0400
-@@ -12,6 +12,9 @@
- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
-
- # Dependencies for shared library (disabled due to problems on Darwin)
--# DLL_LIB = xconnect ncbi_xreader$(DLL)
-+DLL_LIB = xconnect ncbi_xreader$(DLL)
-+
-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
-+
-
- WATCHERS = vasilche
-Index: b/c++/src/util/compress/api/Makefile.compress.lib
-===================================================================
---- a/c++/src/util/compress/api/Makefile.compress.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/util/compress/api/Makefile.compress.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -6,7 +6,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
-+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
- LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS)
-
- WATCHERS = ivanov
-Index: b/c++/src/util/sequtil/Makefile.sequtil.lib
-===================================================================
---- a/c++/src/util/sequtil/Makefile.sequtil.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -3,4 +3,6 @@
- LIB = sequtil
- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
-
-+DLL_LIB = xncbi
-+
- WATCHERS = shomrat
-Index: b/c++/src/corelib/Makefile.test_boost.lib
-===================================================================
---- a/c++/src/corelib/Makefile.test_boost.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/corelib/Makefile.test_boost.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -3,6 +3,8 @@
- SRC = test_boost
- LIB = test_boost
-
-+DLL_LIB = xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
-
- REQUIRES = Boost.Test.Included
-Index: b/c++/src/corelib/Makefile.test_mt.lib
-===================================================================
---- a/c++/src/corelib/Makefile.test_mt.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/corelib/Makefile.test_mt.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -3,6 +3,8 @@
- SRC = test_mt
- LIB = test_mt
-
-+DLL_LIB = xncbi
-+
- # REQUIRES = MT
-
- USE_PCH = no
-Index: b/c++/src/objects/biblio/Makefile.biblio.lib
-===================================================================
---- a/c++/src/objects/biblio/Makefile.biblio.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib 2011-08-27 22:13:52.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = biblio
- SRC = biblio__ biblio___ label_util
-+
-+DLL_LIB = general xser xncbi
-Index: b/c++/src/objects/blastdb/Makefile.blastdb.lib
-===================================================================
---- a/c++/src/objects/blastdb/Makefile.blastdb.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib 2011-08-27 22:11:45.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = blastdb
- SRC = blastdb__ blastdb___
-+
-+DLL_LIB = seq xser xncbi
-Index: b/c++/src/objects/general/Makefile.general.lib
-===================================================================
---- a/c++/src/objects/general/Makefile.general.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/general/Makefile.general.lib 2011-08-27 22:14:06.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = general
- SRC = general__ general___ uoconv
-+
-+DLL_LIB = xser xncbi
-Index: b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-===================================================================
---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib 2011-08-27 22:11:30.000000000 -0400
-@@ -3,4 +3,6 @@
- LIB = genome_collection
- SRC = genome_collection__ genome_collection___
-
-+DLL_LIB = seq general xser xncbi
-+
- WATCHERS = dicuccio
-Index: b/c++/src/objects/id1/Makefile.id1.lib
-===================================================================
---- a/c++/src/objects/id1/Makefile.id1.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/id1/Makefile.id1.lib 2011-08-27 21:59:44.000000000 -0400
-@@ -3,4 +3,6 @@
- LIB = id1
- SRC = id1__ id1___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-Index: b/c++/src/objects/id2/Makefile.id2.lib
-===================================================================
---- a/c++/src/objects/id2/Makefile.id2.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/id2/Makefile.id2.lib 2011-08-27 21:59:51.000000000 -0400
-@@ -1,4 +1,6 @@
- LIB = id2
- SRC = id2__ id2___
-
-+DLL_LIB = seqsplit seq xser xncbi
-+
- WATCHERS = vasilche
-Index: b/c++/src/objects/medline/Makefile.medline.lib
-===================================================================
---- a/c++/src/objects/medline/Makefile.medline.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/medline/Makefile.medline.lib 2011-08-27 22:13:36.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = medline
- SRC = medline__ medline___
-+
-+DLL_LIB = biblio general xser xncbi
-Index: b/c++/src/objects/pub/Makefile.pub.lib
-===================================================================
---- a/c++/src/objects/pub/Makefile.pub.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/pub/Makefile.pub.lib 2011-08-27 22:12:30.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = pub
- SRC = pub__ pub___
-+
-+DLL_LIB = medline biblio xser xncbi
-Index: b/c++/src/objects/seq/Makefile.seq.lib
-===================================================================
---- a/c++/src/objects/seq/Makefile.seq.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/seq/Makefile.seq.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -11,4 +11,6 @@
