[BioC] affxparser & oligo, persistent memory fault

[Kasper Daniel Hansen]

Hi Morten

Most likely this happens because one of your CEL files are corrupted  
somehow. affxparser segfaults when it tries to read a corrupted file.  
The easiest way to detect this is to do something like

celfiles = "" # This should be a character vector of your CEL file names
for(cel in celfiles) {
   print(cel)
   readCelHeader(cel)
}

That way you can identify the culprit.

ANother possibility is that something is wrong with affxparser, but it  
is quite widely used, so for now I will stick to the first explanation.

Could you report back your findings.

Kasper

On Jun 17, 2008, at 5:03 PM, Morten Mattingsdal wrote:

> Hi,
> Ive ran into some trouble here and it seems serious. After  
> installing oligo and running justCRLMM with the freshly downloaded  
> pd.genomewidesnp.6, the genotype calling went on fine for a couple  
> of hours, using about 6GB of RAM. Since I forgot to use "nohup" (so  
> R can work even if I close the shell terminal on the supercomputer),  
> the process got killed by the OS. When I try to rerun the functions,  
> R seems to have some serious trouble.  The below segmentation fault  
> occurs even when I try a fresh re-installation of R-2.7.0 and R-devel.
> Although this seems to be a fundamental memory handling error on  
> this computer, independent of R/Biocondcutor, R is able to read  
> multiple hgu133plus2 CEL files. From the error report below it seems  
> that affxparser is involved somehow.
> Do anyone have any idea of what happened, and why affxparser is  
> persistently dying independent of R versions?
> Would a simple restart be the solution? (not tried since this is a  
> grid computer)
> morten
>
>
>
>
>
>
> *** caught segfault ***
> address 0x2a9f2d9cd9, cause 'memory not mapped'
>
> Traceback:
> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE =  
> "affxparser")
> 2: readCelHeader(x)
> 3: FUN(c("ea07057_0349-01a_genomewidesnp_6_k5166_n2.cel",  
> "ea07057_0349-01b_genomewidesnp_6_k5140.cel",  
> "ea07057_0349-01d_genomewidesnp_6_k-5126.cel",  
> "ea07057_0349-01e_genomewidesnp_6_k5152.cel",  
> "ea07057_0349-01g_genomewidesnp_6_k5111.cel",  
> "ea07057_0349-01h_genomewidesnp_6_k5269.cel",  
> "ea07057_0349-02a_genomewidesnp_6_k5174.cel",  
> "ea07057_0349-02f_genomewidesnp_6_k5138.cel",  
> "ea07057_0349-02g_genomewidesnp_6_k-5262.cel",  
> "ea07057_0351-01b_genomewidesnp_6_u504.cel",  
> "ea07057_0351-01e_genomewidesnp_6_u007.cel",  
> "ea07057_0351-01f_genomewidesnp_6_u-435.cel",  
> "ea07057_0351-02a_genomewidesnp_6_u123.cel",  
> "ea07057_0351-02b_genomewidesnp_6_u004.cel",  
> "ea07057_0351-02e_genomewidesnp_6_u126.cel",  
> "ea07057_0351-02g_genomewidesnp_6_u426.cel",  
> "ea07057_0351-02h_genomewidesnp_6_u524.cel",  
> "ea07057_0351-03a_genomewidesnp_6_u050.cel")[[9L]], ...)
> 4: lapply(X, FUN, ...)
> 5: sapply(filenames, function(x) readCelHeader(x)$chiptype)
> 6: read.celfiles(files)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> > sessionInfo()
> R version 2.8.0 Under development (unstable) (2008-06-16 r45945)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE 
> = 
> en_US 
> ;LC_NUMERIC 
> = 
> C 
> ;LC_TIME 
> = 
> en_US 
> ;LC_COLLATE 
> = 
> en_US 
> ;LC_MONETARY 
> = 
> C 
> ;LC_MESSAGES 
> = 
> en_US 
> ;LC_PAPER 
> = 
> en_US 
> ;LC_NAME 
> = 
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils      
> datasets
> [8] methods   base
> other attached packages:
> [1] oligo_1.5.3          oligoClasses_1.3.3   affxparser_1.13.3  [4]  
> AnnotationDbi_1.3.5  preprocessCore_1.3.1 RSQLite_0.6-9      [7]  
> DBI_0.2-4            Biobase_2.1.7
>
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