[med-svn] r9931 - in trunk/packages/ncbi-blast+/tags: . 2.2.26-1/debian 2.2.26-1/debian/patches
Olivier Sallou
osallou at alioth.debian.org
Wed Mar 7 16:48:26 UTC 2012
Author: osallou
Date: 2012-03-07 16:48:26 +0000 (Wed, 07 Mar 2012)
New Revision: 9931
Added:
trunk/packages/ncbi-blast+/tags/2.2.26-1/
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/control
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/copyright
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_checks
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/hurd_fixes
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/no_multiarch_rpath
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/series
Removed:
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/changelog
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/control
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/copyright
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_checks
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_lib_deps
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/hurd_fixes
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/no_multiarch_rpath
trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/series
Log:
[svn-buildpackage] Tagging ncbi-blast+ 2.2.26-1
Deleted: trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog 2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/changelog 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/changelog (from rev 9926, trunk/packages/ncbi-blast+/trunk/debian/changelog)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/changelog (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/changelog 2012-03-07 16:48:26 UTC (rev 9931)
@@ -0,0 +1,106 @@
+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/2.2.26-1/debian/control
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/control 2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/control 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/control (from rev 9927, trunk/packages/ncbi-blast+/trunk/debian/control)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/control (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/control 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/copyright
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/copyright 2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/copyright 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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
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- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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-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,
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- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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-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>
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-Copyright: 2001-2008 Gennadiy Rozental
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-Files: c++/include/dbapi/driver/odbc/unix_odbc/sqlfront.h
-Copyright: 1998-1999 Brian Bruns
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-Copyright: 1997-1999 Netscape Communications Corp.
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-Files: c++/include/util/bitset/*
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-Files: c++/*
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- PUBLIC DOMAIN NOTICE
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- Please cite the author in any work or product based on this material.
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-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/2.2.26-1/debian/copyright (from rev 9927, trunk/packages/ncbi-blast+/trunk/debian/copyright)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/copyright (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/copyright 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/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/2.2.26-1/debian/patches/fix_checks 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/patches/fix_checks (from rev 9921, trunk/packages/ncbi-blast+/trunk/debian/patches/fix_checks)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_checks (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_checks 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/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/2.2.26-1/debian/patches/fix_lib_deps 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/patches/fix_lib_deps (from rev 9923, trunk/packages/ncbi-blast+/trunk/debian/patches/fix_lib_deps)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_lib_deps (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/fix_lib_deps 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/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/2.2.26-1/debian/patches/hurd_fixes 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/patches/hurd_fixes (from rev 9921, trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/hurd_fixes (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/hurd_fixes 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/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/2.2.26-1/debian/patches/no_multiarch_rpath 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/patches/no_multiarch_rpath (from rev 9923, trunk/packages/ncbi-blast+/trunk/debian/patches/no_multiarch_rpath)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/no_multiarch_rpath (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/no_multiarch_rpath 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/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/2.2.26-1/debian/patches/series 2012-03-07 16:48:26 UTC (rev 9931)
@@ -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/2.2.26-1/debian/patches/series (from rev 9921, trunk/packages/ncbi-blast+/trunk/debian/patches/series)
===================================================================
--- trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/series (rev 0)
+++ trunk/packages/ncbi-blast+/tags/2.2.26-1/debian/patches/series 2012-03-07 16:48:26 UTC (rev 9931)
@@ -0,0 +1,4 @@
+hurd_fixes
+legacy_rename_rpsblast
+fix_lib_deps
+no_multiarch_rpath
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