[BioC] ArrayExpress: missing cdf environment!

[Wolfgang Huber]

Dear Daniel

have you tried with installing the hgu133acdf package manually 
beforehand? (After that, please try to load it to verify it's really there.)

What you see is because the 'print' method for 'AffyBatch' objects from 
the 'affy' package requires the array's CDF package (hgu133acdf in your 
case), and if it does not find it on your computer, it tries to be 
helpful and install it from the Bioconductor repository on the web.

Btw, it should never be necessary to be 'root' to install R packages on 
any sane system configuration.

	Best wishes
	Wolfgang

Il Oct/15/10 5:50 PM, Daniel Rico Rodriguez ha scritto:
> Dear list,
>
> I downloaded a dataset from ArrayExpress using ArrayExpress package, and
> I get an error when I try to see the object created, or a try to
> normalize it with rma.
>
> I am using a Linux Ubuntu. For some reason, a package installation is
> tried (related with cdf, I guess) but I am not root... Is there a way to
> overcome this problem installing some cdf package in my home R library
> folder? I tried installing hgu133a.db, gahgu133acdf and u133x3pcdf, and
> repeating the operation, but I still get the error.
>
> Any help will be really appreciated!
>
> Best,
> Daniel
>
>  > library("ArrayExpress")
>  > library(affy)
>  > GNF <- ArrayExpress("E-TABM-145")
> ...
> The object containing experiment E-TABM-145 has been built.
>  > class(GNF)
> [1] "AffyBatch"
> attr(,"package")
> [1] "affy"
>  > GNF
> Warning in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(), :
> 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable
> AffyBatch object
> size of arrays=712x712 features (228 kb)
> cdf=HG-U133A (??? affyids)
> number of samples=158
> Warning in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(), :
> 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable
> Error in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(), :
> unable to install packages
> In addition: Warning message:
> missing cdf environment! in show(AffyBatch)
>  > GNFnorm <- rma(GNF)
> Warning in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(), :
> 'lib = "/opt/R/R-2.11/lib64/R/library"' is not writable
> Error in install.packages(cdfname, lib = lib, repos =
> Biobase:::biocReposList(), :
> unable to install packages
>
>  > sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] affy_1.26.0 ArrayExpress_1.8.0 Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] XML_2.8-1 affyio_1.16.0 limma_3.4.0
> [4] preprocessCore_1.10.0 tools_2.11.0
>
> ********************************************
>
> Daniel Rico Rodriguez, PhD.
> Structural Computational Biology Group
> Spanish National Cancer Research Center, CNIO
> Melchor Fernandez Almagro, 3.
> 28029 Madrid, Spain.
> Phone: +34 91 224 69 00 #3015
> drico at cnio.es
> http://www.cnio.es
>
> ********************************************
>
>
>
>
>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:3}}
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