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

[Anthony Pemberton]

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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