[BioC] Continued problems with pdInfoBuilder
Rob.Dunne at csiro.au
Tue Nov 18 01:36:50 CET 2008
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 =
> 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,
I got this to work my upgrading to the development version of R (2.9.0)
devel version of pdInfoBuilder.
Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263
CSIRO Mathematical and Information Sciences +61 2 9325 3100
Locked Bag 17, North Ryde, New South Wales, Australia, 1670
http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au
Java has certainly revolutionized marketing and litigation.
More information about the Bioconductor