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For the majority of users, installing from apt is best as it keeps the installation simple and the update patch easy (the package manager takes care of the updates).

There are some cases where building from source is required. For example:

• Using an OS or architecture not officially supported.
  • Each ROS distribution targets only specific platforms and architectures. The ROS buildfarm does not produce binaries for any other platform. In that case the way to install ROS on that platform is to compile from source
• Contributing to core ROS packages:
  • Modifying a ROS package to fix a bug requires compiling that package from source. In order for all the dependant packages to benefit from the change they will also need to be built from source.