[Bioc-devel] Nasty function collision

[James W. MacDonald]

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).

Best,

Jim

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.
>>
>>-Colin
>>
>>On Oct 31, 2006, at 11:08 , James W. MacDonald wrote:
>>
>>  
>>
>>>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.
>>>
>>>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  
>>>getURL()
>>>in RCurl. It seems to me that this method isn't particularly useful  
>>>(is
>>>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
>>>RCurl::getURL().
>>>
>>>Or am I still missing something?
>>>
>>>Best,
>>>
>>>Jim
>>>    
>>
>>_______________________________________________
>>Bioc-devel at stat.math.ethz.ch mailing list
>>https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
> 
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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