When I tried to install Gnome, it was interrupted in IntlTool step. By identifying error message, it should be a Perl XML parser problem. Then I emerged perl-XML-parser separately, and IntlTool could be installed successfully.
So, I suppose IntlTool might have to set dependence relationship with perl-XML-parser.
Most likely you've failed to run perl-cleaner after upgrade to perl 5.16.
*** This bug has been marked as a duplicate of bug 41124 ***