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I manually built the latest version of BlueZ (5.50) and I need to access some tools from Python. Where is the recommended location to put compiled binaries so that they are accessible for all users?

I am running Raspbian Stretch 9.4.

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Either /usr/local/bin (and friends) or /opt/<package name here>/bin/. The latter has the downside people had to manually add the directory to their search paths.

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