Uncaught TypeError: Cannot read property 'setEncoding' of undefined

[fungilation]

[Enter steps to reproduce below:]

1. Simply restarting atom on update

Atom Version: 0.165.0
System: Mac OS X 10.9.5
Thrown From: linter package, v0.9.0

Stack Trace

Uncaught TypeError: Cannot read property 'setEncoding' of undefined

At /Applications/Atom.app/Contents/Resources/app/src/buffered-process.js:126

TypeError: Cannot read property 'setEncoding' of undefined
  at BufferedProcess.module.exports.BufferedProcess.bufferStream (/Applications/Atom.app/Contents/Resources/app/src/buffered-process.js:126:13)
  at new BufferedProcess (/Applications/Atom.app/Contents/Resources/app/src/buffered-process.js:68:14)
  at LinterJshint.Linter.lintFile (/Volumes/System/Users/garyfung/.atom/packages/linter/lib/linter.coffee:142:19)
  at /Volumes/System/Users/garyfung/.atom/packages/linter/lib/linter-view.coffee:138:18
  at Array.forEach (native)
  at /Volumes/System/Users/garyfung/.atom/packages/linter/lib/linter-view.coffee:137:18
  at Object.oncomplete (fs.js:93:15)

Commands

Config

{
  "core": {
    "disabledPackages": [
      "metrics",
      "wrap-guide",
      "autosave",
      "htmlhint",
      "autoclose-html",
      "atom-handlebars",
      "font-awesome-snippetset",
      "underscorejs-snippets",
      "minimap-find-and-replace",
      "minimap-git-diff",
      "minimap-highlight-selected",
      "minimap-selection",
      "emmet",
      "minimap",
      "angularjs",
      "autocomplete"
    ],
    "themes": [
      "seti-ui",
      "base16-tomorrow-dark-theme"
    ],
    "useReactEditor": true,
    "ignoredNames": [
      ".git",
      ".svn",
      ".DS_Store",
      ".gitignore"
    ],
    "projectHome": "/Users/garyfung/Documents/code"
  },
  "linter": {}
}

Installed Packages

# User
atom-color-highlight, v2.0.14
autocomplete-paths, v0.9.0
autocomplete-plus, v1.0.0
autocomplete-snippets, v0.3.1
bezier-curve-editor, v0.6.2
color-picker, v1.2.6
html-entities, v0.2.0
javascript-snippets, v1.0.0
linter, v0.9.0
linter-coffeelint, v0.1.7
linter-csslint, v0.0.11
linter-jshint, v0.1.0
linter-php, v0.0.11
linter-shellcheck, v0.0.6
meteor-api, v2.9.0
script, v2.15.1
seti-ui, v0.5.1
tabs-to-spaces, v0.8.0

# Dev
No dev packages

/cc @atom/core