Re: [R] glmmADMB and the GPL -- formerly-- How to buy R.
On Tue May 23 18:01:03 CEST 2006 Dave Fourier wrote: 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
[R] glmmADMB and the GPL -- formerly-- How to buy R.
I promise the list that this will be my last posting regarding this matter. The package glmmADMB is not and never was the property or a product of Otter Research Ltd. It was simply a probram I wrote using ADMB-RE and gave away. I do this all the time to help various people. I don't monitor or try to control what they do with it. The executable nbmm.exe was produced by using the ADMB-RE package, but under our license executables produced using ADMB are freely distributable. See for example the software Coleraine or stock synthesis. As I stated in my earlier post I was motivated to produce software for negative binomial mixed models by a post of Prof Ripleys, that no such good software existed. I assumed that to mean anywhere not just as a currently existing R package. I originally intended this to be just a stand alone program that anyone could use after they put the data into the proper format. I soon realized, however that R users had a different way of thinking about the methods for specifying these models. Since I have extremely limited R skills I asked Anders Nielsen and Hans Skaug if they would be interested in producing something that could be used more easily by R users. They were not paid for this and acted simply out of a wish to provide a service to the R community. I had no idea how that would go and at that point my involvement in the development (except for modifying the nbmm.exe to deal with difficult data) came to an end. Neither Anders or Hans are employees of or own any part of Otter Research Ltd. I am its sole employee/owner. When the package was finished I agreed to host it on my web site. I also put up a forum because I wanted to see how the software worked for people. I appears that Hans put the GPL on the package. He can speak for himself, but I believe he intended the GPL to apply to the R package which he had taken over from Anders and not the nbmm.exe Certainly he would have no authority to bind Otter Research Ltd in this matter. Now as to flames and Lawyers. As I said Otter Research Ltd is a company of one person. I have successfully sold software for 16 years without a lawyer, mostly to the fisheries management community. I never felt the need for a lawyer until I gave something away for free to the R community. I removed the link that Prof Ripley referred to. If there is another offending link I will be happy to remove it as well if you tell me where it is. For those who want to use the software I will put it up in its original form which means that you will need to put your data into the format that an AD Model Builder program requires. It will still have the same functionality but unfortunately will be more difficult for R users to access. Of course if Hans or Anders or anyone else wants to they are welcome to take the nbmm.exe and make it available with their own R package if they can satisfy whatever the requirements are -- just not on my website. Cheers, Dave -- David A. Fournier P.O. Box 2040, Sidney, B.C. V8l 3S3 Canada Phone/FAX 250-655-3364 http://otter-rsch.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] glmmADMB and the GPL -- formerly-- How to buy R.
- Original Message - From: dave fournier [EMAIL PROTECTED] To: r-help@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
[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, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of
Re: [R] glmmADMB and the GPL -- formerly-- How to buy R.
G'day Dave, I have read your e-mail now several time and can't make up my mind if you want a genuine discussion or just trying to do some flame-baiting. But here are my 2 cents. And, in case that you don't read through the whole reply, let me make it clear to you that this is my personal opinion, that probably few people (if any) on this list might agree with me and that I definitely not speak for the list. DF == dave fournier [EMAIL PROTECTED] writes: DF Some of you have been following the discussion of the GPL and DF its inclusion in the glmmADMB package we created for R users. True in my case. DF I would like to provide a bit of background and include an DF email we received from Prof. Ripley [...] It is usually considered bad form to forward privately sent e-mails to a public forum. Some people are even going so far as to argue that e-mails, as other communications, are copyright protected material and that by posting private e-mails, or other communications, to public forums without the permission of the person who sent the private e-mail the poster is breaching copyright laws. So I hope you asked Brian for his permission to post his private e-mail, because I don't remember seeing it posted to any of the mailing lists related to R. In any case, if you wish to positively engage with a community, I would advise you to learn about the rules according to which that community plays. DF so that everyone can be aware of how some might use the GPL to DF try to force access to proprietary software. Well, that is only possible if the software was released under the GPL. So what is the problem? DF I think this is interesting because many have voiced the DF opinion about the benign nature of the GPL and that commercial DF enterprises who avoid it do so mainly out of ignorance. I must have missed these opinions being expressed in this particular thread, but have a vague idea what you are talking about. Though, I have the impression that you are a bit confused as there are two issues: 1) Commercial enterprises who release their software under the GPL. Since these enterprises released their software under the GPL, they should not be ignorant about it and what it implies. If they are, they should sack their lawyers and get better advise. 2) Commercial enterprises who say that they don't want to port their product to Linux (or other GPL based operation systems) with the argument that this would force them to release the source code of their software. To those enterprises it is usually pointed out that they are misinterpreting (or, if you wish, ignorant of) the GPL and that by providing their software on a GPL'd platform they are not forced to supply source code and they can release their software under other licences if they wish. (And it seems that several commercial enterprises got this message as there is quite a bit of commercial software available under Linux these days: S-PLUS, Matlab, Mathematica, Maple,) The case of glmmADMB seems to fall under the first category, it was released under the GPL and you should have been aware of what this means because you decided to release it under the GPL. DF I have noticed two things: Users of the R-help list appear to DF rely largely on the advice of a rather small number of DF statistical experts. How did you notice this? A lot of readers of mailing list choose to reply in private e-mails instead off replies to the list. My default is to reply-to-sender and not reply-to-all; other people's mail-tool have other defaults. The R mailing lists are (as far as I know) configured that reply-to-sender goes only to the sender of the e-mail, not the whole list. Thus, you should be aware that by looking at what gets posted on R-help will give you a biased sample. DF Second, the R users regard R as being more cutting edge and up DF to date than lists devoted to commercial statistical packages DF like SAS. Sorry, I can't parse this sentence. Do you mean that R users regard commercial statistical statistical packages like SAS as being less cutting edge than R? Or that people on lists devoted to commercial statistical packages like SAS have a different opinion about R than R users? Or that R users regard R as being more cutting edge than some other mailing lists? Was there any purpose in this statement other than flame-baiting? DF For these reasons I was surprised to see the following post on DF the web in reply to a question on negative binomial mixed DF models. DF https://stat.ethz.ch/pipermail/r-help/2005-February/066146.html DF I thought that this was bad advice as certainly our ADMB-RE DF software could handle this problem easily. Fair enough. More flame-baiting or would you kindly let us know whether ADMB-RE was available in February 2005? Was glmmADMB (readily) available at that time? I note that the quoted e-mail
