[med-svn] r1342 - trunk/packages/infernal/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Feb 9 04:26:16 UTC 2008
Author: charles-guest
Date: 2008-02-09 04:26:15 +0000 (Sat, 09 Feb 2008)
New Revision: 1342
Modified:
trunk/packages/infernal/trunk/debian/control
trunk/packages/infernal/trunk/debian/copyright
Log:
Tried to adress the comments of the assistant of the administrators of the ftmpaster machine
Modified: trunk/packages/infernal/trunk/debian/control
===================================================================
--- trunk/packages/infernal/trunk/debian/control 2008-02-08 22:50:05 UTC (rev 1341)
+++ trunk/packages/infernal/trunk/debian/control 2008-02-09 04:26:15 UTC (rev 1342)
@@ -13,7 +13,7 @@
Package: infernal
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: RNA sequence comparison
+Description: inference of RNA secondary structural alignments
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
databases for RNA structure and sequence similarities. It is an
implementation of a special case of profile stochastic context-free
@@ -27,4 +27,4 @@
.
Users of this package should cite:
"Query-Dependent Banding (QDB) for Faster RNA Similarity Searches."
- E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007.
+ E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007.
Modified: trunk/packages/infernal/trunk/debian/copyright
===================================================================
--- trunk/packages/infernal/trunk/debian/copyright 2008-02-08 22:50:05 UTC (rev 1341)
+++ trunk/packages/infernal/trunk/debian/copyright 2008-02-09 04:26:15 UTC (rev 1342)
@@ -1,84 +1,112 @@
-This package was debianized by Steffen Moeller <moeller at debian.org> on
-Mon, 10 Sep 2007 23:15:37 +0200.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Steffen Möller <moeller at debian.org>
+X-Debianized-Date: Mon, 10 Sep 2007 23:15:37 +0200
+X-Source-Downloaded-From: ftp://infernal.janelia.org/pub/software/infernal
+X-Upstream-Author: Infernal developer team at HHMI Janelia Farm:
+ Diana Kolbe <kolbed at janelia.hhmi.org>
+ Eric Nawrocki <nawrockie at janelia.hhmi.org>
+ Sean Eddy <eddy at janelia.hhmi.org>.
+ The "rigfilters" code was contributed by Zasha Weinberg
+ and Larry Ruzzo, University of Washington, Seattle.
-It was downloaded from ftp://infernal.janelia.org/pub/software/infernal
-Upstream Authors:
+Files: debian/*
+Copyright: © 2007-2008 Steffen Möller <moeller at debian.org>
+ © 2007-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+License: GPL-2+
- Infernal developer team at HHMI Janelia Farm:
- Diana Kolbe <kolbed at janelia.hhmi.org>
- Eric Nawrocki <nawrockie at janelia.hhmi.org>
- Sean Eddy <eddy at janelia.hhmi.org>.
-
- The "rigfilters" code was contributed by Zasha Weinberg and Larry
- Ruzzo, University of Washington, Seattle.
-Copyright:
+Files: rigfilters/*
+Copyright: © 2004, Zasha Weinberg
+License: BSD family
+ 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 University of Washington nor the names of
+ its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "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 COPYRIGHT OWNER OR CONTRIBUTORS 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.
- Copyright (C) of "rigfilters": 2004, Zasha Weinberg
+Files: easel/documentation/figures/evd*.pdf, easel/documentation/figures/gev*.pdf
+X-Comment: Those files are figures with only a few words of text, that probably
+ have been generated in a command line session, and therefore have no source.
- Copyright (C) 2001-2007 HHMI Janelia Farm
- Portions Copyright (C) 1991-2007 Sean R. Eddy
- Portions Copyright (C) 2005-2007 Eric P. Nawrocki
- Portions Copyright (C) 2005-2007 Diana L. Kolbe
- Portions Copyright (C) 2004 Zasha Weinberg
- Portions Copyright (C) 1990 Don G. Gilbert
- Portions Copyright (C) 1995-2006 Washington University in St. Louis
- Portions Copyright (C) 1992-1995 Medical Research Council, UK
- Portions Copyright (C) 2004 University of Washington, Seattle
- Portions Copyright (C) 1986,1993,1995 University of Toronto
- Portions Copyright (C) 1989-2001 Free Software Foundation
- Portions Copyright (C) 1991 Massachusetts Institute of Technology
-License:
+Files: Userguide.pdf
+X-Comment: Deleted in the Debian source package (no source available)
- Of "rigfilters":
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
+Files: squid/*
+Copyright: © 1992-2002 Washington University School of Medicine
+License: most likely GPL-2+
+ In squid/00README, it is written:
+ .
+ " If you have any questions about redistributing squid or using
+ squid code in your own work, see the files:
+ COPYRIGHT -- copyright notice, and information on my distribution policy
+ LICENSE -- version 2 of the GNU Public License (see COPYRIGHT)"
+ .
+ However:
+ - There are no COPYRIGHT and LICENSE files in the squid directory;
+ - ../COPYRIGHT ../LICENSE indicate the GNU GPL "version 2 or (at your option)
+ any later version";
+ - a more recent version of the squid library, distributed in Debian's biosquid
+ package, is also disributed under version 2 or later.
- - 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 University of Washington nor the names of
- its contributors may be used to endorse or promote products derived
- from this software without specific prior written permission.
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "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 COPYRIGHT OWNER OR CONTRIBUTORS 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
+Files: *
+Copyright: © 2001-2007 HHMI Janelia Farm
+ © 1991-2007 Sean R. Eddy
+ © 2005-2007 Eric P. Nawrocki
+ © 2005-2007 Diana L. Kolbe
+ © 2004 Zasha Weinberg
+ © 1990 Don G. Gilbert
+ © 1995-2006 Washington University in St. Louis
+ © 1992-1995 Medical Research Council, UK
+ © 2004 University of Washington, Seattle
+ © 1986,1993,1995 University of Toronto
+ © 1989-2001 Free Software Foundation
+ © 1991 Massachusetts Institute of Technology
+License: GPL-2+
+ This suite of programs 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.
+ .
+ In other words, you may modify, copy, or redistribute this source code
+ and its documentation, but if you do, you must preserve all these
+ copyrights and distribute all derivative versions as free software
+ under the GNU General Public License.
+ .
+ This software 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 software, in the file LICENSE; if not, write to the
+ Free Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139
+ USA or see http://www.gnu.org/
- All other files:
-
- 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 package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
-is licensed under the GPL, see above.
+X-Comment: On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL'.
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