[BioC] rma of oligo feature set crashes R

[Benilton Carvalho]

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
>> 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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