[R] Unable to execute lm function within a Rscript launch in the Linux Terminal

[Thomas MORISSEAU]

Hello to the list


I'm using a Rscript launched via the linux terminal as the title of this
mail explains. The following is the code of the Rscript :

myRscript.r
--------------------------------
1 #!/usr/bin/Rscript
2
3 #Read data
4
data=read.table("/home/morisseau/stage/recherche/gwas/data/CFHLC5/CFHLC_format_files_rm_07052010/output/windowstemp.txt")
5
6 data=t(data)
7
phen=read.table("/home/morisseau/stage/recherche/gwas/data/CFHLC/CFHLC_format_files_rm_07052010/input/Admixmap_simphen_simu1_causalsnp61.txt")
8 phen=phen[-1]
9 phen=t(phen)
10 val=c(1,2)
11 for (i in 1:dim(data)[2]){
12	val[1]=data[,i][3]
13	test=chisq.test(phen,data[,i][-(1:4)])
14	val[2]=test$p.value
15	test=lm(phen~data[,i][-(1:4)])
16	print (summary(test))
17	print(val)
18 }
----------------------------------

which call an error :

Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") :
  unable to find "is" function
Calls: lm ... model.matrix -> model.matrix.default -> contrasts<-
Execution stopped


But when I execute the same code in a R console with source("myRscript.r")
command, all works fine.

I'm sure that this is the lm function which entails the error because when
I code off the line 15, the R script works fine in the Linux Terminal.

Can you help me please?

Thank you in advance.

Best regards


Thomas MORISSEAU