[Bioc-devel] Nasty function collision

[Steffen Durinck]

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
>>     
>
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