MySQL 5.6 DESTDIR not work propely
DESTDIR is a variable inserted at the beginning of each target file 

If you wanted to install MySQL in the /usr/local/mysql, you could use the following command sequence

cd /name/of/source/directory
make clean
./configure --prefix=/usr/local/mysql
make &amp;&amp; make install


MySQL would thus be installed in the /usr/local/mysql directory.

The ./configure allows you to control and define how your program will be installed and what options will be included or excluded.

MySQL Source Configuration Options