R SIG Fedora - Nov 2008 - Problem running R from within a script

On Tue, 2008-11-25 at 13:13 -0500, Joshua Kramer wrote:
> Howdy Folks,
> 
> I am running R version 2.7.2 (2008-08-25) on CentOS 5.2 - the standard RPM 
> distribution.
> 
> I am having a curious occurance trying to run a R script from within a 
> shell script.  Basically, I have a small R script that processes a file. 
> It takes two parameters - the input file, and the output file.  I then 
> have a shell script that runs the R script for each file matching a glob.
> 
> R is not picking up the correct parameters *when run from the script*. 
> When I run the command line by itself, it runs fine.
> 
> The command line is this:
> 
> /usr/bin/R CMD BATCH --no-restore --no-save '--args $taxFile
$taxFile.taxonomy' batchMakeTax.R batchMakeTax.log
I'm just guessing here, but those ' ' single quotes don't seem
to make
sense. Try dropping them (or moving them to just be around '$taxFile
$taxFile.taxonomy').

~spot

Howdy Folks,

I am running R version 2.7.2 (2008-08-25) on CentOS 5.2 - the standard RPM 
distribution.

I am having a curious occurance trying to run a R script from within a 
shell script.  Basically, I have a small R script that processes a file. 
It takes two parameters - the input file, and the output file.  I then 
have a shell script that runs the R script for each file matching a glob.

R is not picking up the correct parameters *when run from the script*. 
When I run the command line by itself, it runs fine.

The command line is this:

/usr/bin/R CMD BATCH --no-restore --no-save '--args $taxFile
$taxFile.taxonomy' batchMakeTax.R batchMakeTax.log

Here's the output of the script:
Processing /usr/bin/R CMD BATCH --no-restore --no-save '--args Call0103.xpt
Call0103.xpt.taxonomy' batchMakeTax.R batchMakeTax.log
/usr/lib/R/bin/BATCH: line 55: Call0103.xpt: Permission denied

I do not know why it's trying to write to the input file... any ideas?

Here's the shellscript:

[josh at localhost cr]$ cat batchMakeTax.sh
#!/bin/sh

FILES="*.xpt"

echo MakeCommand is $makeCommand

for taxFile in $FILES
do
         makeCommand="/usr/bin/R CMD BATCH --no-restore --no-save
'--args $taxFile $taxFile.taxonomy' batchMakeTax.R
batchMakeTax.log"
         echo "Processing $makeCommand"
         $makeCommand
done

...and, the R script.  Note that R never gets as far as running the 
script, however - the error occurs in the CMD shell script that is under 
/usr/bin/R/CMD.

[josh at localhost cr]$ cat batchMakeTax.R
library(foreign)
scratchOne <- commandArgs()
inFileArg <- scratchOne[10]
taxFileArg <- scratchOne[11]
sink("debugout.txt", FALSE, "output", FALSE)
print (inFileArg)
print (taxFileArg)
bankData <- read.xport(inFileArg)
sink(NULL)
sink(taxFileArg, FALSE, "output", FALSE)

bdNames <- names(bankData)

numCol <- ncol(bankData)
i=1
while (i <= numCol) {
         myVar <- paste(bdNames[i], typeof(bankData[[bdNames[i]]]), 
sep=":")
         print(myVar)
         i=i+1
}
q()

Thanks!
-josh

-- 

-----
http://www.globalherald.net/jb01
GlobalHerald.NET, the Smarter Social Network! (tm)