There are a few known issues when using cldoc, most of which are related to clang. The following list is non-exclusive. Please file issues on github when you encounter any other problems.
Unsupported compiler flags
There seem to be certain compiler flags which are not supported when using clang as a library. At the moment, at least
-archon OS X seems to cause clang not to parse any files.
Missing system include paths
This is not directly related to cldoc, but it will suffer from this problem. At least on Ubuntu precise, when
gcc-4.7-baseis installed, clang++ will assume to only look for g++ 4.7 system include paths, which cannot be found since g++ 4.7 is not available for Ubuntu precise. I’m not sure at this time how to work around this issue, apart from uninstalling