Christian, You need to use your extended prototype in the function definition within your `setMethod()` call. In particular you do _not_ need to write an explicit `@usage` directive.
See https://github.com/jimhester/examplePrototype/blob/master/R/package.R for an example package without any NOTEs for this situation. Jim On Sun, Sep 20, 2015 at 1:23 PM, Christian Arnold <christian.arn...@embl.de> wrote: > Hi all, > > I am currently producing the documentation for a new hopefully > soon-to-be-submitted Bioconductor package and I am facing some difficulties > with R CMD check. > In summary: I want to dispatch the existing generic for "counts" to make > it usable with my object of type SNPhood as well. > > The original prototype from BiocGenerics: > > standardGeneric for "counts" defined from package "BiocGenerics" > > function (object, ...) > > > > I am calling, as you can see, an internal function for this. Currently, > because of its original prototype, I use: > > setMethod("counts", "SNPhood", function(object, ...) {.getCounts(object, > ...)}) > > > > However, in my case, I want to use an extended prototype to specify which > counts exactly should be extracted. > > .getCounts <- function(SNPhood.o, type, readGroup = NULL, dataset = NULL, > ...) > > > > Everything works, but I want to document the additional arguments > properly. However, with roxygen 2, I am not sure how to achieve that > without producing warnings. > > I am using: > > #' @usage counts (object, type, readGroup, dataset) > > #' @template object > > #' @param type bla > > #' @template readGroup > > #' @template dataset > > > This produces: > > * checking for code/documentation mismatches ... WARNING > Codoc mismatches from documentation object 'counts,SNPhood-method': > counts > Code: function(object, ...) > Docs: function(object, type, readGroup, dataset) > Argument names in code not in docs: > ... > Argument names in docs not in code: > type readGroup dataset > Mismatches in argument names: > Position: 2 Code: ... Docs: type > > > > So, what is the recommended way here? I could write an own "new" counts > function, but I thought if a generics already exists, I should use it > because this is exactly what my function does also... > > > Thanks, > Christian > > -- > ————————————————————————— > Christian Arnold, PhD > Staff Bioinformatician > > SCB Unit - Computational Biology > Joint appointment Genome Biology > Joint appointment European Bioinformatics Institute (EMBL-EBI) > > European Molecular Biology Laboratory (EMBL) > Meyerhofstrasse 1; 69117, Heidelberg, Germany > > Email: christian.arn...@embl.de > Phone: +49(0)6221-387-8472 > Web: http://www.zaugg.embl.de/ > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
