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

[Ruff, Sergej]

I implemented a function to check if limma is available as suggested by Berry and Tiago.

It works fine when limma is pre-installed.
When Limma is not pre-installed, I get the following Note:

"Package suggested but not available for checking: 'limma'".

Seems like the functions isn't installing limma.
Is there something I am missing? I added BiocManager and limma to the suggests and utils to Imports.

check_limma <- function() # Returns TRUE if available, FALSE otherwise
{
  if(requireNamespace("limma", quietly=TRUE)) return(TRUE)
  if(!interactive()) return(FALSE)
  inst <- menu(c("Yes", "No"), title="Package {limma} required but not installed.\nDo you want to install it now?")
  if(inst != 1)
  {
    message("To run this example, first install {limma} following the directions at 'https://bioconductor.org/packages/limma'")
    return(FALSE)
  }
  # the following could be wrapped in try and conditionally return TRUE / FALSE
  if(!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager", quiet=TRUE)
  BiocManager::install("limma", update=FALSE, ask=FALSE, quiet=TRUE)
  return(TRUE)
}

The check also never brings up the menu to ask me, if limma should be installed. Is that normal or should I change something about the
function.

Regards,
Sergej


________________________________
Von: Tiago Olivoto <tiagoolivoto using gmail.com>
Gesendet: Donnerstag, 16. M�rz 2023 17:36:47
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

Hi,
My package pliman depends on EBImage which is in Bioconductor. I have created a function check_ebi() <https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534> that is called in .onAttach() <https://github.com/TiagoOlivoto/pliman/blob/master/R/zzz.R#L36>  and checks if EBImage is installed. If not, the function asks the user to install it. Both EBImage and BiocManager are listed as suggests <https://github.com/TiagoOlivoto/pliman/blob/master/DESCRIPTION#L22>

I believe that this could be a possible solution
Best regards,
Olivoto


Em qui., 16 de mar. de 2023 �s 11:18, Ruff, Sergej <Sergej.Ruff using tiho-hannover.de<mailto:Sergej.Ruff using tiho-hannover.de>> escreveu:
I am currently building a package which uses the "limma"-package as a dependency.

I want to submit my package to CRAN.

Do I need to declare Bioconductor-dependencies such as Limma differently in the Description-File of my Package?

The Check-Function in R shows no Notes, Warnings or Errors, but I am not sure if that means that limma will install when installing my package from CRAN.

Currently I am declaring limma like this:

Suggests:

    limma



Can CRAN identify that limma is a Bioconductor-Package and will it Limma install, when installing my package from CRAN?

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