[BioC] affxparser & oligo, persistent memory fault

[Morten Mattingsdal]

Hi again,
Ive managed to pinpoint the source of my problems, and I'm sorry for 
spamming the list.
1) It seems that reading from another disk-partition is not a good idea.
2) Somehow the computer managed to clean up its dirty memory and 
allowing me to mess it up again
morten

> 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
>
>
>