[Bioperl-l] Can't locate object method "attributes" via package "Bio::SeqFeature::Generic" at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line 703, <DATA> line 192.

Wed Feb 23 16:21:01 UTC 2011

> Hi,
> 
> We had recently updated BioPerl and Bio::Graphics and found
> some applications not working properly. As an example simple
> graphics script like:
> 
> #####################################################
> 
> use Bio::Graphics::Panel;
> use Bio::SeqFeature::Generic;
> 
> use CGI;      # or any other CGI:: form
> handler/decoder
> 
> print "Content-type: text/html\n\n";
> 
> my $panel = Bio::Graphics::Panel->new(-length =>
> 700,
>                
>                
>       -width  => 700
>                
>                
>       );
> 
> my $track = $panel->add_track(-glyph   
>    => 'generic',
>                
>              
> -label       => 1
>                
>               );
> 
> my $feature = Bio::SeqFeature::Generic->new(-start 
>       => 1,
>                
>                
>             -end   
>       => 400
>                
>                
>             );
> $track->add_feature($feature);
> 
> print "<html><body>TEST IMAGE:<br>";
> 
> open GRAPH, "> /srv/www/htdocs/tmp/test.png" or die
> "could not open image file";
> print GRAPH $panel->png;
> close(GRAPH);
> 
> print "<img src=\"/tmp/test.png\">";
> print "</body></html>";
> 
> #####################################################
> 
> is giving following error when I debug:
> 
>   DB<1> n
> Can't locate object method "attributes" via package
> "Bio::SeqFeature::Generic" at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line
> 703.
>  at /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm
> line 703
>        
> Bio::Graphics::Glyph::bgcolor('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)')
> called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line
> 1299
>        
> Bio::Graphics::Glyph::filled_box('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)',
> 'GD::Image=SCALAR(0x2002460)', 0, 0, 400, 7) called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line
> 1471
>        
> Bio::Graphics::Glyph::draw_component('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)',
> 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph/generic.pm
> line 347
>        
> Bio::Graphics::Glyph::generic::draw_component('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)',
> 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph.pm line
> 1050
>        
> Bio::Graphics::Glyph::draw('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)',
> 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph/generic.pm
> line 338
>        
> Bio::Graphics::Glyph::generic::draw('Bio::Graphics::Glyph::generic=HASH(0x1d62f90)',
> 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Glyph/track.pm
> line 35
>        
> Bio::Graphics::Glyph::track::draw('Bio::Graphics::Glyph::track=HASH(0x1d5bb10)',
> 'GD::Image=SCALAR(0x2002460)', 0, 0, 0, 1) called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line
> 588
>        
> Bio::Graphics::Panel::gd('Bio::Graphics::Panel=HASH(0x1b1f6b0)')
> called at
> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/Panel.pm line
> 1067
>        
> Bio::Graphics::Panel::png('Bio::Graphics::Panel=HASH(0x1b1f6b0)')
> called at test.cgi line 37
> Debugged program terminated.  Use q to quit or R to
> restart,
>   use o inhibit_exit to avoid stopping after program
> termination,
>   h q, h R or h o to get additional info.
> 
> #####################################################
> 
> Is it because of some incompatibility between version of
> bioperl and bio::Graphics or some thing else?
> 
> Thanks,
> Mustafa.
> 
> 
>  
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