[BioC] IRanges causes bug in complete.cases

[Seth Falcon]

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.

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