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As became clearer in the comments, the OP had a full clone of all ROS 2 packages in the src space of the workspace.

As rosdep was invoked with the --from-paths option and given the src space as the path, rosdep correctly checked each and every package in the src space for dependencies, which resulted in dependencies being listed as missing which would normally not show up when only ros_base would be considered.

Afaik there is no way to "limit dependencies" with rosdep, so achieve what the OP wants (ie: check dependencies for just the packages contained in ros_base), a workspace with just the packages in ros_base would have to be created.

Using rosinstall_generator, this should be possible:

mkdir -p foxy_ros_base_ws/src
cd foxy_ros_base_ws/src
vcs import < /path/to/foxy_ros_base.rosinstall

As became clearer in the comments, the OP had a full clone of all ROS 2 packages in the src space of the workspace.

As rosdep was invoked with the --from-paths option and given the src space as the path, rosdep correctly checked each and every package in the src space for dependencies, which resulted in dependencies being listed as missing which would normally not show up when only ros_base would be considered.

Afaik there is no way to "limit dependencies" with rosdep, so achieve what the OP wants (ie: check dependencies for just the packages contained in ros_base), a workspace with just the packages in ros_base would have to be created.

Using rosinstall_generator, this should be possible:

rosinstall_generator --deps --tar --rosdistro=foxy ros_base > foxy_ros_base.rosinstall
mkdir -p foxy_ros_base_ws/src
cd foxy_ros_base_ws/src
vcs import < /path/to/foxy_ros_base.rosinstall

As became clearer in the comments, the OP had a full clone of all ROS 2 packages in the src space of the workspace.

As rosdep was invoked with the --from-paths option and given the src space as the path, rosdep correctly checked each and every package in the src space for dependencies, which resulted in dependencies being listed as missing which would normally not show up when only ros_base would be considered.

Afaik there is no way to "limit dependencies" with rosdep, so to achieve what the OP wants (ie: check dependencies for just the packages contained in ros_base), a workspace with just the packages in ros_base would have to be created.

Using rosinstall_generator, this should be possible:

rosinstall_generator --deps --tar --rosdistro=foxy ros_base > foxy_ros_base.rosinstall
mkdir -p foxy_ros_base_ws/src
cd foxy_ros_base_ws/src
vcs import < /path/to/foxy_ros_base.rosinstall