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

[Duncan Murdoch]

On 16/03/2023 12:36 p.m., Tiago Olivoto wrote:
> 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.

If some other package loads but doesn't attach pliman, and is missing 
EBImage, does it fail gracefully?  That's also important.  I'd test what 
happens if a user runs pliman::object_edge( ... ) .  (That function 
isn't in the CRAN version, just the Github version, so I haven't tried 
this.)

Duncan Murdoch


> 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]]
>>
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> 
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