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Within the C/C++ Perspective with the Project Explorer View one can right mouse click on a C++ project to get the Properties window and open the C/C++ Build and go under Settings to see an "All options" window frame with content like "-O0 -g3 -Wall -fPIC -c -fmessage-length=0 -v" for a configuration like "Debug". When using the Make Targets view to invoke a target like "all" with Debug being the active configuration the console window will show the actual make all output. This output does not seem to reflect any of the settings that was shown in the "All options" window that were non-standard - that is any flags added to say the Miscellaneous tool settings for the GCC C Compiler like "-fPIC" are not actually being used in the make invocation. Inspecting the makefiles including the Debug/src/subdir.mk file shows that the "-fPIC" flag is missing from the g++ invocation line which shows something like: g++ -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"src/Myfile.d" -o"$@" "$<" I've tried using the "Tool Settings" interface, changing the optimization level, debug level, and adding defines for the "GCC C Compiler" build stage but in fact none of these changes shows in the make output, is not being used, and is not making it into any of the makefiles. This bug seems to be there in Europa and Ganymede releases of eclipse.
Note that while the "GCC C Compiler" build stage (apparently the compile stage) settings changes in the UI aren't making it into a makefile, the link stage settings are making it in and working as expected. These changes only effect the link stage however and as such aren't useful as a work around to getting changes into the compile stage. All the makefiles are correctly owned by the same user as running eclipse, as are the containing directories.