Run a shell command in a separate thread, terminate it after a time limit, return its output

timeout.rb

# Runs a specified shell command in a separate thread.
# If it exceeds the given timeout in seconds, kills it.
# Passes stdout, stderr, thread, and a boolean indicating a timeout occurred to the passed in block.
# Uses Kernel.select to wait up to the tick length (in seconds) between 
# checks on the command's status
#
# If you've got a cleaner way of doing this, I'd be interested to see it.
# If you think you can do it with Ruby's Timeout module, think again.
def run_with_timeout(*command)
    options = command.extract_options!.reverse_merge(timeout: 60, tick: 1, cleanup_sleep: 0.1, buffer_size: 10240)

    timeout = options[:timeout]
    cleanup_sleep = options[:cleanup_sleep]
    tick = options[:tick]
    buffer_size = options[:buffer_size]

    output = ''
    error = ''

    # Start task in another thread, which spawns a process
    Open3.popen3(*command) do |stdin, stdout, stderr, thread|
        # Get the pid of the spawned process
        pid = thread[:pid]
        start = Time.now

        time_remaining = nil
        while (time_remaining = (Time.now - start) < timeout) and thread.alive?
            # Wait up to `tick` seconds for output/error data
            readables, writeables, = Kernel.select([stdout, stderr], nil, nil, tick)
            next if readables.blank?
            readables.each do |readable|
                stream = readable == stdout ? output : error
                begin
                    stream << readable.read_nonblock(buffer_size)
                rescue IO::WaitReadable, EOFError => e
                    # Need to read all of both streams
                    # Keep going until thread dies
                end
            end
        end

        # Give Ruby time to clean up the other thread
        sleep cleanup_sleep

        if thread.alive?
            # We need to kill the process, because killing the thread leaves
            # the process alive but detached, annoyingly enough.
            Process.kill("TERM", pid)
        end

        yield output, error, thread, !time_remaining
    end
end

I've been using this solution for a while, and it's been working pretty well. Unfortunately, I've recently been ending up with no stdout, when I know there has been stdout. Stderr seems to work fine. Any hints for a reason or solution? I'm trying out upping the tick and cleanup_sleep values.