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