[med-svn] r9986 - in trunk/packages/ncbi-blast+/tags: . 2.2.26-2/debian 2.2.26-2/debian/patches

Olivier Sallou osallou at alioth.debian.org
Tue Mar 13 09:55:40 UTC 2012


Author: osallou
Date: 2012-03-13 09:55:40 +0000 (Tue, 13 Mar 2012)
New Revision: 9986

Added:
   trunk/packages/ncbi-blast+/tags/2.2.26-2/
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/changelog
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/control
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/copyright
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_checks
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_lib_deps
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/hurd_fixes
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/no_multiarch_rpath
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/series
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/wrong_path_to_touch.patch
Removed:
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/changelog
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/control
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/copyright
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_checks
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_lib_deps
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/hurd_fixes
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/no_multiarch_rpath
   trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/series
Log:
[svn-buildpackage] Tagging ncbi-blast+ 2.2.26-2

Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/changelog	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,101 +0,0 @@
-ncbi-blast+ (2.2.25-8) UNRELEASED; urgency=low
-
-  * debian/copyright: Added Upstream-Contact
-
- -- Andreas Tille <tille at debian.org>  Thu, 22 Dec 2011 17:41:16 +0100
-
-ncbi-blast+ (2.2.25-7) unstable; urgency=low
-
-  * Do not output everything to STDERR in
-    c++/src/app/blast/update_blastdb.pl
-    Closes: #644237
-  * debian/control: Depends s/${python:Depends}/python/ because
-    the python dependency of /usr/bin/windowmasker_2.2.22_adapter
-    is not detected obviosely
-  * debian/copyright: Indentation fixes to get DEP5 compatibility
-
- -- Andreas Tille <tille at debian.org>  Wed, 21 Dec 2011 15:47:04 +0100
-
-ncbi-blast+ (2.2.25-6) unstable; urgency=low
-
-   * debian/control:
-     Luca Capello <luca at pca.it>, fix reference for legacy_blast (Closes: #642986).
-     + add a new line to separate the actual description from usage
-      instruction in the long Description:.
-   * debian/rules: add gene_info_reader binary in package
-
- -- Olivier Sallou <olivier.sallou at irisa.fr>  Fri, 30 Sep 2011 12:31:05 -0400
-
-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

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/changelog (from rev 9985, trunk/packages/ncbi-blast+/trunk/debian/changelog)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/changelog	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/changelog	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,113 @@
+ncbi-blast+ (2.2.26-2) unstable; urgency=low
+
+  * debian/patches/wrong_path_to_touch.patch :Fix upstream FTBFS on the Hurd
+    hardcodes wrong path to touch (Closes: #663244)
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 07 Mar 2012 17:29:23 +0100
+
+ncbi-blast+ (2.2.26-1) unstable; urgency=low
+
+  [ Olivier Sallou ]
+  * New upstream release 
+  * Remove some patches, applied upstream
+
+  [ Andreas Tille]
+  * debian/copyright: Added Upstream-Contact
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 07 Mar 2012 09:37:10 +0100
+
+ncbi-blast+ (2.2.25-7) unstable; urgency=low
+
+  * Do not output everything to STDERR in
+    c++/src/app/blast/update_blastdb.pl
+    Closes: #644237
+  * debian/control: Depends s/${python:Depends}/python/ because
+    the python dependency of /usr/bin/windowmasker_2.2.22_adapter
+    is not detected obviosely
+  * debian/copyright: Indentation fixes to get DEP5 compatibility
+
+ -- Andreas Tille <tille at debian.org>  Wed, 21 Dec 2011 15:47:04 +0100
+
+ncbi-blast+ (2.2.25-6) unstable; urgency=low
+
+   * debian/control:
+     Luca Capello <luca at pca.it>, fix reference for legacy_blast (Closes: #642986).
+     + add a new line to separate the actual description from usage
+      instruction in the long Description:.
+   * debian/rules: add gene_info_reader binary in package
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr>  Fri, 30 Sep 2011 12:31:05 -0400
+
+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/2.2.26-2/debian/control
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/control	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/control	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,43 +0,0 @@
-Source: ncbi-blast+
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 7.0.50~), autotools-dev (>= 20100122), libbz2-dev, libpcre3-dev, zlib1g-dev, libboost-test-dev, quilt (>= 0.46-7~), time, libc0.3-dev (>= 2.13-9~) [hurd-i386]
-Standards-Version: 3.9.2
-Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>,
- Andreas Tille <tille at debian.org>
-DM-Upload-Allowed: yes
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast+/trunk/
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/
-
-Package: ncbi-blast+
-Architecture: any
-Enhances: t-coffee
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, python, ncbi-data
-Multi-Arch: foreign
-Description: next generation suite of BLAST sequence search tools
- The Basic Local Alignment Search Tool (BLAST) is the most widely
- used sequence similarity tool. There are versions of BLAST that 
- compare protein queries to protein databases, nucleotide queries 
- to nucleotide databases, as well as versions that translate nucleotide 
- queries or databases in all six frames and compare to protein databases 
- or queries.
- PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting 
- with a protein query, and then uses that PSSM to perform further searches.
- It is also possible to compare a protein or nucleotide query to a 
- database of PSSM’s.
- The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as
- a network service.
-
-Package: ncbi-blast+-legacy
-Architecture: all
-Depends: ncbi-blast+, ${misc:Depends}
-Multi-Arch: foreign
-Description: NCBI Blast legacy call script
- This package adds some fake scripts to call NCBI+ programs
- with the NCBI blast command line. It makes use of the
- legacy_blast script in ncbi-blast+ package.
- .
- To use those scripts, /usr/share/ncbi-blast+/bin must be added
- to the PATH.

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/control (from rev 9927, trunk/packages/ncbi-blast+/trunk/debian/control)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/control	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/control	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,43 @@
+Source: ncbi-blast+
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 7.0.50~), autotools-dev (>= 20100122), libbz2-dev, libpcre3-dev, zlib1g-dev, libboost-test-dev, quilt (>= 0.46-7~), time, libc0.3-dev (>= 2.13-9~) [hurd-i386]
+Standards-Version: 3.9.3
+Uploaders: Olivier Sallou <osallou at debian.org>,
+ Andreas Tille <tille at debian.org>
+DM-Upload-Allowed: yes
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ncbi-blast+/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast+/trunk/
+
+Package: ncbi-blast+
+Architecture: any
+Enhances: t-coffee
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, python, ncbi-data
+Multi-Arch: foreign
+Description: next generation suite of BLAST sequence search tools
+ The Basic Local Alignment Search Tool (BLAST) is the most widely
+ used sequence similarity tool. There are versions of BLAST that 
+ compare protein queries to protein databases, nucleotide queries 
+ to nucleotide databases, as well as versions that translate nucleotide 
+ queries or databases in all six frames and compare to protein databases 
+ or queries.
+ PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting 
+ with a protein query, and then uses that PSSM to perform further searches.
+ It is also possible to compare a protein or nucleotide query to a 
+ database of PSSM’s.
+ The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as
+ a network service.
+
+Package: ncbi-blast+-legacy
+Architecture: all
+Depends: ncbi-blast+, ${misc:Depends}
+Multi-Arch: foreign
+Description: NCBI Blast legacy call script
+ This package adds some fake scripts to call NCBI+ programs
+ with the NCBI blast command line. It makes use of the
+ legacy_blast script in ncbi-blast+ package.
+ .
+ To use those scripts, /usr/share/ncbi-blast+/bin must be added
+ to the PATH.

Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/copyright
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/copyright	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/copyright	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,196 +0,0 @@
-Format: http://dep.debian.net/deps/dep5
-Upstream-Name: ncbi-blast+
-Upstream-Contact: blastsoft at ncbi.nlm.nih.gov
-
-Files: c++/*/util/compress/zlib/*
-Copyright: 1995-2004 Jean-loup Gailly and Mark Adler
-License:
-  This software is provided 'as-is', without any express or implied
-  warranty.  In no event will the authors be held liable for any damages
-  arising from the use of this software.
- .
-  Permission is granted to anyone to use this software for any purpose,
-  including commercial applications, and to alter it and redistribute it
-  freely, subject to the following restrictions:
- .
-  1. The origin of this software must not be misrepresented; you must not
-     claim that you wrote the original software. If you use this software
-     in a product, an acknowledgment in the product documentation would be
-     appreciated but is not required.
-  2. Altered source versions must be plainly marked as such, and must not be
-     misrepresented as being the original software.
-  3. This notice may not be removed or altered from any source distribution.
-
-Files: c++/*/util/regexp/*
-Copyright: 1997-2009 University of Cambridge
-           2008-2009 Google Inc
-License: BSD
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
-   notice, this list of conditions and the following disclaimer.
- 2. The origin of this software must not be misrepresented; you must
-   not claim that you wrote the original software.  If you use this
-   software in a product, an acknowledgment in the product
-   documentation would be appreciated but is not required.
- 3. Altered source versions must be plainly marked as such, and must
-   not be misrepresented as being the original software.
- 4. The name of the author may not be used to endorse or promote
-   products derived from this software without specific prior written
-   permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
- OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
- DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-
-Files: c++/*/util/compress/bzip2/*
-Copyright: 1996-2002 Julian R Seward
-License: BSD
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
-   notice, this list of conditions and the following disclaimer.
- 2. The origin of this software must not be misrepresented; you must
-   not claim that you wrote the original software.  If you use this
-   software in a product, an acknowledgment in the product
-   documentation would be appreciated but is not required.
- 3. Altered source versions must be plainly marked as such, and must
-   not be misrepresented as being the original software.
- 4. The name of the author may not be used to endorse or promote
-   products derived from this software without specific prior written
-   permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
- OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
- DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
- GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
- WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Files: c++/src/build-system/config.*s* c++/src/util/regexp/missing
-Copyright: 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003 Free Software Foundation, Inc
-License: GPLv2
-
-Files: c++/src/build-system/ax_jni_include_dir.m4
-Copyright: 2008 Don Anderson <dda at sleepycat.com>
-License:
-   Copying and distribution of this file, with or without modification, are
-   permitted in any medium without royalty provided the copyright notice
-   and this notice are preserved. This file is offered as-is, without any
-   warranty.
-
-
-Files: c++/include/util/impl/floating_point_comparison.hpp
-Copyright: 2001-2008 Gennadiy Rozental
-License: Boost software license
- Permission is hereby granted, free of charge, to any person or organization
- obtaining a copy of the software and accompanying documentation covered by
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- execute, and transmit the Software, and to prepare derivative works of the
- Software, and to permit third-parties to whom the Software is furnished to
- do so, all subject to the following:
- .
- The copyright notices in the Software and this entire statement, including
- the above license grant, this restriction and the following disclaimer,
- must be included in all copies of the Software, in whole or in part, and
- all derivative works of the Software, unless such copies or derivative
- works are solely in the form of machine-executable object code generated by
- a source language processor.
- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
- SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
- FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
- ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- DEALINGS IN THE SOFTWARE.
-
-Files: c++/include/dbapi/driver/odbc/unix_odbc/sqlfront.h
-Copyright: 1998-1999  Brian Bruns
-License: GPLv2
-
-Files: c++/src/html/ncbi_menu_*.js
-Copyright: 1997-1999 Netscape Communications Corp.
-License: Netscape
- Netscape grants you a royalty free license to use or modify this
- software provided that this copyright notice appears on all copies.
- This software is provided "AS IS," without a warranty of any kind.
-
-
-Files: c++/include/util/bitset/*
-Copyright: 2002-2003 Anatoliy Kuznetsov
-License: MIT
- Permission is hereby granted, free of charge, to any person
- obtaining a copy of this software and associated documentation
- files (the "Software"), to deal in the Software without restriction,
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- and to permit persons to whom the Software is furnished to do so,
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- .
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
- DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
- ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- OTHER DEALINGS IN THE SOFTWARE.
-
-Files: c++/*
-Copyright: NCBI
-License: PD
-                                  PUBLIC DOMAIN NOTICE
-                     National Center for Biotechnology Information
- .
-        This software/database is a "United States Government Work" under the
-        terms of the United States Copyright Act.  It was written as part of
-        the author's official duties as a United States Government employee and
-        thus cannot be copyrighted.  This software/database is freely available
-        to the public for use. The National Library of Medicine and the U.S.
-        Government have not placed any restriction on its use or reproduction.
- .
-        Although all reasonable efforts have been taken to ensure the accuracy
-        and reliability of the software and data, the NLM and the U.S.
-        Government do not and cannot warrant the performance or results that
-        may be obtained by using this software or data. The NLM and the U.S.
-        Government disclaim all warranties, express or implied, including
-        warranties of performance, merchantability or fitness for any particular
-        purpose.
- .
-        Please cite the author in any work or product based on this material.
-
-Files: debian/*
-Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
-License: GPL-2+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/copyright (from rev 9927, trunk/packages/ncbi-blast+/trunk/debian/copyright)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/copyright	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/copyright	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,228 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ncbi-blast+
+Upstream-Contact: blastsoft at ncbi.nlm.nih.gov
+
+Files: c++/*/util/compress/zlib/*
+Copyright: 1995-2004 Jean-loup Gailly and Mark Adler
+License:
+  This software is provided 'as-is', without any express or implied
+  warranty.  In no event will the authors be held liable for any damages
+  arising from the use of this software.
+ .
+  Permission is granted to anyone to use this software for any purpose,
+  including commercial applications, and to alter it and redistribute it
+  freely, subject to the following restrictions:
+ .
+  1. The origin of this software must not be misrepresented; you must not
+     claim that you wrote the original software. If you use this software
+     in a product, an acknowledgment in the product documentation would be
+     appreciated but is not required.
+  2. Altered source versions must be plainly marked as such, and must not be
+     misrepresented as being the original software.
+  3. This notice may not be removed or altered from any source distribution.
+
+Files: c++/*/util/regexp/*
+Copyright: 1997-2009 University of Cambridge
+           2008-2009 Google Inc
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+ 2. The origin of this software must not be misrepresented; you must
+   not claim that you wrote the original software.  If you use this
+   software in a product, an acknowledgment in the product
+   documentation would be appreciated but is not required.
+ 3. Altered source versions must be plainly marked as such, and must
+   not be misrepresented as being the original software.
+ 4. The name of the author may not be used to endorse or promote
+   products derived from this software without specific prior written
+   permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+ OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+
+Files: c++/*/util/compress/bzip2/*
+Copyright: 1996-2002 Julian R Seward
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+ 2. The origin of this software must not be misrepresented; you must
+   not claim that you wrote the original software.  If you use this
+   software in a product, an acknowledgment in the product
+   documentation would be appreciated but is not required.
+ 3. Altered source versions must be plainly marked as such, and must
+   not be misrepresented as being the original software.
+ 4. The name of the author may not be used to endorse or promote
+   products derived from this software without specific prior written
+   permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+ OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+ DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+ GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: c++/src/build-system/config.*s* c++/src/util/regexp/missing
+Copyright: 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003 Free Software Foundation, Inc
+License: GPL-2
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+
+Files: c++/src/build-system/ax_jni_include_dir.m4
+Copyright: 2008 Don Anderson <dda at sleepycat.com>
+License:
+   Copying and distribution of this file, with or without modification, are
+   permitted in any medium without royalty provided the copyright notice
+   and this notice are preserved. This file is offered as-is, without any
+   warranty.
+
+
+Files: c++/include/util/impl/floating_point_comparison.hpp
+Copyright: 2001-2008 Gennadiy Rozental
+License: Boost software license
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
+Files: c++/include/dbapi/driver/odbc/unix_odbc/sqlfront.h
+Copyright: 1998-1999  Brian Bruns
+License: GPL-2
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+
+Files: c++/src/html/ncbi_menu_*.js
+Copyright: 1997-1999 Netscape Communications Corp.
+License: Netscape
+ Netscape grants you a royalty free license to use or modify this
+ software provided that this copyright notice appears on all copies.
+ This software is provided "AS IS," without a warranty of any kind.
+
+
+Files: c++/include/util/bitset/*
+Copyright: 2002-2003 Anatoliy Kuznetsov
+License: MIT
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without restriction,
+ including without limitation the rights to use, copy, modify, merge,
+ publish, distribute, sublicense, and/or sell copies of the Software,
+ and to permit persons to whom the Software is furnished to do so,
+ subject to the following conditions:
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+Files: c++/*
+Copyright: NCBI
+License: PD
+                                  PUBLIC DOMAIN NOTICE
+                     National Center for Biotechnology Information
+ .
+        This software/database is a "United States Government Work" under the
+        terms of the United States Copyright Act.  It was written as part of
+        the author's official duties as a United States Government employee and
+        thus cannot be copyrighted.  This software/database is freely available
+        to the public for use. The National Library of Medicine and the U.S.
+        Government have not placed any restriction on its use or reproduction.
+ .
+        Although all reasonable efforts have been taken to ensure the accuracy
+        and reliability of the software and data, the NLM and the U.S.
+        Government do not and cannot warrant the performance or results that
+        may be obtained by using this software or data. The NLM and the U.S.
+        Government disclaim all warranties, express or implied, including
+        warranties of performance, merchantability or fitness for any particular
+        purpose.
+ .
+        Please cite the author in any work or product based on this material.
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".

Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_checks
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_checks	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_checks	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,45 +0,0 @@
-Subject:  checks misreported as absent when unpacked under /*/src/*
-
- * scripts/common/check/check_add.sh: accept the relative source directory
- * src/build-system/Makefile.meta.in: supply it to check_add.sh
-
-Author: Aaron M. Ucko <ucko at debian.org>
-Last-Update: 2011-05-23
---- a/c++/scripts/common/check/check_add.sh	2011-05-23 18:49:10.000000000 -0400
-+++ b/c++/scripts/common/check/check_add.sh	2011-05-23 18:50:40.000000000 -0400
-@@ -28,14 +28,12 @@
- x_srcdir=`(cd "$1"; pwd)`
- x_test=$2
- x_signature=$3
-+x_srcdir_rel=$4
- x_use_ignore_list=${CHECK_USE_IGNORE_LIST-Y}
- x_delim=" ____ "
- # Default timeout for check (in seconds)
- x_timeout_default=200
- 
--# Convert source dir to relative path
--x_srcdir_rel=`echo "$x_srcdir" | perl -ne 's|^.*?/src/||; print'`
--
- # Check to necessity make test for this application
- if test ! -f "$x_srcdir/Makefile.$x_test.app";  then
-    echo "Warning: File \"$x_srcdir/Makefile.$x_test.app\" not found."
-@@ -46,7 +44,7 @@
- x_app=`grep '^ *APP[ =]' "$x_srcdir/Makefile.$x_test.app"`
- x_app=`echo "$x_app" | sed -e 's/^.*=//' -e 's/^ *//'`
- 
--x_tpath=`echo "$x_srcdir/$x_test" | perl -ne 's|^.*?/src/||; print'`
-+x_tpath=$x_srcdir_rel/$x_test
- if grep -c '^ *CHECK_CMD' $x_srcdir/Makefile.$x_test.app > /dev/null ; then 
-    # Check ignore list
-    x_use_ignore_list=`echo $x_use_ignore_list | tr '[a-z]' '[A-Z]' | sed -e 's/^\(.\).*/\1/g'`
---- a/c++/src/build-system/Makefile.meta.in	2011-05-23 18:48:59.000000000 -0400
-+++ b/c++/src/build-system/Makefile.meta.in	2011-05-23 18:49:20.000000000 -0400
-@@ -188,7 +188,7 @@
-    expendable=false ; \
-    for i in $$x_project ; do \
-       if test "x$$i" = "x-" ; then expendable=true ; continue ; fi ; \
--      $(check_add) $(abs_srcdir) $$i @signature@ @exe_ext@
-+      $(check_add) $(abs_srcdir) $$i @signature@ $(subdir)
- CHECK_ADD_KET = ||  exit 5 ; \
-    done ; \
- fi

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_checks (from rev 9921, trunk/packages/ncbi-blast+/trunk/debian/patches/fix_checks)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_checks	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_checks	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,17 @@
+Subject:  checks misreported as absent when unpacked under /*/src/*
+
+ * src/build-system/Makefile.meta.in: supply it to check_add.sh
+
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-05-23
+--- a/c++/src/build-system/Makefile.meta.in	2011-05-23 18:48:59.000000000 -0400
++++ b/c++/src/build-system/Makefile.meta.in	2011-05-23 18:49:20.000000000 -0400
+@@ -188,7 +188,7 @@
+    expendable=false ; \
+    for i in $$x_project ; do \
+       if test "x$$i" = "x-" ; then expendable=true ; continue ; fi ; \
+-      $(check_add) $(abs_srcdir) $$i @signature@ @exe_ext@
++      $(check_add) $(abs_srcdir) $$i @signature@ $(subdir)
+ CHECK_ADD_KET = ||  exit 5 ; \
+    done ; \
+ fi

Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_lib_deps
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_lib_deps	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,754 +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.
- * 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)

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_lib_deps (from rev 9923, trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_lib_deps	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/fix_lib_deps	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,593 @@
+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
+--- a/c++/src/algo/blast/core/Makefile.blast.lib
++++ b/c++/src/algo/blast/core/Makefile.blast.lib
+@@ -21,5 +21,6 @@
+ CFLAGS  = $(FAST_CFLAGS)
+ LDFLAGS = $(FAST_LDFLAGS)
+ 
++DLL_LIB = composition_adjustment xconnect tables
+ 
+ WATCHERS = coulouri maning madden camacho
+--- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
++++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
+@@ -11,6 +11,8 @@
+ CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
++
+ ASN_DEP = seqset
+ 
+ WATCHERS = morgulis
+--- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
++++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
+@@ -7,6 +7,7 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+ 
+-DLL_LIB = blastxml xhtml xcgi
++DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
++          seq general xser tables xncbi
+ 
+ WATCHERS = jianye zaretska madden camacho fongah2
+--- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
++++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
+@@ -21,3 +21,4 @@
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
++DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
+--- a/c++/src/cgi/Makefile.cgi.lib
++++ b/c++/src/cgi/Makefile.cgi.lib
+@@ -8,6 +8,8 @@
+       cgi_serial cgi_session cgi_exception cgiapp_cached cgi_entry_reader
+ LIB = xcgi
+ 
++DLL_LIB = xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
+ 
+ WATCHERS = vakatov
+--- a/c++/src/html/Makefile.html.lib
++++ b/c++/src/html/Makefile.html.lib
+@@ -7,4 +7,6 @@
+       jsmenu commentdiag indentstream html_exception writer_htmlenc
+ LIB = xhtml
+ 
++DLL_LIB = xncbi
++
+ WATCHERS = ivanov
+--- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
++++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
+@@ -2,3 +2,5 @@
+ 
+ LIB = xnetblastcli
+ SRC = blastclient blastclient_
++
++DLL_LIB = xnetblast xser xconnect xutil xncbi
+--- a/c++/src/objtools/align_format/Makefile.align_format.lib
++++ b/c++/src/objtools/align_format/Makefile.align_format.lib
+@@ -10,6 +10,10 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+ 
++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)
+--- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
++++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
+@@ -12,3 +12,5 @@
+ 
+ WATCHERS = todorov dicuccio grichenk
+ 
++DLL_LIB = xobjmgr seqset seq xser tables xncbi
++
+--- a/c++/src/objtools/readers/Makefile.xobjread.lib
++++ b/c++/src/objtools/readers/Makefile.xobjread.lib
+@@ -19,5 +19,5 @@
+       best_feat_finder source_mod_parser fasta_exception
+ 
+ 
+-DLL_LIB = creaders
++DLL_LIB = seqset seq pub general xser creaders sequtil xutil xncbi
+ 
+--- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
++++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
+@@ -11,6 +11,6 @@
+ mask_writer_blastdb_maskinfo
+ 
+ ASN_DEP = seqset
+-DLL_LIB = seqdb blastdb
++DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
+ 
+ WATCHERS = morgulis camacho
+--- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
++++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
+@@ -7,6 +7,8 @@
+ 
+ ASN_DEP = seqset
+ 
++DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
++
+ LIB = xobjsimple
+ SRC = simple_om
+ 
+--- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
++++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
+@@ -24,6 +24,8 @@
+ 
+ LIB = seqdb
+ 
++DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
+@@ -5,4 +5,6 @@
+ 
+ ASN_DEP = blastdb seqset
+ 
++DLL_LIB = seqdb xobjmgr seqset seq xncbi
++
+ WATCHERS = camacho
+--- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
++++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
+@@ -3,6 +3,8 @@
+ LIB = ncbi_xloader_blastdb_rmt
+ SRC = bdbloader_rmt remote_blastdb_adapter
+ 
++DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
++
+ ASN_DEP = blastdb xnetblast
+ 
+ WATCHERS = camacho
+--- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
++++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
+@@ -4,3 +4,5 @@
+ 
+ LIB = gene_info
+ SRC = gene_info gene_info_reader file_utils
++
++DLL_LIB = xncbi
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib
+@@ -74,11 +74,14 @@
+ deltablast_options \
+ deltablast
+ 
+-SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)
++SRC  = $(SRC_CXX) # $(SRC_C:%=.core_%)
+ 
+ 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
+--- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
++++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
+@@ -24,7 +24,9 @@
+ 
+ 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
+--- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
++++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
+@@ -8,6 +8,8 @@
+ 
+ SRC = symdust
+ 
++DLL_LIB = xobjmgr seq xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+--- a/c++/src/connect/Makefile.xconnect.lib
++++ b/c++/src/connect/Makefile.xconnect.lib
+@@ -14,6 +14,8 @@
+ LIB  = xconnect
+ PROJ_TAG = core
+ 
++DLL_LIB = xncbi
++
+ LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
+ 
+ WATCHERS = lavr
+--- a/c++/src/connect/ext/Makefile.xconnext.lib
++++ b/c++/src/connect/ext/Makefile.xconnext.lib
+@@ -6,4 +6,6 @@
+ 
+ LIB      = xconnext
+ 
++DLL_LIB = xconnect xncbi
++
+ WATCHERS = lavr
+--- a/c++/src/objects/blast/Makefile.blast.lib
++++ b/c++/src/objects/blast/Makefile.blast.lib
+@@ -1,4 +1,6 @@
+ LIB = xnetblast
+ SRC = blast__ blast___ names
+ 
++DLL_LIB = scoremat seqset seq xser xncbi
++
+ WATCHERS = camacho
+--- a/c++/src/objects/blastxml/Makefile.blastxml.lib
++++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
+@@ -1,2 +1,4 @@
+ LIB = blastxml
+ SRC = blastxml__ blastxml___
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/entrez2/Makefile.entrez2.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2.lib
+@@ -2,3 +2,5 @@
+ 
+ LIB = entrez2
+ SRC = entrez2__ entrez2___
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+@@ -4,3 +4,5 @@
+ 
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
++
++DLL_LIB = entrez2 xser xconnect xutil xncbi
+--- a/c++/src/objects/scoremat/Makefile.scoremat.lib
++++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
+@@ -1,2 +1,4 @@
+ LIB = scoremat
+ SRC = scoremat__ scoremat___
++
++DLL_LIB = seqset seq general xser xncbi
+--- a/c++/src/objects/seqedit/Makefile.seqedit.lib
++++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
+@@ -1,3 +1,4 @@
+ LIB = seqedit
+ SRC = seqedit__ seqedit___
+- 
++
