[BioC] Oligo package crlmm method

[Zhu, Julie]

Hi,

I am using the crlmm function in Oligo package to make SNP calls. I
encountered the following segfault error. Could you please let me know what
could be the cause and how to tackle the problem?

Thanks so much for your help!

Kind regards,

Julie

library("oligo")
library("pd.mapping250k.sty")
fullFilenames <- list.celfiles("Sty_CEL_CML", full.names = TRUE)
outputDir <- file.path(getwd(), "crlmmResults_StyCML")
if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir)

 *** caught segfault ***
address 0x12de80000, cause 'memory not mapped'

Traceback:
 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser")
 2: readCelHeader(x)
 3: FUN(c("Sty_CEL_CML/CML-#1-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#1-CP-250ksty.CEL", "Sty_CEL_CML/CML-#10-AP-250ksty.CEL",
"Sty_CEL_CML/CML-#10-CP-250ksty.CEL", "Sty_CEL_CML/CML-#11-AP-250ksty.CEL",
"Sty_CEL_CML/CML-#11-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-AP-250ksty.CEL",
"Sty_CEL_CML/CML-#12-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-CP2-250ksty.CEL",
"Sty_CEL_CML/CML-#13-CP-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP2-250ksty.CEL",
"Sty_CEL_CML/CML-#14-BC-250ksty.CEL", "Sty_CEL_CML/CML-#14-Rem-250ksty.CEL",
"Sty_CEL_CML/CML-#15-BC-250ksty.CEL", "Sty_CEL_CML/CML-#15-CP-250ksty.CEL",
"Sty_CEL_CML/CML-#15-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#16-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#16-BC-GL-250ksty.CEL",
"Sty_CEL_CML/CML-#16-CP-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP2-250ksty.CEL",
"Sty_CEL_CML/CML-#17-AP-250ksty.CEL", "Sty_CEL_CML/CML-#17-CP-250ksty.CEL",
"Sty_CEL_CML/CML-#18-BC-250ksty.CEL", "Sty_CEL_CML/CML-#19-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#19-BC-GL-250ksty.CEL",
"Sty_CEL_CML/CML-#19-CP-250ksty.CEL", "Sty_CEL_CML/CML-#2-CP-250ksty.CEL",
"Sty_CEL_CML/CML-#2-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#20-AP-250ksty.CEL",
"Sty_CEL_CML/CML-#20-BC-250ksty.CEL", "Sty_CEL_CML/CML-#20-CP-250ksty.CEL",
"Sty_CEL_CML/CML-#21-CP-250ksty.CEL", "Sty_CEL_CML/CML-#21-CP2-250ksty.CEL",
"Sty_CEL_CML/CML-#22-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#22-BC-GL-250ksty.CEL",
"Sty_CEL_CML/CML-#22-CP-250ksty.CEL", "Sty_CEL_CML/CML-#23-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#23-BC-GL-250ksty.CEL",
"Sty_CEL_CML/CML-#23-CP-250ksty.CEL", "Sty_CEL_CML/CML-#3-AP-250ksty.CEL",
"Sty_CEL_CML/CML-#3-BC-250ksty.CEL", "Sty_CEL_CML/CML-#4-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#4-CP-250ksty.CEL", "Sty_CEL_CML/CML-#4-Rem-250ksty.CEL",
"Sty_CEL_CML/CML-#5-BC-250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-GL-250ksty.CEL",
"Sty_CEL_CML/CML-#5-Rem-250ksty.CEL", "Sty_CEL_CML/CML-#6-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#6-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#6-CP-250ksty.CEL",
"Sty_CEL_CML/CML-#7-BC-250ksty.CEL", "Sty_CEL_CML/CML-#7-CP-250ksty.CEL",
"Sty_CEL_CML/CML-#8-AP-250ksty.CEL", "Sty_CEL_CML/CML-#8-CP-250ksty.CEL",
"Sty_CEL_CML/CML-#9-BC-250ksty.CEL",
"Sty_CEL_CML/CML-#9-BC-GL-250ksty.CEL")[[16L]], ...)
 4: lapply(X, FUN, ...)
 5: sapply(filenames, function(x) readCelHeader(x)$chiptype)
 6: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate =
recalibrate,     minLLRforCalls = minLLRforCalls, balance = balance, verbose
= verbose)
 7: crlmm(fullFilenames, outputDir)

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 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pd.mapping250k.sty_1.0.0 RSQLite_0.9-2            DBI_0.2-5
[4] oligo_1.12.2             oligoClasses_1.10.0      Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affxparser_1.20.0     affyio_1.16.0         Biostrings_2.16.9
IRanges_1.6.11     
[5] preprocessCore_1.10.0 splines_2.11.1