- seq_id_tree seq_id_handle seq_id_mapper \
- seq_loc_mapper_base seq_align_mapper_base seqlocinfo
-
-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = vasilche grichenk
-Index: b/c++/src/objects/seqcode/Makefile.seqcode.lib
-===================================================================
---- a/c++/src/objects/seqcode/Makefile.seqcode.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib 2011-08-27 22:13:01.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = seqcode
- SRC = seqcode__ seqcode___
-+
-+DLL_LIB = xser xncbi
-Index: b/c++/src/objects/seqset/Makefile.seqset.lib
-===================================================================
---- a/c++/src/objects/seqset/Makefile.seqset.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib 2011-08-27 22:11:14.000000000 -0400
-@@ -1,2 +1,4 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-+
-+DLL_LIB = seq general xser xncbi
-Index: b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-===================================================================
---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib 2011-08-27 22:10:19.000000000 -0400
-@@ -1,4 +1,6 @@
- LIB = seqsplit
- SRC = seqsplit__ seqsplit___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-Index: b/c++/src/serial/Makefile.serial.lib
-===================================================================
---- a/c++/src/serial/Makefile.serial.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/serial/Makefile.serial.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -18,4 +18,6 @@
-
- LIB = xser
-
-+DLL_LIB = xutil xncbi
-+
- WATCHERS = gouriano
-Index: b/c++/src/util/Makefile.util.lib
-===================================================================
---- a/c++/src/util/Makefile.util.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/util/Makefile.util.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -11,6 +11,7 @@
- LIB = xutil
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
- LIBS = $(ORIG_LIBS)
-
- WATCHERS = vakatov
-Index: b/c++/src/util/xregexp/Makefile.xregexp.lib
-===================================================================
---- a/c++/src/util/xregexp/Makefile.xregexp.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib 2011-08-27 21:03:03.000000000 -0400
-@@ -6,7 +6,7 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
-
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS = $(PCRE_LIBS)
-
- WATCHERS = ivanov
-Index: b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-===================================================================
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib 2011-08-27 21:38:35.000000000 -0400
-@@ -8,6 +8,8 @@
-
- SRC = segmask
-
-+DLL_LIB = blast xobjmgr xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-Index: b/c++/src/objmgr/split/Makefile.id2_split.lib
-===================================================================
---- a/c++/src/objmgr/split/Makefile.id2_split.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib 2011-08-27 21:36:26.000000000 -0400
-@@ -17,6 +17,6 @@
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(SOBJMGR_LIBS)
-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
-
- WATCHERS = vasilche
-Index: b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-===================================================================
---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib 2011-08-27 21:03:01.000000000 -0400
-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib 2011-08-27 21:39:32.000000000 -0400
-@@ -8,6 +8,9 @@
-
- LIB = writedb
-
-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
-+ xser sequtil xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-Index: b/c++/src/algo/blast/Makefile.blast_macros.mk
-===================================================================
---- a/c++/src/algo/blast/Makefile.blast_macros.mk 2011-08-27 21:03:02.000000000 -0400
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk 2011-08-27 21:03:03.000000000 -0400
-@@ -15,7 +15,7 @@
- $(BLAST_DB_DATA_LOADER_LIBS) $(BLAST_FORMATTER_MINIMAL_LIBS)
-
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
- xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- xobjread creaders xnetblastcli xnetblast blastdb scoremat tables
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
Copied: trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/fix_lib_deps (from rev 7582, trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/fix_lib_deps (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/fix_lib_deps 2011-08-29 17:21:20 UTC (rev 7584)
@@ -0,0 +1,754 @@
+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 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 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)
+
++DLL_LIB = composition_adjustment xconnect tables
+
+ WATCHERS = blastsoft
+Index: b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+===================================================================
+--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib 2010-03-18 14:56:34.000000000 -0400
++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -11,6 +11,8 @@
+ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
++DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
++
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
+Index: b/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib
+===================================================================