++DLL_LIB = seqset seq general xser xncbi
+--- a/c++/src/objects/submit/Makefile.submit.lib
++++ b/c++/src/objects/submit/Makefile.submit.lib
+@@ -1,2 +1,4 @@
+ LIB = submit
+ SRC = submit__ submit___
++
++DLL_LIB = seqset seq biblio general xser xncbi
+--- a/c++/src/objmgr/util/Makefile.util.lib
++++ b/c++/src/objmgr/util/Makefile.util.lib
+@@ -8,5 +8,7 @@
+ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
+ LIB = xobjutil
+ 
++DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = ucko vasilche
+ 
+--- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
++++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
+@@ -11,6 +11,7 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS)
+ 
++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)
+--- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
++++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
+@@ -8,6 +8,8 @@
+ 
+ LIB = blast_services
+ 
++DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
+@@ -12,4 +12,7 @@
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++           xobjmgr seq xutil xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
++++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
+@@ -14,4 +14,7 @@
+ # Dependencies for shared library
+ DLL_LIB = 
+ 
++DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
++           xser xconnect xcompress xutil xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
++++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
+@@ -12,6 +12,8 @@
+ # Dependencies for shared library
+ DLL_LIB = ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
++++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
+@@ -12,6 +12,8 @@
+ # Dependencies for shared library
+ DLL_LIB = xconnect ncbi_xreader$(DLL)
+ 
++DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+ WATCHERS = vasilche
+--- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
++++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
+@@ -12,6 +12,9 @@
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
+ 
+ # Dependencies for shared library (disabled due to problems on Darwin)
+-# DLL_LIB = xconnect ncbi_xreader$(DLL)
++DLL_LIB = xconnect ncbi_xreader$(DLL)
++
++DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
++
+ 
+ WATCHERS = vasilche
+--- a/c++/src/util/compress/api/Makefile.compress.lib
++++ b/c++/src/util/compress/api/Makefile.compress.lib
+@@ -6,7 +6,7 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+-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
+--- a/c++/src/util/sequtil/Makefile.sequtil.lib
++++ b/c++/src/util/sequtil/Makefile.sequtil.lib
+@@ -3,4 +3,6 @@
+ LIB = sequtil
+ SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
+ 
++DLL_LIB = xncbi
++
+ WATCHERS = shomrat
+--- a/c++/src/corelib/Makefile.test_boost.lib
++++ b/c++/src/corelib/Makefile.test_boost.lib
+@@ -3,6 +3,8 @@
+ SRC = test_boost
+ LIB = test_boost
+ 
++DLL_LIB = xncbi
++
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
+ 
+ REQUIRES = Boost.Test.Included
+--- a/c++/src/corelib/Makefile.test_mt.lib
++++ b/c++/src/corelib/Makefile.test_mt.lib
+@@ -3,6 +3,8 @@
+ SRC = test_mt
+ LIB    = test_mt
+ 
++DLL_LIB = xncbi
++
+ # REQUIRES = MT
+ 
+ USE_PCH = no
+--- a/c++/src/objects/biblio/Makefile.biblio.lib
++++ b/c++/src/objects/biblio/Makefile.biblio.lib
+@@ -1,2 +1,4 @@
+ LIB = biblio
+ SRC = biblio__ biblio___ citation_base
++
++DLL_LIB = general xser xncbi
+--- a/c++/src/objects/blastdb/Makefile.blastdb.lib
++++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
+@@ -1,2 +1,4 @@
+ LIB = blastdb
+ SRC = blastdb__ blastdb___
++
++DLL_LIB = seq xser xncbi
+--- a/c++/src/objects/general/Makefile.general.lib
++++ b/c++/src/objects/general/Makefile.general.lib
+@@ -1,2 +1,4 @@
+ LIB = general
+ SRC = general__ general___ uoconv
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
++++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
+@@ -3,4 +3,6 @@
+ LIB = genome_collection
+ SRC = genome_collection__ genome_collection___
+ 
++DLL_LIB = seq general xser xncbi
++
+ WATCHERS = dicuccio
+--- a/c++/src/objects/id1/Makefile.id1.lib
++++ b/c++/src/objects/id1/Makefile.id1.lib
+@@ -3,4 +3,6 @@
+ LIB = id1
+ SRC = id1__ id1___
+ 
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objects/id2/Makefile.id2.lib
++++ b/c++/src/objects/id2/Makefile.id2.lib
+@@ -1,4 +1,6 @@
+ LIB = id2
+ SRC = id2__ id2___
+ 
++DLL_LIB = seqsplit seq xser xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/objects/medline/Makefile.medline.lib
++++ b/c++/src/objects/medline/Makefile.medline.lib
+@@ -1,2 +1,4 @@
+ LIB = medline
+ SRC = medline__ medline___
++
++DLL_LIB = biblio general xser xncbi
+--- a/c++/src/objects/pub/Makefile.pub.lib
++++ b/c++/src/objects/pub/Makefile.pub.lib
+@@ -1,2 +1,4 @@
+ LIB = pub
+ SRC = pub__ pub___
++
++DLL_LIB = medline biblio xser xncbi
+--- a/c++/src/objects/seq/Makefile.seq.lib
++++ b/c++/src/objects/seq/Makefile.seq.lib
+@@ -12,4 +12,6 @@
+       seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
+       seq_loc_from_string seq_loc_reverse_complementer
+ 
++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
++
+ WATCHERS = vasilche grichenk
+--- a/c++/src/objects/seqcode/Makefile.seqcode.lib
++++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
+@@ -1,2 +1,4 @@
+ LIB = seqcode
+ SRC = seqcode__ seqcode___
++
++DLL_LIB = xser xncbi
+--- a/c++/src/objects/seqset/Makefile.seqset.lib
++++ b/c++/src/objects/seqset/Makefile.seqset.lib
+@@ -1,2 +1,4 @@
+ LIB = seqset
+ SRC = seqset__ seqset___ gb_release_file
++
++DLL_LIB = seq general xser xncbi
+--- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
++++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
+@@ -1,4 +1,6 @@
+ LIB = seqsplit
+ SRC = seqsplit__ seqsplit___
+ 
++DLL_LIB = seqset seq xser xncbi
++
+ WATCHERS = vasilche
+--- a/c++/src/serial/Makefile.serial.lib
++++ b/c++/src/serial/Makefile.serial.lib
+@@ -18,4 +18,6 @@
+ 
+ LIB    = xser
+ 
++DLL_LIB = xutil xncbi
++
+ WATCHERS = gouriano
+--- a/c++/src/util/Makefile.util.lib
++++ b/c++/src/util/Makefile.util.lib
+@@ -11,6 +11,7 @@
+ LIB = xutil
+ PROJ_TAG = core
+ 
++DLL_LIB = xncbi
+ LIBS = $(ORIG_LIBS)
+ 
+ WATCHERS = vakatov
+--- a/c++/src/util/xregexp/Makefile.xregexp.lib
++++ b/c++/src/util/xregexp/Makefile.xregexp.lib
+@@ -6,7 +6,7 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
+ 
+-DLL_LIB = $(PCRE_LIB)
++DLL_LIB = $(PCRE_LIB) xncbi
+ LIBS    = $(PCRE_LIBS)
+ 
+ WATCHERS = ivanov
+--- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
++++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
+@@ -8,6 +8,8 @@
+ 
+ SRC = segmask
+ 
++DLL_LIB = blast xobjmgr xncbi
++
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+ 
+--- a/c++/src/objmgr/split/Makefile.id2_split.lib
++++ b/c++/src/objmgr/split/Makefile.id2_split.lib
+@@ -17,6 +17,6 @@
+ 
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
+ 
+-DLL_LIB = $(SOBJMGR_LIBS)
++DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
+ 
+ WATCHERS = vasilche
+--- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
++++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
+@@ -8,6 +8,9 @@
+ 
+ LIB = writedb
+ 
++DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
++          xser sequtil xutil xncbi
++
+ CFLAGS   = $(FAST_CFLAGS)
+ CXXFLAGS = $(FAST_CXXFLAGS)
+ LDFLAGS  = $(FAST_LDFLAGS)
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk
++++ b/c++/src/algo/blast/Makefile.blast_macros.mk
+@@ -18,7 +18,7 @@
+ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
+ 
+ # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
+-BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
++BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
+ 		xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
+ 		xobjread creaders xnetblastcli xnetblast blastdb scoremat tables xalnmgr
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
+--- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
++++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
+@@ -2,7 +2,7 @@
+ SRC = main mkindex_app
+ 
+ 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)

Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/hurd_fixes	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,81 +0,0 @@
-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

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/hurd_fixes (from rev 9921, trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/hurd_fixes	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/hurd_fixes	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,53 @@
+Subject: fix portability issues that led to Hurd build failures
+
+* src/build-system/configure(.ac):
+  - Reflect the Hurd's support for -Wl,rpath,... .
+* 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
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -5688,7 +5688,7 @@
+     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 )
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1496,7 +1496,7 @@
+     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 )
+--- a/c++/src/connect/ncbi_socket_cxx.cpp
++++ b/c++/src/connect/ncbi_socket_cxx.cpp
+@@ -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
+ 
+--- a/c++/src/connect/ext/ncbi_localnet.c
++++ b/c++/src/connect/ext/ncbi_localnet.c
+@@ -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

Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/no_multiarch_rpath
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/no_multiarch_rpath	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,36 +0,0 @@
-Subject: avoid redundant rpath entries on multiarch systems
-
- * src/build-system/configure(.ac): when ensuring that executables
-   will be able to find libstdc++, don't add rpath entries that files
-   under /etc/ld.so.conf.d already specify, even if they don't resemble
-   traditional single-architecture or biarch locations.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko at debian.org>
-Last-Update: 2011-08-28
-Index: b/c++/src/build-system/configure
-===================================================================
---- a/c++/src/build-system/configure	2011-08-28 11:41:27.000000000 -0400
-+++ b/c++/src/build-system/configure	2011-08-28 11:48:06.000000000 -0400
-@@ -5613,7 +5613,7 @@
-                break
-                ;;
-             /* )
--               found=true
-+               fgrep -qsx $abs_dir /etc/ld.so.conf.d/*  ||  found=true
-                break
-                ;;
-         esac
-Index: b/c++/src/build-system/configure.ac
-===================================================================
---- a/c++/src/build-system/configure.ac	2011-08-28 11:41:27.000000000 -0400
-+++ b/c++/src/build-system/configure.ac	2011-08-28 11:48:11.000000000 -0400
-@@ -1494,7 +1494,7 @@
-                break
-                ;;
-             /* )
--               found=true
-+               fgrep -qsx $abs_dir /etc/ld.so.conf.d/*  ||  found=true
-                break
-                ;;
-         esac

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/no_multiarch_rpath (from rev 9923, trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/no_multiarch_rpath	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/no_multiarch_rpath	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,32 @@
+Subject: avoid redundant rpath entries on multiarch systems
+
+ * src/build-system/configure(.ac): when ensuring that executables
+   will be able to find libstdc++, don't add rpath entries that files
+   under /etc/ld.so.conf.d already specify, even if they don't resemble
+   traditional single-architecture or biarch locations.
+
+Debian-Bug: 633567.
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-08-28
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -5751,7 +5751,7 @@
+                break
+                ;;
+             /* )
+-               found=true
++               fgrep -qsx $abs_dir /etc/ld.so.conf.d/*  ||  found=true
+                break
+                ;;
+         esac
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1558,7 +1558,7 @@
+                break
+                ;;
+             /* )
+-               found=true
++               fgrep -qsx $abs_dir /etc/ld.so.conf.d/*  ||  found=true
+                break
+                ;;
+         esac

Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series	2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/series	2012-03-13 09:55:40 UTC (rev 9986)
@@ -1,8 +0,0 @@
-hurd_fixes
-legacy_rename_rpsblast
-fix_checks
-fix_gcc46_errors
-support_other_cpus
-fix_lib_deps
-no_multiarch_rpath
-do_not_output_everything_to_stderr.patch

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/series (from rev 9983, trunk/packages/ncbi-blast+/trunk/debian/patches/series)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/series	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/series	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,5 @@
+hurd_fixes
+legacy_rename_rpsblast
+fix_lib_deps
+no_multiarch_rpath
+wrong_path_to_touch.patch

Copied: trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/wrong_path_to_touch.patch (from rev 9984, trunk/packages/ncbi-blast+/trunk/debian/patches/wrong_path_to_touch.patch)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/wrong_path_to_touch.patch	                        (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-2/debian/patches/wrong_path_to_touch.patch	2012-03-13 09:55:40 UTC (rev 9986)
@@ -0,0 +1,112 @@
+Subject: upstream bug using hard path for touch
+Description: upstream makes use of a hard path that 
+does not match on hurd systems. Patch comes from upstream
+ and will be included in next release
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 12/03/2012
+--- a/c++/src/build-system/Makefile.meta.in
++++ b/c++/src/build-system/Makefile.meta.in
+@@ -28,7 +28,7 @@
+ 
+ @make_shell@
+ RM    = /bin/rm
+-TOUCH = /usr/bin/touch
++TOUCH = @TOUCH@
+ MKDIR = /bin/mkdir
+ 
+ signature      = @signature@
+--- a/c++/src/build-system/Makefile.mk.in
++++ b/c++/src/build-system/Makefile.mk.in
+@@ -54,7 +54,7 @@
+ RMDIR    = /bin/rm -rf
+ COPY     = /bin/cp -p
+ BINCOPY  = @BINCOPY@
+-TOUCH    = /usr/bin/touch
++TOUCH    = @TOUCH@
+ MKDIR    = /bin/mkdir
+ BINTOUCH = $(TOUCH)
+ LN_S     = @LN_S@
+--- a/c++/src/build-system/NEWS
++++ b/c++/src/build-system/NEWS
+@@ -8,3 +8,5 @@
+ 2011-05-17: new @ncbi_java@ variable for --with-jni builds.
+ 
+ 2011-10-05: new @FEATURES@ variable for the unit test framework.
++
++2012-02-27: new @TOUCH@ variable to avoid hard-coded paths.
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -1965,6 +1965,7 @@
+    AC_MSG_RESULT(no)
+ fi
+ 
++AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH)
+ AC_PROG_EGREP
+ AC_MSG_CHECKING([how to run $EGREP quietly])
+ if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then
+--- a/c++/src/build-system/configure
++++ b/c++/src/build-system/configure
+@@ -318,7 +318,7 @@
+ # include <unistd.h>
+ #endif"
+ 
+-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS'
++ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS PROJECTS build build_cpu build_vendor build_os host host_cpu host_vendor host_os INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CC CFLAGS LDFLAGS CPPFLAGS ac_ct_CC EXEEXT OBJEXT CXX CXXFLAGS ac_ct_CXX MT_SFX DLL DLL_LIB_SETTING IF_WITH_DLL UNLESS_WITH_DLL STATIC USUAL_AND_DLL USUAL_AND_LIB LN_S RANLIB ac_ct_RANLIB AR STRIP DISTCC CCACHE TAIL TOUCH EGREP VALGRIND_PATH CXXCPP TCHECK_CL AMQ CPP Z_INCLUDE Z_LIBS BZ2_INCLUDE BZ2_LIBS LZO_INCLUDE LZO_LIBS PCRE_INCLUDE PCRE_LIBS LIBGNUTLS_CONFIG GNUTLS_INCLUDE GNUTLS_LIBS OPENSSL_INCLUDE OPENSSL_LIBS FTDS64_INCLUDE FTDS64_LIBS FTDS64_LIB FTDS64_CTLIB_INCLUDE FTDS64_CTLIB_LIBS FTDS64_CTLIB_LIB FTDS_INCLUDE FTDS_LIBS FTDS_LIB freetds ftds64 mysql_config PYTHON PYTHON_INCLUDE PYTHON_LIBS PYTHON23 PYTHON23_INCLUDE PYTHON23_LIBS PYTHON24 PYTHON24_INCLUDE PYTHON24_LIBS PYTHON25 PYTHON25_INCLUDE PYTHON25_LIBS _ACJNI_JAVAC X_CFLAGS X_PRE_LIBS X_LIBS X_EXTRA_LIBS wxconf EXPAT_INCLUDE EXPAT_LIBS SABLOT_INCLUDE SABLOT_LIBS LIBXML_INCLUDE LIBXML_LIBS LIBXSLT_INCLUDE LIBXSLT_LIBS XSLTPROC SQLITE3_INCLUDE SQLITE3_LIBS OECHEM_INCLUDE OECHEM_LIBS SGE_INCLUDE SGE_LIBS MUPARSER_INCLUDE MUPARSER_LIBS HDF5_INCLUDE HDF5_LIBS JPEG_INCLUDE JPEG_LIBS PNG_INCLUDE PNG_LIBS TIFF_INCLUDE TIFF_LIBS UNGIF_INCLUDE UNGIF_LIBS GIF_INCLUDE GIF_LIBS XPM_INCLUDE XPM_LIBS freetype_config MAGIC_INCLUDE MAGIC_LIBS CURL_INCLUDE CURL_LIBS signature build_root top_srcdir srcdir status_dir builddir runpath ncbi_runpath c_ncbi_runpath LINK C_LINK TAIL_N EGREP_Q FAST_CFLAGS FAST_CXXFLAGS OBJCXX_CXXFLAGS DEPFLAGS DEPFLAGS_POST FAST_LDFLAGS APP_LDFLAGS DLL_LDFLAGS C_LIBS OBJCXX_LIBS GCCPCH