I have a very similar problem with my CPAN on RedHat 9, that is Net::FTP fails to download from any FTP location (as if the Net::FTP module was broken). So, as soon as CPAN switches to ncftpget, the file gets downloaded properly. I'm afraid I don't know how to disable Net::FTP, but in order to add ncftpget (or ftp) to your FTP downloading alternatives, you should edit the CPAN/Config.pm file in your Perl5 installation path (on Linux, this is /usr/local/lib/perl5/5.x.y). The file contains a list of all FTP, HTTP, proxy and other downloading settings. I believe that as soon as you get one of the utilities right (like ftp), downloading off the Internet should work with CPAN.
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