[BioC] Oligo package crlmm method
Zhu, Julie
Julie.Zhu at umassmed.edu
Wed Sep 15 17:27:55 CEST 2010
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
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