[Bioperl-l] Bio:Das 1.11 installation problem

[Bernd Jagla]

Hi, 

 

I am working on a MAC 10.5.7; try to install Bio::Das using perl -MCPAN -e
'install Bio::Das'
This is perl, v5.8.9 built for darwin-2level
(please let me know if you need anything else)

 

I am trying to install Bio::Das 1.11

 

I get the following error:

 

not ok 3

not ok 4

Can't call method "description" on an undefined value at t/01das.t line 62.

 

When going into the sources for 01das.t and printing out $db I get:

 

$VAR1 = \bless( {

                   'autotypes' => undef,

                   'default_dsn' => undef,

                   'autocategories' => undef,

                   'sockets' => {},

                   'aggregators' => [

                                      bless( {

                                               'sub_parts' => [

 
'coding_exon'

                                                              ],

                                               'require_whole_object' =>
undef,

                                               'main_method' => 'CDS',

                                               'method' => 'alignment'

                                             }, 'Bio::DB::GFF::Aggregator'
),

                                      bless( {

                                               'sub_parts' => [

                                                                'EST_match'

                                                              ],

                                               'require_whole_object' =>
undef,

                                               'main_method' => 'alignment',

                                               'method' => 'alignment'

                                             }, 'Bio::DB::GFF::Aggregator' )

                                    ],

                   'timeout' => undef,

                   'oldstyle_api' => 1,

                   'default_server' => 'http://www.wormbase.org/db/seq/das'

                 }, 'Bio::Das' );

 

 

@sources is empty

And test(3, at sources) fails.

 

Please advise.

 

Thanks,

 

Bernd