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Whenever audio starts playing, or stops playing, a 'popping' sound can be heard from my headphones. I am running Elementary OS 0.3.2 Freya, and the issue only happens when I am using headphones. The 'popping' also happens when I plug my headphones in and when wifi has connected or disconnected.

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If you happen to be using TLP, this could be caused by TLP's default config turning your audio stuff off when you're not playing audio to save power. I noticed my laptop was doing the same thing while playing audio through my headphone port on battery power. When it was "power saving" I noticed a hissing noise coming from my speakers too.

Try setting the following parameters in /etc/default/tlp to disable audio power saving:

# Enable audio power saving for Intel HDA, AC97 devices (timeout in secs).
# A value of 0 disables, >=1 enables power saving (recommended: 1).
SOUND_POWER_SAVE_ON_AC=0
SOUND_POWER_SAVE_ON_BAT=0

# Disable controller too (HDA only): Y/N.
SOUND_POWER_SAVE_CONTROLLER=N

Then restart the tlp service:

sudo systemctl restart tlp

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