TLTR: This is a known issue, without solution. The work-around is to restart Atom.

---

[Enter steps to reproduce below:]

1. click “Update All”

Atom Version: 1.5.4 System: Mac OS X 10.11.3 Thrown From: sync-settings package, v0.7.0

Stack Trace

Uncaught Error: ENOENT: no such file or directory, open ‘/Users/jhs/.atom/packages/sync-settings/node_modules/github/api/v3.0.0/routes.json’

At fs.js:549

Error: ENOENT: no such file or directory, open '/Users/jhs/.atom/packages/sync-settings/node_modules/github/api/v3.0.0/routes.json'
    at Error (native)
    at Object.fs.openSync (fs.js:549:18)
    at Object.module.(anonymous function) [as openSync] (ATOM_SHELL_ASAR.js:137:20)
    at Object.fs.readFileSync (fs.js:397:15)
    at Object.fs.readFileSync (ATOM_SHELL_ASAR.js:385:29)
    at Object.module.exports (/Users/jhs/.atom/packages/sync-settings/node_modules/github/api/v3.0.0/index.js:22:33)
    at new module.exports (/Users/jhs/.atom/packages/sync-settings/node_modules/github/index.js:184:26)
    at Object.SyncSettings.createClient (/Users/jhs/.atom/packages/sync-settings/lib/sync-settings.coffee:300:16)
    at Object.SyncSettings.checkForUpdate (/Users/jhs/.atom/packages/sync-settings/lib/sync-settings.coffee:61:21)
    at Immediate._onImmediate (/Users/jhs/.atom/packages/sync-settings/lib/sync-settings.coffee:44:19)
    at processImmediate [as _immediateCallback] (timers.js:374:17)

Commands

     -9:09.0 core:close (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:23.4.0 fuzzy-finder:toggle-file-finder (atom-workspace.workspace.scrollbars-visible-when-scrolling.seti-ui-no-icons.theme-monokai.theme-one-dark-ui)
     -3:21.4.0 core:confirm (atom-text-editor.editor.mini.is-focused)
  2x -3:20.8.0 core:move-down (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:20.3.0 editor:move-to-end-of-screen-line (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:19.7.0 core:save (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:15.3.0 core:backspace (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:15 core:save (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:13.8.0 core:close (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:13.5.0 fuzzy-finder:toggle-file-finder (atom-workspace.workspace.scrollbars-visible-when-scrolling.seti-ui-no-icons.theme-monokai.theme-one-dark-ui)
     -3:12.4.0 core:confirm (atom-text-editor.editor.mini.is-focused)
     -3:11.3.0 editor:move-to-end-of-screen-line (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:10.7.0 core:save (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:06.5.0 core:backspace (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -3:06.3.0 core:save (atom-text-editor.editor.vim-mode.insert-mode.is-focused)
     -0:50.2.0 settings-view:check-for-package-updates (atom-workspace.workspace.scrollbars-visible-when-scrolling.seti-ui-no-icons.theme-monokai.theme-one-dark-ui)

Config

{
  "core": {
    "audioBeep": false,
    "disabledPackages": [
      "editorconfig",
      "linter-jscs"
    ],
    "themes": [
      "one-dark-ui",
      "monokai"
    ]
  },
  "sync-settings": {
    "_analyticsUserId": "...",
    "_lastBackupHash": "...",
    "gistId": "...",
    "personalAccessToken": "..."
  }
}

Installed Packages

# User
api-docs, v0.0.4
atom-beautify, vundefined
atom-cli-diff, v1.3.0
atom-handlebars, v1.3.0
atom-html-preview, v0.1.16
autoclose-html, v0.23.0
autocomplete-paths, v1.0.2
autocomplete-ruby, v0.1.0
color-picker, v2.1.1
cson, v2.0.1
file-icons, v1.6.18
git-diff-details, v0.23.0
highlight-selected, v0.11.2
language-haml, v0.23.15
language-javascript-jsx, v0.3.7
language-matlab, v0.2.0
language-slim, v0.5.0
language-spacebars, v0.2.2
linter, v1.11.3
linter-bootlint, v1.0.2
linter-coffeelint, v1.1.2
linter-haml, v1.1.0
linter-htmlhint, v1.0.3
linter-js-standard, v3.2.1
linter-ruby, v1.2.2
monokai, v0.18.0
pdf-view, v0.48.0
pigments, v0.24.4
react, v0.14.1
relative-numbers, v0.5.0
set-syntax, v0.3.0
standard-formatter, v2.0.0
sync-settings, v0.7.0
vim-mode, v0.64.0
vim-surround, v0.8.1

# Dev
No dev packages