[BioC] affxparser & oligo, persistent memory fault

[Morten Mattingsdal]

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