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

From: David Ruau <David.Ruau_at_rwth-aachen.de>
Date: Thu 20 Oct 2005 - 00:39:12 EST

Thanks a lot Professor Ripley, it works that way. I will upgrade to v 2.2 one day when I have time and see if it still happen.

David

On Oct 19, 2005, at 15:58, Prof Brian Ripley wrote:

> On Wed, 19 Oct 2005, Duncan Murdoch wrote:
>
>> 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.
>
> Something in that workspace requires the Biobase namespace, and that
> needs to import the methods namespace. It does not in the version I
> have.
>
> A solution is to use R --vanilla and then load(".RData").
>
> --
> Brian D. Ripley, ripley@stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
>



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