[Bioc-devel] NAMESPACE issue, possibly related to AnnotationDbi

[Martin Morgan]

J.J.Goeman at lumc.nl wrote:
>  Dear Seth and Martin,
> 
> Thank you very much for your explanation. So, what is happening is that
> we have two functions
> 
> - as.list, the base function, from the base package and therefore always
> in my namespace.
> - as.list, the S4 generic based on the function above, in AnnotationDbi
> which had been attached to the user workspace with require().
> 
> In the namespace hierarchy the function (in the namespace) takes
> precedence over the generic (in the user workspace), resulting in R
> stubbornly trying to apply the base function to an object from the
> AnnotationDbi package, even though a method for that object is
> available.
> 
> I can see that this makes perfect sense from a namespace perspective,
> but it is rather peculiar from an S4 classes perspective. Would it not
> be sensible if generics would always override the base functions they
> are based on?

Hi Jelle --

Yes, if S4 generics and base functions were more tightly integrated, one
might expect methods attached in the user name space to be reached. One
would still like name space protection -- the package author would want
to specify that the desired method comes from AnnotationDbi.

Martin

> 
> Best regards,
> 
> Jelle
> 
>  
> 
>> -----Original Message-----
>> From: bioc-devel-bounces at stat.math.ethz.ch 
>> [mailto:bioc-devel-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon
>> Sent: 04 December 2009 20:35
>> To: bioc-devel at stat.math.ethz.ch
>> Subject: Re: [Bioc-devel] NAMESPACE issue, possibly related 
>> to AnnotationDbi
>>
>> Hi Jelle,
>>
>> I think I have an explanation for you.  Prior to your change, 
>> you had AnnotationDbi listed in the 'Imports' field of the 
>> DESCRIPTION file for your globaltest package.  Listing a 
>> package in Imports tells R that these packges are 
>> dependencies, but does not actually cause these packages to 
>> be imported into your package's name space.  For that you 
>> have to add something to NAMESPACE.
>>
>> The addition you made is fine.  You can also do a wholesale import as:
>>
>>    import("AnnotationDbi")
>>
>> And then you should not need the more granular imports.  
>> However, the granular imports where you import specific 
>> symbols is generally a good practice since it avoids 
>> unintentional name conflicts.  A change in a package you 
>> import could introduce a symbol clash, but this will not be 
>> an issue if you have imported the minimal set of symbols.
>>
>> Does that help?
>>
>> + seth
>>
>> --
>> Seth Falcon
>> Program in Computational Biology | Fred Hutchinson Cancer 
>> Research Center
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list 
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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