Error in opening .RData containing a genefilter object

Wed, Oct 19, 2005 7:39 AM

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 at 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