[Bioperl-l] installing Bio::DB::GFF

[Jason Stajich]

On Wed, 18 Dec 2002, Chester Langin wrote:

> Am using SuSE 7.1 and installing with CPAN.
>
> Have completely installed Bundle::BioPerl,
> which, BTW, does not inlcude bioperl 1.0.2.
>
By design.

Just force install, XEMBL and EBI DB server seems to be down.

The warnings about not having programs installed are because, you don't
have those programs installed.  These aren't necessary and it should fail
gracefuly by skipping the tests.  Future releases separate the application
running portions into a different package so you won't be bothered by
this.

> Was installing GMOD, which said that I needed
> Bio::DB::GFF.
>
> Instructed CPAN to install Bio::DB::GFF and it
> attempted to install bioperl-1.0.2, which gave
> these errors on testing...
>
Bio::DB::GFF is part of bioperl-1.0.2

> t/BioFetch_DB:  Couldn't connect to EMBL with
>   Bio::DB::EMBL.pm
>   --- Exception ---
>   MSG: Can't parse fasta entry
>   ...
>
> t/BioGraphics:  failed test 2
>
> t/Clustalw:  4/10 Clustalw program not found
>
> t/RefSeq:  11/13 Couldn't connect to RefSeq with
>   Bio::DB::RefSeq.pm
>   --- Execption ---
>   MSG:  Can't parse fasta entry
>   ...
>
> t/TCoffee:  4/16tcoffee program not found.
>
> What, if anything, do I need to fix before I
> force install and move on?
>
> TIA.
>
> ,,Chet Langin,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
> <http://cs.siu.edu/~langin> <langin@cs.siu.edu>
> ~~~Diagonally parked in a parallel universe ~~~
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu