[BioC] Problem loading affy using a saved workspace

[Rafael A. Irizarry]

this type of error has occured to me when the definition of a class
changes and an object created that was create to an old definition exists.
vince, hasthe definition of exprSet changed? james, what version did you use to
create the exprSet and what version of Biobase are you using now?

On Thu, 27 Mar 2003, James MacDonald wrote:

> A little more information. The workspace I am loading contains two AffyBatch objects, and an exprSet object that was created by running rma on one of the AffyBatch objects.
> 
> If I load the workspace, delete the exprSet, and then load either Biobase or affy, things work as expected. It doesn't help to delete either of the AffyBatch objects.
> 
> Is there any reason that an existing exprSet object should be mucking things up?
> 
> Jim
> 
> 
> 
> James W. MacDonald
> UMCCC Microarray Core Facility
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> Vincent Carey 525-2265 <stvjc at channing.harvard.edu> 03/27/03 03:34PM >>>
> what version of R
> 
> exprSet undefined suggests package Biobase has not been loaded.
> not clear to me why library(affy) does not accomplish the load.
> try manually library(Biobase) before library(affy)
> 
> > Hi all,
> >
> > I am running R/Bioconductor on WinXP using affy 1.1.1. (Biobase 1.3.10)
> >
> > If I decide to open up an existing workspace that contains e.g., an AffyBatch and exprSet, I can open the workspace, but when I try to attach the affy package, I get the following error message.
> >
> > [Previously saved workspace restored]
> >
> > > library(affy)
> > Loading required package: tkWidgets
> > Loading required package: widgetTools
> 
> -----> this second load of tkWidgets is also strange -- i see it myself
> 
> > Loading required package: tkWidgets
> >
> > Attaching package `tkWidgets':
> >
> >
> >         The following object(s) are masked from package:tkWidgets :
> >
> >          [snip]
> >
> > Error in mlistMetaName(f) : No way to associate a generic function with an object of class "NULL"
> > Error in mlistMetaName(f) : No way to associate a generic function with an object of class "NULL"
> > Error in reconcilePropertiesAndPrototype(name, slots, prototype, superClasses) :
> >         Class "AffyBatch" extends an undefined class ("exprSet"
> > Error in library(affy) : .First.lib failed
> > >
> >
> > Any ideas?
> >
> > Jim
> >
> >
> >
> >
> > James W. MacDonald
> > UMCCC Microarray Core Facility
> > 1500 E. Medical Center Drive
> > 7410 CCGC
> > Ann Arbor MI 48109
> > 734-647-5623
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch 
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor 
> >
> 
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