[Bioperl-l] Failed tests for FeatureIO

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Mon Sep 25 05:43:36 EDT 2006


Chris,

> I am getting failed tests for FeatureIO.t on make test using bioperl- 
> live on Mac OS X (10.4.7, perl 5.8.6):
> pyr:~/src/bioperl-live cjfields$ perl -I. -w t/FeatureIO.t
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Invalid protein count
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:331
> STACK: Bio::FeatureIO::ptt::_initialize Bio/FeatureIO/ptt.pm:147
> STACK: Bio::FeatureIO::new Bio/FeatureIO.pm:266
> STACK: Bio::FeatureIO::new Bio/FeatureIO.pm:286
> STACK: t/FeatureIO.t:189
> -----------------------------------------------------------

Hmmm, I committed that module last week. I just did a fresh complete checkout 
of current CVS, and all the tests pass fine for me on Linux 2.6 + Perl 5.8.5 ?

Do you have t/data/test.ptt ? (the .pm isn't completely robust yet...)

I can't think of any other issues - here's the offending code:

sub _initialize {
   my($self,%arg) = @_;

   $self->SUPER::_initialize(%arg);

   if ($self->mode eq 'r') {
     # Line 1
     my $desc = $self->_readline();
     chomp $desc;
     $self->description($desc);
     # Line 2
     my $line = $self->_readline();
     $line =~ m/^(\d+) proteins/ or $self->throw("Invalid protein count");
     $self->protein_count($1);
     # Line 3
     $self->_readline();
   }
}

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia


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