From mtmorgan at fhcrc.org  Fri Mar 11 07:36:16 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 10 Mar 2011 22:36:16 -0800
Subject: [Rd] Problem with defining new method for residuals()
In-Reply-To: <AA818EAD2576BC488B4F623941DA74270336BD@inbomail.inbo.be>
References: <AA818EAD2576BC488B4F623941DA74270336BD@inbomail.inbo.be>
Message-ID: <4D79C2E0.5020703@fhcrc.org>

On 03/10/2011 08:21 AM, ONKELINX, Thierry wrote:
> Dear all,
> 
> I'm writing a package and I would like to reuse the residuals()
> function. When I use a function which calls the redefined residuals
> (for my custom class) I get an error (see below). It looks like the
> wrong method is used. The strange this is, that when it execute the
> code manually it get no error.

Hi Thierry --

I think this is a bug in the methods package.

Your package promotes stats::residuals to an S4 generic. Normally this
should work.

However, your package Depends: on lme4, which also promotes
stats::residuals to an S4 generic. Apparently, this interferes with your
own attempt to make a generic, even though you do not import lme4 into
your name space. As a consequence of the (putative) bug, your package
sees the original stats::residuals.

A work-around seems to be to importFrom(lme4, residuals) and do NOT
import residuals from stats, so that your own method is associated with
the generic defined in lme4.

Martin

> 
> Any suggestions?
> 
> Best regards,
> 
> Thierry
> 
> The entire source code is at
> svn://scm.r-forge.r-project.org/svnroot/aflp
> 
> The code with the error.
> 
>> normalise(dummy)
> Error in object$na.action : $ operator not defined for this S4 class
>> traceback()
> 5: naresid(object$na.action, object$residuals) at normalise.R#30 4:
> residuals.default(outliers(data)) at normalise.R#30 3:
> residuals(outliers(data)) at normalise.R#30 2:
> nrow(residuals(outliers(data))) at normalise.R#30 1:
> normalise(dummy) #This works fine
>> data <- dummy nrow(residuals(outliers(data)))
> [1] 0
> 
> NAMESPACE importFrom(stats, residuals, resid, hclust, princomp) 
> exportPattern(".")
> 
> METHODS setMethod("residuals", signature(object = "AFLP.outlier"), 
> function(object, ...){ object at Residual } )
> 
> setMethod("resid", signature(object = "AFLP.outlier"), 
> function(object, ...){ object at Residual } )
> 
> ----------------------------------------------------------------------------
>
> 
ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek team Biometrie &
> Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium
> 
> Research Institute for Nature and Forest team Biometrics & Quality
> Assurance Gaverstraat 4 9500 Geraardsbergen Belgium
> 
> tel. + 32 54/436 185 Thierry.Onkelinx at inbo.be www.inbo.be
> 
> To call in the statistician after the experiment is done may be no
> more than asking him to perform a post-mortem examination: he may be
> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
> 
> The plural of anecdote is not data. ~ Roger Brinner
> 
> The combination of some data and an aching desire for an answer does
> not ensure that a reasonable answer can be extracted from a given
> body of data. ~ John Tukey
> 
> ______________________________________________ R-devel at r-project.org
> mailing list https://stat.ethz.ch/mailman/listinfo/r-devel


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[Rd] Problem with defining new method for residuals()
Martin Morgan