[Bioperl-l] bioperl-run t/EMBOSS.t

Brian Osborne bosborne11 at verizon.net
Thu Oct 19 15:06:08 UTC 2006


Yes, I see. Those EMBOSS programs work a bit differently from the typical
app run by bioperl-run, there's no need for WrapperBase methods like
program_dir(), executable(), it seems. Well, I can try and take a look at
this tonight but there's probably someone better suited to this than me,
I've spent very little time with bioperl-run. Volunteer?

Brian O.

On 10/19/06 11:37 AM, "Nathan S. Haigh" <n.haigh at sheffield.ac.uk> wrote:

> Thanks for committing that change Brian. Now the tests proceed from this
> point, I get the following error:
> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> MSG: Abstract method "Bio::Tools::Run::WrapperBase::program_dir" is not
> implemented by package Bio::Tools::Run::EMBOSSApplication.
> This is not your fault - author of Bio::Tools::Run::EMBOSSApplication
> should be blamed!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /home/bo1nsh/cvswc/bioperl-1-5-2/Bio/Root/Root.pm:350
> STACK: Bio::Root::RootI::throw_not_implemented
> /home/bo1nsh/cvswc/bioperl-1-5-2/Bio/Root/RootI.pm:522
> STACK: Bio::Tools::Run::WrapperBase::program_dir
> /home/bo1nsh/cvswc/bioperl-1-5-2/Bio/Tools/Run/WrapperBase.pm:346
> STACK: Bio::Tools::Run::WrapperBase::program_path
> /home/bo1nsh/cvswc/bioperl-1-5-2/Bio/Tools/Run/WrapperBase.pm:327
> STACK: Bio::Tools::Run::WrapperBase::executable
> /home/bo1nsh/cvswc/bioperl-1-5-2/Bio/Tools/Run/WrapperBase.pm:297
> STACK: t/EMBOSS.t:58
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