[Bioperl-l] Bio::Graphics dependencies

Lincoln Stein lincoln.stein at gmail.com
Tue Jan 27 13:55:42 UTC 2009

Hi Alex,

I've just uploaded version 1.84 to PAUSE. The dependency on
Bio::Graphics::Browser::Util was spurious and has been removed. The
Bio::Graphics::Glyph::trace module implements an ABI sequencing trace
display, and  does require an external module called Bio::SCF. This module
is on CPAN, but it in turn requires a binary library called io-lib from the
STADEN (http://staden.sourceforge.net/) package. So I have made this into a
"recommendation" in the META.yml file.


On Tue, Jan 27, 2009 at 3:17 AM, Alex Lancaster <alexl at users.sourceforge.net
> wrote:

> 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:
> Bio::Graphics::Browser::Util
> Bio::SCF
> 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:
> lib/Bio/Graphics/Wiggle/Loader.pm
> 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:
> http://koji.fedoraproject.org/koji/buildinfo?buildID=80400
> and the full requires are found here:
> http://koji.fedoraproject.org/koji/rpminfo?rpmID=973748
> Thanks,
> Alex
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Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>

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