R help - Feb 2005 - passing command line arguments to 'R CMD BATCH myScript.R'

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

Oleg Sklyar wrote:
> 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
> 
See ?commandArgs

Uwe Ligges

I have never understood the difference between 
> R CMD BATCH --vanilla --slave myScript.R outFile.txt
and
> R --vanilla --slave < myScript.R > outFile.txt
I use the latter method, and then the --args construction works
great:
> R --vanilla --slave --args myArg1 myArg2 < myScript.R > outFile.txt
In fact, I define "R --vanilla --slave --args" to be an environment
variable $R, and then it's just
> $R myArg1 myArg2 < myScript.R > outFile.txt
-- David Brahm (brahm at alum.mit.edu)

Hi,
I recently solved the problem: I ran a program from Linux. The basic
idea is using enviroment variables and ?Sys.getenv

This is a general approach to calling R from a script file.

Here is part of my codes and explanation:

# assign some values to the arguments
dvar=5
categorical=3
....

# export them as env. var.
export dvar mod_min mod_max tree_no cp categorical

#run your r program in a batch mode
R CMD BATCH < $HOME/r/batch/mk_trees.r

The following is part of my mk_trees.r:
#load arguments
cargs<-Sys.getenv(c('dvar','mod_min','mod_max','tree_no','cp','categorical'))
dvar<-as.numeric(cargs[1])
mod_min<-as.numeric(cargs[2])
mod_max<-as.numeric(cargs[3])
tree_no<-as.numeric(cargs[4])
cp<-as.numeric(cargs[5])
cc<-strsplit(cargs[6], "\n")
categorical<-as.numeric(cc[[1]])


HTH,

Ed

On Fri, 25 Feb 2005 14:57:57 +0000, Oleg Sklyar <osklyar at ebi.ac.uk>
wrote:
> 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
> 
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