Hi, what OS do you have? Try
uname -a
What source do you have? r960 should be the last commit for 0.9.6. Try
cd /usr/local/src/indi
svn update -r 960
Try to remove cmake cache, execute it one more time and copy & paste complete result here:
cd /usr/local/src/indi/libindi
rm -rf CMakeFiles CMakeCache.txt
cmake -DCMAKE_INSTALL_PREFIX=/usr .
I had exactly the same problem yesterday on OSX Mavericks and the problem was, that /usr/local/include (/usr/include in case of Raspbian ) wasn't on compiler search path. There is a feature (or a bug in my opinion) in cmake_modules/FindNova.cmake that it is referencing libnova as
#include <libnova.h>
instead of
#include <libnova/libnova.h>
BTW, It is not a good idea to do experiments like this under root account