[R] Append to outfile in R CMD BATCH mode

Turchin, Michael Michael.Turchin at childrens.harvard.edu
Fri Mar 12 03:18:57 CET 2010

So I have a semi-answer for myself. I don't think this way is preferable, but if you're going through the same thing as me, maybe it'll help.

If you pass your desired outfile as an argument in '--args filename', you can redirect the output the following way:

cmd_args = commandArgs()
print (cmd_args) #To figure out which number argument your outfile is
sink(cmd_args[2], append=TRUE) #Or whatever number argument your filename is
sink() #at the end of your script

Stderr I think still gets directed to your outfile location in the R CMD BATCH... command (see start of thread), but Stdout should now go to wherever you directed it with sink, plus, now you can append.

HTH (and if you're aware of a better way, please let me know!)
~Michael Turchin
Children's Hospital Boston
The Broad Institute

From: r-help-bounces at r-project.org [r-help-bounces at r-project.org] On Behalf Of Turchin, Michael [Michael.Turchin at childrens.harvard.edu]
Sent: Thursday, March 11, 2010 5:27 PM
To: r-help at r-project.org
Subject: [R] Append to outfile in R CMD BATCH mode

Is there a way to append to the outfile when using R CMD BATCH? My code, right now, is:

R CMD BATCH --slave --vanilla '--args place .2 -.1 .9 .6' StratificationSimulation example.output

Everything else is working the way I'd like it. The first few lines of code of my script file are:

cmd_args = commandArgs()
print (cmd_args)
#d <- read.table("/dev/stdin")

if that helps any. However, I cannot currently change the output to append, rather than override, the designated outfile. Maybe I could potentially use sink(__, append=TRUE) if I could somehow reference the outfile from within the script (and assuming my understanding of sink() is correct)?

Any thoughts, or help? They're all greatly appreciated.
Children's Hospital Boston
The Broad Institute
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