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

[Jason Stajich]

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
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu