[Bioperl-l] Bio::DB::Sam error: undefined symbol: Perl_Gthr_key_ptr

Leon Timmermans l.m.timmermans at students.uu.nl
Mon Oct 8 14:40:49 EDT 2012


On Fri, Oct 5, 2012 at 11:06 PM, Georg Otto <gwo at well.ox.ac.uk> wrote:
> Hi
>
> I have a problem using Bio::DB::Sam
>
>
> Like other perl modules I installed Bio-SamTools-1.36 in my home
> directory, since I do not have administration rights to the server I am
> using. When I call
>
> use Bio::DB::Sam
>
> I get the following error:
>
> /usr/local/bin/perl: symbol lookup error: /home/gwo/perl/modules/lib/perl/5.10.1/auto/Clone/Clone.so: undefined symbol: Perl_Gthr_key_ptr
>
> Both Bio::DB::Sam and Clone.pm were installed under the same version of
> perl (perl v5.10.1, Ubuntu 11.04)
>
> Any idea what is going on?
>
> Best wishes,
>
> Georg

This is definitely a mixup of perls.I guess you have compiled
Bio-SamTools for your system's perl (which is threaded), but try to
run in on the perl in /usr/local (which is apparently unthreaded. That
doesn't work. The easiest fix may be to change «#!
/usr/local/bin/perl» in your script to «/usr/bin/perl».

Leon



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