[R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

[Uwe Ligges]

On 17.03.2023 13:09, Ruff, Sergej wrote:
> Thanks,
> 
> 
> I thought about changing it to "Imports", but will it cause any issues when CRAN runs checks on my package and limma isn´t available on CRAN?

No, BioC is a mainstream repository.

Best,
Uwe Ligges



> 
> 
> ________________________________
> Von: Ivan Krylov <krylov.r00t using gmail.com>
> Gesendet: Freitag, 17. März 2023 12:31:23
> An: Ruff, Sergej
> Cc: r-package-devel using r-project.org
> Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
> 
> В Fri, 17 Mar 2023 11:02:18 +0000
> "Ruff, Sergej" <Sergej.Ruff using tiho-hannover.de> пишет:
> 
>> I would like to ask, if I need to add something to the
>> DESCRIPTION-file when declaring Bioconductor dependencies for CRAn
>> Submission.
> 
> Strictly speaking, no. Once you list limma under Suggests, it's
> possible and proper to install your package using
> BiocManager::install('YOUR_PACKAGE', dependencies = TRUE) and have
> limma installed too, as Martin Morgan said above in the thread.
> 
>> Some recommend adding biocViews:
> 
> This field is required on Bioconductor, not CRAN:
> https://contributions.bioconductor.org/description.html?q=biocViews#description-biocviews
> 
>> some recommend adding Remotes: bioc::limma
> 
> Not a standard R/CRAN field, only used by the remotes package:
> https://remotes.r-lib.org/articles/dependencies.html
> 
>> Others add Biocmanager to the suggests file
> 
> I suppose it could help a user who doesn't initially know to use
> BiocManager in order to install your package, and could also be used to
> install limma on behalf of your users (with their permission!), but
> it's additional work, may be hard to get right (see the CRAN policy
> about installing packages and touching user files), and is not required
> at all.
> 
>> What should I add to my Description File to make sure that limma gets
>> installed from Bioconductor when needed?
> 
> See Martin Morgan's e-mail above in the thread. In short, tell your
> users to install your package using BiocManager::install(...,
> dependencies = TRUE) if they want limma to work. They are still free to
> install.packages() if they don't want limma or can set things up
> themselves.
> 
> Move limma to Imports (better) or Depends (may be worse)
> if you want limma to be always available, at the cost of always
> requiring Bioconductor to be set up to have your package installed.
> There are other ways besides BiocManager::install(), but they all
> depend on the user having set up Bioconductor repos in their R session
> somehow, be it BiocManager::repositories() or setRepositories().
> 
> --
> Best regards,
> Ivan
> 
> 	[[alternative HTML version deleted]]
> 
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