[BioC] Continued problems with pdInfoBuilder

[Rob Dunne]

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

Hi Harry,
I got this to work my upgrading to the development version of  R (2.9.0) 
and the
devel version of pdInfoBuilder.

Bye
Rob


-- 
Rob Dunne         Fax: +61 2 9325 3200     Tel: +61 2 9325 3263
CSIRO Mathematical and Information Sciences     +61 2 9325 3100
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http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au

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