I've been building RT 387 of late and use cpans Bundle::RT install using cpan.
All this comes down and istalls OK (takes ages), but for the libgd library.
To get round that problem I use the ./configure of:-
./configure  --prefix=/usr/local/Rt/rt-3.8.7    \
      --disable-graphviz    \
      --disable-gd  \
      --with-web-handler=modperl2   \

I have built RT into Sun's VirtualBox guesting FreeBSD_8, not that that should 
make any difference.

Try Cpan, that got me over several problems I was having with the RT installing 
procedure(s).
Then your problems re-appear when setting up apache - yet another hurdle.
The internet is full of RT's this un that and all are old and almost useless 
for todays procedures.

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