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

[Marcin Kierczak]

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
_______________________________________