I think you just want to use the "select" argument. For example,
multiple=FALSE before would correspond to select="arbitrary" now, while
multiple=TRUE corresponds to the default select="all". There are other
values for select.

Michael

On Sat, Apr 28, 2012 at 12:23 AM, <Michael.Dondrup@uni.no> wrote:

> Hi,
> I have some R-scripts that rely on the argument multiple=TRUE
> in findOverlaps(). However, this option has been removed in the latest
> release it seems, as it was said to be deprecated before. But now
> our scripts don't work any more, and removing the parameter
> simply yields a different output format and is not an option.
>
> Is there a quick way to  bring the behavior of it back, with respect to
> output format and overlap matching?
>
> Thank you very much for your help
> Michael
>
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