[R] R[1304] general protection rip - Error running R file in Batch mode

From: Srinivas Iyyer <srini_iyyer_bio_at_yahoo.com>
Date: Wed 22 Feb 2006 - 12:24:52 EST

hi group,
 I have a list of 100 elements (genes), that are to be queried in postgres. The out of the file is processed for fisher test and written back as a file with pvalues.
For one such operation there are 54 lines of code.

I replicated the same code changing the query element and file name to write back.

I created a jumbo 100*54 = 5400 lines of code by replication.

I saved this file as .R and ran it as:
R CMD BATCH myfile.R..

The program ran for ~40 mins. ( each operation takes 5 mins). after going home, I checked the stats and saw that the program got aborted leaving 8 output files in directory.

I checked /var/log/messages and found :

localhost kernel: R[1304] general protection rip:2a988c919e rsp:7fbfff87f0 error:0

postgres did not log any error message.

This is my first time I am running my R code in BATCH mode. I am a new to programming in R and I have been working directly with R interface.

Could any one guess what could have been the problem.


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