Great, thanks for updating. I legitimately wanted to use %in%, not %over%.

Michael


On Wed, Nov 6, 2013 at 10:59 AM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Michael,
>
>
> On 11/05/2013 04:30 PM, Michael Lawrence wrote:
>
>> I'm getting a little tired of this one popping up:
>>
>> In x %in% other :
>>     Starting with BioC 2.12, the behavior of %in% on GenomicRanges objects
>>    has changed to use *equality* instead of *overlap* for comparing
>>    elements between GenomicRanges objects 'x' and 'table'. Now 'x[i]' and
>>    'table[j]' are considered to match when they are equal (i.e. 'x[i] ==
>>    table[j]'), instead of when they overlap. This new behavior is
>> consistent
>>    with base::`%in%`(). If you need the old behavior, please use:
>>
>>      query %over% subject
>>
>> Now that even release is Bioc 2.13, can we remove it? And there might be
>> others.
>>
>
> If you use %over% you don't get the warning ;-)
>
> Anyway this is gone in BioC 2.14 as part of the normal process of
> removing features that were defunct in BioC 2.13.
>
> Cheers,
> H.
>
>
>
>> Thanks,
>> Michael
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>>
> --
> 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@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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