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Buildroot does not reconfigure pkgconf system library and system include dirs to STAGING_DIR. This means that pkgconf prints the sysroot system library and system include dirs instead of letting the compiler handle the logical sysroot. This breaks the -isystem compiler flag, as it increases the priority of the system library and system include directories. For example: $ output/host/bin/pkg-config --cflags glib-2.0 -Ioutput/host/bin/../x86_64-buildroot-linux-gnu/sysroot/usr/include/glib-2.0 -Ioutput/host/bin/../x86_64-buildroot-linux-gnu/sysroot/usr/lib/glib-2.0/include -Ioutput/host/bin/../x86_64-buildroot-linux-gnu/sysroot/usr/include A header in `.../sysroot/usr/include` will be included before a header in any directory specified with -isystem flags. Specifically, this breaks the Chromium build system, which expects a C++ math.h in a bundled LLVM C++ library, and gets a GNU C math.h instead. Fix this by telling pkgconf about the sysroot's system library and system include directories, so that it doesn't accidentally print them. Signed-off-by: Thomas Preston <thomas.preston@codethink.co.uk> [Arnout: change order of variables] Signed-off-by: Arnout Vandecappelle (Essensium/Mind) <arnout@mind.be>