[BioC] readChp (affxparser) segfaults

[Kasper Daniel Hansen]

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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