This bug was fixed in the package ntp - 1:4.2.8p4+dfsg-3ubuntu5

---------------
ntp (1:4.2.8p4+dfsg-3ubuntu5) xenial; urgency=medium

  * debian/apparmor-profile: allow 'rw' access to /dev/pps[0-9]* devices.
    Patch thanks to Mark Shuttleworth. (LP: #1564832)

 -- Jamie Strandboge <ja...@ubuntu.com>  Thu, 07 Apr 2016 15:12:41 -0500

** Changed in: ntp (Ubuntu)
       Status: In Progress => Fix Released

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https://bugs.launchpad.net/bugs/1564832

Title:
  Apparmor profile for NTPd needs to allow read/write access to
  /dev/ppsX

Status in ntp package in Ubuntu:
  Fix Released

Bug description:
  Am trying to get NTP to work with the kernel PPS subsystem, for high-
  accuracy GPS-based clocks. On startup of NTPd I see this:

  Apr  1 11:18:58 doorway kernel: [  300.387443] audit: type=1400
  audit(1459505938.042:9): apparmor="DENIED" operation="open"
  profile="/usr/sbin/ntpd" name="/dev/pps0" pid=1668 comm="ntpd"
  requested_mask="wr" denied_mask="wr" fsuid=0 ouid=0

  Adding this to the usr.sbin.ntpd apparmor profile eliminated the
  error:

    /dev/pps[0-9]* rw,

  
  I'm not sure why ntpd needs *write* access to ppsN though, perhaps that can 
be improved.

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