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

[Prof Brian Ripley]

Soemone broke contrasts<- in 2.10.0 to require the 'methods' package, 
but this was corrected in R-patched on Jan 4.

Thus you need to add 'methods' to the default packages in Rscript (see 
its help) or update your R.

This has come up before, so a search of the archives was likely to 
have found it.

On Tue, 23 Mar 2010, Paul.Rustomji at csiro.au wrote:

> 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)
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595