[R-pkg-devel] Documenting dependencies on Bioconductor packages

[Kristian Hovde Liland]

Hi.

No one knows how to properly document Bioconductor dependencies, or is it too obvious to warrant a response?

Best regards,
Kristian Hovde Liland

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Fra: R-package-devel <r-package-devel-bounces at r-project.org> på vegne av Kristian Hovde Liland <kristian.liland at nmbu.no>
Sendt: 21. juni 2016 09:00
Til: r-package-devel at r-project.org
Emne: [R-pkg-devel] Documenting dependencies on Bioconductor packages

​Dear package developers.

We are developing a set of R packages that perform statistics and classification on nucleotide sequence data. For efficient reading and writing of such data the package depends on the Biostrings package hosted by Bioconductor.

Being a mainstream repository, dependencies on Bioconductor packages have been considered okay; minus out-of-sync package updates and different hosting structure (separate devel branch at Biostrings and different recommended installation strategy).

CRAN policy enforcing is becoming stricter (which is very good considering the sheer amount of new packages arriving and future proofing), and thus we received a reply after submitting one of our packages as follows:
"Can you pls improve the Description to make clearer that you refer to the 'Biostrings' package from BioC?".

I haven't found any good examples on how to include such information in the descriptions. Is it sufficient to write at the end: "This package depends on the Biostrings package hosted by Bioconductor.", or is there a formal or more elegant way of including this information? I find documentation and CRAN policies to be a bit sparse on the subject. From other previous mailing list and forum discussions I gather that Bioconductor should not be added to the Additional_repositories list.

Best regards,
Kristian Hovde Liland
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