[Bioperl-l] Problems installing latest stable bioperl-db (1.6)

[Chris Fields]

Tony,

The error should point out the problem: install Graph::Directed via  
CPAN.

Saying that, we need to add that as a 'recommends' for the db package  
and skip those tests if Graph::Directed isn't present.  Will do that  
now.

chris

On Sep 24, 2009, at 10:08 AM, Anthony Pemberton wrote:

> Chris, Mark,
>
> Thank you, I have made significant progress with the install. I had  
> to do a
>
> Cpan> force install Array::Compare
>
> To get the model properly installed.
>
> However, I now have a new error. When I do
>
> Cpan> install CJFIELDS/BioPerl-db-1.6.0.tar.gz
>
> I get the following error (now only 1 of the 16 tests fails):
>
> t/12ontology.t .... 1/740 Bio::OntologyIO: soflat cannot be found
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::OntologyIO::soflat. Can't locate  
> Graph/Directed.pm in @INC (@INC contains: t/lib t /root/.cpan/build/ 
> BioPerl-db-1.6.0-xim2YV/blib/lib /root/.cpan/build/BioPerl-db-1.6.0- 
> xim2YV/blib/arch /root/.cpan/build/BioPerl-db-1.6.0-xim2YV /usr/ 
> lib64/perl5/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/5.8.5 / 
> usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi /usr/lib/ 
> perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib64/perl5/ 
> vendor_perl/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/ 
> vendor_perl/5.8.5 /usr/lib64/perl5/vendor_perl/5.8.3/x86_64-linux- 
> thread-multi /usr/lib/perl5/vendor_perl .) at /usr/lib/perl5/ 
> site_perl/5.8.5/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm line 118.
> BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.5/ 
> Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm line 118.
>
>
> Can you help with this one?
>
> Regards,
>
> Tony Pemberton
>
>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at illinois.edu]
>> Sent: 23 September 2009 18:48
>> To: Mark A. Jensen
>> Cc: Anthony Pemberton; bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] Problems installing latest stable bioperl-db
>> (1.6)
>>
>> Appears Array::Compare is used for Test::Warn, so it isn't a true
>> requirement (probably a test_requires or somesuch).
>>
>> chris
>>
>> On Sep 23, 2009, at 10:36 AM, Mark A. Jensen wrote:
>>
>>> hi Tony- missing prereqs are the issue with this message,yes-
>>> the brute force approach would be to install each of these
>>> as they come up; you can do
>>>
>>> $ cpan
>>> cpan> install Array::Compare
>>>
>>> etc., then attempt the bioperl-db install again; lather, rinse,
>>> repeat.
>>> MAJ
>>> ----- Original Message ----- From: "Anthony Pemberton"
>> <A.J.Pemberton at bham.ac.uk
>>>>
>>> To: <bioperl-l at bioperl.org>
>>> Sent: Tuesday, September 22, 2009 1:06 PM
>>> Subject: [Bioperl-l] Problems installing latest stable bioperl-db
>>> (1.6)
>>>
>>>
>>>> Folks,
>>>>
>>>> I am experiencing problems installing bioperl-db. I followed the
>>>> instructions on the website both installing via CPAN and
>>>> downloading the source tarball. Get the same error. I think I have
>>>> missing prerequistes, the first error I get is:
>>>>
>>>> Can't locate Array/Compare.pm in @INC (@INC contains: t/lib t /usr/
>>>> local/BioPerl-db-1.6.0/blib/lib
>>>> /usr/local/BioPerl-db-1.6.0/blib/arch /usr/local/BioPerl-db-1.6.0 /
>>>> usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/5.8.5 /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-
>>>> thread-multi /usr/lib/perl5/site_perl/5.8.5
>>>> /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-
>>>> linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5
>>>> /usr/lib64/perl5/vendor_perl/5.8.3/x86_64-linux-thread-multi /usr/
>>>> lib/perl5/vendor_perl .) at t/lib/Test/Warn.pm line 228.
>>>>
>>>> Can anyone help?
>>>>
>>>> Regards,
>>>>
>>>> Tony P.
>>>>
>>>>
>>>> **************************************************************
>>>> Mr. A. Pemberton Tel:+44 121 414 3388
>>>> School of Biosciences, Fax:+44 121 414 5925
>>>> The University of Birmingham
>>>> Email:a.j.pemberton at bham.ac.uk
>>>> Birmingham B15 2TT U.K.
>>>> **************************************************************
>>>>
>>>>
>>>>
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>>>>
>>>
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