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

From: Duncan Murdoch <murdoch_at_stats.uwo.ca>
Date: Wed 22 Feb 2006 - 14:05:44 EST

On 2/21/2006 8:24 PM, Srinivas Iyyer wrote:
> 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.

That's a fairly strange way to write such a thing. Why not write a single function, and run it in a loop?

>
> 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.

You haven't really given us much to go on. You haven't stated the version, or what packages and functions you are using.

I'd guess this is a bug with one of the packages you're using, but it could be a bug in R. Can you determine which line causes the error? Does it happen if you extract just that line, and enough previous ones to set things up for it?

Duncan Murdoch



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