On Fri, Dec 11, 2009 at 2:10 PM, Seth Falcon <sfalcon@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).


> I expect an update next week.
>
>
>  To avoid stuff like this in the future, perhaps it would make sense
>> to think of some kind of testing for packages making an S4 generic
>> out of a "base" function.
>>
>
> Do you have a specific idea of how we could achieve this?  Adding a sanity
> test, like running the example, for a base function within a package that
> promotes the function into a generic would have helped this case, but might
> not catch other issues?
>
> + seth
>
> --
> Seth Falcon
> Program in Computational Biology | Fred Hutchinson Cancer Research Center
>
>
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