[Bioperl-l] Budle::BioPerl dependency issues

Nathan Haigh N.Haigh at sheffield.ac.uk
Sat Nov 18 03:22:00 EST 2006


Hi Gang,

At the moment we are having a few teathing problems with CPAN packages. I notice that you are trying to install the 1.5.2 release candidate 3 - we are
in the final stages of getting out the official 1.5.2 developer release (hopefully in the next couple of weeks). There are indeed a few things wrong
with the latest Bundle::BioPerl package but we thought we'd hold off updating it until the 1.5.2 release (or shortly before).

I think that the problem with CPAN installing dependencies is that it has no way to correctly ordering the installation of dependencies, such that it
may be neccessary to run the install several time in order to get everything installed. For example, if prerequisite 2 depends on prerequisite 1 and
CPAN installs prerequisite 2 first, then it's test suite will probably fail and thus the installation of the package siting both these as
dependencies will fail to install.

I believe you are correct in the way you are installing bioperl, but we still have a few issues to sort out with regards to the CPAN packages - these
will definately be sorted out by the time of the 1.5.2 release in a matter of weeks.

If anyone is aware of a way to force CPAN to install modules in a specific order, please let Sendu know - we may be able to make the install process
much easier to the users.

Thanks
Nathan


Quoting gang wu <gwu at molbio.mgh.harvard.edu>:

> 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. 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.
> 
> 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.
> 
> So my question is : Is this the right way to install BioPerl? It took me
> two days to figure it out but still not 100% sure all packages are
> installed properly.
> 
> Any feedback is appreciated.
> 
> Gang
> 
> =================================================
> cpan> install Bundle::BioPerl
> Ace is up to date.
> Bio::ASN1::EntrezGene is up to date.
> Class::AutoClass is up to date.
> Clone is up to date.
> Convert::Binary::C is up to date.
> Running install for module Data::Stag::writer
> 
>   The module Data::Stag::writer isn't available on CPAN.
> 
>   Either the module has not yet been uploaded to CPAN, or it is
>   temporary unavailable. Please contact the author to find out
>   more about the status. Try 'i Data::Stag::writer'.
> DBD::mysql is up to date.
> GD::SVG is up to date.
> GD is up to date.
> Graph::Directed is up to date.
> HTML::Parser is up to date.
> Running install for module HTTP::Request::Common-
> 
>   The module HTTP::Request::Common- isn't available on CPAN.
> 
>   Either the module has not yet been uploaded to CPAN, or it is
>   temporary unavailable. Please contact the author to find out
>   more about the status. Try 'i HTTP::Request::Common-'.
> LWP::UserAgent is up to date.
> Set::Scalar is up to date.
> SOAP::Lite is up to date.
> Running install for module Spreadhseet::ParseExcel
> 
>   The module Spreadhseet::ParseExcel isn't available on CPAN.
> 
>   Either the module has not yet been uploaded to CPAN, or it is
>   temporary unavailable. Please contact the author to find out
>   more about the status. Try 'i Spreadhseet::ParseExcel'.
> Storable is up to date.
> SVG is up to date.
> SVG::Graph is up to date.
> Text::Shellwords is up to date.
> XML::DOM::XPath is up to date.
> XML::Parser::PerlSAX is up to date.
> XML::SAX is up to date.
> XML::SAX::Base is up to date.
> XML::SAX::Writer is up to date.
> XML::Simple is up to date.
> XML::Twig is up to date.
> XML::Writer is up to date.
> Bundle summary: The following items in bundle Bundle::BioPerl had
> installation problems:
>   Data::Stag::writer HTTP::Request::Common- Spreadhseet::ParseExcel
> ====================================================
> 
> 
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