Audio is "clippy" when playback speed is not 1.0X

[booga]

I was trying to play an MKV file on my VLC. When I change the playback speed, the audio becomes clippy/choppy. (When I bring back the playback speed to normal, the audio is perfect again.) I run VLC in verbose mode and got this:

$ vlc -v foo.mkv
VLC media player 3.0.0-git Vetinari (revision 3.0.0~~git20160813+r65787+62~ubuntu16.04.1)
[00000000009ad1a8] core libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface.
[00007f0aa800c4e8] transport stream error: cannot resolve services.tvrage.com port 80: Temporary failure in name resolution
[00007f0aa800c4e8] access stream error: HTTP connection failure
[00007f0aa800c4e8] core stream error: cannot resolve services.tvrage.com port 80 : Temporary failure in name resolution
[00007f0aa0c1ef38] avcodec decoder warning: thread type 1: disabling hardware acceleration
[00007f0a84000f88] transport stream error: cannot resolve services.tvrage.com port 80: Temporary failure in name resolution
[00007f0a84000f88] access stream error: HTTP connection failure
[0000000000ab4be8] core audio output error: cannot find decoder for conversion pipeline
[00007f0a64003c68] core audio filter error: cannot add user audio filter "scaletempo" (skipped)
[0000000000ab4be8] core audio output error: cannot find decoder for conversion pipeline
[0000000000ab4be8] core audio output error: cannot setup filtering pipeline
[00007f0aa0d73ae8] core decoder error: failed to create audio output
Failed to open VDPAU backend libvdpau_va_gl.so: cannot open shared object file: No such file or directory
[00007f0aa0c1ef38] avcodec decoder warning: plane 0 not aligned: disabling direct rendering
[0000000000ab4be8] pulse audio output warning: starting late (-23093 us)
[00007f0aa0c1ef38] avcodec decoder warning: thread type 1: disabling hardware acceleration
[0000000000ab4be8] pulse audio output warning: starting late (-29422 us)
[0000000000ab4be8] core audio output warning: playback way too late (643183): flushing buffers
[0000000000ab4be8] pulse audio output warning: starting late (-375869 us)
[0000000000ab4be8] core audio output warning: playback way too late (348108): flushing buffers
[0000000000ab4be8] pulse audio output warning: starting late (-351468 us)
[0000000000ab4be8] core audio output warning: playback way too late (324917): flushing buffers
[0000000000ab4be8] pulse audio output warning: starting late (-338824 us)
[0000000000ab4be8] core audio output warning: playback way too late (309336): flushing buffers
[0000000000ab4be8] pulse audio output warning: starting late (-326640 us)

[Rémi Denis-Courmont]

Because "scaletempo" filter is missing. Are you using S/PDIF?

[booga]

Sorry, what's S/PDIF? The MKV file is on my hard drive. I'm not using any s/pdif cable/connector.

[Rémi Denis-Courmont]

If you are not using S/PDIF, the problem comes from lack of scaletempo filter. With no further details, I have to suspect build or installation problem.