[BioC] Oligo package crlmm method

Benilton Carvalho beniltoncarvalho at gmail.com
Wed Sep 15 17:43:18 CEST 2010


Start a new session of R and try the following:

cels = list.files("Sty_CEL_CML", pattern="CEL$", full=TRUE)
library(affxparser)
table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]]))

and let me know what you get.

b

On 15 September 2010 16:27, Zhu, Julie <Julie.Zhu at umassmed.edu> wrote:
> 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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