From murdoch at stats.uwo.ca  Wed Oct 11 22:26:40 2006
From: murdoch at stats.uwo.ca (murdoch at stats.uwo.ca)
Date: Wed, 11 Oct 2006 22:26:40 +0200 (CEST)
Subject: [Rd] Possible bug in accessing methods documentation? (PR#9291)
Message-ID: <20061011202640.39C2A4BEC6@slim.kubism.ku.dk>

On 10/11/2006 2:48 PM, Seth Falcon wrote:
> Hi,
> 
> Reading help("Documentation"), I'm led to believe that a help call
> like:
> 
>     ?myFun(x, sqrt(wt))
> 
> Will search for help on the appropriate method in the case that myFun
> is generic.  This isn't working for me.  Here is an example using the
> Biobase package:
> 
> ## If Biobase is not installed
> source("http://bioconductor.org/biocLite.R")
> biocLite("Biobase")
> 
>> library("Biobase")
>> data(sample.ExpressionSet)
>> class(sample.ExpressionSet)
> [1] "ExpressionSet"
> attr(,"package")
> [1] "Biobase"
>> z <- featureNames(sample.ExpressionSet)
>> z[1:2]
> [1] "AFFX-MurIL2_at"  "AFFX-MurIL10_at"
>> ?featureNames(sample.ExpressionSet)
> Warning message:
> no method defined for function 'featureNames' and signature 'object = "missing"' in: .helpForCall(e1Expr, parent.frame()) 
> Error in .helpForCall(e1Expr, parent.frame()) : 
>         no documentation for function 'featureNames' and signature 'object = "missing"'
> 
> 
> Am I expecting the wrong thing or is this broken?  

I think it's broken.  The line that looks broken is in .helpForCall, 
where it has

methods::"elNamed<-"(sigClasses, arg, class(argVal))

Looking at the elNamed<- function, I think this is supposed to be 
equivalent to

sigClasses[[arg]] <- class(argVal)

but it is not making any assignment.  I don't understand the point of 
doing the assignment that way, or why it's not working, so I'll leave 
this for someone else.

Duncan Murdoch




[Rd] Possible bug in accessing methods documentation? (PR#9291)
murdoch at stats.uwo.ca