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Installation

Compiling and building bayesmix requires a modern C++ compiler, git, the GNU make utility, cmake (version >= 3.16) and pkg-config. Make these packages available varies between operating systems.

Warning: Check the version of cmake available in your package manager default repository. This requirement is already satisfied in Ubuntu 20.04 LTS, so in fairly updated distros this requirement will already be satisfied. If your system is too old and the binary cmake package does not satisfy the minimum requiremens, please go to the official CMake GitHub repository and follow the installation instructions.

Requirements - Linux

On Linux systems, the required packages can be installed via the system's default package manager. For instance, in Ubuntu or other Debian based distros it is sufficient to run

sudo apt install git g++ make cmake pkg-config

For other Linux distributions, you need to adapt the above instruction to the syntax of your package manager. This table shows the correspondence of package management commands among some of the most popular Linux distributions.

Requirements - MacOS

On MacOS, the required packages can be installed via Homebrew. Once installed, it is sufficient to run

brew install git g++ make cmake pkg-config

Requirements - Windows

First of all, install git via the Git for Windows project. Download the installer and complete the prompts leaving default choices to install.

On Windows, we also need the installation of a proper C++ toolchain and install the other required packages. bayesmix can be successfully compiled and installed with RTools40, RTools42 and RTools43 toolchains. This choice simplified the development on a lightweight R interface working on all platforms.

Rtools is a toolchain bundle used for building R packages from source (those that need compilation of C/C++ or Fortran code) and for building R itself. Rtools usually consists of Msys2 build tools, GCC/MinGW-w64 compiler toolchain and libraries. These require slightly different steps to configure, so please follow the appropriate steps below.

All toolchains will require updating your PATH variable, See these instructions for details on changing the PATH if you are unfamiliar. The following instructions will assume that the default installation directory was used, so be sure to update the paths accordingly if you have chosen a different directory.

Configure RTools40

Download the installer and complete the prompts to install. Next, add the following lines to your PATH:

C:\rtools40\usr\bin
C:\rtools40\mingw64\bin

The C++ compiler is now available on your system. All the other dependencies can be installed by typing the following commands into Windows Command Prompt or Windows PowerShell:

pacman -Sy mingw-w64-x86_64-make
pacman -Sy mingw-w64-x86_64-cmake
pacman -Sy mingw-w64-x86_64-pkg-config

Configure RTools42 / RTools43

These two versions of RTools toolchain are quite similar. Of course, RTools43 offers newer version of the packages, but in both cases the installation and configuration is identical. Download either the RTools42 installer or the RTools43 installer and complete the prompts to install. Next, add the following lines to your PATH:

RTools42

C:\rtools42\x86_64-w64-mingw32.static.posix\bin
C:\rtools42\ucrt64\bin
C:\rtools42\usr\bin

RTools43

C:\rtools43\x86_64-w64-mingw32.static.posix\bin
C:\rtools43\ucrt64\bin
C:\rtools43\usr\bin

The C++ compiler is now available on your system. All the other dependencies can be installed by typing the following commands into into Windows Command Prompt or Windows PowerShell:

pacman -Sy mingw-w64-ucrt-x86_64-make
pacman -Sy mingw-w64-ucrt-x86_64-cmake
pacman -Sy mingw-w64-ucrt-x86_64-pkgconf

Important remarks :

  • Use the native Windows Command Prompt (or Windows PowerShell) to execute these commands. If PATH environment variable has been configured correctly, all requirements will be satisfied.
  • In order for bayesmix to be properly linked to Intel's TBB library, the absolute path to tbb must be added to the User PATH variable. This is done automatically during build but to make this change effective user need to close and open a new shell.

Build bayesmix

To install and use bayesmix, please cd to the folder to which you wish to install it, and clone this repository with the following command-line instruction:

git clone https://github.com/bayesmix-dev/bayesmix.git

Then, by using cd bayesmix, you will enter the newly downloaded folder.

To build the executable for the main file run_mcmc.cc, please use the following list of commands:

mkdir build
cd build
cmake .. -DDISABLE_TESTS=ON
make run_mcmc
cd ..

Remark: Configuring and compiling bayesmix for the first time will require several minutes, since cmake needs to provide and compile all the libraries on which bayesmix depends.

Finally, to compile unit tests, please use the following commands:

cd build
cmake .. -DDISABLE_TESTS=OFF
make test_bayesmix
cd ..

The corresponding executable is located at build/test/test_bayesmix.