[BioC] snapCGH, runBioHMM, Error: segfault from C stack overflow
seth at userprimary.net
Mon Mar 15 16:30:55 CET 2010
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:
- 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
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?
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