When setting the smoother in the alsa modules we use the htimestamp, but when interpolating (using get) we use pa_rtclock. pa_rtclock is not guaranteed to be the same as htimestamp. Specifically in the case where CLOCK_MONOTONIC is not defined, alsa will use getnstimeofday. Also in the case where HAVE_CLOCK_GETTIME is not defined in alsa-lib (can happen in Android) then alsa-lib will not use CLOCK_MONOTONIC. The fix is to use snd_pcm_status to get the time from alsa when calculating latency. A less accurate alternative would be to simply use pa_rtclock_get during the smoother_put.
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