Hi all,

When I do ram of oligo, R crashed. It is very similar to https://stat.ethz.ch/pipermail/bioconductor/2011-October/041567.html. Here is the output of console,

> library(oligo)
> library(limma)
> library(pd.hugene.1.0.st.v1)
Loading required package: RSQLite
Loading required package: DBI
> targets<-readTargets(file="filelist.txt",sep=" ",row.names="cel_files")
> affyGeneFS <- read.celfiles(targets$cel_files)
Platform design info loaded.
Reading in : Control-1-1_(HuGene-1_0-st-v1).CEL
Reading in : CONTROL-1-2-(HuGene-1_0-st-v1).CEL
Reading in : Control-2-3_(HuGene-1_0-st-v1).CEL
Reading in : CONTROL-2-4-(HuGene-1_0-st-v1).CEL
Reading in : Control-3-5_(HuGene-1_0-st-v1).CEL
Reading in : CONTROL-3-6-(HuGene-1_0-st-v1).CEL
Reading in : kd-1_7-(HuGene-1_0-st-v1).CEL
Reading in : KD-1-8_(HuGene-1_0-st-v1).CEL
Reading in : kd-2_9-(HuGene-1_0-st-v1).CEL
Reading in : KD-2-10_(HuGene-1_0-st-v1).CEL
Reading in : kd-3_11-(HuGene-1_0-st-v1).CEL
Reading in : KD-3-12_(HuGene-1_0-st-v1).CEL
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.3
[3] DBI_0.2-7                 limma_3.16.3
[5] oligo_1.24.0              Biobase_2.20.0
[7] oligoClasses_1.22.0       BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] affxparser_1.32.0     affyio_1.28.0         BiocInstaller_1.10.1
 [4] Biostrings_2.28.0     bit_1.1-10            codetools_0.2-8
 [7] ff_2.2-11             foreach_1.4.0         GenomicRanges_1.12.2
[10] IRanges_1.18.0        iterators_1.0.6       preprocessCore_1.22.0
[13] splines_3.0.0         stats4_3.0.0          zlibbioc_1.6.0

> geneCore <- rma(affyGeneFS, target = "core")
Background correcting

 *** caught segfault ***
address 0x1029fb000, 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(affyGeneFS, target = "core")
 5: rma(affyGeneFS, 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: 1
aborting ...
Segmentation fault: 11

Any ideas?

Yours sincerely,

Jianhong Ou

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