On Mon, Nov 17, 2008 at 7:00 PM, Harry Mangalam <harry.mangalam@uci.edu>wrote:

> Like Rob Dunne previously, I'm trying to use pdInfoBuilder to generate
> a pkg for the RaGene-1_0-st-v1 series, but am getting the same error
> that he was finally able to resolve.  Unlike him, I am not.
>
> R version 2.6.2 (2008-02-08) (from Ubuntu 8.04.1 deb)
> pdInfoBuilder 1.6.0
> > library(pdInfoBuilder)
> > pgfFile <- "RaGene-1_0-st-v1.r3.pgf"
> > clfFile <- "RaGene-1_0-st-v1.r3.clf"
> > transFile <- " RaGene-1_0-st-v1.na26.rn4.transcript.csv"
> > probeFile <- "RaGene-1_0-st-v1.probe.tab"
> > pkg <- new("AffyGenePDInfoPkgSeed", author = "hjm", email
> = "harry.mangalam@uci.edu", version = "0.0.1", genomebuild = "Mon Nov
> 17 14:23:44 PST 2008",biocViews = "Rat Gene 1.0 ST Array", pgfFile =
> pgfFile, clfFile = clfFile, transFile = transFile, probeFile =
> probeFile)
> Error in getClass(Class, where = topenv(parent.frame())) :
>  "AffyGenePDInfoPkgSeed" is not a defined class
>
> Is this a version mismatch or am I missing something more obvious?
>

Hi, Harry.  The oligo package and associates has changed very significantly
since R-2.6.2.  I would suggest upgrading to the current version of R and
re-installing bioconductor.  As for the direct question as to whether or not
this is a version mismatch, it is not possible to say without the output of
sessionInfo(), but I would guess that it is.

Hope that helps,
Sean

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