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 <tiagooliv...@gmail.com>
Gesendet: Donnerstag, 16. M�rz 2023 17:36:47
An: Ruff, Sergej
Cc: r-package-devel@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.r...@tiho-hannover.de<mailto:sergej.r...@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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