On 10/31/23 07:22, Wolfgang Huber wrote: > 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.
My pleasure, and that's the cleanest solution. But it will only help if the package that defines the "other" results() function is a Bioconductor package and not a CRAN package. Has this package been identified? A 4th option is to make sure that the other package gets loaded _before_ SNPhood e.g. by putting an explicit library(<the other package>) before library(SNPhood) in your vignette, even though that's kind of hacky. Best, H. > > 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 -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
