Hi, On Wed, Jul 30, 2014 at 11:42:03AM +0100, Dave Love wrote: > > RNA-seq results by using TopHat and Cufflinks softwares. > > cufflinks appears to be non-free, in which case it can't go into Fedora, > though there doesn't seem to have been a ruling from fedora-legal on it. The "non-free-ness" in Debian is caused by the use of locfit. I'm quoting the relevant section from debian/copyright: Files: src/locfit/* Copyright: © 1996-2001 Lucent Technologies, Bell Laboratories. © 1996-2001 Catherine Loader. 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 Source: http://stat.bell-labs.com/project/locfit So while the code is free software the restriction: ... should not, and can not, be used to derive meaningful benchmarks, either for the speed or accuracy of algorithms. is something what is regarded as non-free by Debian. I several times tried to contact the authors about this but never got any response. I'd be interested about the opinion of fedora-legal. Kind regards Andreas. -- http://fam-tille.de _______________________________________________ scitech mailing list scitech@xxxxxxxxxxxxxxxxxxxxxxx https://admin.fedoraproject.org/mailman/listinfo/scitech
