[Bioperl-l] Problem with : EUtilities - Proxy

[Chris Fields]

On Dec 19, 2006, at 10:40 AM, Anthony Ferrari wrote:

> Hi all,
>
> I've just installed BioPerl 1.5.2 (devel) on a linux mandrake  
> machine with
> the cpan shell.
> I want to use the Bio::DB::EUtilities to retrieve data (id's) from  
> NCBI
> 'gene' database (first step of my pipeline).
>
> But the installation of this package doesn't seem to be correct :
> The simple example given on the documentation doesn't work. (this  
> one :
> http://doc.bioperl.org/bioperl-live/Bio/DB/EUtilities.html#SYNOPSIS)
>
> Here is the error message I got :
> "Can't use an undefined value as an ARRAY reference at
> /usr/lib/perl5/site_perl/5.8.7/LWP/UserAgent.pm line 779."
>
> In the UserAgent package, line 779 is in the private "_need_proxy"
> subroutine and corresponds to the code :    ...if (@{ $self-> 
> {'no_proxy'} })
> ...
>
> If I comment this line in the UserAgent package and the  
> corresponding "}",
> the example works. But obviously, I prefer to solve the problem in  
> a regular
> way :)
>
> Indeed, my computer accesses the internet via a http proxy and I  
> didn't tell
> this to BioPerl at any moment.
> As I read on the BioPerl Wiki site, I tried to configure an  
> $http_proxy
> environment variable but it still doesn't work.
>
> One last maybe important information is that I saw during the  
> installation
> that the tests 't/EUtilities' were skipped because of an unrevealed  
> reason.
>
>
> So finally I got two questions :
> 1. Is there somebody who can figure out what is my problem ?
> 2. At the moment, is the Bio::DB::EUtilities package really  
> efficient or
> using directly the NCBI eutilities with the LWP::Simple package  
> could be an
> good alternative ?
>
> Many thanks in advance,
> Best Regards,
> Anthony Ferrari

First things first: at the moment the BioPerl EUtilities interface is  
very experimental (as specifically outlined in the POD), so I can't  
really recommend it for production use until the API is cleaned up.   
However, I do appreciate any feedback or comments re:EUtilities (the  
reason it's out there in the 1.5.2 release).

You might check out this bug report, which relates directly to your  
issue:

http://bugzilla.open-bio.org/show_bug.cgi?id=2109

After I worked out the proxy issue Torsten got it working.  Let me  
know if this doesn't help or fix the problem.

chris