[Bioperl-l] Bio::Root::IO possible bug?

[Vamsi]

Yes, I rewrote the lines as

if ( ! ref($self->{'_filehandle'}) ||
     (ref($self->{'_filehandle'}) eq 'IO::String') ) {
   close($self->{'_filehandle'});
}

and it works fine. The trouble seems to be with the use of 'isa'

Thanks,
Vamsi
> 
> This seems like a perl 5.005 bug I guess - we obviously did't see this
> error in any of our tests.
> 
> You can try and add this to the logic in the if statement on line 487
> which is causing you grief:
> 
> if( ref($self->{'_filehandle'}) =~ /GLOB/i  ||
>     ! ref($self->{'_filehandle'}) ||
>     ! $self->{'_filehandle'}->isa('IO::String') ) {
>   close($self->{'_filehandle'});
> }
> 
> -jason
> On Fri, 3 Oct 2003, Vamsi wrote:
> 
> > Hi,
> >
> > After I upgraded to Bioperl 1.2.3 having problems with even
> > simple scripts.
> >
> > For instance
> >
> > --------------
> > use Bio::SeqIO;
> > my $in = Bio::SeqIO->new(-file => $ARGV[0], -format => 'Fasta');
> > $in->next_seq;
> > $in->close;
> > --------------
> >
> > results in
> >
> > Can't call method "isa" on unblessed reference at /usr/perl5/site_perl/5.005/Bio/Root/IO.pm line 487, <GEN0> chunk 1.
> >
> > Is there a bug in Bio::Root::IO.pm?
> >
> > Thanks,
> > Vamsi
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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