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Yes you can set specific flags needed by you. I prefer using GUI or ccmake . Enter following commands in your terminal
Step1. Change the directory to opencv build folder.
Step2. $ ccmake .
List of all the modules and flags will be displayed on the screen.
Step3. Now set the flags ON/OFF using enter key.
Step4. Press c to configure changes.
Step5. Press g to generate files.
After this you can do make and install