These logs are printed once I try to upgrade cling and llvm from their respective repositories.
There are multiple problems with compiling the current version of cppyy.
First of all, the distributed cling version is too old and doesn't support the GCC 5 ABI which means that you can't compile it with the GCC version I have. This can be fixed by upgrading cling to 0.3 or higher.
Second of all, there's a bug in clang that doesn't allow to compile llvm with the clib headers that are distributed with GCC 6.
I can download and install an older compiler but I don't see a reason since upgrading cling will fix the issue.

I tried to find the source code repository for the package in order to try to share my contributions to upgrade cling to 0.3 but I could not find it. If it doesn't exist can you please create one, preferably under the pypy project in Bitbucket?