vagga + ubuntu16.04 with kernel 4.6

Vagrantfile

# -*- mode: ruby -*-
# vi: set ft=ruby :

# All Vagrant configuration is done below. The "2" in Vagrant.configure
# configures the configuration version (we support older styles for
# backwards compatibility). Please don't change it unless you know what
# you're doing.

$script = <<SCRIPT
echo "deb [trusted=true] http://ubuntu.zerogw.com vagga-testing main" | sudo tee /etc/apt/sources.list.d/vagga.list
sudo apt-get update
sudo apt-get install -Vy vagga
wget -q "http://kernel.ubuntu.com/~kernel-ppa/mainline/v4.6-yakkety/linux-headers-4.6.0-040600-generic_4.6.0-040600.201605151930_amd64.deb" \
    "http://kernel.ubuntu.com/~kernel-ppa/mainline/v4.6-yakkety/linux-headers-4.6.0-040600_4.6.0-040600.201605151930_all.deb" \
    "http://kernel.ubuntu.com/~kernel-ppa/mainline/v4.6-yakkety/linux-image-4.6.0-040600-generic_4.6.0-040600.201605151930_amd64.deb"
sudo dpkg --install ./linux-*
cat > vagga.yaml <<EOF
containers:
  alpine:
    setup:
    - !Alpine v3.3
    - !Sh echo "Hello"
  ubuntu:
    setup:
    - !Ubuntu xenial
    - !Sh echo "Hello"
EOF
SCRIPT

Vagrant.configure("2") do |config|
  config.vm.box = "ubuntu/xenial64"
  config.vm.provider "virtualbox" do |v|
    v.memory = 1024
    v.cpus = 2
  end
  config.vm.provision "shell", inline: $script
end

reproduce errors:

vagrant up
vagrant halt && vagrant up  # reboot with new kernel
vagrant ssh -c "vagga _build alpine"