[Bioperl-l] Bio:Das 1.11 installation problem
Bernd Jagla
bernd.jagla at pasteur.fr
Wed Jun 10 04:16:08 EDT 2009
To whom it may concern:
I added
$self->proxy($ENV{'HTTP_PROXY'}) if $ENV{'HTTP_PROXY'};
Around line 72 before:
$self->proxy($proxy) if $proxy;
In Das.pm. This did the trick.
For completeness I also edited Fetch.pm:
Around line 134:
$proxy = $ENV{'HTTP_PROXY'} if $ENV{'HTTP_PROXY'};
Before:
my $dest = $proxy || $request->url;
Best,
Bernd
-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Kevin Brown
Sent: Tuesday, June 09, 2009 5:26 PM
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Bio:Das 1.11 installation problem
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
> >>
> >>
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
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