Hi,
     I have met one problem when I used justRMA() under Linux. Under R GUI,
the code can work, but when I use Rscript to call, it can't work. The code
is as follows,

inputPath="/data1/caozf/CCLE/expression/cel"
outputPath="/data1/caozf/CCLE/expression/processed"
phenoinfo="/data1/caozf/CCLE/expression/para/CCLE_Expression.Arrays.sif_2010-09-29.txt"
prefix="CCLE_Expression_Entrez_2012-03-09"
cdfname="hgu133plus2hsentrezgcdf"

#input cel files and phenoinfo
library("affy")
print("normal1")
#input cel files
    sampleInfo<- read.delim(phenoinfo,sep="\t",header=TRUE)
    sampleNames<- as.character(sampleInfo$CCLE.name)
    filelist<- paste(as.character(sampleInfo$Array),".CEL",sep="")
print("normal2")

#RMA normalization
    eset<-
justRMA(filenames=filelist,celfile.path=inputPath,sampleNames=sampleNames,cdfname
= cdfname)
print("normal3")
    e <- exprs(eset)
    e<- round(e,3)
print("normal4")

#  output
   e<- cbind(rownames(e),e)
   colnames(e)[1]<- "CCLE.Name"

write.table(e,paste(outputPath,"/",prefix,"_rma.txt",sep=""),sep="\t",quote=FALSE,row.names=F,append=F,
               col.names=T)

The code file was named PreprocessAffyExp.CCLE.r, and the log are as
follows,
[caozf@helix para]$ Rscript  PreprocessAffyExp.CCLE.r
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

[1] "normal1"
[1] "normal2"
Execution halted

So, we can make sure that, justRMA can not work. But I don't know how to
deal with?
Any help is appriciate.

-- 

Zongfu Cao

*BeiGene(Beijing) Co.,Ltd*
No.30 Science Park Road
Zhong-Guan-Cun Life Science Park
Changping District, Beijing P.R.China
Postal Code: 102206

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