Since check_all_disks is internally defined in Nagios, you might well
see a "duplicate definition" error if you define your own
check_all_disks command. I'd recommend

define command{
    command_name check_all_physical_disks
    command_line /usr/lib/nagios/plugins/check_disk -w '$ARG1$' -c '$ARG2$' -e 
-A --exclude-type=tracefs --exclude-type=cgroup 
--exclude_device=/run/lxcfs/controllers
}

instead, and then call that in your host definition:

define service {
        use                             generic-service
        hostgroup_name                  all
        service_description             Disk Space
        check_command                   check_all_physical_disks!6%!4%
}

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which is subscribed to the bug report.
https://bugs.launchpad.net/bugs/1516451

Title:
  check_disk plugin broken after upgrade to 15.10

Status in nagios-plugins package in Ubuntu:
  Triaged

Bug description:
  I didn't touch my Nagios config, just update my system from 15.04 to
  15.10. Suddenly the default localhost/Disk Space check fails with the
  following output:

  DISK CRITICAL - /sys/kernel/debug/tracing is not accessible:
  Permission denied

  This can be reproduced when manually running the underlying command as
  user "nagios":

  $ /usr/lib/nagios/plugins/check_disk -w '20%' -c '10%' -e
  DISK CRITICAL - /sys/kernel/debug/tracing is not accessible: Permission denied

  When I run it as root it works:

  # /usr/lib/nagios/plugins/check_disk -w '20%' -c '10%' -e
  DISK OK| /dev=0MB;1186;1334;0;1483 /run=8MB;239;269;0;299 
/=17157MB;57386;64559;0;71733 /dev/shm=0MB;1199;1349;0;1499 
/run/lock=0MB;4;4;0;5 /sys/fs/cgroup=0MB;1199;1349;0;1499 
/boot=48MB;181;204;0;227 /run/user/0=0MB;239;269;0;299

  Seems "nagios" user can't access the dir it tries to access:

  # ls -la /sys/kernel/debug/tracing
  drwx------  7 root root 0 Nov 15 19:40 .

  # lsb_release -rd
  Description:    Ubuntu 15.10
  Release:        15.10

  # apt-cache policy nagios-plugins-basic
  nagios-plugins-basic:
    Installed: 1.5-3ubuntu1
    Candidate: 1.5-3ubuntu1
    Version table:
   *** 1.5-3ubuntu1 0
          500 http://de.archive.ubuntu.com/ubuntu/ wily/main amd64 Packages
          100 /var/lib/dpkg/status

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