[BioC] segfault during rma using oligo on Nimblegen data

Piet Jones pietjones at gmail.com
Wed Oct 24 14:37:13 CEST 2012

Dear Bioconductors,

I have a problem when it comes to trying to normalize a Nimblegen data
set using the oligo package. I have generated the appropriate package
using the ndf file and the package 'pdInfoBuilder' (which generated
'pd.fixed.gpl13936.090918.vitus.exp'). I have installed it using:

R CMD INSTALL pd.fixed.gpl13936.090918.vitus.exp

My problem comes in when I trying to run the actual normalization
using 'rma', specifically when it starts to do the background
correction, R dies with a segfault. I have no idea how to debug this,
below I have provided my R session with a sessionInfo() output, I have
also provided the information that I could gleam from the core dump.

Does anybody have any suggestion on what may be the problem, or how I
should proceed to solve this (not that proficient with debugging R)?



> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [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

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

other attached packages:
[1] pd.fixed.gpl13936.090918.vitus.exp_0.0.1
[2] RSQLite_0.11.1
[3] DBI_0.2-5
[4] oligo_1.16.2
[5] preprocessCore_1.14.0
[6] oligoClasses_1.14.0
[7] Biobase_2.12.2

loaded via a namespace (and not attached):
[1] affxparser_1.24.0 affyio_1.20.0     Biostrings_2.20.4 bit_1.1-8
[5] ff_2.2-7          IRanges_1.10.6    splines_2.13.0

>xys <- list.files(pattern=".xys",full.names=T)
> data_raw <- read.xysfiles(xys,pkgname='pd.fixed.gpl13936.090918.vitus.exp')
Platform design info loaded.
Checking designs for each XYS file... Done.
Allocating memory... Done.
Reading ./fixed_GSM881517_anther_a_431086A01.xys.
Reading ./fixed_GSM881518_anther_b_431086A03.xys.
Reading ./fixed_GSM881519_anther_m_431086A02.xys.
Reading ./fixed_GSM881520_berry_06_10_a_364214A08.xys.

I truncated the above there are a total of 162 xys files
> data_norm <- rma(data_raw)
Background correcting

 *** caught segfault ***
address 0xa2ca000, cause 'memory not mapped'

 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(data_raw)
 5: rma(data_raw)

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

Here is the information that is in the core dump:
14657880 at head002:~/Work/ilse/data/paper/GSE36128/test_all/fixed> gdb --core=core
GNU gdb (GDB) SUSE (7.2-3.3)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
For bug reporting instructions, please see:
BFD: Warning: /export/home/14657880/Work/ilse/data/paper/GSE36128/test_all/fixed/core
is truncated: expected core file size >= 757334016, found: 5304320.
Missing separate debuginfo for the main executable file
Try: zypper install -C
[New Thread 5677]
[New Thread 5488]
Failed to read a valid object file image from memory.
Core was generated by `/usr/lib64/R/bin/exec/R'.
Program terminated with signal 11, Segmentation fault.
#0  0x00007fcf9d3fda13 in ?? ()


Kind Regards,
Piet Jones

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