R devel - Jul 2005 - mac os x crashes with bioconductor microarray code (PR#8013)

Full_Name: Eric Libby
Version: 2.1.1
OS: OS Tiger
Submission from: (NULL) (65.93.158.117)


I am trying to analyze microarray data of 42 human arrays. I typed in the
following instructions:
library(affy)
Data <-ReadAffy()
eset <- expresso(Data, normalize.method="invariantset",
bg.correct=FALSE,
pmcorrect.method="pmonly",summary.method="liwong") 

And I get some sort of memory error that crashes the R program. Specifically it
states:
R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3)
R(1763) malloc: *** error: can't allocate region
R(1763) malloc: *** set a breakpoint in szone_error to debug
R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3)
R(1763) malloc: *** error: can't allocate region
R(1763) malloc: *** set a breakpoint in szone_error to debug
Error: cannot allocate vector of size 338724 Kb
R(1763) malloc: *** vm_allocate(size=8421376) failed (error code=3)
R(1763) malloc: *** error: can't allocate region
R(1763) malloc: *** set a breakpoint in szone_error to debug


Any ideas? My computer has 2gb of RAM and 100 gb free. I would think that
analyzing 42 microarrays would not be too difficult. Thanks,
Eric

On Jul 19, 2005, at 12:34 AM, cireeric at alumni.rice.edu wrote:
> R(1763) malloc: *** vm_allocate(size=346857472) failed (error code=3)
> R(1763) malloc: *** error: can't allocate region
As the error says, you're obviously running out of contiguous wired  
memory (RAM).
> Any ideas? My computer has 2gb of RAM and 100 gb free. I would  
> think that analyzing 42 microarrays would not be too difficult.
You didn't tell us anything about the size of the data - and it seems  
to be of considerable size, because it fails on allocating ca. 350MB  
bytes at once. Whether what you do is difficult or not, that I don't  
know, but obviously you don't have enough memory for what you're  
trying to do. Basically that means you should reconsider your  
approach. Once you provide more information you may want to ask  
Bioconductor users about this issue, but it's definitely not a bug in R.

Cheers,
Simon