+--- a/c++/src/algo/blast/dbindex_search/Makefile.xalgoblastdbindex_search.lib 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)
+
++DLL_LIB = xobjmgr xncbi
++
+ ASN_DEP = seqset
+
+ WATCHERS = morgulis
+Index: b/c++/src/algo/blast/format/Makefile.xblastformat.lib
+===================================================================
+--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib 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)
+
+-DLL_LIB = blastxml xhtml xcgi
++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
++ seq general xser tables xncbi
+
+ WATCHERS = blastsoft
+Index: b/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib
+===================================================================
+--- a/c++/src/algo/blast/gumbel_params/Makefile.gumbelparams.lib 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
+
++DLL_LIB = tables xutil xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+Index: b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+===================================================================
+--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib 2011-02-10 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)
+
++DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
+Index: b/c++/src/cgi/Makefile.cgi.lib
+===================================================================
+--- a/c++/src/cgi/Makefile.cgi.lib 2010-02-26 12:16:17.000000000 -0500
++++ b/c++/src/cgi/Makefile.cgi.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -8,6 +8,8 @@
+ cgi_serial cgi_session cgi_exception cgiapp_cached cgi_entry_reader
+ LIB = xcgi
+
++DLL_LIB = xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+
+ WATCHERS = vakatov
+Index: b/c++/src/html/Makefile.html.lib
+===================================================================
+--- a/c++/src/html/Makefile.html.lib 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
+
++DLL_LIB = xncbi
++
+ WATCHERS = ivanov
+Index: b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+===================================================================
+--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib 2004-02-25 12:11:43.000000000 -0500
++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -2,3 +2,5 @@
+
+ LIB = xnetblastcli
+ SRC = blastclient blastclient_
++
++DLL_LIB = xnetblast xser xconnect xutil xncbi
+Index: b/c++/src/objtools/align_format/Makefile.align_format.lib
+===================================================================
+--- a/c++/src/objtools/align_format/Makefile.align_format.lib 2010-08-03 09:56:32.000000000 -0400
++++ b/c++/src/objtools/align_format/Makefile.align_format.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -10,6 +10,10 @@
+
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+
++DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
++ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
++ xcgi xhtml tables xncbi
++
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
+ # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
+ # CFLAGS = $(FAST_CFLAGS)
+Index: b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+===================================================================
+--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib 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
+
+-
++DLL_LIB = xobjmgr seqset seq xser tables xncbi
+
+ WATCHERS = todorov
+Index: b/c++/src/objtools/readers/Makefile.xobjread.lib
+===================================================================
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib 2011-02-02 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
+
+-DLL_LIB = creaders
++DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi
+
+Index: b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+===================================================================
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib 2010-08-06 12:57:00.000000000 -0400
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -11,6 +11,6 @@
+ mask_writer_blastdb_maskinfo
+
+ ASN_DEP = seqset
+-DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
+
+ WATCHERS = morgulis camacho
+Index: b/c++/src/objtools/simple/Makefile.xobjsimple.lib
+===================================================================
+--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib 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
+
++DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
++
+ LIB = xobjsimple
+ SRC = simple_om
+
+Index: b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+===================================================================
+--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib 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
+
++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib 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
+
++DLL_LIB = seqdb xobjmgr seqset seq xncbi
++
+ WATCHERS = camacho
+Index: b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib 2010-06-16 12:03:59.000000000 -0400
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -3,6 +3,8 @@
+ LIB = ncbi_xloader_blastdb_rmt
+ SRC = bdbloader_rmt remote_blastdb_adapter
+
++DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
++
+ ASN_DEP = blastdb xnetblast
+
+ WATCHERS = camacho
+Index: b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+===================================================================
