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Source: INSTALL_FSBRAIN_FROM_SOURCE.md

Installing fsbrain from from source

Some platforms, like Linux, default to building fsbrain from source.

While fsbrain is written in plain R, some of its dependencies are written in C++, and building from source thus requires a compiler and the specific libraries required to build each dependency. These are known as system dependencies.

System dependencies

A system dependency is a non-R software that is needed for the installation of a package. System dependencies cannot be installed automatically using the R package system, so you need to install them manually or using the package manager of your operating system.

The fsbrain package itself does not have any system dependencies, however, it uses rgl for rendering. You can check the SystemRequirements section on the rgl page at CRAN for the full list of rgl dependencies or read on. To get GIFTI format support, you will also need libxml2-dev.

Note: If you use the scimesh backend, none of the rgl system dependencies are required — scimesh is a pure C++ software renderer with no external library dependencies beyond a C++ compiler.

To install the system dependencies for rgl and xml2:

Linux System dependencies (or: building from source)

R packages are compiled from source by default under Linux, so you need some development libraries. Before installing fsbrain, run the following command in your system shell (not in R):

  • for deb-based Linux distributions (Debian, Ubuntu, …):
sudo apt-get install build-essential cmake libmagick++-dev libx11-dev libgl1-mesa-dev libglu1-mesa-dev mesa-common-dev libfreetype6-dev libxml2-dev libssh-dev libcurl4-openssl-dev gfortran libblas-dev liblapack-dev libgfortran5

Note: For older Ubuntu versions, you may have to replace libgfortan5 in the command above with libgfortan4.

  • for rpm-based Linux distributions (Fedora, CentOS, RHEL, …):
sudo yum install ImageMagick-c++-devel libX11-devel mesa-libGLU-devel freetype-devel libxml2-devel

If you want to compile the package under any other operating system, you will need the libraries as well, of course.

MacOS System dependencies

Recent macOS versions do not ship with an X11 environment. If you want to use the default rgl backend for interactive viewing, you will need to install XQuartz. If you want to create GIF movies, make sure you have imagemagick installed (easiest via homebrew: brew install imagemagick@6).

Recommended for static image export: Use the scimesh backend, which requires neither X11 nor XQuartz and produces identical publication-ready images.

Note that X11 is not needed for rendering, but only for opening interactive windows. If you only need publication-quality static images (which is the typical use case), the scimesh backend or the browser-based rglwidget are better options.