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 <chrarn...@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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
