[BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow

Seth Falcon seth at userprimary.net
Mon Mar 15 16:30:55 CET 2010

Hi Robert,

On 3/15/10 6:46 AM, Ivanek, Robert wrote:
> I tried to run the runBioHMM function on my data (Nimblegen HD 2.1
> Arrays), however I am always getting the error: "Error: segfault from C
> stack overflow".

You need to provide us with more information so that we can help you.  A
good start would include:

- sessionInfo()
- the exact code you are running
- more details on the input data.

> What is the reason for that error? Are the data too big? I tried to
> split the array according the chromosomes but it did not help. Only
> after splitting the data into small pieces the function run
> successfully. 

That does suggest that data size is the issue.  Are you able to obtain
any details on where the segfault occurs?  R-devel includes a fix for an
issue in gsub that could cause a stack overflow segfault for long
strings.  You might try installing latest R-devel, Bioconductor devel
packages and see if the problem is reproducible there.

> I preprocessed the data according the snapCGH manual (snapCGHguide.pdf),
> below is the code that produced the error, object class and sessionInfo.

Maybe you forgot to copy/paste?

+ seth

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