[BioC] past bioc releases

Simon Anders anders at ebi.ac.uk
Sat May 16 12:55:10 CEST 2009


wangchuanming wrote:
> On a Windows XP (SP2) machine, when I use the package Affy (R 2.0.1,
> bioconductor 1.6),the following error message appears:
>> library(affy) Data <- ReadAffy() eset <- rma(Data)
> Error in load(zfile, envir = envir) : ReadItem: unknown type 242 In
> addition: Warning message: package 'hgu133plus2cdf' was built under R
> version 2.9.0 Error in library("hgu133plus2cdf", lib.loc = NULL) : 
> .First.lib failed for 'hgu133plus2cdf'

It seems that your are mixing binary packages built with R 2.0.1 with
those built with R 2.9.0. This will cause trouble.

> The reason why I use the old version of R is some functions whicn I
> saw in some books and manuals were not found in the latest version of
> R,such as "rowSds " and "heatmap ". I also can't find the download
> website of the package 'hgu133plus2cdf' built under R 2.0.1.

This is not agood reason, as the functions "heatmap" and "rowSds" have
not been removed from R, of course. "heatmap" is in the "stats" package
and should always be available in a proper installation of R.

If you type "??rowSds" (in newer R versions, only), R will search all
packages, even those not loaded, for the function rowSds and inform you
that is is in the "genefilter" package, which is one of the Bioconductor
default packages installed by "biocLite()".

It seems that your installation of R 2.9 is completely missed up and
missing essential parts. Try fixing it, and if you still have trouble,
please ask again and give details of how you installed R and
Bioconductor and also post the output of the "sessionInfo" command.

Best regards

| Dr. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
| office phone +44-1223-492680, mobile phone +44-7505-841692
| preferred (permanent) e-mail: sanders at fs.tum.de


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