R script in batch mode on Mac

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Hi list,

I would like the run a R script in a batch mode.  So i use a command line like this :

for i in *.xlsx; do cat $i | echo 'argv <- $i; source("path/to/script.R")' | R --vanilla --slave ; done

which gives the error " Erreur : '$' inattendu(e) dans "argv <- $" "

i've also tried  :

for i in *.xlsx; do cat $i | R CMD BATCH --args $i "path/to/script.R" ; done

which gives me nothing.  

The idea is to read dozens of similar excel files in a folder with gdata package and to write their content in another single file.  
My script works fine with a read.xls when i specify a file name, but and here I get the name of the file with :
argv <- commandArgs(TRUE)

This is all I've been able to find from various docs and I'm not familiar with the command line.  
What am I doing wrong ?
Could anyone help me ?
You need to read up on shell command syntax. In particular, the "cat $i | command" bit would pipe the content of the file $i into the command, which makes no sense when the command is "echo" or "R". Also check up on the use of single and double quotes.
Didier
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Peter Dalgaard, Professor
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Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

Hi list,

I would like the run a R script in a batch mode.  So i use a command line like this :

for i in *.xlsx; do cat $i | echo 'argv <- $i; source("path/to/script.R")' | R --vanilla --slave ; done

which gives the error " Erreur : '$' inattendu(e) dans "argv <- $" "

i've also tried  :

for i in *.xlsx; do cat $i | R CMD BATCH --args $i "path/to/script.R" ; done

which gives me nothing.  

The idea is to read dozens of similar excel files in a folder with gdata package and to write their content in another single file.  
My script works fine with a read.xls when i specify a file name, but and here I get the name of the file with :
argv <- commandArgs(TRUE)

This is all I've been able to find from various docs and I'm not familiar with the command line.  
What am I doing wrong ?
Could anyone help me ?
Try Rscript like this

for k in *.R; do
    Rscript -e "source('path/to/script.R')" $k
done

and get the name of the file to process from commandArgs()

or

Rscript -e "source('path/to/script.R')" *.xlsx

and loop over the elements of commandArgs() in the script.

or

use list.files() -- something like list.files(pattern="^.*\\.xlsx") -- in the script then you don't need to loop in the shell script.

Berend