[Bioperl-l] Budle::BioPerl dependency issues

Nathan Haigh N.Haigh at sheffield.ac.uk
Sat Nov 18 04:56:57 EST 2006


Hi Chris,

Would it be possible to pull Bundlle::BioPerl 2.1.6 from CPAN - it contains some errors. I think Sendu *may* have some further instructions regarding
this package a bit closer to the 1.5.2 release.

Cheers
Nathan



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

> Hi Nathan,
> 
> Thanks for your message. I saw the 
> C/CR/CRAFFI/Bundle-BioPerl-2.1.6.tar.gz is now the default one if you 
> use 'install Bundle::BioPerl', which will definitely frustrate a bunch 
> of users. Can this release be held for a while before most of the bugs 
> are cleared?
> 
> Thanks again.
> Gang
> 
> 
> Gang
> 
> Nathan Haigh wrote:
> > 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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> >>
> >>     
> >
> >
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