[R] passing command line arguments to 'R CMD BATCH myScript.R'

[Oleg Sklyar]

Hi Community,

I have a question about how to pass command line parameters to R script 
running in the batch mode. The problem is: there is a banch of data 
files which are to be processed by R script called from a web-server, 
i.e. in the batch mode. The web server generates data files and passes 
their names calling 'R CMD BATCH' one by one for every file. Now the 
question is how to call 'R CMD BATCH myScript.R' with parameters, like 
file name to process? I know how to read the parameters passed to an R 
script, but I don't know how to pass them.

There is an option --args that should cut the rest of the line off the 
command line. The problem is however that BATCH syntax is: 'R CMD BATCH 
[options] inFile [outFile]', i.e. if I write
'R CMD BATCH --args myDataFile myScript.R' or 'R CMD BATCH --args 
myDataFile < myScript.R' (similar was posted on some R help under 
Windows) it is not going to work because then BATCH doesn't know about 
myScript.R - it is considered as a parameter, so only 'R CMD BATCH' is 
executed. If however I use 'R CMD BATCH myScript --args myDataFile' then 
R understands --args as an output file and generates a file with that name.

Does anyone has a solution for the problem?

Best regards
Oleg

-- 
Dr Oleg Sklyar
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD
England
phone/fax  +44(0)1223 49 4478/4468
e-mail osklyar at ebi.ac.uk