no template named 'auto_ptr' in namespace 'std'
This error message is sourced from the abolition of auto_ptr in -std=c++11.
As is described in ClusterSequence.hh, you need to compile the source files without using it.
Just comment out the related part in config_auto.h as
/* compile the deprecated parts of the interface using auto-ptr */
#ifndef FASTJET_HAVE_AUTO_PTR_INTERFACE
/* #define FASTJET_HAVE_AUTO_PTR_INTERFACE */
#endif