[Bioperl-l] Bio:Das 1.11 installation problem

[Lincoln Stein]

Hi,

The regression tests require an active Internet connection, as well as the
DAS test server being up and running. It may be there was a temporary
failure of one of those two. I just tested on my end and the regression
tests ran ok, so could you try it again?

Lincoln

On Mon, Jun 8, 2009 at 12:24 PM, Bernd Jagla <bernd.jagla at pasteur.fr> wrote:

> 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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>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>