From murdoch at stats.uwo.ca  Tue Jul 15 21:00:57 2008
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Tue, 15 Jul 2008 15:00:57 -0400
Subject: [Rd] methods/namespaces/possible bug
In-Reply-To: <8B255C3E-603A-4FA9-9E11-42C2A1E34C92@stat.berkeley.edu>
References: <8B255C3E-603A-4FA9-9E11-42C2A1E34C92@stat.berkeley.edu>
Message-ID: <487CF3E9.9040509@stats.uwo.ca>

On 7/15/2008 2:11 PM, Kasper Daniel Hansen wrote:
> Using
> 
>  > methods("plot")
>   [1] plot.Date*          plot.HoltWinters*   plot.POSIXct*
>   [4] plot.POSIXlt*       plot.TukeyHSD       plot.acf*
>   [7] plot.data.frame*    plot.decomposed.ts* plot.default
> [10] plot.dendrogram*    plot.density        plot.ecdf
> [13] plot.factor*        plot.formula*       plot.hclust*
> [16] plot.histogram*     plot.isoreg*        plot.lm
> [19] plot.medpolish*     plot.mlm            plot.ppr*
> [22] plot.prcomp*        plot.princomp*      plot.profile.nls*
> [25] plot.spec           plot.spec.coherency plot.spec.phase
> [28] plot.stepfun        plot.stl*           plot.table*
> [31] plot.ts             plot.tskernel*
> 
>     Non-visible functions are asterisked
> 
> I don't see plot.function listed. As I read the man page for methods I  
> would say that the search is just looking for functions with the right  
> type of name.

In a package with a NAMESPACE (like the graphics package, where 
plot.function lives), a function needs to be declared to be an S3method 
to show up in this list.  plot.function is not declared as an S3 method.

I don't know the reason for this, but I assume it's intentional:  take a 
look at the plot() generic:  it has special case code to handle functions.

So if this is a bug, I think it's a documentation bug in the 
?plot.function man page, where plot.function should be documented to act 
a lot like an S3 method, but not identically like one:  notice the 
special handling of the y axis label.


> If I define a plot.function in my global workspace, methods("plot")  
> picks it up
> 
>  > plot.function = function() {print("blah")}
>  > methods("plot")
>   [1] plot.Date*          plot.HoltWinters*   plot.POSIXct*
>   [4] plot.POSIXlt*       plot.TukeyHSD       plot.acf*
>   [7] plot.data.frame*    plot.decomposed.ts* plot.default
> [10] plot.dendrogram*    plot.density        plot.ecdf
> [13] plot.factor*        plot.formula*       plot.function
> [16] plot.hclust*        plot.histogram*     plot.isoreg*
> [19] plot.lm             plot.medpolish*     plot.mlm
> [22] plot.ppr*           plot.prcomp*        plot.princomp*
> [25] plot.profile.nls*   plot.spec           plot.spec.coherency
> [28] plot.spec.phase     plot.stepfun        plot.stl*
> [31] plot.table*         plot.ts             plot.tskernel*


Functions declared in the global workspace are handled by patterns on 
the name, since you can't declare things there:  there's no NAMESPACE file.

>     Non-visible functions are asterisked
> 
> Based on this, I think that methods("plot") should return  
> plot.function, so I am almost ready to take the bug word in my mouth.
> 
> When I debug the methods function it gets to the line
>    S3reg <- ls(get(".__S3MethodsTable__.", envir = defenv), pattern =  
> name)
> where it searches the .__S3MethodsTable__. object. Consulting the help  
> page it seems that this object is part of the namespace functionality.
> 
> My guess is that something goes wrong because function is a reserved  
> word?

I don't think so.

Duncan Murdoch
	
> 
> Kasper
> 
> This has been tested under R-2.7.1 on Mac OS X and under a not too  
> recent version of R-devel under x86_64. My sessionInfo for the Mac  
> version is
> 
>  > sessionInfo()
> R version 2.7.1 (2008-06-23)
> i386-apple-darwin8.10.1
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] tools_2.7.1
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] methods/namespaces/possible bug
Duncan Murdoch