Hm, cant find any verboose option with -h, but i've tried with the -W options to enable all warnings, nothing file related

perl -MCPAN -e 'CPAN::Shell->o("conf")' -W
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If its a different command, please enlighten me.

Since script is runned as root and the config files are owned by root i doubt this is the problem though

Your language isn't very clear. If I understand the question correctly, then I would try this:

perl -MCPAN::FirstTime -e 'CPAN::FirstTime::init();'
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And from a script:

#!/usr/bin/perl

use strict;
use warnings;
use CPAN;
use CPAN::FirstTime;

CPAN::FirstTime::init();
CPAN::Shell->install(
"Bundle::CPAN",
"Bundle::LWP");
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thanks, i solved the problem with CPAN::HandleConfig->load; Wasnt aware that i had to explicity load the configuration file.