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I'm trying to remove package X entirely from my /nix/store/, but nix-garbage-collect wont remove it as its probably referenced by some garbage collection root (gc-root) somewhere. Is it possible to list which gc-roots reference a given package X?

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The program nix-du can provide you with a graph showing which gc-roots reference which packages, but it also does the additional work of calculating the size of each package.

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