[R-pkg-devel] Conditionally use packages from Bioconductor

[Daniel Lüdecke]

Thanks for the quick reply! I was a bit uncertain about this due to the CRAN check notes from this package:
https://cran.r-project.org/web/checks/check_results_BiocManager.html

That made me think that the reason why the packages which are not available for testing are hosted on Bioconductor.

Daniel

-----Ursprüngliche Nachricht-----
Von: Uwe Ligges [mailto:ligges using statistik.tu-dortmund.de] 
Gesendet: Mittwoch, 5. Februar 2020 16:08
An: Daniel Lüdecke <d.luedecke using uke.de>; r-package-devel using r-project.org
Betreff: Re: [R-pkg-devel] Conditionally use packages from Bioconductor



On 05.02.2020 16:05, Daniel Lüdecke wrote:
> Dear all,
> 
> for a package that is already published on CRAN, we plan to include a 
> function that relies on the M3C-package, which is on Bioconductor only.
> Since this function in M3C is not essential for most other functions 
> of our package, we thought about adding M3C to the "Suggests" field in 
> the DESCRIPTION file, and from the "Writing R Extensions" page we 
> found that we could also add the URL to the "Additional_repositories" 
> field of the DESCRIPTION file (Additional_repositories:
> https://bioconductor.org/packages/release/bioc/html/M3C.html).

BioC is a standard repository that you do not need to delcare.

Best,
Uwe Ligges



> Would this be the correct way to conditionally use a package from 
> Bioconductor in own packages?
> 
> Best
> Daniel
> 
> 
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Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de
Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Marya Verdel
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SAVE PAPER - THINK BEFORE PRINTING