[BioC] rma of oligo feature set crashes R

[Hervé Pagès]

Hi Thomas,

On 11-10-04 12:24 PM, Benilton Carvalho wrote:
> What's your *complete* output of sessionInfo()? And is it reproducible
> with any public data?
>
> b
>
> On 4 October 2011 20:17, Thomas H. Hampton
> <Thomas.H.Hampton at dartmouth.edu>  wrote:
>>
>> Ideas?
>>
>>> sessionInfo()
>> R version 2.13.0 (2011-04-13)
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>
>>
>> library(oligo)
>> library(pd.hugene.1.0.st.v1)
>>
>> exonCELs<- list.celfiles(full.names = TRUE)
>> affyExonFS<- read.celfiles(exonCELs)
>> exonCore<- rma(affyExonFS, target = "core")
>>
>> Leads to this:
>>
>> Welcome to oligo version 1.16.2
>> ================================================================================
>>> library(pd.hugene.1.0.st.v1)
>> Loading required package: RSQLite
>> Loading required package: DBI
>>>
>>> exonCELs<- list.celfiles(full.names = TRUE)
>>> affyExonFS<- read.celfiles(exonCELs)
>> Platform design info loaded.
>> Reading in : ./MD01.CEL
>> Reading in : ./MD02.CEL
>> Reading in : ./MD03.CEL
>> Reading in : ./MD04.CEL
>> Reading in : ./MD05.CEL
>> Reading in : ./MD06.CEL
>> Reading in : ./MD07.CEL
>> Reading in : ./MD08.CEL
>> Reading in : ./MD09.CEL
>> Reading in : ./MD10.CEL
>> Reading in : ./MD11.CEL
>> Reading in : ./MD12.CEL

FWIW, it will be more informative for Benilton if you call
sessionInfo() here, that is, just before the call that causes
the crash. Thanks!  H.

>>> exonCore<- rma(affyExonFS, target = "core")
>> Background correcting
>>
>>   *** caught segfault ***
>> address 0x2addb000, cause 'memory not mapped'
>>
>> Traceback:
>>   1: .Call("rma_c_complete_copy", pmMat, pnVec, nPn, normalize, background,     bgversion, verbose, PACKAGE = "oligo")
>>   2: basicRMA(pms, pnVec, normalize, background)
>>   3: .local(object, ...)
>>   4: rma(affyExonFS, target = "core")
>>   5: rma(affyExonFS, target = "core")
>>
>> 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:
>>
>>
>>
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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