Building the rSPDE package from source on Mac and Linux

David Bolin and Alexandre B. Simas

2023-01-18

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

Adjusting 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:

CC = clang
CXX = clang++

One should also confirm the location of the Eigen library. The default location is /usr/local/include/eigen3/ 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.