EPROTO: protocol error, symlink '../semver/bin/semver' when using ember new

I have a Vagrant virtual machine created with ubuntu/trusty64 box (it runs Ubuntu 14.04.3 LTS (GNU/Linux 3.13.0-66-generic x86_64)) with Ruby on Rails, Node.js (5.x, but previously 0.12) and Ember CLI.

I'm trying to create a new Ember application by running ember new frontend and it always gives me some errors:

Successfully initialized git.
Installing packages for tooling via npm...
npm ERR! tar.unpack untar error /home/vagrant/.npm/underscore.string/2.3.3/package.tgz
npm ERR! tar.unpack untar error /home/vagrant/.npm/underscore.string/2.3.3/package.tgz
npm ERR! tar.unpack untar error /home/vagrant/.npm/underscore.string/2.3.3/package.tgz
npm ERR! tar.unpack untar error /home/vagrant/.npm/underscore.string/2.3.3/package.tgz
npm ERR! tar.unpack untar error /home/vagrant/.npm/underscore.string/2.3.3/package.tgz
npm ERR! tar.unpack untar error /home/vagrant/.npm/acorn/1.2.2/package.tgz
npm ERR! tar.unpack untar error /home/vagrant/.npm/npm/2.14.10/package.tgz
npm ERR! tar.unpack untar error /home/vagrant/.npm/bower/1.7.0/package.tgz
EPROTO: protocol error, symlink '../semver/bin/semver' -> '/vagrant/emberrails/frontend/node_modules/ember-cli-dependency-checker/node_modules/.bin/semver'
Error: EPROTO: protocol error, symlink '../semver/bin/semver' -> '/vagrant/emberrails/frontend/node_modules/ember-cli-dependency-checker/node_modules/.bin/semver'
    at Error (native)

Why? How can I fix this?

This problem occurs when I try to install some packages through NPM on my own, but then I add --no-bin-links to the command and it's all fine, but I don't have this option on ember new.