[BioC] Oligo package crlmm method

Zhu, Julie Julie.Zhu at umassmed.edu
Wed Sep 15 18:46:20 CEST 2010 

Benilton,

Thanks for the debugging code! It helped me to get down to two files with
unreadable header. 

Best regards,

Julie


On 9/15/10 11:55 AM, "Julie Zhu" <julie.zhu at umassmed.edu> wrote:

> 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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