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

Georg Otto gwo at well.ox.ac.uk
Mon Oct 8 20:23:56 UTC 2012

Leon Timmermans <l.m.timmermans at students.uu.nl> writes:

> On Fri, Oct 5, 2012 at 11:06 PM, Georg Otto <gwo at well.ox.ac.uk> wrote:

>> 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)
> 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».

thanks a lot, that did the trick!


Georg Otto
The Wellcome Trust Centre for Human Genetics

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