+--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib 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
+ SRC = gene_info gene_info_reader file_utils
++
++DLL_LIB = xncbi
+Index: b/c++/src/algo/blast/api/Makefile.xblast.lib
+===================================================================
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib 2010-03-18 14:56:34.000000000 -0400
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -69,11 +69,14 @@
+ winmask_filter \
+ subj_ranges_set
+
+-SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
++SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
+
+ LIB = xblast
+
+-DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
++DLL_LIB = xalgoblastdbindex blast composition_adjustment xalgowinmask \
++ xalgodustmask seqdb xobjread xobjutil xobjmgr \
++ xnetblastcli xnetblast scoremat seqset seq general \
++ xser xconnect sequtil tables xutil xncbi
+
+ CFLAGS = $(FAST_CFLAGS)
+ # Strict gcc flags
+Index: b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+===================================================================
+--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib 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
+
+-DLL_LIB = xblast $(OBJMGR_LIBS)
++DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \
++ ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader seqdb xobjread \
++ xobjmgr scoremat seqset seq xser xutil xncbi
+
+ # should be redundant, given the above :-/
+ ASN_DEP = seqset xnetblast
+Index: b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+===================================================================
+--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib 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
+
++DLL_LIB = xobjmgr seq xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+Index: b/c++/src/connect/Makefile.xconnect.lib
+===================================================================
+--- a/c++/src/connect/Makefile.xconnect.lib 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
+
++DLL_LIB = xncbi
++
+ LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
+
+ WATCHERS = lavr
+Index: b/c++/src/connect/ext/Makefile.xconnext.lib
+===================================================================
+--- a/c++/src/connect/ext/Makefile.xconnext.lib 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
+
++DLL_LIB = xconnect xncbi
++
+ WATCHERS = lavr
+Index: b/c++/src/objects/blast/Makefile.blast.lib
+===================================================================
+--- a/c++/src/objects/blast/Makefile.blast.lib 2010-05-12 15:03:57.000000000 -0400
++++ b/c++/src/objects/blast/Makefile.blast.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,4 +1,6 @@
+ LIB = xnetblast
+ SRC = blast__ blast___ names
+
++DLL_LIB = scoremat seqset seq xser xncbi
++
+ WATCHERS = camacho
+Index: b/c++/src/objects/blastxml/Makefile.blastxml.lib
+===================================================================
+--- a/c++/src/objects/blastxml/Makefile.blastxml.lib 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___
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/entrez2/Makefile.entrez2.lib
+===================================================================
+--- a/c++/src/objects/entrez2/Makefile.entrez2.lib 2010-10-15 14:36:49.000000000 -0400
++++ b/c++/src/objects/entrez2/Makefile.entrez2.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -2,3 +2,5 @@
+
+ LIB = entrez2
+ SRC = entrez2__ entrez2___
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+===================================================================
+--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib 2010-10-15 14:36:49.000000000 -0400
++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -4,3 +4,5 @@
+
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
++
++DLL_LIB = entrez2 xser xconnect xutil xncbi
+Index: b/c++/src/objects/scoremat/Makefile.scoremat.lib
+===================================================================
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib 2003-06-05 16:20:42.000000000 -0400
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
++
++DLL_LIB = seqset seq general xser xncbi
+Index: b/c++/src/objects/seqedit/Makefile.seqedit.lib
+===================================================================
+--- a/c++/src/objects/seqedit/Makefile.seqedit.lib 2006-01-25 12:11:00.000000000 -0500
++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,3 +1,4 @@
+ LIB = seqedit
+ SRC = seqedit__ seqedit___
+-
++
++DLL_LIB = seqset seq general xser xncbi
+Index: b/c++/src/objects/submit/Makefile.submit.lib
+===================================================================
+--- a/c++/src/objects/submit/Makefile.submit.lib 2003-06-05 16:21:46.000000000 -0400
++++ b/c++/src/objects/submit/Makefile.submit.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = submit
+ SRC = submit__ submit___
++
++DLL_LIB = seqset seq biblio general xser xncbi
+Index: b/c++/src/objmgr/util/Makefile.util.lib
+===================================================================
+--- a/c++/src/objmgr/util/Makefile.util.lib 2010-02-26 11:33:57.000000000 -0500
++++ b/c++/src/objmgr/util/Makefile.util.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -8,5 +8,7 @@
+ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
+ LIB = xobjutil
+
++DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = ucko vasilche
