R help - Oct 2005 - Error in opening .RData containing a genefilter object

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

[gaia:admin]$
-------
I am working under OS X 10.3.9.

David

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

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
>