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For any nontrivial binary, generally several challenges must be overcome to make analysis of that binary less difficult. Examples of challenges you might encounter include
Binaries that have been stripped of some or all of their symbol information
Binaries that have been linked with static libraries
Binaries that make use of complex, user-defined data structures
Compiled C++ programs that make use of polymorphism
Binaries that have been obfuscated in some manner to hinder analysis
Binaries that use instruction sets with which IDA Pro is not familiar
Binaries that use file formats with which IDA Pro is not familiar