manifests.init.pp

notify {'Hello world': }
include rundeck

provision.puppet.sh

#!/usr/bin/env bash
rpm -Uvh https://yum.puppet.com/puppet5-release-el-7.noarch.rpm
yum install -y puppet-agent

Puppetfile

mod 'puppetlabs-stdlib'
mod 'pltraining-dirtree'
mod 'puppetlabs-inifile'
mod 'puppet-archive'
mod 'puppetlabs-java_ks'
mod 'puppet-rundeck'

Vagrantfile

Vagrant.configure(2) do |config|
  config.vm.box = "bento/centos-7.4"
  config.vm.synced_folder File.dirname(__FILE__), "/puppet"
  config.vm.provision :shell, path: "provision/puppet.sh"
  config.vm.provision "puppet" do |puppet|
    puppet.manifests_path = "manifests"
    puppet.manifest_file = "init.pp"
    puppet.module_path = "modules"
  end
end

Ran

r10k puppetfile install
vagrant up

Using Vagrant 2.2.4 and latest VirtualBox.