[R] issues with "write.table"

[Foadi, J (James)]

Dear R gurus and users,
I'm having problems with the use of write.table.
I have a 28-variables data frame create at each cycle of a loop; it can contain between 2000 and 3000 rows for each cycle.
After each cycle the data frame is written out to a file with the "append=TRUE" option and then removed from memory.
These are the couple of lines involved:

> data2 <- format.data.frame(sorted_data)
> write.table(data2,file="R_toscala.txt",append=TRUE,quote=FALSE,sep="\t",row.names=FALSE,col.names=FALSE)
> rm(tmp,new_xyz,u0,u1,data,data0,data1,data2,data3,data4,templ0,templ1,f0,f1,frac,Xdet,Ydet,tthr,tth,tras_coef,sc,srs,sup,sdown,rs,lorentz,pola,rot,sorted_data)

You can see that data2 is removed at each cycle together with other objects in order to free memory.

Now everything is OK when the written file, "R_toscala.txt" grows roughly to 100000 lines. But my code writes wrong values after that. I suspect there might
be issues with files size or with stack size, but am absolutely not sure about it. I am running Ubuntu 8 - 64bit. The ulimit -a gives:

core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 40960
max locked memory       (kbytes, -l) 32
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 40960
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

Any idea of what is going wrong here?

Many thanks,

James


Dr James Foadi PhD
Membrane Protein Laboratory (MPL)
Diamond Light Source Ltd
Diamond House
Harewell Science and Innovation Campus
Chilton, Didcot
Oxfordshire OX11 0DE

Email    :  james.foadi at diamond.ac.uk
Alt Email:  j.foadi at imperial.ac.uk

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