ShimWarning: The `IPython.html` package has been deprecated since IPython 4.0

I'm not sure if the warning in the subject is itself a problem, but I can't seem to run your example. I have a new installation of Anaconda with Python3 and have installed notedown by pip install https://github.com/aaren/notedown/tarball/master. Following is from the r-examples directory:

$ notedown r-example.Rmd --knit --rmagic > r-example-me.ipynb
/anaconda3/lib/python3.6/site-packages/IPython/html.py:14: ShimWarning: The `IPython.html` package has been deprecated since IPython 4.0. You should import from `notebook` instead. `IPython.html.widgets` has moved to `ipywidgets`.
  "`IPython.html.widgets` has moved to `ipywidgets`.", ShimWarning)
$

And I don't get a complete .ipynb output file:

$ cat r-example-me.ipynb 
{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext rpy2.ipython"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Introduction to ggplot2\n",
    "\n",
    "This is a short demo on how to convert an R Markdown Notebook into an IPython Notebook using knitr and notedown.\n",
    "\n",
    "Adding a Python Chunk"
   ]
  }
 ],
 "metadata": {},
 "nbformat": 4,
 "nbformat_minor": 2
}

aaren / notedown

ShimWarning: The `IPython.html` package has been deprecated since IPython 4.0 #70