I put together an example package that generates a bash script:

# default.nix
with import <nixpkgs> {};
stdenv.mkDerivation {
  name = "varSubTest";
  src = ./.;
  inherit R; rByAnotherName = R;
  builder = ./builder.sh;
}

# builder.sh
#!/usr/bin/env bash
source $stdenv/setup
mkdir -p $out/bin
substituteAll $src/varSubTest.sh $out/bin/varSubTest
chmod +x $out/bin/varSubTest

# varSubTest.sh
#!/usr/bin/env bash
echo "R is substituted with @R@"
echo "rByAnotherName is substituted with @rByAnotherName@"

If you run `nix-build && ./result/bin/varSubTest`, you'll see that @R@ is 
skipped.
Is there a restriction that single uppercase letters can't be used as variable 
names?
Jeff
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