Trying to update mcrypt on yosemite

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I went through the steps at updating mcrypt on yosemite

And when I went to run

sudo make install

and this is what came back

Tariks-Mac-mini:mcrypt tam3$ sudo make install
Installing shared extensions:     /Applications/MAMP/bin/php/php5.4.10/lib/php/extensions/no-debug-non-zts-20100525/

Why is it sharing extensions to MAMP? I have set my bash_profile to /usr/bin/php

How do I get everything pointing to the native php?

BTW, I have tried:

./configure --prefix=/usr/bin/php
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I had such problem installing Mcrypt with following commands in the site you mentioned and finally I could solve the problem after installing Command Line Tools for OS X 10.9 for Xcode 6.1.1 GM Seed which you can download form Downloads for Apple Developers.