[Bioc-devel] subsetByOverlaps export missing from NAMESPACE in GenomicRanges
mtmorgan at fhcrc.org
Mon Dec 24 02:46:24 CET 2012
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)
so that the methods are associated with the correct generic, and
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
and likely have Imports: GenomicRanges in the DESCRIPTION file, whereas if you
were implementing a new method you'd say
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.
> 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:
>>> I have noticed that subsetByOverlaps is not exported in GenomicRanges
>>> NAMESPACE. Would be nice if someone could put it in :)
>>> [[alternative HTML version deleted]]
>>> Bioc-devel at r-project.org mailing list
>> *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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