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1) Create a new c++-project with some sources and a makefile 2) Select GCC per file scanner info profile 3) Build the project 4) Generate a parser-log for one of the files in the project and see that the built-in includes of the compiler are missing. The reason is, that the makefile that is dumped into .metadata/.plugins/org.eclipse.cdt.make.core is incorrect. It contains the line: gcc ... -f ${project_name}_scd.mk specs.c where it should read gcc ... -E -P -v -dD specs.c I can fix the issue for my project by editing .cproject and using: <runAction arguments="-f ${project_name}_scd.mk | -E -P -v -dD" command="make" instead of <runAction arguments="-f ${project_name}_scd.mk" command="make" The syntax looks crazy, it was introduced via bug 261280
I found that the problem does not occur when I use a new workspace. Because my workspace was pretty old, I don't think this is much of a problem.