[Bioc-devel] Package problems due to results() function from other package?

[Wolfgang Huber]

Dear Christian

If your vignette attaches another package that exports a “results” function, after it attached SNPhood which defines its own results function, then the R interpreter has no other choice than doing what it does.

Other people adding additional functionality to their packages is probably not something one can really complain about, so I see three options
- you use SNPhood::results in your vignette
- you don’t attach the other package, and rather just use what you need from it using “::”
- you convince Hervé to add ‘results' to BiocGenerics and everyone who exports such a function converts it to a method for that generic.

Thank you and kind regards
Wolfgang

--
Wolfgang Huber
EMBL
https://www.huber.embl.de/









> Il giorno 2023-10-28, alle ore 16:15, Christian Arnold <chrarnold using web.de> ha scritto:
> 
> For my package SNPhood that did not receive any code changes or updates
> in quite a while, I suddenly see errors with Bioc 3.18:
> https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html
> 
> Error: processing vignette 'workflow.Rmd' failed with diagnostics:
> unused argument (type = "allelicBias")
> 
> This comes from this line I think:
> 
> names(results(SNPhood.o, type = "allelicBias"))
> 
> For literally years, this didnt cause any problems, and the results
> function is actually (re)defined in the SNPhood package:
> 
> results <- function(SNPhood.o, type, elements = NULL)
> 
> I am not sure now what causes this. Should I use the syntax
> SNPhood::results to make it clear, or I am wrongly assuming that the
> wrong result function is taken that causes the error?
> 
> Any pointers?
> 
> 
> Best
> 
> Christian
> 
> 
> [[alternative HTML version deleted]]
> 
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