[BioC] Error in function (classes, fdef, mtable)

[Martin Morgan]

Several of your packages seem to be out of date with the version
released in Bioconductor 1.9 and intended for use with R 2.4.0, e.g.,

affyio (version in 1.9: 1.2.0; your version: 1.0.0)
affyQCReport (1.12.0, versus 1.10.0)
simpleaffy (1.8.0, versus 1.6.0)

After running the command

update.packages(repos="http://bioconductor.org")

(my message on 11/09 was not clear about the repos argument, sorry) do
you still receive the errors?

Martin

"D.Enrique ESCOBAR ESPINOZA" <escobarebio at yahoo.com> writes:

> I would like some help to solve my little problem using affyQCReport:
> I don t know why but I m having troubles to call proper libraries.
> I wrote the following method:
> =============================
> #* @param		aPrefix	a string representing a png filename
> #* @param		aData	an AffyBatch object to plot
> plotCorr2png	<- function	(aTitle	= "",
> 							aData	= NULL
> 							){
> 				doCat	(":::::::plotCorr2png::")
> 				print(aTitle)
> 				print(aData)
> 				require(affyQCReport)
> 				print(sessionInfo())
> 				aTitlePNG	= paste(aTitle,"Corr.png",sep="")
> 				png	(filename=aTitlePNG,
> 					width=600,height=800,res=600)
> 					
> 					correlationPlot(aData)
> 					
> 				dev.off()
> 				pkg		<- "package:affyQCReport";
> 				detach(pos = match(pkg, search()))
> }
> ==============================
> the error appear when I plot into apng file
> correlationPlot...
> It use to say no correlationPlot function, i solved that requiring
> affyQCReport.
> Then I m still having the output even if simpleaffy is loaded
>>>>>>>>>>>>>>>>>>>>>>>>
> :::::::plotCorr2png::
> [1] "affylimsgenechipanalyze-doVESICULES-qc_AffyQC"
> AffyBatch object
> size of arrays=1002x1002 features (39230 kb)
> cdf=Mouse430_2 (45101 affyids)
> number of samples=5
> number of genes=45101
> annotation=mouse4302
> Loading required package: affyQCReport
> Welcome to 'affyQCReport' V 1.6-1
> Further information available at: www.bifix.org
>       mailto: craig.parman at bifix.org
> R version 2.4.0 (2006-10-03)
> x86_64-redhat-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics" 
> "grDevices"
> [7] "utils"     "datasets"  "base"
>
> other attached packages:
> affyQCReport   simpleaffy   reposTools   genefilter     survival     
>  xtable
>     "1.10.0"      "2.6.0"     "1.10.0"     "1.12.0"       "2.29"     
> "1.4-2"
> mouse4302cdf      affyPLM        gcrma  matchprobes     affydata     
>    affy
>     "1.12.0"     "1.10.0"      "2.6.0"      "1.6.0"     "1.10.0"    
> "1.12.1"
>       affyio      Biobase
>      "1.0.0"     "1.12.2"
> Error in function (classes, fdef, mtable)  :
>         unable to find an inherited method for function "pData", for
> signature "phenoData"
> In addition: Warning message:
> X11 used font size 25 when 28 was requested
> Execution halted
> Total files in  directory  : 47
>>>>>>>>>>>>>>>>>>>>>>>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org