################################
Set Up Data Analysis Environment
################################

Download and run the `Anaconda`_ installation script.  Unless
:envvar:`PATH` is modified permanently, each terminal session needs to redefine
the path as follows

.. code:: bash

   export PATH=<absolute_path_to_anaconda>/bin:$PATH

.. _Anaconda: https://www.anaconda.com/distribution/#download-section

The `Jupyter`_ notebook installation is as easy as running a single command.

.. _Jupyter: http://jupyter.readthedocs.org/en/latest/install.html

In order to enhance the notebook with `R`_, install :program:`rpy2`.

.. _R: http://sites.psu.edu/theubunturblog/installing-r-in-ubuntu/

.. code:: bash

   sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
   echo "deb http://cran.r-project.org/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
   sudo apt-get update
   sudo apt-get install r-base
   sudo apt-get install r-base-dev
   export PATH=<absolute-path-to-anaconda>/bin:$PATH
   pip install rpy2

R packages can be `installed directly`_ or via `rpy2`_.  Note that direct
installation requires the notebook to be relaunched in order to access the new
packages.

.. _installed directly: https://cran.r-project.org/doc/manuals/R-admin.html#Installing-packages
.. _rpy2: http://rpy.sourceforge.net/rpy2/doc-dev/html/robjects_rpackages.html#installing-removing-r-packages

PyMathProg
==========

`PyMathProg`_ is an easy to use solver for linear programming.

.. _PyMathProg: http://pymprog.sourceforge.net/index.html

ImportError: :file:`<path>/anaconda3/lib/libgomp.so.1`: version 'GOMP_4.0' not found (required by /usr/lib/R/lib/libR.so)
=========================================================================================================================

This error may be resolved by telling the run-time shared library loader where
to look for the shared library before launching the notebook.

.. code:: bash

   export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/:$LD_LIBRARY_PATH
   jupyter-notebook

ImportError: :file:`<path>/anaconda3/bin/../lib/libreadline.so.6`: undefined symbol: PC
=======================================================================================

This error may be resolved by manually importing :program:`readline` before
executing the notebook :program:`rpy2` magic command.

.. code:: python

   import readline
   %load_ext rpy2.ipython

:file:`libgfortran.so.3`: version GFORTRAN_1.4 not found
========================================================

This error usually means the library was installed incorrectly.

.. code:: bash

   conda remove libgfortran
   conda install libgcc --force