Duplicate identifier 'export='

I know this question was asked here before, but none of the solutions is working for me. I have the following tsconfig:

{"compilerOptions": {"module": "commonjs","target": "es6","declaration": true,"outDir": "./dist"  },"typeRoots": ["./node_modules/@types/*"],"include": ["./src/**/*"  ]}

but when I run tsc I get:

../node_modules/@types/passport/index.d.ts(100,5): error TS2300: Duplicate identifier 'export='.node_modules/@types/passport/index.d.ts(100,5): error TS2300: Duplicate identifier 'export='.

How is it possible that I still get ../node_modules/@types/ (etc) when I specifically said only include the ./src folder and only types from ./node_modules/@types?

I'm using typescript Version 2.4.0 (but have the same problem with version 2.3.4)