[Bioperl-l] Bio:Das 1.11 installation problem

[bernd at pasteur.fr]

I tested the connection with wget and everything works fine.
I suspect that our proxy might be the problem but all variables are set
correctly (ftp_proxy, http_proxy and many more) I am not sure which
environment variable are being used...
I am not too familiar with all this and don't know where to look for the
right configurations.

Thanks,

Bernd

> 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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> 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>
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