[med-svn] [SCM] cufflinks branch, master, updated. upstream/1.0.2-23-gef4edb3

Sun May 29 14:46:39 UTC 2011

The following commit has been merged in the master branch:
commit ef4edb3f6bf4d9a5742765f03245d2faf7be1601
Author: Charles Plessy <plessy at debian.org>
Date:   Sun May 29 23:46:18 2011 +0900

    Reviewed copyright and license notices, and found that locfit is non-free…
    
    The license of locfit forbids to make benchmarks.

diff --git a/debian/copyright b/debian/copyright
index 5477bde..af50c87 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,9 +2,124 @@ Format: http://dep.debian.net/deps/dep5
 Source: http://cufflinks.cbcb.umd.edu/downloads/cufflinks-1.0.2.tar.gz
 
 Files: *
-Copyright: Copyright (C) 2003-2009 Cole Trapnell et al
+Copyright: Copyright (C) 2003-2010 Cole Trapnell et al
+ © 2010 Adam Roberts
+ © 2009 Geo Pertea
+ © 2001 Vladimir Prus <ghost at cs.msu.su>
+ © 2001 Jeremy Siek <jsiek at cs.indiana.edu>
+ © 2009 Eric Bose-Wolf
 License: BSL-1.0
 
+Files: ax_bam.m4
+Copyright: © 2010 Cole Trapnell <cole at cs.umd.edu>
+License: GAP
+
+Files: ax_boost_base.m4 ax_boost_thread.m4
+Copyright: © 2008,2009 Thomas Porschberg <thomas at randspringer.de>
+ © 2009 Michael Tindal
+Source: http://autoconf-archive.cryp.to/
+License: GAP
+
+Files: ax_check_zlib.m4
+Copyright: © 2008 Loic Dachary <loic at senga.org>
+Source: http://www.gnu.org/software/autoconf-archive/ax_check_zlib.html
+License: GPL-2+_with_Autoconf_exception
+ This program 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 program 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/>.
+ .
+ As a special exception, the respective Autoconf Macro's copyright owner
+ gives unlimited permission to copy, distribute and modify the configure
+ scripts that are the output of Autoconf when processing the Macro. You
+ need not follow the terms of the GNU General Public License when using
+ or distributing such scripts, even though portions of the text of the
+ Macro appear in them. The GNU General Public License (GPL) does govern
+ all other use of the material that constitutes the Autoconf Macro.
+ .
+ This special exception to the GPL applies to versions of the Autoconf
+ Macro released by the Autoconf Archive. When you make and distribute a
+ modified version of the Autoconf Macro, you may extend this special
+ exception to the GPL to apply to your modified version as well.
+Comment: On Debian systems, the full text of the GNU General Public
+ license version 2 can be consulted in ‘/usr/share/common-licenses/GPL-2’.
+
+Files: src/lemon/*
+Source: http://lemon.cs.elte.hu/trac/lemon
+Copyright: © 2003-2008 Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport (Egervary Research Group on Combinatorial Optimization, EGRES)
+ © 2003 The Trustees of Indiana University
+ © Jeremy Siek 2000
+License: BSL-1.0
+Comment: The files contain the following header:
+  This file is a part of LEMON, a generic C++ optimization library
+ . 
+  Copyright (C) 2003-2008
+  Egervary Jeno Kombinatorikus Optimalizalasi Kutatocsoport
+  (Egervary Research Group on Combinatorial Optimization, EGRES).
+ .
+  Permission to use, modify and distribute this software is granted
+  provided that this copyright notice appears in all copies. For
+  precise terms see the accompanying LICENSE file.
+ .
+  This software is provided "AS IS" with no warranty of any kind,
+  express or implied, and with no claim as to its suitability for any
+  purpose.
+ .
+ The license file at http://lemon.cs.elte.hu/trac/lemon/browser indicates
+ the Boost Software License, Version 1.0.
+
+Files: src/locfit/*
+Copyright: © 1996-2001 Lucent Technologies, Bell Laboratories.
+ © 1996-2001 Jiayang Sun.
+Source: http://stat.bell-labs.com/project/locfit
+License: Locfit
+  ABOUT ALGORITHMS:
+ The Locfit implementation has been designed largely from the point
+ of view of generality: to provide a set of functions that can be
+ used for as wide a range of local fitting problems as possible.
+ It is not intended to be the fastest or most efficient implementation
+ possible. In addition to generality, the code in many places makes
+ extensive trade-offs made between speed and numerical accuracy (some
+ of which can be controlled through optional arguments). Many of Locfit's
+ options will only be used in a small fraction of cases; for other cases,
+ they add to the cost of overhead (an obvious example is multi-dimensional
+ fitting: when used in 1-d, many loops reduce to for(i=0;i<1;i++)).
+ Additionally, the user interfaces (i.e. the R and S-Plus code) add
+ significantly to the computational overhead. For these reasons, the
+ Locfit code, as distributed, should not, and can not, be used to
+ derive meaningful benchmarks, either for the speed or accuracy of algorithms.
+ Anyone wishing to use Locfit in any kind of comparative benchmark
+ study must contact and obtain permission from the Author.
+ .
+  COPYRIGHT:
+ .
+  Copyright (c) 1996-2001 Lucent Technologies, Bell Laboratories.
+  SCB code is
+  Copyright (c) 1996-2001 Jiayang Sun.
+ .
+ Permission to use, copy, modify, and distribute this software for any
+ purpose (with the exceptions noted in `About Algorithms' above)
+ without fee is hereby granted, and provided that this entire notice is
+ included in all copies of any software which is or includes a copy or
+ modification of this software and in all copies of the supporting
+ documentation for such software.
+ .
+ THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTY.  IN PARTICULAR, NEITHER THE AUTHOR NOR LUCENT TECHNOLOGIES
+ MAKE ANY REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE
+ MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE.
+Comment: the files contain “See README file for details.” and the license
+ displayed above is from the README file of the locfit source available at
+ http://stat.bell-labs.com/project/locfit/dist/locfit.tgz
+
 Files: debian/*
 Copyright: 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>
 License: BSL-1.0
@@ -33,3 +148,10 @@ License: BSL-1.0
  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.
+
+License: GAP
+ 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.
+Comment: GAP stands for GNU All Permissive, see:
+ http://www.gnu.org/s/hello/manual/texinfo/All_002dpermissive-Copying-License.html

-- 
Transcript assembly, differential expression, and differential regulation for RNA-Seq.

