[Bioc-devel] cleaning up obsolete warnings

Hervé Pagès hpages at fhcrc.org
Wed Nov 6 19:59:45 CET 2013

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.


> Thanks,
> Michael
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

More information about the Bioc-devel mailing list