From nigel.delaney at outlook.com  Sun Nov 10 22:32:50 2013
From: nigel.delaney at outlook.com (Nigel Delaney)
Date: Sun, 10 Nov 2013 16:32:50 -0500
Subject: [Rd] Embedded R Fails When Run on LSF Queue System
Message-ID: <BAY176-W4686BF21116D18A83FEBE5E5FC0@phx.gbl>

Hi,

I had a quick question I was hoping someone might be able to answer, as my journey through the source code so far has not been very profitable. I have a command line program that embeds R, and the program works just fine when run from the command line. However, when I run the program as a job in the LSF cluster at my institute, the following error occurs:

Fatal error: you must specify '--save', '--no-save' or '--vanilla'

This is confusing becasue I believe I have set this by changing the startup parameters so that the no-save option is in use. I initialize R with the following collection of function calls:

1-Rf_initialize_R
2-R_SetParams
3-setup_Rmainloop

At step 2 I pass in a structure that specifies the no-save option (as well as interactive=true, verbose=false), so I would expect it to be okay, but I still receive this error. Again, not at the terminal but only when run as a separate process.

I gathered from this thread that someone else has experienced this (https://stat.ethz.ch/pipermail/r-help/2008-March/155935.html), but am not sure how best to rectify it as I believe I have already changed the setting.

Does anyone know what a good solution or work around might be?

Thanks for any help,
Nigel 		 	   		  


[Rd] Embedded R Fails When Run on LSF Queue System
Nigel Delaney