[BioC] segfault during rma using oligo on Nimblegen data

[Benilton Carvalho]

The first recommendation is to update R. The current version is
2.15.x. The reason I ask you this is because it is really hard to
offer support for versions that are long gone (I always work with the
current version and the devel one).

After updating, try again. (I guess you'll have the same problem)

If you do (run into problems again), my suggestion is for you to
explain how you got the "fixed" part into the NDF name. I guess
someone manipulated the file and possibly not as expected... Improper
handling of the NDF causes NA values to appear where they're not
expected.

benilton

On 24 October 2012 13:37, Piet Jones <pietjones at gmail.com> wrote:
> 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)?
>
> ----------------------------------------------------------------------------------------------------
>
>>library(oligo)
>>library('pd.fixed.gpl13936.090918.vitus.exp')
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-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
>
> 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'
>
> 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(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:
> <http://www.gnu.org/software/gdb/bugs/>.
> 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
> "debuginfo(build-id)=81f375e003a6b0d50c77cf51d91f35f3526920fb"
> [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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