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Installation Tutorial for MacOS

The following is a more detailed description of the installation process of BanditPAM for MacOS.

Prerequisites

Please ensure the following dependencies are installed:

  • The most recent version of the Xcode Command Line Tools: via xcode-select --install. If you get errors about C++ standard library headers not being found, see the known issues
  • Homebrew: via /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  • LLVM's clang: via brew install llvm
  • The OpenMP and and Armadillo libraries: via brew install libomp armadillo
  • CARMA: via the instructions in its guide
  • Python3: if not installed, we recommend installing Python3 via Anaconda, which is CPython compiled with clang
  • pip for your Python3 installation; this should be completed if installing via Anaconda above
  • The necessary python packages: via python -m pip install -r requirements.txt

(NOT RECOMMENDED): Instead of LLVM's clang, you can also use another C++ compiler and point your CC environment variable to it. Please ensure this is the same compiler used to compile your Python installation if using CPython. If you open a python REPL it will show the compiler used during the language installation:

>> python
Python 3.7.9 (default, Mar  1 2021, 13:32:26)
[Clang 11.0.0 (clang-1100.0.33.17)] :: Intel Corporation on darwin
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution

For the default Python2 installed on Mac, the Apple clang compiler is used; for Intel python, clang is used as well. Do not attempt to compile the BanditPAM extension with gcc if your Python used clang.

BanditPAM Installation

BanditPAM can then be installed via one of the following ways:

  1. Running python -m pip install banditpam, OR
  2. Running python -m pip install . in the home directory (/BanditPAM)

Known Issues

The following is a list of issues seen when installing BanditPAM on MacOS. To report a bug, please file an issue at https://github.com/motiwari/BanditPAM/

  • MacOS users may get an error like the one below. If so, you likely need to update your Xcode Tools. Open the XCode app and install the additional software when prompted. If that still does not work, delete your XCode command line tools, re-install them, open the Xcode app and install the additional software when prompted. If that still does not work, restart your computer and try again. Original Thread
/usr/local/opt/llvm/bin/../include/c++/v1/stdlib.h:93:15: fatal error: 'stdlib.h' file not found
#include_next <stdlib.h>
              ^~~~~~~~~~
1 error generated.
error: command '/usr/local/opt/llvm/bin/clang' failed with exit code 1
  • Building the wheels for PyPy on MacOS via cibuildwheel do not work. As such, it's necessary to build the package from source if using PyPy. For more information, see the Developer Notes