Did you try the precompiled versions available at: ftp://toolkit.lmb.uni-muenchen.de/HHsearch/HHsearch1.5.1/ ?
If you don't know already, find out whether you are running a 32 or 64bit version of the os by typing into the command line
For 64bit it should end like this: 'x86_64 GNU/Linux'.
If it ends in 'i686 GNU/Linux' use hhsearch instead of hhsearch64 in the following line. Type this into the Terminal to download the file, make it executable and execute it:
chmod +x hhsearch64
See if this works already then you don't have to compile the source.
You will probably want to run if from everywhere on your system. The easiest way to do this is copying the exectuable to a path that is in your $PATH variable like so:
sudo cp hhsearch64 /usr/local/bin