without trying it myself, I see two possible problems:
1) Classes still use prototypes under the hood, so if you are testing an instance method, you still need spyOn(Store.prototype, 'allPackages'); If this is the case, this will avoid problem number 2....
2) es6 Classes freeze all of their properties, so you aren't allowed to change them. This includes changing them for spies. This is what causes your TypeError. All the solutions for this are kinda annoying. You need to expose something down the chain from 'allPackages' and mock it out in your test. In the above code, the only thing is the variable `_allPackages`. Sometimes you can wrap some other function that isn't on a class and spy on that function.
Hope that helps,
Charles