[Bioc-devel] Proper way of documenting a BiocGenerics generics with extended prototypes

[Jim Hester]

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.arnold at 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.arnold at embl.de
> Phone: +49(0)6221-387-8472
> Web: http://www.zaugg.embl.de/
>
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>

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