[Bioperl-l] Budle::BioPerl dependency issues

gang wu gwu at molbio.mgh.harvard.edu
Sat Nov 18 03:07:47 EST 2006


It turned out that most of the modules of BioPerl were not installed at 
all. And none of the scripts were installed. I had to download and 
install bioperl-1.5.2-RC3.tar.gz 
<http://bioperl.org/DIST/bioperl-1.5.2-RC3.tar.gz> again. A similar 
problem when installing bioperl-db-1.5.2-RC3.tar.gz. So I manually 
copied all stuff under Bio folder to the corresponding Perl library 
folder. Is it Ok to do it in this way?

Gang

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. 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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