[Bioc-devel] BiocGenerics / NAMESPACE question
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Mon Dec 5 20:36:25 CET 2011
2011/12/5 Hervé Pagès <hpages at fhcrc.org>:
> Hi Kapser,
> On 11-12-04 10:40 AM, Kasper Daniel Hansen wrote:
>> I have looked a bit at BiocGenerics. I may not be up to date on the
>> latest in export/NAMESPACE, but why are (almost) all the generics
>> exported as
>> and not
>> and why is combine/updateObject different. Is it because you need
>> export() to register the generic and only exportMethod if the package
>> defines a method aside from the generic?
> Yep. export() is for a function (a generic is a function),
> exportMethod() is for a method. There is no "lapply" method defined
> in BiocGenerics, just the "lapply" generic function.
>> And does that mean I need to
>> treat exporting a method differently depending on whether or not the
>> package I am writing defines the generic or not?
> If the package you are writing defines a method for a generic that is
> defined elsewhere, then you need to import the generic and to export
> only the method. If your package defines the generic and at least one
> method for it, then you don't need to import anything (besides the
> method package of course) and you need to export the generic (with
> export()) and the method (with exportMethod()).
Thanks a lot, this is a clear explanation and it also makes sense.
However, I suspect that many packages do not follow this. At least
Biobase does not, since it only uses exportMethods() without exporting
the generic separately for all the methods (like sampleNames,
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