[Bioperl-l] Problem with : EUtilities - Proxy

Anthony Ferrari ferraria at gmail.com
Tue Dec 19 12:06:31 EST 2006


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


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