How to compile R packages without sudo?

An short description of the key steps

Published

October 31, 2021

Most of the time, if you are installing packages that are available on CRAN, the following command will do the trick.

install.packages(pkgs, type = "binary")

However, if you are installing packages that requires compiling, especially if needs specific compiling versions, and your default compiler is too old (gcc 4.8), and you see errors like lib/libstdc++.so.6: version GLIBCXX_3.4.20 not found. This post can hopefully help you.

Some headlines

Easy fix

Ask system admin for sudo, then do the following

sudo apt-get install libstdc++6

In case this still have not fixed your problem, you may need the following, (find out where your libstdc++.so.6 is, cd there)

sudo mv libstdc++.so.6 libstdc++.so.6.orig
sudo ln -s YOUR_NEW_lib64/libstdc++.so.6.SOME_MINOR_VERSION libstdc++.so.6

Will fix things most of the time. I have run into this problem a few times when having trouble installing stringi.

For reference, see this post.

Install gcc and compile R packages

See this previous post, you may want to use newer gcc such as gcc-11.2.0. Let’s say you have followed the instruction, and installed gcc-11.2.0 at YOUR_PATH. You can modify your Makevars file to configure some of the compiling flags.

Create ~/.R/Makevars with the following content

CC=YOUR_PATH/gcc-11.2.0/bin/gcc -std=gnu99
CXX=YOUR_PATH/gcc-11.2.0/bin/g++
CXX14=YOUR_PATH/gcc-11.2.0/bin/g++

Most likely you will need to recompile Rcpp after this step.

Static linking gcc

By default, R uses the following flags for compiling

CC = gcc -std=gnu99
CFLAGS = -g -O2

You want to add the following lines into your Makevars, replace YOUR_PATH

CXXFLAGS=-O0 -march=native -mtune=native
CXXFLAGS += -fPIC -flto -static-libgcc -static-libstdc++ -LYOUR_PATH/gcc-11.2.0/lib64

In the case you need c++14

Add the following lines

CXX14FLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -fPIC
CXX14FLAGS+=-flto -Wno-unused-local-typedefs -static-libgcc -static-libstdc++ -LYOUR_PATH/gcc-11.2.0/lib64

Add the following line to .bash_profile

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:YOUR_PATH/gcc-11.2.0/lib64

Static linking fortran

This doesn’t happen often, but when it does,

By default

FLIBS = -lgfortran -lm -lquadmath

You want to add the following lines into your Makevars, replace YOUR_PATH

FLIBS = -static-libgfortran -LYOUR_PATH/gcc-11.2.0/lib64/ -lm -lquadmath