Perhaps this is a permissions issue with the nix shepherd service? I haven't tried the patch linked above, but found that I could run
$ sudo nix-channel --update
without running into the issue. Then, I got the same error again when trying to install any package with nix-env. Once again, I could run
$ sudo nix-env -i <some-package>
which would successfully install it to the root profile. After doing this, however, I found that I now could run
$ nix-env -i <some-package>
to install the package to my user profile, presumably because the nix store was populated by the run with sudo.