[Rd] Embedded R Fails When Run on LSF Queue System
Nigel Delaney
nigel.delaney at outlook.com
Sun Nov 10 22:32:50 CET 2013
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
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