Hi Jim, Kasper, and Hervé, thanks a lot for the quick answer. For some reason, I was under the impression that I have to use exactly the original prototype from the generics, but I didn't fully realize I can extend this arbitrarily as long as the original arguments - object and ... in this case, are among the extended list.
It works now, perfect, no complaints. * **A related question that I have is the following, maybe someone can share with me his or her thoughts: * In addition to counts (for which a generics already exists), users can extract "enrichment" instead of counts out of my object. Because there is a generics for counts, I thought it makes conceptually sense to also have a generics for enrichment then, because "enrichment" may also be something that other packages may use as a general terminology in a genomic context. So currently, I am creating one in an identical fashion to counts. Similarly, I defined one for "parameters" to extract parameters out of the object that were defined previously in the main function that creates the object. For both "enrichment" and "parameters", I could of course also regular functions, but I was wondering which of the two approaches I should take. Any thoughts? Thanks a lot, very much appreciated! Christian On 20.09.2015 21:09, Jim Hester wrote: > 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 <mailto: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 <mailto:christian.arn...@embl.de> > Phone: +49(0)6221-387-8472 <tel:%2B49%280%296221-387-8472> > Web: http://www.zaugg.embl.de/ > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- ————————————————————————— 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/ [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel