The following *.pc file illustrates the issue: libdir=/home/software/plplot_svn/HEAD/comprehensive_test_disposeable/shared/install_tree/lib includedir=/home/software/plplot_svn/HEAD/comprehensive_test_disposeable/shared/install_tree/include/plplot drvdir=/home/software/plplot_svn/HEAD/comprehensive_test_disposeable/shared/install_tree/lib/plplot5.9.10/driversd Name: PLplot Qt Description: Scientific plotting library (Qt4 bindings, double precision) Requires.private: plplotd Version: 5.9.10 Libs: -L${libdir} -lplplotqtd -L/home/wine/newstart/build_script/install-linux/lib -lQtSvg -L/home/wine/newstart/build_script/install-linux/lib -lQtGui -L/home/wine/newstart/build_script/install-linux/lib -lQtCore Cflags: -I${includedir} -isystem /home/wine/newstart/build_script/install-linux/include -isystem /home/wine/newstart/build_script/install-linux/include/QtSvg -isystem /home/wine/newstart/build_script/install-linux/include/QtGui -isystem /home/wine/newstart/build_script/install-linux/include/QtCore The result for the -cflags option is -isystem /home/wine/newstart/build_script/install-linux/include /home/wine/newstart/build_script/install-linux/include/QtSvg /home/wine/newstart/build_script/install-linux/include/QtGui /home/wine/newstart/build_script/install-linux/include/QtCore -I/home/software/plplot_svn/HEAD/comprehensive_test_disposeable/shared/install_tree/include/plplot I assume the missing -isystem tags in that result are because pkg-config is being too enthusiastic about cleaning up repeat tags. But in the -isystem case they should be left as they are.
Thanks for the report. Should be fixed in master. See commit abdbaba. This probably needs to be more robust against all the other -ifoo gcc options, but that's a project for another day.
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