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

uname -a

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:

wget 'ftp://toolkit.lmb.uni-muenchen.de/HHsearch/HHsearch1.5.1/hhsearch64'
chmod +x hhsearch64
./hhsearch64

See if this works already then you don't have to compile the source.

*Edit:
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