[Bioperl-l] Budle::BioPerl dependency issues

Sendu Bala bix at sendu.me.uk
Sat Nov 18 03:04:14 EST 2006


gang wu wrote:
> Hi everyone,
> 
> I saw some problems when installing BioPerl
> 1.5.2R3(Bundle-BioPerl-2.1.6.tar.gz) with CPAN. But obviously CPAN could
> not solve all the dependency issues with one shot of 'install
> Bundle::BioPerl'. Some packages such as GD-2.35 just could not be
> installed.

What problems did you run into specifically with GD?


> And it turned out that CPAN refused to install BioPerl with
> some test return value 255. Then I went to /root/.cpan/build to
> configure, test, rebuild those problematic packages. After several more
> runs of 'install Bundle::BioPerl', CPAN finally installed BioPerl
> successfully.

Do you remember what the other problematic packages were, and what you 
had to do to get them working?


> Below attached is the output of CPAN, which stills complains three
> packages have issues: Data::Stag::writer HTTP::Request::Common-
> Spreadhseet::ParseExcel. I think the first two are typos somewhere in
> the Bundle::BioPerl. And the third module is not on the server and could
> be found on the CPAN site.

All three are typos. We'll get those fixed.


> So my question is : Is this the right way to install BioPerl?

At the present moment, yes. For 1.5.2 I'll probably be recommending not 
using Bundle::BioPerl once I fix some other things.


> It took me two days to figure it out but still not 100% sure all packages are
> installed properly.

I'm sorry for the troubles you ran into. We'll try and do better for the 
final release of 1.5.2.


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