On 07-11-2012, at 12:08, didier peeters wrote:
> 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
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