[R] Problem with factors in lm() when using Rscript but not GUI

[Paul.Rustomji at csiro.au]

Hello R-help

I am having a curious problem.  I am using a batch file to call an R script and am getting an error when performing a lm() fit using factorial data only when running in batch mode (see below).  I do not get the error when executing the same code in GUI mode in R 2.10.1.  Nor do I get the error when using Rscript version 2.9.2....


#######################################
#windows batch file contains this line to call tnp2.r r-script
#Rscript ./tnp2.r  --slave
########################################

########################################
#tnp2.r - contents of tnp2.r script file are below

print(R.Version()$version.string)

#generate some data
x <- rep(c(1:12),3)
y <- 1:length(x)+rnorm(length(x))

print(x)
print(y)

#this bit works OK
xtemp <- lm(y ~ x )
print(xtemp)
print("got to here (without factor part)")

monthfac <- as.factor(x)
print(monthfac)

#this line below causes probs in R v2.10.1 when run from Rscript.....
xtemp2 <- lm(y ~ monthfac)

print(xtemp2)
stop("stopped on purpose",call.=F)

#end of file tnp2.r
###############################################



#error message is thus:

Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") :
  could not find function "is"
Calls: lm ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted


As I say - all works ok in GUI mode but not in Rscript mode (v2.10.1).....

This problem seemed to commence after upgrading to R 2.10.1 from R2.9.2, as the same code works fine in Rscript in version 2.9.2.

Paul.

###########################
> Sys.info()
                     sysname                      release 
                   "Windows"                         "XP" 
                     version                     nodename 
"build 2600, Service Pack 3"                      "XXXX" 
                     machine                        login 
                       "x86"                     "xxxxxx" 
                        user 
                    "xxx"

$platform
[1] "i386-pc-mingw32"

$arch
[1] "i386"

$os
[1] "mingw32"

$system
[1] "i386, mingw32"

$status
[1] ""

$major
[1] "2"

$minor
[1] "10.1"

$year
[1] "2009"

$month
[1] "12"

$day
[1] "14"

$`svn rev`
[1] "50720"

$language
[1] "R"

$version.string
[1] "R version 2.10.1 (2009-12-14)"






Paul Rustomji
CSIRO Land and Water (Lucas Heights, NSW)