You can issue a
urequire AMD ... or use
build:template:'AMD' config option instead of the default uRequire UMD (Universal Module Definition) format.
The AMD template is safe & 100% equivalent for Web/AMD execution with its UMD counterpart (and smaller in size). Its also what you need to r.js optimize your package on your own (although you can save your self time & hassle and use the 'combined' template that does this for you).
If you want AMD along with simple nodejs execution consider 'UMDplain' template, which runs as Web/AMD & nodejs without any nodejs dependencies (but has nodejs template limitations).