Installing monocle3

Table of Contents

In this short post I will demonstrate how to install package monocle3 in R on your macOS. If you are using default compilers provided by Apple, you might have encounter some errors like

clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [leidenbase.so] Error 1 ERROR: compilation failed for package ‘leidenbase’

ERROR: compilation failed for package ‘leidenbase’ ...

Solution #

To solve this issue you first have to update your current gcc compiler as well as installing llvm. The problem is that macOS does not come with gFortran package which is required by sub-package leidenbase. In this case I recommend installing/upgrading the packages using brew illustrated below.

brew install gcc llvm
# copy and paste the code in your shell to enable llvm

Secondly, now we have to tell R to use these packages by updating ~/.R/Makevars path. If you do not have .R folder in your home directory, you can create it by running mkdir ~\.R.

Before changing the variables you have to verify which gcc version have you installed. You can do so by running gcc-<TAB>. The example below shows how to setup the variables for gcc-9.

vim ~/.R/Makevars
# Copy and paste the code below.
VER=-9
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/9.2.0/lib/gcc/9/

# Restart R

Good job, now restart R and run the monocle3 installation again.

BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
                       'limma', 'S4Vectors', 'SingleCellExperiment',
                       'SummarizedExperiment'))
devtools::install_github('cole-trapnell-lab/leidenbase')
devtools::install_github('cole-trapnell-lab/monocle3')

Solution #

Resources #