Re: [R-pkg-devel] extending as.mcmc.list

2018-04-12 Thread Joe Thorley 
Hi Georgi

That fixed it

Thanks

Joe

> On Apr 12, 2018, at 08:27, Georgi Boshnakov 
>  wrote:
> 
> The following is in your NAMESPACE:
> 
> export(as.mcmc.list)
> 
> Don't export as.mcmc.list, presumably this is the one from 'coda ' it is 
> rarely your responsibility.
> 
> 
> Georgi Boshnakov
> 
> -Original Message-
> From: R-package-devel [mailto:r-package-devel-boun...@r-project.org 
> ] On Behalf Of Joe Thorley
> Sent: 12 April 2018 16:01
> To: r-package-devel@r-project.org 
> Subject: [R-pkg-devel] extending as.mcmc.list
> 
> The S3 generic function coda::as.mcmc.list has a check exclusion in 
> R-devel/src/library/tools/R/utils.R.
> 
> I am trying to extend it to objects of various classes
> 
> https://github.com/poissonconsulting/mcmcr/blob/master/R/as.mcmc.list.R 
>   >
> 
> However I get the note 
> 
> Found the following apparent S3 methods exported but not registered:
>  as.mcmc.list
> See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
> manual.
> 
> Although this note is discussed on r-package-devel
> 
> https://stat.ethz.ch/pipermail/r-package-devel/2017q2/001531.html 
>   >
> 
> I am unclear about how I should resolve the issue.
> 
> Currently I am considering renaming the function to as.mcmc_list although 
> this feels somewhat unsatisfactory.
> 
> Any advice is appreciated
> 
> Joe
> 
> Joe Thorley PhD, RPBio
> Computational Biologist
> Poisson Consulting Ltd.
> 4216 Shasheen Road
> Nelson, BC
> V1L 6X1, Canada
> Tel: +1 250 551 2194
> Email: j...@poissonconsulting.ca
> Web: www.poissonconsulting.ca
> Skype: joethorley
> 
> 
> 
> 
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> 
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> 
Joe Thorley PhD, RPBio
Computational Biologist
Poisson Consulting Ltd.
4216 Shasheen Road
Nelson, BC
V1L 6X1, Canada
Tel: +1 250 551 2194
Email: j...@poissonconsulting.ca
Web: www.poissonconsulting.ca
Skype: joethorley




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Re: [R-pkg-devel] extending as.mcmc.list

2018-04-12 Thread Georgi Boshnakov 
The following is in your NAMESPACE:

export(as.mcmc.list)

Don't export as.mcmc.list, presumably this is the one from 'coda ' it is rarely 
your responsibility.


Georgi Boshnakov

-Original Message-
From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf 
Of Joe Thorley
Sent: 12 April 2018 16:01
To: r-package-devel@r-project.org
Subject: [R-pkg-devel] extending as.mcmc.list

The S3 generic function coda::as.mcmc.list has a check exclusion in 
R-devel/src/library/tools/R/utils.R.

I am trying to extend it to objects of various classes

https://github.com/poissonconsulting/mcmcr/blob/master/R/as.mcmc.list.R 


However I get the note 

Found the following apparent S3 methods exported but not registered:
  as.mcmc.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

Although this note is discussed on r-package-devel

https://stat.ethz.ch/pipermail/r-package-devel/2017q2/001531.html 


I am unclear about how I should resolve the issue.

Currently I am considering renaming the function to as.mcmc_list although this 
feels somewhat unsatisfactory.

Any advice is appreciated

Joe

Joe Thorley PhD, RPBio
Computational Biologist
Poisson Consulting Ltd.
4216 Shasheen Road
Nelson, BC
V1L 6X1, Canada
Tel: +1 250 551 2194
Email: j...@poissonconsulting.ca
Web: www.poissonconsulting.ca
Skype: joethorley




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[R-pkg-devel] extending as.mcmc.list

2018-04-12 Thread Joe Thorley 
The S3 generic function coda::as.mcmc.list has a check exclusion in 
R-devel/src/library/tools/R/utils.R.

I am trying to extend it to objects of various classes

https://github.com/poissonconsulting/mcmcr/blob/master/R/as.mcmc.list.R 


However I get the note 

Found the following apparent S3 methods exported but not registered:
  as.mcmc.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

Although this note is discussed on r-package-devel

https://stat.ethz.ch/pipermail/r-package-devel/2017q2/001531.html 


I am unclear about how I should resolve the issue.

Currently I am considering renaming the function to as.mcmc_list although this 
feels somewhat unsatisfactory.

Any advice is appreciated

Joe

Joe Thorley PhD, RPBio
Computational Biologist
Poisson Consulting Ltd.
4216 Shasheen Road
Nelson, BC
V1L 6X1, Canada
Tel: +1 250 551 2194
Email: j...@poissonconsulting.ca
Web: www.poissonconsulting.ca
Skype: joethorley




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Re: [R-pkg-devel] GPL + other licence

2018-04-12 Thread David C Sterratt 
Thanks to all for your helpful replies.

It seems reasonable to consider that the whole package is indeed
licensed under GPL >= 3, and I can therefore remove the LICENSE file.
The Qhull COPYING.txt notice is included in the inst/doc directory, as
required by the Qhull licence, so I think all should be OK.

If the CRAN maintainers are happy with this proposal, that will resolve
a major R-packaging headache, so thanks again.

Best wishes,

David.


On Wed 11 Apr 2018 at 16:58 BST, Martyn Plummer  wrote:

> I agree with Brian. This type of license is classified by the Free
> Software Foundation as "lax" or "permissive" because it does not
> prevent incorporation of the code into proprietary software.
>
> Here is what Richard Stallman has to say: https://www.gnu.org/licenses/
> license-compatibility.en.html
>
> "[L]ax licenses are usually compatible with any copyleft license. In
> the combined program, the parts that came in under lax licenses still
> carry them, and the combined program as a whole carries the copyleft
> license."
>
> Hence you can license your package under the GPL.
>
> Martyn
>
> On Tue, 2018-04-10 at 08:14 -0500, Brian G. Peterson wrote:
>> I'm not a lawyer, but I don't see why the entire package can't be
>> released under GPL, while also respecting the QHull license for the
>> QHull code and the derived QHull portions.
>>
>> Many existing R packages released under GPL, and R itself, include BSD
>> and MIT licensed code.
>>
>> The QHull license is a very permissive license, basically BSD or MIT-
>> like in its permissions.
>>
>> BSD and MIT code may be included in GPL'd code, as long as its license
>> (inclusion of the copyright notice, etc.) is also included where
>> required.
>>
>> GPL applies to the entire work, in this case the R package.  I think
>> you should discuss this with the CRAN maintainers and release the
>> package under GPL.
>>
>> Regards,
>>
>> Brian
>>


--
David C Sterratt, Senior Research Associate
Institute for Adaptive and Neural Computation, School of Informatics
University of Edinburgh, 10 Crichton Street, Edinburgh EH8 9AB, Scotland, UK
http://homepages.inf.ed.ac.uk/sterratt - tel: +44 131 651 1739

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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