Building the rSPDE package from source on Mac and Linux

Building from source

To build rSPDE from source you need to obtain the GitHub version. If you have all the dependencies (see below how to install some of them), you can install the rSPDE package from source by running the following command on R (for the development version):

remotes::install_github("davidbolin/rspde", ref = "devel-src")

or, if you want to install the stable version:

remotes::install_github("davidbolin/rspde", ref = "stable-src")

Dependencies on Linux

The rSPDE package depends on the Eigen C++ library.

To install Eigen on Ubuntu, run:

sudo apt install libeigen3-dev

To install Eigen on Arch-Linux or Manjaro, run:

sudo pacman -S eigen3

To install Eigen on Red Hat, Fedor or CentOS, run:

sudo yum install eigen3-devel

To install Eigen on OpenSuse, run:

sudo zypper install eigen3-devel

Dependencies on Mac

We can install Eigen on MacOS with Homebrew.

To install Homebrew, run:

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

To install Eigen using Homebrew, run:

brew install eigen

Finally, if after installing eigen with brew it gives you an error that it cannot find eigen library, you can create a symbolic link to eigen’s path as:

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

You also need to create the following symbolic links related to homebrew:

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

Finally, you need to install gcc-14:

brew install gcc@14

and also create the symbolic links associated to gcc:

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

Adjusting the Makefile

If you experience trouble while installing the rSPDE package, you might need to adjust the Makefile. Before that, you will need to have rSPDE source files locally on your computer. To such an end, you can, for instance, close the rSPDE repository by running the following command on a terminal:

git clone https://github.com/davidbolin/rSPDE.git

You can also download the source files.

Now, let us discuss the Makefile. The Makefile has the following base form:

toInclude = ${R_LIBRARY_DIR}/INLA/include/

obj = cgeneric_mvnormdens.o cgeneric_aux_nonstat.o cgeneric_aux_nonstat_fixed.o \
      cgeneric_rspde_stat_frac_model.o cgeneric_rspde_nonstat_general.o \
      cgeneric_rspde_stat_general.o cgeneric_rspde_stat_parsim_gen.o \
      cgeneric_rspde_stat_parsim_fixed.o cgeneric_rspde_stat_int.o \
      cgeneric_rspde_nonstat_gen_fixed.o cgeneric_rspde_nonstat_int.o \
      cgeneric_aux_nonstat_int.o

all : rSPDE.so

CC = clang
CXX = clang++

EIGEN_MAC = /usr/local/include/eigen3/
EIGEN_LINUX = /usr/include/eigen3/

flags = -O2 -Wall -Wextra -fpic

%.o: %.c
    $(CC) $(flags) -Iinclude -I$(toInclude)  -c $^ -o $@

%.o: %.cpp
    $(CXX) $(flags)  -I$(toInclude) -I$(EIGEN_MAC) -I$(EIGEN_LINUX) -c $^ -o $@

rSPDE.so: $(obj)
    $(CXX) -shared *.o -o ../inst/shared/rspde_cgeneric_models.so -lblas -llapack

clean :
    rm -f *.o

.PHONY: all clean

Adjusts on Linux

For linux, we recommend to use the gcc-12 and g++-12 compilers. To this end, one must install gcc and g++, then change the following lines on the Makefile:

CC = gcc
CXX = g++

One should also confirm the location of the Eigen library. The default location is /usr/include/eigen3/ and is already set at the Makefile. If you have Eigen installed in a different location, you will need to update the Makefile by changing the EIGEN_LINUX variable:

EIGEN_LINUX = /correct_path/

To install gcc and g++ on Ubuntu, run

sudo apt install gcc g++

To install gcc and g++ on Arch-Linux or Manjaro, run:

sudo pacman -S gcc g++

To install gcc and g++ on Red Hat, Fedor or CentOS, run:

sudo yum install gcc g++

To install gcc and g++ on OpenSuse, run:

sudo zypper install gcc g++

Adjusts on Mac

For Mac, especially with intel processors, we found the most stable compiler to be clang and clang++. Thus, one must have the following lines on the Makefile:

One should also confirm the location of the Eigen library. The default location is /usr/local and is already set at the Makefile.

If you installed Eigen using Homebrew, you can check the location of the Eigen installation by using the following command:

brew --prefix eigen

You can, then, update the EIGEN_MAC variable in the Makefile with the correct path.

David Bolin and Alexandre B. Simas