[BioC] variable "mgu74av2cdf" was not found

[Ben Bolstad]

I can duplicate your errors on a fresh windows 2000 installation of R
1.6.1 and bioconductor (getBioC), both using mgu74av2cdf and hgu95acdf 
data. 

No such problem trying the equivalent on a linux machine. 

On a linux machine

> library(mgu74av2cdf)
> mgu74av2cdf
<environment: 0x8b3a8b0>

On a windows machine

> library(mgu74av2cdf)
> mgu74av2cdf
Error: object "mgu74av2cdf" not found

Rafael: have the cdfenvs been tested on win? digging around in the
installed cdfenvs on win i can't find the equivalent to the .First.lib,
does not appear that the datafiles are being attached properly on win.

Thanks,

Ben


> I did a complete reinstall of R 1.6.1 and Bioconductor 1.1.  I also got mgu74av2cdf_0.1.zip from http://www.bioconductor.org/data/cdfenvs/cdfenvs.html and installed that.
> 
> Here are the main details:
> 
> > library(affy)
> > library(Biobase)
> > library(mgu74av2cdf)
> > Data <- ReadAffy()
> > eset <- rma(Data)
> Error in get(x, envir, mode, inherits) : variable "mgu74av2cdf" was not found
> > Data
> AffyBatch object
> size of arrays=640x640 features (12803 kb)
> Error in get(x, envir, mode, inherits) : variable "mgu74av2cdf" was not found
> Error in inherits(cdf.env, "try-error") : Object "cdf.env" not found
> > 
> 
> I am using Windows 2000 and I use:
> 
> "C:\Program Files\R\rw1061\bin\Rgui.exe" --max-mem-size=768M
> 
> to start R.
> 
> 
> In Bioconductor 1.0, things work better.  For example:
> >Data <- ReadAffy()
> >Data
> object
> CDF used=MG_U74Av2.CDF
> number of chips=4
> number of genes=12488
> number of probe pairs=197993
> annotation=
> description=
> notes=
> size of chip=640x640
> chip names=
> NL_OMCATHR_H1A
> NL_OWTHR_H1A
> NL_YMCATHR_H1A
> NL_YWTHR_H1A
> 
> I am not sure what to do next.
> 
> Thanks much,
> Dick
> 
> *******************************************************************************
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Environmental Health, Box 354695
> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
> 			Seattle, WA 98105-6099
> *******************************************************************************
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