[R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran

Uwe Ligges ||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de
Mon Jun 26 21:03:28 CEST 2023 


On 26.06.2023 02:52, Bernd.Gruber wrote:
> Thanks, just to make sure:
> 
> In the policy I find the entry:
> 
> Additional_repositories:

You can use this for CRAN-style repositories. Not for other inds of 
storage. In that case you need to decalre it as written text in the 
Description field.

Best,
Uwe Ligges


> The ‘Additional_repositories’ field is a comma-separated list of repository URLs where the packages named in the other fields may be found. It is currently used by R CMD check to check that the packages can be found, at least as source packages (which can be installed on any platform).
> 
> And here I would have to provide an url that links to the tar.gz file of the package, or can I also provide
> 
> The ‘Additional_repositories’ field is a comma-separated list of repository URLs where the packages named in the other fields may be found. It is currently used by R CMD check to check that the packages can be found, at least as source packages (which can be installed on any platform).
> 
> github::green-striped-gecko/dartR.popgenomics
> 
> similar to the Remotes: field (which I think is not possible to use).
> 
> Thanks,
> 
> 
> ==============================================================================
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> From: Uwe Ligges <ligges using statistik.tu-dortmund.de>
> Sent: Sunday, 25 June 2023 20:51
> To: Bernd.Gruber <Bernd.Gruber using canberra.edu.au>
> Cc: r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran
> 
> 
> 
> On 25.06.2023 09:00, Bernd.Gruber wrote:
>> Hi,
>>
>> Thanks for the advice.
>>
>> Still not 100% sure if that is okay to submit to CRAN.
>>
>> As mentioned I have new packages that have others in the suggest (and yes the examples/tests run fine by making the dependent),
>>
>> But if I have a package that is not yet on CRAN in the suggest I see that running winbuilder.
>>
>> Suggests or Enhances not in mainstream repositories:
>> dartR.sim
> 
> If it is not in a mainstream repo, you can declare where users can get
> it from, see the explanation in the CRAN policies how to declare it.
> 
> 
> 
>> * checking package namespace information ... OK
>> * checking package dependencies ... NOTE
>> Package suggested but not available for checking: 'dartR.sim'
> 
> This is OK, once the former is explained.
> 
> Best,
> Uwe Ligges
> 
> 
>>
>>
>>
>>
>> Can I explain when I submit that dartR.sim will be there (as mentioned the examples run fine), but obviously is not yet on CRAN.
>>
>> I assume the same would happen if I put the new packages in Enhances…
>>
>> Regards, Bernd
>>
>>
>>
>>
>> From: Thierry Onkelinx <thierry.onkelinx using inbo.be<mailto:thierry.onkelinx using inbo.be>>
>> Sent: Friday, June 23, 2023 5:51 PM
>> To: Simon Urbanek <simon.urbanek using r-project.org<mailto:simon.urbanek using r-project.org>>
>> Cc: Bernd.Gruber <Bernd.Gruber using canberra.edu.au<mailto:Bernd.Gruber using canberra.edu.au>>; r-package-devel using r-project.org<mailto:r-package-devel using r-project.org>
>> Subject: Re: [R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran
>>
>> Dear Bernd,
>>
>> You could contact the maintainer of the spatstat package. They did the same thing (splitting a large package into several smaller ones) a few years ago.
>>
>> Having the base package suggesting an add-on and the add-on depending on or suggesting the base package might create an unwanted loop.
>>
>> Best regards,
>>
>> ir. Thierry Onkelinx
>> Statisticus / Statistician
>>
>> Vlaamse Overheid / Government of Flanders
>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>> thierry.onkelinx using inbo.be<mailto:thierry.onkelinx using inbo.be<mailto:thierry.onkelinx using inbo.be%3cmailto:thierry.onkelinx using inbo.be>>
>> Havenlaan 88 bus 73, 1000 Brussel
>> www.inbo.be<http://www.inbo.be><http://www.inbo.be<http://www.inbo.be>>
>> ///////////////////////////////////////////////////////////////////////////////////////////
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>> The plural of anecdote is not data. ~ Roger Brinner
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>>
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>>
>>
>> Op vr 23 jun 2023 om 06:52 schreef Simon Urbanek <simon.urbanek using r-project.org<mailto:simon.urbanek using r-project.org<mailto:simon.urbanek using r-project.org%3cmailto:simon.urbanek using r-project.org>>>:
>> Bernd,
>>
>> the sequence in which you submit doesn't matter - the packages have to work regardless of the sequence. Suggests means that the dependency is optional, not that it can break tests. You have to skip the tests that cannot be run due to missing dependencies (see 1.1.3.1<http://1.1.3.1><http://1.1.3.1<http://1.1.3.1>> in R-exts)
>>
>> Cheers,
>> Simon
>>
>>
>>
>>> On Jun 23, 2023, at 2:35 PM, Bernd.Gruber <Bernd.Gruber using canberra.edu.au<mailto:Bernd.Gruber using canberra.edu.au<mailto:Bernd.Gruber using canberra.edu.au%3cmailto:Bernd.Gruber using canberra.edu.au>>> wrote:
>>>
>>> Hi,
>>>
>>> I have a question regarding the separation of a package into smaller pieces (to avoid long testing/installation times and more important to avoid to many dependencies)
>>>
>>> I am the maintainer of an R package (dartR) which has grown and is now at the limit in terms of testing/run time and also dependencies. To further develop the package we started to break the package into smaller packages namely
>>>
>>>
>>> Two core packages (dartR.base and dartR.data) and here dartR.base has dartR.data in the depends. (dartR.base is 60% of the previous package) and dartR.data is our data.package for test data (dartR.data is already on CRAN)
>>>
>>>
>>>
>>>
>>> Next to the two core packages we also have 3 more addon packages that deal with specialised analysis
>>>
>>> dartR.sim
>>> dartR.spatial
>>> dartR.popgenomics.
>>>
>>> Those packages depend on dartR.base and dartR.data.
>>>
>>> All addon packages and core packages should have the other addon packages as suggests, hence here comes the question.
>>>
>>>
>>> How do I submit the packages? All of them at once? Or step by step.
>>>
>>> If I submit step by step (e.g. dartR.base) it obviously cannot have the other dartR addon packages as suggests (cannot be tested and will break the CRAN tests).
>>>
>>> So would be the correct way to:
>>> Submit dartR.base (without dartR.sim, dartR.spatial and dartR.popgenomics in the suggest.)
>>> Then submit dartR.sim, then dartR.spatial and finally dartR.popgenomics (all without suggests of the other packages)
>>>
>>> And finally update all packages (only their description file and add the suggests once they are on CRAN).
>>>
>>> Hope that makes sense and thanks in advance,
>>>
>>> Bernd
>>>
>>
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