GNU bug report logs - #28946
licence problem with cufflinks

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Dave Love <fx <at> gnu.org>
To: bug-guix <at> gnu.org
Subject: licence problem with cufflinks
Date: Sun, 22 Oct 2017 17:52:42 +0100

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>.

Message #8 received at 28946 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Dave Love <fx <at> gnu.org>
Cc: 28946 <at> debbugs.gnu.org
Subject: Re: bug#28946: licence problem with cufflinks
Date: Sun, 22 Oct 2017 23:39:11 +0200

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

    http://web.archive.org/web/20070616194305/http://cm.bell-labs.com/cm/ms/departments/sia/project/locfit/dist/locfit.tgz

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/

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Message #11 received at 28946 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Dave Love <fx <at> gnu.org>
Cc: 28946 <at> debbugs.gnu.org
Subject: Re: bug#28946: licence problem with cufflinks
Date: Tue, 24 Oct 2017 09:10:51 +0200

Ricardo Wurmus <rekado <at> elephly.net> writes:

> 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 have written email to coletrap <at> uw.edu to report my findings and ask
about details.

> 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.

That’s still what I intend to do.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

Message #14 received at 28946 <at> debbugs.gnu.org (full text, mbox):

From: Dave Love <fx <at> gnu.org>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 28946 <at> debbugs.gnu.org
Subject: Re: bug#28946: licence problem with cufflinks
Date: Tue, 24 Oct 2017 11:03:02 +0100

Ricardo Wurmus <rekado <at> elephly.net> writes:

> Ricardo Wurmus <rekado <at> elephly.net> writes:
>
>> 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 have written email to coletrap <at> uw.edu to report my findings and ask
> about details.

Sorry, I could probably have saved you effort.  I think I already mailed
before cufflinks moved to github, and I also tried to track down the
author of the problematic component, though they probably wouldn't hold
the copyright as far as I remember..

Message #19 received at 28946-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Dave Love <fx <at> gnu.org>
Cc: 28946-done <at> debbugs.gnu.org
Subject: Re: bug#28946: licence problem with cufflinks
Date: Tue, 31 Oct 2017 08:19:10 +0100

Dave Love <fx <at> gnu.org> writes:

> Ricardo Wurmus <rekado <at> elephly.net> writes:
>
>> Ricardo Wurmus <rekado <at> elephly.net> writes:
>>
>>> 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 have written email to coletrap <at> uw.edu to report my findings and ask
>> about details.
>
> Sorry, I could probably have saved you effort.  I think I already mailed
> before cufflinks moved to github, and I also tried to track down the
> author of the problematic component, though they probably wouldn't hold
> the copyright as far as I remember..

I have not received any response; neither to the bug report, nor to the
email I sent.  I have removed cufflinks from Guix with commit 7bf59f702.

Thanks again for the report!

So… I’ll try to see if I can adapt the GPL code from r-locfit in a fork
of Cufflinks at some point.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
https://elephly.net

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