Re: [R] Error in opening .RData containing a genefilter object

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Wed 19 Oct 2005 - 23:03:50 EST

On 10/19/2005 8:37 AM, David Ruau wrote:
> Hi,
> I discover that when I save a workspace containing a genefilter (pkg
> from Bioconductor) object I cannot open no more after. I have to
> restore the .RData file from a backup to be able to start R again.
> I didn't upgrade to Version 2.2 but I'm not sure that it will solve the
> problem.
> Did anyone have encounter the same problem?
> Below is a short r session to reproduce the error:
> ...
> [Previously saved workspace restored]
>
> > library(genefilter)
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> Vignettes contain introductory material. To view,
> simply type: openVignette()
> For details on reading vignettes, see
> the openVignette help page.
> Loading required package: survival
> Loading required package: splines
> > f1 <- kOverA(5, 60)
> > q()
> Save workspace image? [y/n/c]: y
> [computer:admin]$ r
>
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.1.1 (2005-06-20), ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for a HTML browser interface to help.
> Type 'q()' to quit R.
>
> Error in .initContents() : couldn't find function "isGeneric"
> Error: .onLoad failed in 'loadNamespace' for 'Biobase'
> Fatal error: unable to restore saved data in .RData

Looks like it might be a bug in Biobase. I'd first confirm that it happens in a current release of R, then post again to the Bioconductor list.

Duncan Murdoch



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