[Bioperl-l] Bio:Das 1.11 installation problem

[Kevin Brown]

Dumb question, but are you exporting the variables after you set them?

FTP_PROXY=http://...
HTTP_PROXY=http://...
export FTP_PROXY HTTP_PROXY 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Bernd Jagla
> Sent: Tuesday, June 09, 2009 12:06 AM
> To: 'Stefan Kirov'; bernd at pasteur.fr
> Cc: 'Lincoln Stein'; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio:Das 1.11 installation problem
> 
> 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
> >>
> >>     
> >
> >
> > _______________________________________________
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> >
> >   
> 
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