+
+Index: b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+===================================================================
+--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib 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)
+
++DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
+
+ ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
+ # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
+Index: b/c++/src/objtools/blast/services/Makefile.blast_services.lib
+===================================================================
+--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib 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
+
++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2010-05-04 11:42:43.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -12,4 +12,7 @@
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++ xobjmgr seq xutil xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib 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 =
+
++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
++ xser xconnect xcompress xutil xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib 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)
+
++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2010-05-04 11:42:43.000000000 -0400
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -12,6 +12,8 @@
+ # Dependencies for shared library
+ DLL_LIB = xconnect ncbi_xreader$(DLL)
+
++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+===================================================================
+--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib 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) $(Z_INCLUDE)
+
+ # Dependencies for shared library (disabled due to problems on Darwin)
+-# DLL_LIB = xconnect ncbi_xreader$(DLL)
++DLL_LIB = xconnect ncbi_xreader$(DLL)
++
++DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
++
+
+ WATCHERS = vasilche
+Index: b/c++/src/util/compress/api/Makefile.compress.lib
+===================================================================
+--- a/c++/src/util/compress/api/Makefile.compress.lib 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)
+
+-DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
++DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
+ LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS)
+
+ WATCHERS = ivanov
+Index: b/c++/src/util/sequtil/Makefile.sequtil.lib
+===================================================================
+--- a/c++/src/util/sequtil/Makefile.sequtil.lib 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
+
++DLL_LIB = xncbi
++
+ WATCHERS = shomrat
+Index: b/c++/src/corelib/Makefile.test_boost.lib
+===================================================================
+--- a/c++/src/corelib/Makefile.test_boost.lib 2010-02-26 12:16:17.000000000 -0500
++++ b/c++/src/corelib/Makefile.test_boost.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -3,6 +3,8 @@
+ SRC = test_boost
+ LIB = test_boost
+
++DLL_LIB = xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
+
+ REQUIRES = Boost.Test.Included
+Index: b/c++/src/corelib/Makefile.test_mt.lib
+===================================================================
+--- a/c++/src/corelib/Makefile.test_mt.lib 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
+
++DLL_LIB = xncbi
++
+ # REQUIRES = MT
+
+ USE_PCH = no
+Index: b/c++/src/objects/biblio/Makefile.biblio.lib
+===================================================================
+--- a/c++/src/objects/biblio/Makefile.biblio.lib 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
++
++DLL_LIB = general xser xncbi
+Index: b/c++/src/objects/blastdb/Makefile.blastdb.lib
+===================================================================
+--- a/c++/src/objects/blastdb/Makefile.blastdb.lib 2003-08-06 12:13:02.000000000 -0400
++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = blastdb
+ SRC = blastdb__ blastdb___
++
++DLL_LIB = seq xser xncbi
+Index: b/c++/src/objects/general/Makefile.general.lib
+===================================================================
+--- a/c++/src/objects/general/Makefile.general.lib 2006-03-14 16:14:34.000000000 -0500
++++ b/c++/src/objects/general/Makefile.general.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = general
+ SRC = general__ general___ uoconv
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+===================================================================
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib 2010-08-20 12:43:35.000000000 -0400
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -3,4 +3,6 @@
+ LIB = genome_collection
+ SRC = genome_collection__ genome_collection___
+
++DLL_LIB = seq general xser xncbi
++
+ WATCHERS = dicuccio
+Index: b/c++/src/objects/id1/Makefile.id1.lib
+===================================================================
+--- a/c++/src/objects/id1/Makefile.id1.lib 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___
+
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objects/id2/Makefile.id2.lib
+===================================================================
+--- a/c++/src/objects/id2/Makefile.id2.lib 2010-05-04 11:42:43.000000000 -0400
++++ b/c++/src/objects/id2/Makefile.id2.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,4 +1,6 @@
+ LIB = id2
+ SRC = id2__ id2___
+
