[R] Append to outfile in R CMD BATCH mode

[Turchin, Michael]

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
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code
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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:

options(echo=FALSE)
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.
Thanks!
~Michael
Children's Hospital Boston
The Broad Institute
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