[Bioperl-l] Budle::BioPerl dependency issues

gang wu gwu at molbio.mgh.harvard.edu
Sat Nov 18 03:44:45 EST 2006


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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