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Installation

Since this package contains C++ source code, pip needs a C++ compiler to install PySurvival.

1 - Installing C++ compiler

On MacOS

  1. Install brew - go on http://brew.sh/ and follow the provided instructions

  2. Install the latest version of gcc with the command :

    • If you have never installed gcc, use: 

      brew install gcc

    • If you have already installed gcc and want the latest version: 

      brew upgrade gcc

  3. Get the list all the gcc files with the command:

    brew ls gcc
    PySurvival - List of gcc variables

  4. Assign the environment variables CC and CXX to the previously found addresses, by entering the following lines in the terminal: 

    export CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
export CC=/usr/local/Cellar/gcc/8.2.0/bin/gcc-8

Note: As of October 18, 2018, the latest version on MacOS is 8.2.0, hence the use of 8.2.0; feel free to use the version that matches your situation instead.

On Linux

CentOS7

  1. Install GCC with the command : 

    sudo yum install centos-release-scl
sudo yum install devtoolset-8-gcc devtoolset-8-gcc-c++  -y
    Note: As of March 2019, the latest version of gcc is 8, hence the use of devtoolset-8; feel free to use the version that matches your situation instead.

  2. Assign the environment variables CC and CXX to the appropriate files: 

    export CXX=/opt/rh/devtoolset-8/root/usr/bin/x86_64-redhat-linux-g++
export CC=/opt/rh/devtoolset-8/root/usr/bin/x86_64-redhat-linux-gcc

Ubuntu

  1. Install GCC with the command : 

    sudo apt install gcc-8 g++-8
    Note: As of March 2019, the latest version of gcc is 8, hence the use of gcc-8 g++-8; feel free to use the version that matches your situation instead.

  2. Assign the environment variables CC and CXX to the appropriate files: 

    export CXX=/usr/bin/g++-8
export CC=/usr/bin/gcc-8

The easiest way to install pySurvival is to use to pip:

pip install pysurvival

Potential Issues

Issues with matplotlib on MacOS

If you encounter the following error:

Error with matplotlib

RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework.

You'll need to ensure that there exists a file ~/.matplotlib/matplotlibrc containing the code: backend: TkAgg. To do this, run the following code in your Terminal:

cd
echo "backend: TkAgg" >> ~/.matplotlib/matplotlibrc