findOverlaps documentation mentions that G/IRanges is moving a Nested Containment List objects implementation with slightly changed behaviour. The documentation mentions that special meaning of maxgap in conjunction with start/end/within is not respected in the new algorithm. What is alarming to me is that there is no error or warning given for the new behavior. Shouldn't an error (or at least a warning) be raised given the nature of the change and the high likelihood of an unnoticed change analysis results?

Edit: additionally, different results are also returned for type="equal", which is not mentioned in the documentation of the change

Thanks Daniel for pointing this out. I agree that this kind of subtle change in semantic deserves a warning. I just added the warning to IRanges and GenomicRanges in release and devel, and also added the type="equal" case that was missing to the documentation of the changes between the old and new implementations (in ?NCList).

Cheers,

H.