[Bioc-devel] Namespace and function 'open'

Robert Gentleman rgentlem at fhcrc.org
Fri Feb 15 19:30:27 CET 2008


Hi,
   It might help if folks read Luke Tierney's description of name spaces 
in R News, in the hopes of removing some of the confusion here.  In 
particular pay attention to the discussion of how resolution of symbols 
is done during evaluation (and the fact that base plays a special role).

The problem is indeed that Markus (and please do not post the same 
question to two lists, or cross post, that is not viewed as appropriate 
behavior, reporting sessionInfo is helpful) wants open from Affy, not 
from base, and that by putting a name space on his package he makes it 
hard to do that, since the point of name spaces is essentially to give 
some priority to functions in base.

Until affy has a namespace then importing won't work (anyone care to put 
one on it?).  I suspect that using get is going to be the easiest solution.

best wishes
   Robert


Markus Schmidberger wrote:
> Error: package 'affy' does not have a name space
> 
> With
> importMethod(affy, open)
> I can build and install the package. But I still have the error
> 
> Fehler in UseMethod("open") : keine anwendbare Methode für "open"
> 
> Best
> Markus
> 
> Sean Davis schrieb:
>> On Fri, Feb 15, 2008 at 11:25 AM, Markus Schmidberger
>> <schmidb at ibe.med.uni-muenchen.de> wrote:
>>   
>>> But there is no NAMESPACE in the package "affy". Therefore I can not
>>>  import the variables.
>>>
>>>  importClassesFrom(affy, ProgressBarText)
>>>
>>>  Error: package 'affy' does not have a name space
>>>     
>> How about:
>>
>> import(affy)
>>
>> Does that do it?
>>
>> Sean
>>
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org



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