[R] R memory issue for writing out the file

Henrik Bengtsson hb at stat.berkeley.edu
Tue Apr 15 19:45:44 CEST 2008

Try to write the data.frame to file in blocks of rows by calling
write.table() multiple times - see argument 'append' for
write.table().  That will probably require less memory.


On Tue, Apr 15, 2008 at 6:12 PM, Xiaojing Wang <timanwang at gmail.com> wrote:
> Hello, all,
>  First thanks in advance for helping me.
>  I am now handling a data frame, dimension 11095400 rows and 4 columns. It
>  seems work perfect in my MAC R (Mac Pro, Intel Chip with 4G RAM) until I was
>  trying to write this file out using the command:
>  write.table(all,file="~/Desktop/alex.lgen",sep="
>  ",row.names=F,na="0",quote=F,col.names=F)
>  I got the error message:
>  R(319,0xa000d000) malloc: *** vm_allocate(size=88764416) failed (error
>  code=3)
>  R(319,0xa000d000) malloc: *** error: can't allocate region
>  R(319,0xa000d000) malloc: *** set a breakpoint in szone_error to debug
>  I then confirmed in Windows (Windows XP, 1G RAM) R by trying it again. It
>  seems that it has to do with my R memory limit allocation.
>  I read all the online help and still could not figure out the way to solve
>  the problem. Also I do not understand why the data could be easily handled
>  within R but could not write out due to the insufficient memory. I am not
>  good at both R and computers.  Sorry for my naive questions if it sounds
>  bothersome.
>  --
>  Xiaojing WANG
>  Dept. of Human Genetics
>  Univ. of Pittsburgh, PA 15261
>  Tel: 412-624-8157
>         [[alternative HTML version deleted]]
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