One problem I run up against again and again is module installation problems. I run Mac OS X Tiger and Fedora Linux machines online and offline and can never be sure I'm going to be able to install the modules I need. Just now one of my Mac OS X Tiger machines failed to install Date::Calc and CGI::Application due to being unable to "create a new distribution object". I'm afraid I find module errors well over my head and don't think your average Perl developer should have to understand such internals. Perl is still held back, in my opinion, by the precarious business of installing CPAN modules. Something needs to be done about it otherwise Perl will end up being used only by developers who understand compiler error messages. I've had to switch to PHP lately simply because I can't gurantee a complete Perl setup for client servers and their projects which is a shame because I love Perl as a language - it's just a pity its packaged so badly.
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