PHP mcrypt not compiled properly

brew reinstall mcrypt --build-from-source php56-mcrypt --build-from-source

Build from source is an option which will force brew to compile from source rather than using a bottle.

Since you had a previous installation of PHP (5.3), and now you just installed a newer version (5.5.1), maybe the new PHP installation are pointing to some old locations.

Look for any php.ini you're using, and verify the extension_dir directive.

The last suggestion would be to reinstall PHP 5.5.1.

The warning is because of mismatch between php-mcrypt module version and php version in the server. I am not that familiar with brew as I am a Macports user however depending on your unix ditro you can do something like:

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yum list installed | grep php55

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Sample output:=======php55-gd.x86_64                        5.2.14-2.el5.art                   installedphp55-imap.x86_64                      5.2.14-2.el5.art                  installedphp55-mbstring.x86_64                  5.2.14-2.el5.art                installed**php55-mcrypt.x86_64                    5.1.6-15.el5.centos.1        installed**php55-mysql.x86_64                     5.2.14-2.el5.art                  installed=======

We can see the php-mcrypt module associated with earlier version of PHP.

How to fix the error?

Update php-mcrypt module to fix the error.

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yum update php-mcrypt

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hope that helps