[R] glmmADMB and the GPL -- formerly-- How to buy R.

Jason Barnhart jasoncbarnhart at msn.com
Wed May 24 17:52:09 CEST 2006

----- Original Message ----- 
From: "dave fournier" <otter at otter-rsch.com>
To: <r-help at stat.math.ethz.ch>
Sent: Tuesday, May 23, 2006 9:01 AM
Subject: [R] glmmADMB and the GPL -- formerly-- How to buy R.

> Dear List,
> Some of you have been following the discussion of the GPL and its 
> inclusion
> in the glmmADMB package we created for R users. I would like to provide
> a bit of background and include an email we received from
> Prof. Ripley so that everyone can be aware of how some might use the
> GPL to try to force access to proprietary software. I think this is
> interesting because many have voiced the opinion about the benign nature
> of the GPL and that commercial enterprises who avoid it do so mainly out
> of ignorance.
> I have noticed two things:
> Users of the R-help list appear to rely largely on the advice of a
> rather small number of statistical experts. Second, the R users regard R
> as being more cutting edge and up to date than lists devoted to
> commercial statistical packages like SAS.
> For these reasons  I was surprised to see the following post on the web
> in reply to a question on negative binomial mixed models.
>     https://stat.ethz.ch/pipermail/r-help/2005-February/066146.html
> I thought that this was bad advice as certainly our ADMB-RE software
> could handle this problem easily.  However one never knows exactly what
> sort of data people might use in a particular example that could lead to
> difficulties so I decided to code up a program that R users could test
> for this problem.  However R users are used to a different approach for
> model formulation so that it was difficult for the average R user to
> access the program. I approached Anders Nielsen who is both an
> experienced ADMB user and R user and asked him to write an interface in
> R which would make the program more accessible to R users. He created a
> package and the whole thing seems to have had some success with at least
> one PhD thesis based on calculations using it. The R code that Anders
> wrote is simply an interface which takes the R specification for the
> model and outputs a data file in the format the an ADMB program expects.
> The ADMB program is a stand alone exe. The R script then reads the ADMB
> output files and presents the results to the user in a more familiar R
> format. Now it appears at some revision someone put a GPL notice on this
> package although Anders states that he did not do so, and and he is
> certain that it was not originally included by him. In any event the R
> script is easily extracted from the package by those who know how to do
> so and we have no problem with making the ADMB-RE source to the  exe
> (TPL file) available. In fact the original was on our web site but was
> modified as we made to program more robust to deal with difficult data
> sets.  The compiled TPL file links with our proprietary libraries and we
> have no intention of providing the source for these, but that is exactly
> what Prof. Ripley seems to be demanding since he claims that he wants
> the program to run on his computer which it apparently does not do at
> present. Prof. Ripley seems to feel that he is a qualified spokesman for
> the open source community. I have no idea what the community at large
> feels about this.
> What follows is Hans Skaug's post with Prof. Ripley's reply.
> > On Mon, 22 May 2006, H. Skaug wrote:
> >
> >> > About glmmADMB and GPL:
> >> >
> >> > We were not very cautious when we put in the GPL statement.
> >> > What we wanted to say was that the use of glmmADMB is free, and
> >> > does not require a license for AD Model Builder.
> >
> > But that is not what you said, and you are legally and morally bound to
> > fulfill the promise you made.
> >
> >> > Am I correct in interpreting this discussion so that all
> >> > we have to do is to remove the "License: GPL" statement
> >> > from the DESCRIPTION file (and everywhere else it may occur),
> >> > and there will be no conflict between glmmADMB and the
> >> > rules of the R community?
> >
> > I have made a request under the GPL. `All' you have to do is to fulfill
> > it.
> >
> >> > We have temporarily withdrawn glmmADMB until this question has been
> >> > settled.
> >
> > You can withdraw the package, but it has already been distributed under
> > GPL, and those who received it under GPL have the right to
> redistribute it
> > under GPL, including the sources you are obliged to give them.  That's
> > part of the `freedom' that GPL gives.
> >
> >> > hans
> >> >
> >> >
> >> >
> >>> >> Brian Ripley wrote:
> >>> >>
> >>> >> The issue in the glmmADMB example is not if they were required
> to release
> >>> >> it under GPL (my reading from the GPL FAQ is that they probably
> were not,
> >>> >> given that communication is between processes and the R code is
> >>> >> interpreted).
> >> >
> >>> >> Rather, it is stated to be under GPL _but_ there is no source
> code offer
> >>> >> for the executables (and the GPL FAQ says that for anonymous FTP
> it should
> >>> >> be downloadable via the same site, and the principles apply
> equally to
> >>> >> HTTP sites).  As the executables are not for my normal OS and I
> would like
> >>> >> to exercise my freedom to try the GPLed code, I have requested
> the sources
> >>> >> from the package maintainer.
> >> >
> >> >
> >
> > -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied
> Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford,
> Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
> Hans' post was an attempt to reach some sort of consensus with the R
> community so that users who so wished could continue to use the glmmADMB
> software.  So far this is the only response we have received. I guess it
> is up to the R community to decided whether Prof. Ripley speaks for all
> of you.
>     Cheers,
>      Dave


While the background information is appreciated I think some of your
comments are not germane to the glmmADMB issue.  Here are my thoughts:

    1) Perceiving our reliance upon a small group of experts on the
       r-help list is a bit presumptuous.  Personally, I have several
       friends and colleagues elsewhere to rely upon.  I try not to
       wear out my welcome with them, just as I endeavor the same with
       the R-help list.

    2) Clearly, Prof. Ripley does not speak for the entire community and
       he doesn't appear to make that claim to in any of the material below
       or that I've seen in archives. He's one member exercising his right
       as a list member, developer, etc. to pursue an issue that he
       deems important.  (One need not even be an R user to challenge your
       choice of license and source code availability.)

       Clearly you have a right to state your opinions.  It just appears
       gratuitous when you do so in this manner.

    3) IMHO the status of the proprietary code is possibly in doubt from
       purely a legal perspective.

       Prior posts note your intent was to keep certain portions of the
       source code proprietary.  *I* think it is reasonable
       to agree that you intended this and attempted to communicated this.

       It is unclear how much rigor you applied to ensure your legal rights
       were protected when documenting your choice of license.

       However, withdrawing the glmmADMB package itself seems "a day late
       and a dollar short."  The package itself appears to be GPL'ed and it
       appears that Otter Research is aware of that.

    4) I agree w/ those comments made by Berwin Turlach and Marc Schwartz.

Otherwise, I would extend a general thank you for contributing an R package.
Although I don't use glmmADMB, your generosity as a contributor is noted 
perhaps not always explicitly recognized.

I do hope that Otter Research finds a solution to its current predicament.


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