[R-pkg-devel] Import package countreg that is not on CRAN

[Duncan Murdoch]

Yes, thanks, I missed that option.

On 13/11/2020 10:11 a.m., Henrik Bengtsson wrote:
> You can change your package from using:
> 
>    Imports: countreg
> 
> to use:
> 
>    Suggests: countreg
> 
> For this to work, you'll have to update your code, package tests,
> examples, and vignettes, to run conditionally on 'countreg' being
> installed, e.g.
> 
> if (requireNamespace("countreg", quietly = TRUE)) {
>    ...
> }
> 
> Whether or not this makes sense depends on how central 'countreg' is
> to your package.  If it is only needed optionally and for a small part
> of your functionality, then it's doable but if it's a mission-critical
> dependency, it might be too much of a hack.
> 
> This is in compliance with CRAN and in agreement with what Uwe says too.
> 
> I've used this myself in for instance
> https://cran.r-project.org/web/package=aroma.core where small parts of
> the functionality depend on packages not in the mainstream (= CRAN &
> Bioconductor) repositories. This allows those who wish to use
> alternative methods, if they want to go the extra mile to install
> them.  Also, if they're popular enough it might nudge the maintainers
> of those enough to submit to CRAN or Bioconductor - a process that
> might take years, if at all.
> 
> /Henrik
> 
> On Fri, Nov 13, 2020 at 3:23 AM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>>
>> On 13/11/2020 3:10 a.m., Jason Luo wrote:
>>> Hi,
>>>
>>> I'm submitting a new package (https://github.com/Penncil/pda/) to CRAN. It
>>> relies on some function (zerotrunc and hurdle in R/ODAP.R) from countreg (
>>> https://rdrr.io/rforge/countreg/) , which is not on CRAN. The submission
>>> returns error as below
>>>
>>> https://win-builder.r-project.org/incoming_pretest/pda_1.0_20201113_083442/Debian/00check.log
>>>
>>> Seems the r-forge repo is identified in the DESCRIPTION
>>> Additional_repositories, but countreg is still not available. I assume this
>>> is not a rare problem but didn't find useful solutions online. Any
>>> suggestions? Thanks!
>>
>> If countreg is not in one of the mainstream repositories (CRAN or
>> Bioconductor), then it may not have been subject to careful testing, so
>> CRAN sees it as unreliable.  Since your package depends on it, yours is
>> also unreliable, so CRAN won't publish it.
>>
>> I don't know anything about the pda or countreg packages, so this is
>> general advice on what you could do, and may not be applicable here:
>>
>>     - you could take over maintenance of countreg (if its current
>> maintainer agrees), and put in the work to get it on CRAN.
>>     - you could copy parts of countreg to your own package (if its
>> license allows that), and drop your dependence on it.
>>     - you could substitute some other CRAN package that provides
>> equivalent functionality and depend on that instead.
>>     - you could drop the parts of your package that need countreg, and
>> submit a smaller package to CRAN without that dependency.
>>     - you could publicize that your package is on Github, and give up on
>> publishing it on CRAN.
>>
>> Duncan Murdoch
>>
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