Limit of matrix + naming

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. 

Thanks
Sri

Hi group, 
I ran the file again and after 10 min. of run, the
process got interrupted.  

Here is the output of the file

$bash: R CMD BATCH grand.R > grand.log


 R CMD BATCH grand.R


/usr/local/lib64/R/bin/BATCH: line 55:  1758 Broken
pipe             ( echo "invisible(options(echo =
TRUE))"; cat ${in}; echo ''; echo "proc.time()" )
      1760 Segmentation fault      | ${R_HOME}/bin/R
${opts} >${out} 2>&1


Is this because of the excess query code in one .R
file?

Any suggestions, will help me .

thanks
Sri

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. 

Thanks
Sri

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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