[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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>> 
> 



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