[Bioc-devel] cleaning up obsolete warnings

[Hervé Pagès]

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

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