Same issue is happening to me. Here are minimal steps to reproduce:

Create an empty directory containing a single file "main.rs", containing the 
following single line:

extern crate arena;

Then, with that directory as the current directory, run:

rustc main.rs


The error is "error[E0523]: found two different crates with name `std` that are 
not distinguished by differing `-C metadata`. This will result in symbol 
conflicts between the two.". The use of "arena" here is not critical; any 
stable, public crate that's part of the standard library will do (e.g. for the 
original reporter, it happened with "proc_macro").

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https://bugs.launchpad.net/bugs/1676169

Title:
  rustc (1.16.0+dfsg1-1~exp1ubuntu1) gives an error when compiling with
  std

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