[Bioperl-l] bio::graphics::panel under mod_perl

Lincoln Stein lstein at cshl.edu
Wed Dec 22 11:55:05 EST 2004

Funny; this problem is not occurring for me, and I use 
Bio::Graphics::Panel under mod_perl all the time on multiple web 

It sounds like a GD problem. My usual advice on these occasions (when 
GD is acting up) is to search and destroy all old versions of libgd, 
then reinstall libgd and GD from source.  In your case, you might 
also try doing the same for libpng and libz -- particularly if you 
haven't updated in a while since there is a security hole in libpng 


On Thursday 16 December 2004 04:44 pm, Sean Davis wrote:
> I know this is a very esoteric question, but here goes:
> I have two scripts, one home-brewed (using bioperl-live from recent
> CVS), and gbrowse (1.62), both running under mod_perl (apache 1.3).
> Each has the same behavior--in some requests, seemingly at random,
> several colors become black.  I haven't been able to sort this out,
> but since it happens in gbrowse and my custom app using
> bio::graphics, I wonder if there is an issue there.  It could just
> as likely be gd or some other supporting package.  I guess I am
> wondering if anyone else has noticed these issues or how I might
> sort it out.  Note that these work fine as straight CGI.  Two files
> are attached (as I am behind a firewall, so can't show the
> sites....).  The second has the correct color scheme.
> Sean

Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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