[Bioperl-l] Bio:Das 1.11 installation problem
Bernd Jagla
bernd.jagla at pasteur.fr
Mon Jun 8 16:24:12 UTC 2009
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
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