[Bioc-devel] License question

Robert Gentleman rgentlem at fhcrc.org
Thu Jan 10 20:42:27 CET 2008


pingou wrote:
> Dear all,
> Packaging the Bioconductor libraries for Fedora, we are facing a

   First it is great that you are interested in packaging (I am guessing 
rpm or what ever variant is now popular).  I am sure many authors will 
be glad to help you out.  I have a few comments and questions.

   Could you clarify what you mean by "libraries" here? Bioconductor is 
a loosely connected set of packages (no libraries), each with 
potentially different licenses and some with non-standard licenses.  We 
do not require users to adhere to any particular set of licenses, so 
there will always be packages that do not meet pretty much any set of 

> problem, that I think could be easily solved.
> Many packages are not clear about their license, most of them are
> declared to be under the LGPL license,
> but some of them do not precise clearly which version of this license.

   Some specific examples might be nice. Last time I checked most were 
quite specific, with some exceptions (as I noted above).  You might also 
want to check with Kurt Hornik who not very long ago sent a list of 
anomalies to us and as far as I know most were resolved, and those that 
were not are not easily resolvable.

> Would it be possible to add a copy of the license used in every package?

   Why not do that as part of your packaging if you need it there? In my 
experience license files get out of date, and references to standard 
licenses in more or less standard locations tends to be a better 
practice.  In the old days, distributing the LICENSE file was useful as 
some folks would have had trouble locating it. But these days that is 
just not true.

> Adding this file to R packages is now straightforward, indeed the
> announce of the release of R 2.6.0 [1] says :
>      A standard for specifying package license information in the
>          DESCRIPTION License field was introduced, see 'Writing R
>          Extensions'.  In addition, files LICENSE or LICENCE in a package
>          top-level source directory are now installed (so putting copies
>          into the 'inst' subdirectory is no longer necessary).
> Could you possibly add to on the Bioconductor guidelines/requirements
> that a copy of the license be added to each package, and which version
> of the LGPL is being used?  Usually this will be LGPL v2.1 "or any later
> version" (saying "or any later version" is very important for
> compatibility with newer GNU licenses like LGPL v3 or GPL v3).

   We do from time to time ask authors to clarify their licenses, if 
they can (and some cannot).  Personally I am not in favor of either LGPL 
or GPL v3, and think that such changes are so substantial that package 
authors would need to make those decisions themselves and should 
carefully consider the ramifications of such decisions. I would not be 
comfortable suggesting that they adopt language of the form "or any 
later version" in regard to the GPL or its variants (or any other 
license for that matter).

> In addition the GNU licenses recommend that the version of the license
> be added near the top of each source file (e.g. in a comment block):

  I can't see how that is of any real benefit to anyone, and certainly a 
burden on package authors. But your request here may get some to do it.
What it does do is to make it harder to change licenses (as every file 
needs to be modified) or to release under multiple licenses.

>      This file is part of Biconductor package Foobar.
>      Foobar is free software: you can redistribute it and/or modify
>      it under the terms of the GNU Lesser General Public License as
> published by
>      the Free Software Foundation, either version 2.1 of the License, or
>      (at your option) any later version.
>      Foobar is distributed in the hope that it will be useful,
>      but WITHOUT ANY WARRANTY; without even the implied warranty of
>      GNU General Public License for more details.
>      You should have received a copy of the GNU General Public License
>      along with Foobar.  If not, see <http://www.gnu.org/licenses/>.
> The GNU project page[2] and Fedora's licensing page[3] have more
> information.

   Yes, and they seem to require that license changes be announced. That 
is really not going to happen. In particular from [3]:

A license change in a package is a very serious event - it has as many, 
if not more, implications for related packages as ABI changes do.

Therefore, if your package changes license, even if it just changes the 
license version, it is required that you announce it on fedora-devel-list.

Note that any license change to a more restrictive license or license 
version may affect the legality of portions of Fedora as a whole; ergo, 
FESCo reserves the right to block upgrades of packages to versions with 
new licenses to ensure the legal distribution of Fedora.

Please contact FESCo if you have any questions.

Seems like it imposes restrictions on us that we don't want. I am not 
sure how you might deal with it, but there is no way we could agree to 
these terms.

  thanks for your interest


> Adding these license clarifications will greatly increase the speed by
> which Bioconductor packages can be reviewed and included in Fedora, as
> we won't have to go manually verifying the license for each package with
> the individual maintainer, but can simply check the source code.
> Thanks in advance for this clarification,
> Best regards,
> P.Yves
> [1] https://stat.ethz.ch/pipermail/r-announce/2007/000832.html
> [2] http://www.gnu.org/licenses/gpl-howto.html
> [3] http://fedoraproject.org/wiki/Licensing
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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