Android: How do I stop Runnable?

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Instead implement your own thread.kill() mechanism, using existing API provided by the SDK. Manage your thread creation within a threadpool, and use Future.cancel() to kill the running thread:

ExecutorService executorService = Executors.newSingleThreadExecutor();
Runnable longRunningTask = new Runnable();

// submit task to threadpool:
Future longRunningTaskFuture = executorService.submit(longRunningTask);

... ...
// At some point in the future, if you want to kill the task:
longRunningTaskFuture.cancel(true);
... ...

Cancel method will behave differently based on your task running state, check the API for more details.

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