Dear Martin, Thank you very much for your solution. It works fine.
Best regards, Thierry ---------------------------------------------------------------------------- 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.onkel...@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 > -----Oorspronkelijk bericht----- > Van: Martin Morgan [mailto:mtmor...@fhcrc.org] > Verzonden: vrijdag 11 maart 2011 7:36 > Aan: ONKELINX, Thierry > CC: r-devel@r-project.org; John Chambers > Onderwerp: Re: [Rd] Problem with defining new method for residuals() > > 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@Residual } ) > > > > setMethod("resid", signature(object = "AFLP.outlier"), > > function(object, ...){ object@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.onkel...@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@r-project.org > > mailing list https://stat.ethz.ch/mailman/listinfo/r-devel > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
