[Bioc-devel] Nasty function collision

James W. MacDonald jmacdon at med.umich.edu
Tue Oct 31 21:43:40 CET 2006

Thanks Steffen. FWIW, Colin's suggestion appears to work as well (and I 
am certainly not averse to messy hackery - I may well make a living at 
it ;-D).



Steffen Durinck wrote:
> I agree with Colin and will modify the biomaRt code so it uses 
> RCurl::getURL().
> Thanks Jim, for pointing out this problem.
> Cheers,
> Steffen
> Colin A. Smith wrote:
>>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. I think the best  
>>option would be to have biomaRt use RCurl::getURL() instead of getURL 
>>(). Short of that, you might be able to write a function in  
>>affycoretools which redefines the behavior of getURL with an "ANY"  
>>argument in the global namespace:
>>setMethod("getURL", "ANY", function(object) {
>>     RCurl::getURL(object)
>>Because annaffy is in its own namespace, it shouldn't be affected by  
>>that change. (?) I'm not sure if this suggestion would actually work  
>>and it could be regarded as messy hackery.
>>Just my two cents.
>>On Oct 31, 2006, at 11:08 , James W. MacDonald wrote:
>>>Thanks for the input. However, I am not sure if any of these  
>>>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.
>>>It seems to me that Laurent has the best suggestion - getURL() in
>>>annaffy has a method:
>>>setMethod("getURL", "ANY", function(object) {
>>>     return(character(0))
>>>Which to an S4 maven may be useful, but pretty much torches the  
>>>in RCurl. It seems to me that this method isn't particularly useful  
>>>it?), so maybe the best course of action is to convince Colin Smith to
>>>remove this particular method.
>>>The other possibility is to get Steffen Durinck to change biomaRt  
>>>to use
>>>Or am I still missing something?
>>Bioc-devel at stat.math.ethz.ch mailing list
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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