[Bioperl-l] Bio:Das 1.11 installation problem

[Bernd Jagla]

Great, that works!!!
But since I am using Bio::Das within GBrowse I can't/don't want to  change
those sources. I tried setting some environment variable but that doesn't
seem to work either...
So far I have the set the following:
FTP_PROXY=http://...
HTTP_PROXY=http://...
PROXYFTP=http://...
PROXYHTTP=http://...
ftp_proxy=http://...
http_proxy=http://...
PROXY=http://...

Any suggestions are welcome.

Thanks,

Bernd


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Stefan Kirov
Sent: Monday, June 08, 2009 11:26 PM
To: bernd at pasteur.fr
Cc: Lincoln Stein; Bernd Jagla; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Bio:Das 1.11 installation problem

bernd at pasteur.fr wrote:
Try to add this line
-proxy => 'http:<YOUR PROXY HERE>',
in t/01das.t where the Bio::Das object is created (I think line 41).
Hope this works for you, it did for me.
Stefan
> 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
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> 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>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>     
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l