From: https://llvm.org/bugs/show_bug.cgi?id=13237 "clang mirrors gcc in that it allows an optional space when specifying include paths, i.e. it supports both `-I/DIR and `-I /DIR` or along the same line `-isystem/DIR` and `-isystem /DIR`. scan-build understands most of these as well, but not the `-isystem/DIR` form without the extra space." a simple patch to scan-build will allow for -isystem arguments patch from: Thomas Hauth https://llvm.org/bugs/attachment.cgi?id=13705 not committed yet, and it still present in all versions of clang. This is especially a problem using cmake as it uses -isystem for system libraries by default.