[BioC] IRanges causes bug in complete.cases

Seth Falcon seth at userprimary.net
Sat Dec 12 01:59:03 CET 2009


On 12/11/09 4:54 PM, Michael Lawrence wrote:
> On Fri, Dec 11, 2009 at 2:10 PM, Seth Falcon<sfalcon at fhcrc.org>  wrote:
>
>> On 12/10/09 12:17 PM, Kasper Daniel Hansen wrote:
>>
>>> After loading IRanges, complete.cases ceases to work (see below).
>>> Test via example("complete.cases", package = "stats")
>>>
>>
>> I can reproduce this on R-devel, but not on R-patched and am not certain
>> yet where the problem lies.  There have been some non-trivial fixes to some
>> methods package code in recent R-devel.  This is likely related and will
>> take some more looking to understand if the bug is in the IRanges method def
>> or in R.
>>
>>
> Just in case this didn't get through, I did work around this by forcing
> IRanges to provide the generic (package = "IRanges"), rather than relying on
> the implicit generic. I don't see from the S4 documentation how this could
> be required of IRanges. The code shouldn't be coming anywhere near the
> actual IRanges method (on DataTable).

Yes, I see your workaround in IRanges (and it works around for me too).

I agree that IRanges should not have to do this.  I think for this case, 
IRanges should be able to simply call setMethod with no setGeneric call 
and the right thing should happen.

I'll look into it more.

+ seth

-- 
Seth Falcon | @sfalcon | http://userprimary.net/users



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