use Math::RungeKutta;

sub outer {
   my $var = sub_from_other_package();

   my $differ = sub {
      my $y = shift;
      $var->[...]{...}{...}; etc.
      ...
      return $res;
   };

   my $dydt = sub {
      my ($t,@y) = @_;
      return $differ->($y);
   };

   ($t, @y) = rkXXX(\@y, $dydt, $t, $dt);  
}