https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129
--- Comment #5 from chuck cranor <chuck at ece dot cmu.edu> --- I don't think anyone would manually add "-isystem /usr/include" ... but build systems that provide variables for third party headers that may or may not be installed in /usr/include often trigger this. e.g. if boost is installed in prefix /pkg, then you want to include /pkg/include in the search path. if boost is installed in /usr then you want /usr/include in the search path. if you have "-isystem ${BOOST_PREFIX}/include" in your CXXFLAGS and BOOST_PREFIX happens to be set to /usr somewhere earlier, you lose. For what it's worth, this definitely crops up in cmake-based builds: https://gitlab.kitware.com/cmake/cmake/issues/16291 I triggered it with cmake and Boost on a Cray. It is partly cmake's fault too. Its handling of CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES isn't correct.