some of node_modules directories are empty

[webmake]

I'm opening this issue because:

• npm is producing an incorrect install.

What's going wrong?

First of all I thought that I have an issue #10399, so reinstalled everything from scratch. But still got repeating error:

$ npm install --no-bin-links
module.js:540
    throw err;
    ^

Error: Cannot find module 'extend'
    at Function.Module._resolveFilename (module.js:538:15)
    at Function.Module._load (module.js:468:25)
    at Module.require (module.js:587:17)
    at require (internal/module.js:11:18)
    at Object.<anonymous> (/var/www/app/node_modules/request/index.js:17:14)
    at Module._compile (module.js:643:30)
    at Object.Module._extensions..js (module.js:654:10)
    at Module.load (module.js:556:32)
    at tryModuleLoad (module.js:499:12)
    at Function.Module._load (module.js:491:3)

After some code investigation of that failing library, I decided to delete downloaded folder, now I got an issue

$ npm install --no-bin-links
module.js:540
    throw err;
    ^

Error: Cannot find module 'extsprintf'
    at Function.Module._resolveFilename (module.js:538:15)
    at Function.Module._load (module.js:468:25)
    at Module.require (module.js:587:17)
    at require (internal/module.js:11:18)
    at Object.<anonymous> (/var/www/app/node_modules/jsprim/lib/jsprim.js:8:22)
    at Module._compile (module.js:643:30)
    at Object.Module._extensions..js (module.js:654:10)
    at Module.load (module.js:556:32)
    at tryModuleLoad (module.js:499:12)
    at Function.Module._load (module.js:491:3)

Even more as you can see from image, there is not only one directory empty

supporting information:

• npm -v prints:
  5.6.0

• node -v prints:
  v8.9.4

• Windows, OS X/macOS, or Linux?:
  Ubuntu 16.04.3 LTS

• Container:

  • I develop using Vagrant on Windows.