[med-svn] [SCM] abyss branch, master, updated. upstream/1.3.4-13-gfd8fdf4

Fri Jun 1 06:47:52 UTC 2012

The following commit has been merged in the master branch:
commit 8e6fc942fbd07bbca557730445437d9d0fe1c621
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 1 08:21:54 2012 +0200

    Shaun Jackman accidentially uploaded new upstream and forgot that package is team maintained now - just commiting his changes

diff --git a/debian/changelog b/debian/changelog
index bfd218c..cf63965 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,17 @@
-abyss (1.3.3-3) UNRELEASED; urgency=low
+abyss (1.3.4-2) UNRELEASED; urgency=low
 
   * debian/upstream: BibTeX compliant authors
 
  -- Andreas Tille <tille at debian.org>  Wed, 16 May 2012 16:16:49 +0200
 
+abyss (1.3.4-1) unstable; urgency=low
+
+  * New upstream release.
+  * debian/copyright: Add CityHash, which has an Expat license.
+  * debian/control: Bump Standards-Version to 3.9.3.1.
+
+ -- Shaun Jackman <sjackman at debian.org>  Thu, 31 May 2012 11:39:13 -0700
+
 abyss (1.3.3-2) unstable; urgency=low
 
   * debian/control:
diff --git a/debian/copyright b/debian/copyright
index 7ef0c28..7188bbb 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,102 +2,6 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: ABySS
 Upstream-Contact: Shaun Jackman <sjackman at bcgsc.ca>
 Source: http://www.bcgsc.ca/platform/bioinfo/software/abyss
-        https://github.com/sjackman/abyss
-
-Files: *
-Copyright: Copyright 2012 Genome Sciences Centre
-License: BCCA-Academic
-
-Files: Common/* DistanceEst/* ParseAligns/*
-Copyright: Copyright 2012 Genome Sciences Centre
-License: BCCA-Academic or GPL-3+
-
-Files: Common/HashFunction.cpp
-Copyright: public-domain
-License: public-domain
- You can use this free for any purpose. It's in the public domain.
- It has no warranty.
-
-Files: dialign/*
-Copyright: Copyright 2008 Amarendran R. Subramanian
-License: LGPL-2.1+
- On Debian systems, see `/usr/share/common-licenses/LGPL-2.1'.
- .
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
- .
- This library 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
- Lesser General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
- .
- Amarendran R. Subramanian, hereby disclaims all copyright interest in the
- DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian.
- .
- Amarendran R. Subramanian, 2004-2008
- .
- DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig.
- .
- Research work using DIALIGN-TX should cite:
- .
- DIALIGN-TX: improvement of the segment-based approach for multiple
- sequence alignment by combining greedy and progressive alignment
- strategies
- Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern,
- Algorithms for Molecular Biology 3:6, 2008
- .
- DIALIGN-T: An improved algorithm for segment-based multiple
- sequence alignment
- Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,
- Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005
-
-Files: FMIndex/bit_array.h
-Copyright: Copyright 2010 Daisuke Okanohara
-License: BSD-3-clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- .
- Redistributions of source code must retain the above Copyright
- notice, this list of conditions and the following disclaimer.
- .
- Redistributions in binary form must reproduce the above Copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- .
- Neither the name of the authors nor the names of its contributors
- may be used to endorse or promote products derived from this
- software without specific prior written permission.
-
-Files: FMIndex/sais.hxx
-Copyright: Copyright 2010 Yuta Mori
-License: Expat
- 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.
 
 License: BCCA-Academic
  Debian may redistribute this software package.
@@ -330,6 +234,107 @@ License: BCCA-Academic
  obligations hereunder without BCCA's prior written consent. BCCA, at
  its sole discretion may assign this Agreement without notice to You.
 
+Files: *
+Copyright: Copyright 2012 Genome Sciences Centre
+License: BCCA-Academic
+
+Files: Common/* DistanceEst/* ParseAligns/*
+Copyright: Copyright 2012 Genome Sciences Centre
+License: BCCA-Academic or GPL-3+
+
+Files: Common/cholesky.hpp
+Copyright: Copyright 2005 Gunter Winkler, Konstantin Kutzkow
+License: LGPL-2.1+
+
+Files: Common/city.cc Common/city.h
+Copyright: Copyright 2011 Google, Inc.
+License: Expat
+
+Files: dialign/*
+Copyright: Copyright 2008 Amarendran R. Subramanian
+License: LGPL-2.1+
+
+License: LGPL-2.1+
+ On Debian systems, see `/usr/share/common-licenses/LGPL-2.1'.
+ .
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This library 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
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ .
+ Amarendran R. Subramanian, hereby disclaims all copyright interest in the
+ DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian.
+ .
+ Amarendran R. Subramanian, 2004-2008
+ .
+ DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig.
+ .
+ Research work using DIALIGN-TX should cite:
+ .
+ DIALIGN-TX: improvement of the segment-based approach for multiple
+ sequence alignment by combining greedy and progressive alignment
+ strategies
+ Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern,
+ Algorithms for Molecular Biology 3:6, 2008
+ .
+ DIALIGN-T: An improved algorithm for segment-based multiple
+ sequence alignment
+ Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,
+ Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005
+
+Files: FMIndex/bit_array.h
+Copyright: Copyright 2010 Daisuke Okanohara
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ Redistributions of source code must retain the above Copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ Redistributions in binary form must reproduce the above Copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ .
+ Neither the name of the authors nor the names of its contributors
+ may be used to endorse or promote products derived from this
+ software without specific prior written permission.
+
+Files: FMIndex/sais.hxx
+Copyright: Copyright 2010 Yuta Mori
+License: Expat
+
+License: Expat
+ 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.
+
 License: GPL-3+
  This program is free software; you can redistribute it
  and/or modify it under the terms of the GNU General Public
@@ -351,4 +356,3 @@ License: GPL-3+
  On Debian systems, the full text of the GNU General Public
  License version 3 can be found in the file
  `/usr/share/common-licenses/GPL-3'.
-

-- 
Packaging of abyss in Debian

