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

[Ruff, Sergej]

Thanks.


I would like to ask, if I need to add something to the DESCRIPTION-file when declaring Bioconductor dependencies for CRAn Submission.


Right now I only listed limma under "suggests".


I asked online and get conflicting answers. Some recommend adding biocViews: above suggests and some recommend adding

Remotes: bioc::limma


Others add Biocmanager to the suggests file in Addition to limma.


Is that necessary? What should I add to my Description File to make sure that limma gets installed from Bioconductor when needed?



________________________________
Von: Ivan Krylov <krylov.r00t using gmail.com>
Gesendet: Freitag, 17. März 2023 11:45:57
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 10:19:37 +0000
"Ruff, Sergej" <Sergej.Ruff using tiho-hannover.de> пишет:

> Thats the source of my worries. Will the same error appear when CRAN
> checks the examples of my package? Or should I not be worried?

Yes, part of CRAN checks is running your package without the packages
listed under Suggests:
https://www.stats.ox.ac.uk/pub/bdr/noSuggests/README.txt [*]

See WRE 1.1.3.1 for the official guidance on how to handle optional
dependencies that might not be installed:
https://cran.r-project.org/doc/manuals/R-exts.html#Suggested-packages

In short, your code should check the return value of
requireNamespace('limma', quietly = TRUE) before trying to run code
from it. Your code can (and probably should) raise an error if asked to
do something using limma when it's not available, but then in your
tests/vignettes/examples you should check whether limma is available
before trying to run that code.

--
Best regards,
Ivan

[*] See also:
https://cran.r-project.org/web/checks/check_issue_kinds.html

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