For instance, if we run one of the included python tests using the raw build directory from cmake+ninja: $ LD_LIBRARY_PATH=/scratchl/jgg/llvm/build/lib/ PYTHONPATH=/scratchl/jgg/llvm/tools/clang/bindings/python python /scratchl/jgg/llvm/tools/clang/bindings/python/examples/cindex/cindex-dump.py t.c -v Here! ../tools/clang/lib/Driver/Driver.cpp:68 Dir= clang version 3.4 Target: x86_64-unknown-linux-gnu Thread model: posix Found candidate GCC installation: /usr/lib/gcc/i686-linux-gnu/4.7 Found candidate GCC installation: /usr/lib/gcc/i686-linux-gnu/4.7.3 Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/4.7 Found candidate GCC installation: /usr/lib/gcc/x86_64-linux-gnu/4.7.3 Selected GCC installation: /usr/lib/gcc/x86_64-linux-gnu/4.7 Here! ../tools/clang/lib/Frontend/ASTUnit.cpp:2038 ResourceFilesPath=/scratchl/jgg/llvm/build/lib/clang/3.4 ignoring nonexistent directory "../lib/clang/3.4/include" The 'ignoring nonexistent directory' line shows the wrong path, it should be prefixed with the bin dir. Eg when running clang natively that doesn't print and the search path properly includes: /scratchl/jgg/llvm/build/bin/../lib/clang/3.4/include Which is missing from the libclang version. This problem causes parses through libclang to fail, typically with cannot find stddef.h warnings. I've edited the source (using GIT as of today) and added some Here! prints to show some of the flow. Analysis: libclang uses the code in CIndexer::getClangResourcesPath() to locate the installation relative to the shared library location. This code is working fine, the 2nd Here! above prints the result of that function as it shows up in ASTUnit::LoadFromCommandLine as ResourceFilesPath However, the value ResourceFilesPath is no longer used on Linux because InitHeaderSearch::AddDefaultIncludePaths exits early. On Linux the include files are found via the Driver constructor's ClangExecutable argument, which is wired to 'clang' when libclang is being used. Which is because of this code in clang::createInvocationFromCommandLine // FIXME: We shouldn't have to pass in the path info. driver::Driver TheDriver("clang", llvm::sys::getDefaultTargetTriple(), "a.out", *Diags); The driver should probably be created with something like ResourceFilesPath + "../bin/clang" until the FIXME is solved properly..