[Bioc-devel] Nasty function collision

[Seth Falcon]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:

> Thanks for the input. However, I am not sure if any of these
> suggestions are applicable. I don't ever call getURL() directly; it
> gets called as a result of calling saveHTML() in annaffy, which
> outputs an HTML table, or it gets called by useMart() in biomaRt when
> trying to connect to a Biomart using the RCurl package.

Then the problem is in these packages and they need to take advantage
of the name space utilities. 

Ah, annaffy has this:

if( !isGeneric("getURL") )
    setGeneric("getURL", function(object) standardGeneric("getURL"))

This is familiar legacy code that worked around issues in the S4
system.  It is no longer needed, and in this case, I'm pretty sure it
is causing trouble.  Removing the check and just defining the generic
in the annaffy package should help.

For biomaRt, it might make sense to import RCurl or at least getURL in
the NAMESPACE file.

Jim, can you try patching annaffy as suggested and see if this
resolves the issue?

+ seth