I am using highland.js and have installed it with its type definition:
jq .dependencies package.json | grep highland
  "@types/highland": "https://registry.npmjs.org/@types/highland/-/highland-1.14.30.tgz",
  "highland": "^2.9.0",
I am using PhpStorm (which uses the WebStorm component for TypeScript).
When I typehint for:
Highland.Stream<any>
PhpStorm complains about the Stream:
Corresponding file not included in tsconfig.json

Yet the go to declaration works and it jumps to node_modules/@types/highland/index.d.ts:367:
interface Stream<R> extends NodeJS.EventEmitter { ... }
I can compile the code fine with tsc without errors and it's working as expected. What is PhpStorm's / WebStorm's problem?
$ jq . tsconfig.json
{
  "compilerOptions": {
    "module": "commonjs",
    "lib": [
      "es2016",
      "dom"
    ],
    "target": "es6",
    "noImplicitAny": true,
    "sourceMap": true,
    "outDir": "dist",
    "strictNullChecks": true,
    "skipLibCheck": true,
    "types": [
      "node",
      "mocha",
      "chai",
      "sinon"
    ]
  },
  "exclude": [
    "node_modules",
    "src/typings-custom/main.d.ts"
  ]
}
I tried adding highland to types to no avail, and I have no idea what the error is telling me.
                        
I had the same issue with Webstorm 2018. I closed and reopened Webstorm and, voilĂ : the red lines were gone! I just needed to refresh Webstorm I guess. Since Webstorm and PHPStorm are both under the same umbrellas, maybe this will work for you as well.