[Bioc-devel] subsetByOverlaps export missing from NAMESPACE in GenomicRanges

[Martin Morgan]

On 12/23/2012 05:19 PM, Jesper Gådin wrote:
> Yes thanks that is probably the reason why it is missing from
> GenomicRanges. Noticed that it was in IRanges and had already put it in the
> import, but forgot to also put in my export... After I put it in exports it
> works as intended.

actually, GenomicRanges 1.11.20 defines new methods on subsetByOverlaps, and so 
has (not literally, but in effect)

   importFrom(IRanges, subsetByOverlaps)

so that the methods are associated with the correct generic, and

   exportMethods(subsetByOverlaps)

so that the new methods (and generic) are available to the end user.

Not sure what your use case is, but if you were _using_ this method in your 
package you would say

   importFrom(GenomicRanges, subsetByOverlaps)

and likely have Imports: GenomicRanges in the DESCRIPTION file, whereas if you 
were implementing a new method you'd say

   importFrom(IRanges, subsetByOverlaps)
   exportMethods(subsetByOverlaps)

and have at least Imports: IRanges in the DESCRIPTION file (but likely Depends: 
GenomicRanges or Depends: IRanges, as it might be reasonable for the user to 
have access to functionality from these packages when using your package).

I think subsetByOverlaps methods should have been exported in the release 
version of GRanges (1.10.5) but were not.

Also, in passing (and probably obvious from the last couple of responses), since 
you're developing a package it makes sense to track the devel branch of R and 
Bioconductor. That way, your package will be ready for use when the new R / Bioc 
release come out in a few months.

Martin

>
> Jesper
>
> On Mon, Dec 24, 2012 at 1:57 AM, Tim Triche, Jr. <tim.triche at gmail.com>wrote:
>
>> that's probably because it is exported from IRanges
>>
>>
>>
>> On Sun, Dec 23, 2012 at 4:19 PM, Jesper Gådin <jesper.gadin at gmail.com>wrote:
>>
>>> Hey,
>>>
>>> I have noticed that subsetByOverlaps is not exported in GenomicRanges
>>> NAMESPACE. Would be nice if someone could put it in :)
>>>
>>> /Jesper
>>>
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>>>
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>>
>>
>>
>> --
>> *A model is a lie that helps you see the truth.*
>> *
>> *
>> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>>
>
> 	[[alternative HTML version deleted]]
>
>
>
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