[Bioc-devel] seqnames as a candidate for BiocGenerics

[Michael Lawrence]

Probably because that would mean genomeIntervals depending on IRanges.
Because GenomeInfoDb needs CompressedList.

On Mon, Apr 27, 2015 at 11:14 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Nico,
>
> On 04/26/2015 09:58 AM, Nicolas Delhomme wrote:
>
>> Hej Hervé (I guess)!
>>
>> Could it be possible to move the generic from "seqnames" and "seqnames<-"
>> from GenomeInfoDb to BiocGenerics? I would then deprecate the "seq_name"
>> and "seq_name<-" functions of the genomeIntervals package and import them
>> in the easyRNASeq package.
>>
>
> I guess I could.
>
> However I want to make it clear that a generic function doesn't have
> to go to BiocGenerics before it can be shared across packages. There
> are situations where this kind of move actually helps to resolve
> conflicts but it doesn't seem to be the case here. Any reason why
> you can't just import GenomeInfoDb? This is what all the packages that
> need the "seqnames" and "seqnames<-" generics currently do. Moving
> these generics to BiocGenerics will likely break many of them.
>
> Thanks,
> H.
>
>
>> Cheers,
>>
>> Nico
>>
>> ---------------------------------------------------------------
>> Nicolas Delhomme
>>
>> The Street Lab
>> Department of Plant Physiology
>> Umeå Plant Science Center
>>
>> Tel: +46 90 786 5478
>> Email: nicolas.delhomme at umu.se
>> SLU - Umeå universitet
>> Umeå S-901 87 Sweden
>> ---------------------------------------------------------------
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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