thats because long long (guaranteed 64 bit integer) is not defined in the c++98 standard.
compilers define the 64 bit types but use different names.
long long is the name in the C99 Standard so for example g++ decided to use long long too where as Visual Studio (windows) uses __int64
so root typedefs these to a common name so the code can be compiled on different plattforms as long as the common name (e.g. Long64_t) is used.
so this “error” shouldn’t be a problem.
you can still compile with pedantic if you disable this error with -Wno-long-long
(another possiblity would be to compile with -std=c++0x but I doubt that would be wise as the new standard has not yet been finalized)