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In SCons manual: ================= In order to inform the C compiler about the repositories, SCons will add appropriate -I flags to the compilation commands for each directory in the $CPPPATH list. So if we add the current directory to the construction environment $CPPPATH like so: env = Environment(CPPPATH = ['.']) env.Program('hello.c') Repository('/usr/repository1') Then re-executing SCons yields: % scons -Q cc -o hello.o -c -I. -I/usr/repository1 hello.c cc -o hello hello.o ================= The additional include directory is definitely not what we want. Just remove the additional Repository line.