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Installing packages to a foreign system

I'm trying to debootstrap a system and when I chroot into it to install more packages, many fail because their configure scripts assume they are being called from a running system and try to interact with it and modify the running state, instead of just the filesystem. For example, daemon packages try to start the daemon in the configure script, which you can't do running inside a chroot. So my question is, what is the proper way to install packages into a foreign system's filesystem such that they do not attempt to modify the running host system?

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