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

[Tiago Olivoto]

Hi Sergej,

I sincerely don't know if the position of biocView really matters (I'll try
it when preparing for the new CRAN release of pliman). I believe that
biocView will not allow you to put limma in the imports field and
automatically install it from Bioconductor, as you can see here in this
discussion <
https://stackoverflow.com/questions/54411495/bioconductor-packages-not-installing-with-biocviews-specification-in-description
>

In my case, I had no errors when submitting pliman to CRAN using EBImage as
suggests (I haven't yet tried to use biocView: and EBImage in the Imports
section).

Best regards,
Olivoto

Em qui., 16 de mar. de 2023 às 14:01, Ruff, Sergej <
Sergej.Ruff using tiho-hannover.de> escreveu:

> thank you.
>
>
> I see you added biocView: below your suggested Dependencies. Is it
> necessary for CRAN to identify Bioconductor Dependencies and if so, should
> I add it below or above the suggested packages? Do I also need BiocManager
> among my Suggests?
>
>
> Last question: How does CRAN work with Bioconductor Dependencies? Will
> CRAN accept limma as a dependency or will my submission be rejected?
>
>
> Best regards,
>
> Sergej
> ------------------------------
> *Von:* Tiago Olivoto <tiagoolivoto using gmail.com>
> *Gesendet:* Donnerstag, 16. März 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 às 11:18, Ruff, Sergej <
> 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?
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-package-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>

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