[Bioperl-l] Bio::Graphics dependencies

Alex Lancaster alexl at users.sourceforge.net
Tue Jan 27 08:17:49 UTC 2009

Hi there,

Now that it is split out from BioPerl proper, I'm packaging up the
Bio::Graphics CPAN module as an RPM for Fedora but have run into
dependency problems:

perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::SCF)
perl-Bio-Graphics-1.83-2.fc11.noarch requires perl(Bio::Graphics::Browser::Util)

So it appears that Bio::Graphics possibly requires some other CPAN
modules that aren't mentioned in the META.yml file, specifically:


In Fedora, Perl dependencies are automatically generated by inspecting
the 'use Module' statements in the .pm files and the RPM is probably
generating the dependency because of the line:

"use Bio::Graphics::Browser::Util 'shellwords';" in:

and "use Bio::SCF;" inlib/Bio/Graphics/Glyph/trace.pm

Are these spurious "use" statements, or should Bio::Graphics have a
hard requirement on other CPAN modules that should be mentioned in the
META.yml file?  Or are they optional features that could skipped in
the installation?  If they are optional it would be good to provide a
means of detecting that the optional CPAN deps aren't installed and
not install those modules.

There is some mention of a Generic-Genome-Browser in the README file,
is that where this functionality lies?

You can find the build is here:


and the full requires are found here:



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