[Bioperl-l] Budle::BioPerl dependency issues

gang wu gwu at molbio.mgh.harvard.edu
Sat Nov 18 01:39:46 EST 2006


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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