[Bioc-devel] Nasty function collision

[Seth Falcon]

"Colin A. Smith" <colin at colinsmith.org> writes:

> This is sort of passing the buck but it seems like it is the  
> responsibility of client code to resolve collisions like this when  
> both colliding packages already use namespaces. 

Yes, but your code, Colin, is attaching a rather broad method on
someone else's generic (can't say who's actually).  Since getURL in
RCurl is _not_ generic, it really slams getURL.

Code that does the optional generic definition really needs to go away
at this point (I know it was needed at some point, so I'm not trying
to point a finger or anything).  To be specific, I'm referring to any
code that does something along the lines of:

    if (!isGeneric("foo"))
       setGeneric("foo") ...


Yes, biomaRt and other RCurl user's should import getURL from RCurl (I
think that is enough, I don't think you need RCurl::getURL), but you
may be right that there is a larger issue when a generic gets
defined... will explore that one.

Best,

+ seth