++DLL_LIB = seqsplit seq xser xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/objects/medline/Makefile.medline.lib
+===================================================================
+--- a/c++/src/objects/medline/Makefile.medline.lib 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___
++
++DLL_LIB = biblio general xser xncbi
+Index: b/c++/src/objects/pub/Makefile.pub.lib
+===================================================================
+--- a/c++/src/objects/pub/Makefile.pub.lib 2003-06-05 16:21:46.000000000 -0400
++++ b/c++/src/objects/pub/Makefile.pub.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = pub
+ SRC = pub__ pub___
++
++DLL_LIB = medline biblio xser xncbi
+Index: b/c++/src/objects/seq/Makefile.seq.lib
+===================================================================
+--- a/c++/src/objects/seq/Makefile.seq.lib 2010-08-05 12:25:14.000000000 -0400
++++ b/c++/src/objects/seq/Makefile.seq.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -11,4 +11,6 @@
+ seq_id_tree seq_id_handle seq_id_mapper \
+ seq_loc_mapper_base seq_align_mapper_base seqlocinfo
+
++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = vasilche grichenk
+Index: b/c++/src/objects/seqcode/Makefile.seqcode.lib
+===================================================================
+--- a/c++/src/objects/seqcode/Makefile.seqcode.lib 2003-06-05 16:21:46.000000000 -0400
++++ b/c++/src/objects/seqcode/Makefile.seqcode.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = seqcode
+ SRC = seqcode__ seqcode___
++
++DLL_LIB = xser xncbi
+Index: b/c++/src/objects/seqset/Makefile.seqset.lib
+===================================================================
+--- a/c++/src/objects/seqset/Makefile.seqset.lib 2004-05-19 10:49:26.000000000 -0400
++++ b/c++/src/objects/seqset/Makefile.seqset.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,2 +1,4 @@
+ LIB = seqset
+ SRC = seqset__ seqset___ gb_release_file
++
++DLL_LIB = seq general xser xncbi
+Index: b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+===================================================================
+--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib 2010-05-04 11:42:43.000000000 -0400
++++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -1,4 +1,6 @@
+ LIB = seqsplit
+ SRC = seqsplit__ seqsplit___
+
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+Index: b/c++/src/serial/Makefile.serial.lib
+===================================================================
+--- a/c++/src/serial/Makefile.serial.lib 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
+
++DLL_LIB = xutil xncbi
++
+ WATCHERS = gouriano
+Index: b/c++/src/util/Makefile.util.lib
+===================================================================
+--- a/c++/src/util/Makefile.util.lib 2010-02-26 11:33:57.000000000 -0500
++++ b/c++/src/util/Makefile.util.lib 2011-08-29 12:15:27.000000000 -0400
+@@ -11,6 +11,7 @@
+ LIB = xutil
+ PROJ_TAG = core
+
++DLL_LIB = xncbi
+ LIBS = $(ORIG_LIBS)
+
+ WATCHERS = vakatov
+Index: b/c++/src/util/xregexp/Makefile.xregexp.lib
+===================================================================
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib 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)
+
+-DLL_LIB = $(PCRE_LIB)
++DLL_LIB = $(PCRE_LIB) xncbi
+ LIBS = $(PCRE_LIBS)
+
+ WATCHERS = ivanov
+Index: b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+===================================================================
+--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib 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
+
++DLL_LIB = blast xobjmgr xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+
+Index: b/c++/src/objmgr/split/Makefile.id2_split.lib
+===================================================================
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib 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)
+
+-DLL_LIB = $(SOBJMGR_LIBS)
++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
+
+ WATCHERS = vasilche
+Index: b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+===================================================================
+--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib 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
+
++DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
++ xser sequtil xutil xncbi
++
+ CFLAGS = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+Index: b/c++/src/algo/blast/Makefile.blast_macros.mk
+===================================================================
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk 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)
+
+ # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
+-BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
++BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
+ xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
+ xobjread creaders xnetblastcli xnetblast blastdb scoremat tables
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
+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)
Deleted: trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes 2011-08-29 13:23:07 UTC (rev 7579)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/hurd_fixes 2011-08-29 17:21:20 UTC (rev 7584)
@@ -1,61 +0,0 @@
-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/connect/ncbi_socket_cxx.cpp, src/connect/ext/ncbi_localnet.c:
- cope with missing PATH_MAX everywhere, not just under Windows.
