[Bioperl-l] doing a 1.2.3 release

[Ewan Birney]

Jason or other Perl Gods...


There is something very, very kooky going on with the new DESTROY method
in Bio::SeqIO. What is happening is that on the line:


    if( $db ) {
        if( ref($db) &&  !$db->isa('Bio::DB::RandomAccessI') ) {
            $self->warn("Must pass in a valid Bio::DB::RandomAccessI
object for access to remote l\
ocations for spliced_seq");
            $db = undef;
        }
    }


if( $db)

in SeqFeatureI (I broke up the if statement to isolate it), perl is
somehow calling the garbage collector, and for reasons beyond me ends up
saying:


Bio::SeqFeatureI::spliced_seq(Bio/SeqFeatureI.pm:459):
459:        my ($mixed,$mixedloc,$fstrand) = (0);
  DB<3> n
Bio::SeqFeatureI::spliced_seq(Bio/SeqFeatureI.pm:461):
461:        if( $db ) {
  DB<3> s
Can't call method "isa" on an undefined value at Bio/SeqFeatureI.pm line
461.
Bio::SeqIO::DESTROY(Bio/SeqIO.pm:627):
627:        my $self = shift;



Notice that the debugger has just now entered the Bio::SeqIO::DESTROY
method. Commenting out though just moves this towards Bio/Root/RootI
DESTROY...


Really confused. Perl is at:

Ewan-Birneys-Computer:~/src/bioperl-branch-1-2] birney% perl -version

This is perl, v5.6.0 built for darwin

Copyright 1987-2000, Larry Wall

Perl may be copied only under the terms of either the Artistic License or
the
GNU General Public License, which may be found in the Perl 5.0 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using `man perl' or `perldoc perl'.  If you have access to the
Internet, point your browser at http://www.perl.com/, the Perl Home Page.



Is there a "gotcha" here? This is v. annoying....