[BioC] readChp (affxparser) segfaults

[Gábor Csárdi]

Kasper, thanks. Btw. is there anything against reading in the raw data
from the .chp files, besides the called genotype? I have a patch for
this if you are interested.

Best,
Gabor

On Mon, May 11, 2009 at 2:14 AM, Kasper Daniel Hansen
<khansen at stat.berkeley.edu> wrote:
> Fixed in the devel branch, affxparser version 1.17.2
>
> Kasper
>
> On May 1, 2009, at 9:18 , Gábor Csárdi wrote:
>
>> Dear All,
>>
>> I am trying to read in a .chp file with readChp from the affxparser
>> package, without much success. It used to work fine, but for this new
>> file (and a lot of other new files as well) it segfaults.
>>
>> The file is for the Affymetrix 5.0 SNP chip, and it was produced by
>> Affymetrix Power Tools. I have uploaded it here:
>> http://www2.unil.ch/cbg/readChp_segfault.chp.gz
>>
>> Sometimes it segfaults for the first read attempt, sometimes only for
>> the second:
>>>
>>> library(affxparser)
>>> chp <- readChp("readChp_segfault.chp")
>>
>> *** caught segfault ***
>> address 0x1ab8000, cause 'memory not mapped'
>>
>> Traceback:
>> 1: .Call("R_affx_get_chp_file", filename, withQuant)
>> 2: readChp("readChp_segfault.chp")
>>
>> 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:
>>
>> A more detailed backtrace:
>>
>>> library(affxparser)
>>> chp <- readChp("readChp_segfault.chp")
>>
>> Program received signal SIGSEGV, Segmentation fault.
>> 0x0000003d53a70c2e in strlen () from /lib64/tls/libc.so.6
>> (gdb) bt
>> #0  0x0000003d53a70c2e in strlen () from /lib64/tls/libc.so.6
>> #1  0x0000002a95606029 in Rf_mkChar (
>>   name=0x1a35988 "./apt-probeset-genotype -o
>> /home/zoltan/apt-1.10.1-20081103-amd64-pc-linux/results/ --cdf-file
>> GenomeWideSNP_5.cdf --chrX-snps GenomeWideSNP_5.chrx
>> --read-models-brlmmp GenomeWideSNP_5.models --output"...)
>>   at envir.c:3238
>> #2  0x0000002a9562ba93 in Rf_mkString (
>>   s=0x1a35988 "./apt-probeset-genotype -o
>> /home/zoltan/apt-1.10.1-20081103-amd64-pc-linux/results/ --cdf-file
>> GenomeWideSNP_5.cdf --chrX-snps GenomeWideSNP_5.chrx
>> --read-models-brlmmp GenomeWideSNP_5.models --output"...)
>>   at ../../src/include/Rinlinedfuns.h:537
>> #3  0x0000002a9948a191 in R_affx_GetList (params=
>>
>> {<std::_List_base<affymetrix_calvin_parameter::ParameterNameValueType,std::allocator<affymetrix_calvin_parameter::ParameterNameValueType>
>>>>
>>>> = {_M_impl =
>>
>>
>> {<std::allocator<std::_List_node<affymetrix_calvin_parameter::ParameterNameValueType>
>>>>
>>>> =
>>>> {<__gnu_cxx::new_allocator<std::_List_node<affymetrix_calvin_parameter::ParameterNameValueType>
>>>> = {<No data fields>}, <No data fields>}, _M_node = {_M_next =
>>
>> 0x1968ca0, _M_prev = 0x1a1f510}}}, <No data fields>})
>>   at R_affx_chp_parser.cpp:122
>> #4  0x0000002a9948d76f in R_affx_ReadCHP (chp=0xf878b0, isBrief=false)
>>   at R_affx_chp_parser.cpp:789
>> #5  0x0000002a9948e0d5 in R_affx_get_chp_file (fname=0x69a588,
>>   withQuantifications=0xfcc1a8) at R_affx_chp_parser.cpp:917
>> ---Type <return> to continue, or q <return> to quit---
>> #6  0x0000002a955e515a in do_dotcall (call=0x192b970, op=Variable "op"
>> is not available.
>> ) at dotcode.c:859
>> #7  0x0000002a9561359a in Rf_eval (e=0x1a35988, rho=0x192b778) at
>> eval.c:487
>> #8  0x0000002a95616d20 in Rf_applyClosure (call=0x192aa98, op=0x192a830,
>>   arglist=0x192b820, rho=0x544aa8, suppliedenv=0x544ae0) at eval.c:667
>> #9  0x0000002a95613359 in Rf_eval (e=0x192aa98, rho=0x544aa8) at
>> eval.c:505
>> #10 0x0000002a956154a3 in do_set (call=0x192a9f0, op=0x522a88,
>> args=0x192aa28,
>>   rho=0x544aa8) at eval.c:1422
>> #11 0x0000002a95613452 in Rf_eval (e=0x192a9f0, rho=0x544aa8) at
>> eval.c:461
>> #12 0x0000002a956317e8 in Rf_ReplIteration (rho=0x544aa8, savestack=0,
>>   browselevel=Variable "browselevel" is not available.
>> ) at main.c:257
>> #13 0x0000002a95631920 in R_ReplConsole (rho=0x544aa8, savestack=0,
>>   browselevel=0) at main.c:306
>> #14 0x0000002a95631c20 in run_Rmainloop () at main.c:966
>> #15 0x00000000004008ab in main ()
>> (gdb)
>>
>>> sessionInfo()
>>
>> R version 2.8.1 (2008-12-22)
>> x86_64-redhat-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] affxparser_1.16.0
>>
>> So this is for the development version of affxparser, but I get the
>> same result with the BioC 2.3 version (1.14.2) as well. Moreover, this
>> is not the only file that fails, so probably the file is not corrupt.
>>
>> Any help is appreciated, Best Regards,
>> Gabor
>>
>> --
>> Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM
>>
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>
>



-- 
Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM