[Bioc-devel] cleaning up obsolete warnings

[Hervé Pagès]

On 11/06/2013 11:29 AM, Michael Lawrence wrote:
> Great, thanks for updating. I legitimately wanted to use %in%, not %over%.

Great to hear you have a use case for %in% (with the new behavior). So
I'm not the only one ;-)

H.

>
> Michael
>
>
> On Wed, Nov 6, 2013 at 10:59 AM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at 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 at fhcrc.org <mailto:hpages at fhcrc.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
>

-- 
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 fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319