[BioC] R crashes on winXP with 2G memory

Henrik Bengtsson hb at maths.lth.se
Sat Apr 1 12:45:49 CEST 2006


R should never crash, that's true.  What's your version of R?  Are you
running R v.2.2.1?  Then try to download the latest "patched" version.
 Are you running R v2.3.0 devel?  Then try to download a newer
version, because bugs get introduced once in a while in the devel
version which are fixed a few days later.

When does it crash?  In the read.table() call?  Try to narrow it down.
 If it is a memory problem, you can always try to through in a gc() in
the end of your for loop.  Also, if you're only interested in a few of
the columns, you can the read.table() to ignore all others.  See the
help and argument 'colClasses'.  That will speed up your reading and
decrease the memory usage. R should still not crash, but you might
avoid the bug this way.

In your script, 'Count' and 'count' are two different objects!  Also,
your 'assign(print(i,quote=FALSE),x)' statement is very misleading
(although correct).  It's better to split it up in two lines:



On 3/31/06, Hao Liu <liuha at umdnj.edu> wrote:
> Dear All:
> I encountered this several times, could someone point out where the problem
> is? I don't think it is the memory restriction or something...
> I have 345 MAS5 results formated as: probeset_id, expression_value, PA_call
> in 345 text file. I tried to combine them into one single file, but only
> retain one probeset_ID column.
> This is my commend:
> Files<-list.files(pattern=".txt$");
> Count<-0;
> for(i in files) {x<-read.table(i, header=TRUE,sep="\t"); assign(print(i,
> quote=FALSE),x);if(count==0){combined<-x;rm(x);count<-count+1;} else
> {combined<-cbind(combined,x[,2:3]);rm(x);count<-count+1;}}
> After processing over 200 files, the program crashes.
> Is there a better way to get it done? And, for this large dataset, if I
> don't want to use RMA -- which is easier to get using justrma, I am stuck
> here...
> Thanks
> Hao
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Henrik Bengtsson
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