Building the rSPDE package from source on Mac and Linux

Overview

Starting with this release of rSPDE, the C/C++ cgeneric sources used by INLA live on a single branch (devel) together with the R code, and compilation is opt-in. The default install — including the CRAN release and the regular GitHub install — is pure R and requires no compiler.

When you opt in, the configure script copies the sources from inst/src-optional/ into src/ and then R CMD INSTALL builds inst/shared/rspde_cgeneric_models.so (or .dll on Windows). At runtime rSPDE detects this shared object and uses it directly; otherwise it falls back to the shared object that ships with INLA. The legacy devel-src and stable-src branches are deprecated.

Asking for the compiled build

Pick one of the following — both have the same effect:

# Via configure args
remotes::install_github(
  "davidbolin/rSPDE",
  ref = "devel",
  configure.args = "--enable-compiled"
)

# Via an environment variable
withr::with_envvar(
  c(RSPDE_COMPILE = "1"),
  remotes::install_github("davidbolin/rSPDE", ref = "devel")
)

Without the flag (or RSPDE_COMPILE=1), configure writes a no-op Makevars and the install stays pure R.

If you have already cloned the repository and want to build locally:

git clone https://github.com/davidbolin/rSPDE.git
cd rSPDE
RSPDE_COMPILE=1 R CMD INSTALL .

You can verify the compiled path is active from R with:

getOption("rspde.compiled")  # TRUE when the local shared object is loaded

Toolchain prerequisites

The Makefile shipped in inst/src-optional/ is the same one that used to live on devel-src. It expects:

Eigen headers (the cgeneric C++ helpers #include <Eigen/...>),
gcc-14 / g++-14 (Homebrew on macOS, distro packages on Linux),
BLAS / LAPACK (linked via -lblas -llapack),
on macOS, the Homebrew prefix exposed at the symlinked locations /usr/local/brewlib and /usr/local/brewinclude.

Linux

Install Eigen:

sudo apt install libeigen3-dev          # Debian / Ubuntu
sudo pacman -S eigen                    # Arch / Manjaro
sudo yum install eigen3-devel           # RHEL / Fedora / CentOS
sudo zypper install eigen3-devel        # openSUSE

Install gcc-14 / g++-14 (or the most recent gcc available; the Makefile defaults to gcc-14):

sudo apt install gcc-14 g++-14          # Debian / Ubuntu
sudo pacman -S gcc                      # Arch / Manjaro
sudo dnf install gcc gcc-c++            # Fedora
sudo zypper install gcc gcc-c++         # openSUSE

If your gcc is not at /opt/homebrew/bin/gcc-14, edit the CC / CXX lines in inst/src-optional/Makefile (or in src/Makefile after running configure --enable-compiled) before running R CMD INSTALL. The Makefile auto-detects Linux and emits the correct architecture flags.

macOS

Install Homebrew:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install Eigen, gcc@14, and the Homebrew copies of BLAS/LAPACK that the package links against:

brew install eigen
brew install gcc@14

If eigen is not picked up automatically, create the symlinks the Makefile looks for:

sudo ln -s $(brew --prefix eigen)/include/eigen3 /usr/local/include/eigen3
sudo ln -s $(brew --prefix)/lib /usr/local/brewlib
sudo ln -s $(brew --prefix)/include /usr/local/brewinclude

The Makefile sets CC = /opt/homebrew/bin/gcc-14 and CXX = /opt/homebrew/bin/g++-14. On Apple Silicon (Homebrew under /opt/homebrew) the path is correct out of the box. On Intel Macs (Homebrew under /usr/local) either edit those two lines to point at your gcc-14 binary, or expose a symlink:

sudo ln -s $(brew --prefix gcc@14)/bin/gcc-14 /opt/homebrew/bin/gcc-14
sudo ln -s $(brew --prefix gcc@14)/bin/g++-14 /opt/homebrew/bin/g++-14

The Makefile also codesigns the produced .so ad-hoc, which is required by the macOS dynamic linker on macOS 26+.

Inspecting and adjusting the Makefile

The Makefile shipped in inst/src-optional/ is reproduced (truncated) below. After running ./configure --enable-compiled you will find the same file in src/, where any tweaks for an unusual environment should be made before running R CMD INSTALL .:

toInclude = $(R_LIBRARY_DIR)/INLA/include/
PKG_CFLAGS = -I$(R_HOME)/include

CC  = /opt/homebrew/bin/gcc-14
CXX = /opt/homebrew/bin/g++-14

EIGEN_MAC     = /opt/homebrew/
EIGEN_MAC_VAR = /usr/local
EIGEN_LINUX   = /usr
MAC_LIB       = /usr/local/brewlib
MAC_INCLUDE   = /usr/local/brewinclude

# --- platform-specific flags follow; see the file for the full content ---

Most users only need to update CC / CXX (if gcc-14 lives elsewhere) and the Eigen / Homebrew paths. The first time you build, the Makefile will fetch cgeneric.h from the upstream r-inla repository if it is not already present in ${R_LIBRARY_DIR}/INLA/include/.

Windows

The Makefile is not maintained for Windows. Windows users should stick with the default pure-R install (remotes::install_github("davidbolin/rSPDE", ref = "devel")), which delegates the cgeneric implementation to the shared object that ships with INLA.

David Bolin and Alexandre B. Simas