[Bioc-devel] BiocGenerics request

Stephanie M. Gogarten sdmorris at u.washington.edu
Sat Oct 14 01:00:51 CEST 2017

On 10/13/17 3:32 PM, Hervé Pagès wrote:
> Hi Stephanie,
> Can you provide a little bit more context? Have you observed
> conflicts between VariantAnnotation:::asVCF() and other asVCF()
> functions defined elsewhere? Any reason why you can't use/import
> VariantAnnotation:::asVCF() in your package?

I would prefer to leave VariantAnnotation in "Suggests" rather than 
"Imports" for performance reasons - it adds substantially to package 
load time, but will be used only rarely.

> Alternatively, have you considered using/defining a coercion method
> to VCF instead? That should work (and would be preferred) if you
> don't need the extra arguments that an "asVCF" method would allow
> you to support.

I will look into coercion methods; thanks for the suggestion! Can one 
define a coercion method where the "to" class is in a package that's not 
attached until the method is called (with requireNamespace)?


> The VCF class is defined in the VariantAnnotation package so it
> would be weird to have the asVCF() generic in BiocGenerics.
> Cheers,
> H.
> On 10/13/2017 01:55 PM, Stephanie M. Gogarten wrote:
>> Can we move the "asVCF" generic to BiocGenerics?
>> thanks,
>> Stephanie
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