RUNPATH_ORIGIN NO_STRICT_ALIASING D_SFX DEBUG_SFX LIB_OR_DLL FORCE_STATIC_LIB APP_LIB_SETTING APP_LIBS_SETTING LINK_DLL has_dll_loadable LINK_LOADABLE CFLAGS_DLL CXXFLAGS_DLL ALLOW_UNDEF FORBID_UNDEF OPT_GROUPS local_lbsm ncbi_crypt CONNEXT XCONNEXT serial bdb dbapi objects gui algo app internal sra check CHECK_ARG CHECK_TOOLS CHECK_TIMEOUT_MULT CHECK_OS_NAME FEATURES script_shell make_shell obj_ext lib_pre lib_l_pre lib_ext dll_ext loadable_ext lib_l_ext exe_ext f_compile f_outobj f_outlib f_libpath f_runpath f_outexe BDB_LIB BDB_CACHE_LIB DBAPI_DRIVER DBAPI_CTLIB DBAPI_DBLIB DBAPI_MYSQL DBAPI_ODBC THREAD_LIBS NCBIATOMIC_LIB NETWORK_LIBS NETWORK_PURE_LIBS RESOLVER_LIBS MATH_LIBS KSTAT_LIBS RPCSVC_LIBS CRYPT_LIBS DL_LIBS RT_LIBS UUID_LIBS DEMANGLE_LIBS ICONV_LIBS Z_LIB BZ2_LIB PCREPOSIX_LIBS PCRE_LIB OPENSSL_STATIC_LIBS TLS_INCLUDE TLS_LIBS SYBASE_PATH SYBASE_LCL_PATH SYBASE_INCLUDE SYBASE_LIBS SYBASE_DLLS SYBASE_DBLIBS MYSQL_INCLUDE MYSQL_LIBS BERKELEYDB_INCLUDE BERKELEYDB_LIBS BERKELEYDB_STATIC_LIBS BERKELEYDB_CXX_LIBS BERKELEYDB_CXX_STATIC_LIBS ODBC_INCLUDE ODBC_LIBS BOOST_INCLUDE BOOST_LIBPATH BOOST_TAG BOOST_REGEX_LIBS BOOST_REGEX_STATIC_LIBS BOOST_TEST_PEM_LIBS BOOST_TEST_PEM_STATIC_LIBS BOOST_TEST_TEM_LIBS BOOST_TEST_TEM_STATIC_LIBS BOOST_TEST_UTF_LIBS BOOST_TEST_UTF_STATIC_LIBS BOOST_THREAD_LIBS BOOST_THREAD_STATIC_LIBS NCBI_C_INCLUDE NCBI_C_LIBPATH OPENGL_INCLUDE OPENGL_LIBS OPENGL_STATIC_LIBS OSMESA_INCLUDE OSMESA_LIBS OSMESA_STATIC_LIBS GLUT_INCLUDE GLUT_LIBS GLEW_INCLUDE GLEW_LIBS GLEW_STATIC_LIBS FLTK_INCLUDE FLTK_LIBS FLTK_LIBS_GL FLTK_LIBS_IMAGES FLTK_LIBS_ALL FLTK_STATIC_LIBS FLTK_STATIC_LIBS_GL FLTK_STATIC_LIBS_IMAGES FLTK_STATIC_LIBS_ALL FLTK_CONFIG WXWIDGETS_INCLUDE WXWIDGETS_LIBS WXWIDGETS_STATIC_LIBS WXWIDGETS_GL_LIBS WXWIDGETS_GL_STATIC_LIBS WXWIDGETS_POST_LINK FASTCGI_INCLUDE FASTCGI_LIBS FASTCGI_OBJS NCBI_SSS_INCLUDE NCBI_SSS_LIBPATH LIBSSSUTILS LIBSSSDB sssutils SP_INCLUDE SP_LIBS ORBACUS_INCLUDE ORBACUS_LIBPATH LIBOB LIBIMR ICU_CONFIG ICU_INCLUDE ICU_LIBS ICU_STATIC_LIBS EXPAT_STATIC_LIBS SABLOT_STATIC_LIBS LIBXML_STATIC_LIBS LIBXSLT_STATIC_LIBS XERCES_INCLUDE XERCES_LIBS XERCES_STATIC_LIBS XALAN_INCLUDE XALAN_LIBS XALAN_STATIC_LIBS SQLITE3_STATIC_LIBS FREETYPE_INCLUDE FREETYPE_LIBS ncbi_xreader_pubseqos ncbi_xreader_pubseqos2 UNLESS_PUBSEQOS JDK_PATH JDK_INCLUDE ncbi_java NCBI_C_ncbi BINCOPY APP_NOCOPY APP_OR_NULL IF_REBUILDING_LIBS IF_REBUILDING_CONDITIONALLY IF_DEACTIVATING configurables_mfname CC_FILTER CXX_FILTER AR_FILTER LINK_FILTER CC_WRAPPER CXX_WRAPPER AR_WRAPPER LINK_WRAPPER KeepStateTarget Rules serial_ws50_rtti_kludge ncbicntr UNIX_SRC UNIX_USR_PROJ compiler compiler_root compiler_version COMPILER OSTYPE NCBI_PLATFORM_BITS LIBOBJS LTLIBOBJS'
+ ac_subst_files=''
+ 
+ # Initialize some variables set by options.
+@@ -6615,6 +6615,46 @@
+ echo "${ECHO_T}no" >&6
+ fi
+ 
++# Extract the first word of "touch", so it can be a program name with args.
++set dummy touch; ac_word=$2
++echo "$as_me:$LINENO: checking for $ac_word" >&5
++echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6
++if test "${ac_cv_path_TOUCH+set}" = set; then
++  echo $ECHO_N "(cached) $ECHO_C" >&6
++else
++  case $TOUCH in
++  [\\/]* | ?:[\\/]*)
++  ac_cv_path_TOUCH="$TOUCH" # Let the user override the test with a path.
++  ;;
++  *)
++  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
++as_dummy="/bin:/usr/bin:$PATH"
++for as_dir in $as_dummy
++do
++  IFS=$as_save_IFS
++  test -z "$as_dir" && as_dir=.
++  for ac_exec_ext in '' $ac_executable_extensions; do
++  if $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
++    ac_cv_path_TOUCH="$as_dir/$ac_word$ac_exec_ext"
++    echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
++    break 2
++  fi
++done
++done
++
++  ;;
++esac
++fi
++TOUCH=$ac_cv_path_TOUCH
++
++if test -n "$TOUCH"; then
++  echo "$as_me:$LINENO: result: $TOUCH" >&5
++echo "${ECHO_T}$TOUCH" >&6
++else
++  echo "$as_me:$LINENO: result: no" >&5
++echo "${ECHO_T}no" >&6
++fi
++
+ echo "$as_me:$LINENO: checking for egrep" >&5
+ echo $ECHO_N "checking for egrep... $ECHO_C" >&6
+ if test "${ac_cv_prog_egrep+set}" = set; then
+@@ -33848,6 +33888,7 @@
+ s, at DISTCC@,$DISTCC,;t t
+ s, at CCACHE@,$CCACHE,;t t
+ s, at TAIL@,$TAIL,;t t
++s, at TOUCH@,$TOUCH,;t t
+ s, at EGREP@,$EGREP,;t t
+ s, at VALGRIND_PATH@,$VALGRIND_PATH,;t t
+ s, at CXXCPP@,$CXXCPP,;t t




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