-
-Author: Aaron M. Ucko <ucko at 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
-@@ -11416,7 +11416,7 @@
- #ifdef HAVE_UNISTD_H
- # include <unistd.h>
- #endif
-- RETSIGTYPE handler(int sig) { }
-+ RETSIGTYPE handler(int sig) { alarm(0); }
- int
- main ()
- {
-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
-@@ -2811,7 +2811,7 @@
- #ifdef HAVE_UNISTD_H
- # include <unistd.h>
- #endif
-- RETSIGTYPE handler(int sig) { }]],
-+ RETSIGTYPE handler(int sig) { alarm(0); }]],
- [[struct timeval timeout = { 5, 0 };
- signal(SIGALRM, &handler);
- 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
-@@ -34,7 +34,7 @@
- #include <ncbi_pch.hpp>
- #include <connect/ncbi_socket_unix.hpp>
- #include <limits.h> // for PATH_MAX
--#if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
-+#ifndef PATH_MAX
- # define PATH_MAX 512 // will actually use less than 32 chars
- #endif
-
-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
-@@ -64,6 +64,8 @@
-
- #if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
- # define PATH_MAX _MAX_PATH
-+#elif !defined(PATH_MAX)
-+# define PATH_MAX 4096
- #endif /*NCBI_OS_MSWIN && !PATH_MAX*/
-
- #if PATH_MAX < 256
Copied: trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/hurd_fixes (from rev 7582, trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/hurd_fixes (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.25-5/debian/patches/hurd_fixes 2011-08-29 17:21:20 UTC (rev 7584)
@@ -0,0 +1,81 @@
+Subject: fix portability issues that led to Hurd build failures
+
+* 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.
+
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-06-10
+Index: b/c++/src/build-system/configure
+===================================================================
+--- 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>
+ #endif
+- RETSIGTYPE handler(int sig) { }
++ RETSIGTYPE handler(int sig) { alarm(0); }
+ int
+ main ()
+ {
+Index: b/c++/src/build-system/configure.ac
+===================================================================
+--- 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>
+ #endif
+- RETSIGTYPE handler(int sig) { }]],
++ RETSIGTYPE handler(int sig) { alarm(0); }]],
+ [[struct timeval timeout = { 5, 0 };
+ signal(SIGALRM, &handler);
+ alarm(1);
+Index: b/c++/src/connect/ncbi_socket_cxx.cpp
+===================================================================
+--- 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>
+ #include <limits.h> // for PATH_MAX
+-#if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
++#ifndef PATH_MAX
+ # define PATH_MAX 512 // will actually use less than 32 chars
+ #endif
+
+Index: b/c++/src/connect/ext/ncbi_localnet.c
+===================================================================
+--- 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)
+ # define PATH_MAX _MAX_PATH
++#elif !defined(PATH_MAX)
++# define PATH_MAX 4096
+ #endif /*NCBI_OS_MSWIN && !PATH_MAX*/
+
+ #if PATH_MAX < 256
More information about the debian-med-commit
mailing list