[BioC] Oligo package crlmm method
Zhu, Julie
Julie.Zhu at umassmed.edu
Wed Sep 15 17:55:01 CEST 2010
Benilton,
Thank you so much for such a quick response!
I tried the following code and got the following error.
Best regards,
Julie
table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]]))
*** caught segfault ***
address 0x1abb9000, 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")[[12L]], ...)
4: lapply(X, FUN, ...)
5: sapply(cels, function(x) readCelHeader(x)[["chiptype"]])
6: table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]]))
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:
On 9/15/10 11:43 AM, "Benilton Carvalho" <beniltoncarvalho at gmail.com> wrote:
> 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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