[Bioperl-l] Budle::BioPerl dependency issues

gang wu gwu at molbio.mgh.harvard.edu
Sat Nov 18 03:30:30 EST 2006


Sendu Bala wrote:
> 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.
>
> What problems did you run into specifically with GD?
If I enable JPEG, GIFS and  XPM,  none of the test could pass. Since I 
usually use only PNG for output, I can live without them. I am not sure 
if it's system related problem. All of them work fine with my 32 bit 
Xeon server running Redhat AS 4, while the new Xeon AMD/EM64T with newer 
libgd runnig Redhat AS4 AMD/EM64T does not work.
>
>> 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.
>
> Do you remember what the other problematic packages were, and what you 
> had to do to get them working?
>
XML-DOM-XPath-0.12 has a test trying to locate XML::XPath.pm while I 
guess it should be XML::DOM::XPath.pm. I could not recall what other 
packages had issues, but basically it's special package configuration issue.
>> 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.
>
> All three are typos. We'll get those fixed.
>
>
>> So my question is : Is this the right way to install BioPerl?
>
> At the present moment, yes. For 1.5.2 I'll probably be recommending 
> not using Bundle::BioPerl once I fix some other things.
>
See my another message for other issues.
>
>> It took me two days to figure it out but still not 100% sure all 
>> packages are
>> installed properly.
>
> I'm sorry for the troubles you ran into. We'll try and do better for 
> the final release of 1.5.2.
Actually your hard work is benifiting the whole community and we all owe 
you a Thank You.



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