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bug#28946: licence problem with cufflinks

From: Ricardo Wurmus
Subject: bug#28946: licence problem with cufflinks
Date: Sun, 22 Oct 2017 23:39:11 +0200
User-agent: mu4e 0.9.18; emacs 25.3.1

Hi Dave,

> I noticed that there's a package for cufflinks, but it has a non-free
> component.  It isn't packaged for Debian or Fedora because of that.  See
> <https://github.com/cole-trapnell-lab/cufflinks/issues/16>.

Thank you for the information! I’m going to investigate this.

I downloaded an original release of C locfit from


and compared it to the copy in the Cufflinks repository at commit
d402b182fabd9a831ccb4173e3cb3a2d2dd2e75e (May 2011).

After copying a couple of files from src-c to src they do seem rather
similar, but with about a thousand lines worth of differences (excluding
whitespace changes).  However, it doesn’t look like the code is based on
any of the GPL versions on CRAN[1], because the archives there do not
contain certain files (such as “ar_funs.c”).

If we could be reasonably sure that the code is a derivative of the
GPL’d locfit code from CRAN we essentially deal with a GPL violation,
and not a case of non-free software.

I’ll review this problem and will remove cufflinks by the end of this if
we come to the conclusion that it cannot be considered free.

[1]: https://cran.r-project.org/src/contrib/Archive/locfit/


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