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which setup.bash to source?

If you want to build Autoware using the binary ROS packages, you should not source the setup.bash for your from source installation. Likewise if you want to build using your from-source installation you should not source the setup.bash from the binary installation. With the exception of using the binaries as an underlay workspace for customizations in the source installation there are very few circumstances where you would source both setup scripts in the same session and I would recommend you avoid it.

Both error messages indicate that some packages required by A are not available in the workspace. Did you run the rosdep command indicated in the installation instructions?

What is the output of dpkg -s ros-foxy-geometry-msgs for your environment?