[GenABEL-dev] Possible convert.snp.ped(GenABEL) bug

[Yurii Aulchenko]

Hi Marcin,

many thanks for this bug report. I have tested this using data from
GenABEL/inst/exdata with

convert.snp.ped(ped="pedin.18",mapfile="map.18",out="genos123.raw")

and also get

"Error: segfault from C stack overflow"

Interestingly, 1.6-5 works just fine.

have filed in bug report on your behalf

https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1388&group_id=505&atid=2058


On Thu, May 12, 2011 at 11:48 AM, Marcin Kierczak
<marcin.kierczak at slu.se> wrote:
> Hej,
>
> for those of you who do not know me - my name is Marcin and I am working at the Comp. Genetics Group, SLU Uppsala, Sweden. I am using GenABEL quite a lot in my work and recently have organized a workshop on using GenABEL for the analysis of stratified canine populations.
>
> It seems that calling convert.snp.ped on OsX, GenABEL 1.6.6 rises the following errors:
>
> 1. "Error: segfault from C stack overflow" or even "R quit unexpectedly". (32 bit version)
>
> R 64 either
>
> 1. *** caught segfault ***
> Traceback:
> 1: .C("convert_snp_merlin", as.character(pedfile), as.character(mapfile),     as.character(outfile), as.integer(intstrand), as.integer(bcast),     as.character(alcodes), as.integer(length(alcodes)), as.integer(intfmt),     as.integer(traits), as.integer(mapHasHeaderLine), PACKAGE = "GenABEL")
> 2: convert.snp.ped("Sw_ej_opheno.ped", "Sw_ej_opheno.map", "Sw.raw")
>
> or
>
> 2. invalid permissions and than segfault
>
> When I modified permissions to 777, still segfault.
>
> When downgraded to 1.6.5 - everything went smooth!
>
> Marcin
> _______________________________________
>
> Marcin Kierczak, PhD
> Postdoctoral Researcher
> Department of Animal Breeding and Genetics
> Swedish University of Agricultural Sciences
>
> Box 7023
> SE-75 007 Uppsala
> Sweden
> phone: +46 18 672 065
> e-mail: Marcin.Kierczak at hgen.slu.se
> web: http://www.computationalgenetics.se
> _______________________________________
>
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