The solution is, as has been pointd out, to redefine the WARN signal handler.

To redirect warnings for the command

my $allofit = buildData(\%Edina::SSR::Common::everything);
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I simply created a subroutine:

sub makeData {
  my @warns = ();
  local $SIG{__WARN__} = sub { push @warns, @_; };

  my $allofit = buildData(\%Edina::SSR::Common::everything);

  return ($allofit, \@warns);
}
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and called it with:

my ($allofit, $error) = makeData();
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then the value of $error->... can be tested for any warnings

-- Ian Stuart
A man depriving some poor village, somewhere, of a first-class idiot.