[BioC] readChp (affxparser) segfaults

[Gábor Csárdi]

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