Just doing an "apt-get dist-upgrade" on a 16.04 VM:

...
Setting up grub-common (2.02~beta2-36ubuntu3.11) ...
Installing new version of config file /etc/grub.d/10_linux ...
update-rc.d: warning: start and stop actions are no longer supported; falling 
back to defaults
Setting up grub-pc-bin (2.02~beta2-36ubuntu3.11) ...
Setting up grub2-common (2.02~beta2-36ubuntu3.11) ...
Setting up grub-pc (2.02~beta2-36ubuntu3.11) ...
Installing for i386-pc platform.
File descriptor 3 (pipe:[136263]) leaked on vgs invocation. Parent PID 18940: 
grub-install
File descriptor 3 (pipe:[136263]) leaked on vgs invocation. Parent PID 18940: 
grub-install
File descriptor 3 (pipe:[136263]) leaked on vgs invocation. Parent PID 18940: 
grub-install
Installation finished. No error reported.
Generating grub configuration file ...
Found linux image: /boot/vmlinuz-4.4.0-83-generic
Found initrd image: /boot/initrd.img-4.4.0-83-generic
Found linux image: /boot/vmlinuz-4.4.0-21-generic
Found initrd image: /boot/initrd.img-4.4.0-21-generic
done
...
Setting up initramfs-tools-core (0.122ubuntu8.8) ...
Setting up initramfs-tools (0.122ubuntu8.8) ...
update-initramfs: deferring update (trigger activated)
Setting up mdadm (3.3-2ubuntu7.2) ...
update-initramfs: deferring update (trigger activated)
Generating grub configuration file ...
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19859: 
grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19859: 
grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19899: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19899: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19909: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19909: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19919: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19919: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19929: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19929: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19979: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 19979: 
/usr/sbin/grub-probe
Found linux image: /boot/vmlinuz-4.4.0-83-generic
Found initrd image: /boot/initrd.img-4.4.0-83-generic
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20061: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20061: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20072: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20072: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20082: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20082: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20092: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20092: 
/usr/sbin/grub-probe
Found linux image: /boot/vmlinuz-4.4.0-21-generic
Found initrd image: /boot/initrd.img-4.4.0-21-generic
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20335: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on vgs invocation. Parent PID 20335: 
/usr/sbin/grub-probe
File descriptor 3 (pipe:[140340]) leaked on lvs invocation. Parent PID 20417: 
/bin/sh
done
update-rc.d: warning: start and stop actions are no longer supported; falling 
back to defaults
...

It updated 119 packages, but lvm2 was not one of them.

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https://bugs.launchpad.net/bugs/591823

Title:
  "File descriptor \d+ (\S+) leaked on lvs invocation."

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