Installation of CAIBIrnaseq

This guide explains how to install the CAIBIrnaseq package from GitHub, including required dependencies and system setup.

System setup

R version

This package is available for R version above the 4.1.0. Verify your version with :

version

System dependencies

For some systems, there are command lines to run in the Terminal so that the system has all the dependencies to install correctly the package.

Linux Ubuntu/Debian

# Upgrade of the system
sudo apt update && sudo apt upgrade -y

# System dependencies
sudo apt install -y r-base r-base-dev libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev build-essential zlib1g-dev pandoc git

MacOS

# If not already done, install Homebrew
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# System dependencies 
brew install libgit2 pkg-config freetype harfbuzz fribidi libpng libtiff jpeg pandoc git

Windows

For Windows, you must only install Rtools (https://cran.r-project.org/bin/windows/Rtools/). Then, restart Rstudio and verify Rtools is installed :

# In R Console
pkgbuild::has_build_tools(debug = TRUE)

Packages to install before CAIBIrnaseq

To install the CAIBIrnaseq package from GitHub, you have to install 2 basic packages:

# If not already installed
install.packages("devtools")
install.packages("BiocManager")

devtools will allows us to install the package from Github BiocManager to install the Bioconductor dependencies.

Now, you are ready to install the package ! Just run this line :

# Installation from Github : 
devtools::install_github("crcordeliers/CAIBIrnaseq", dependencies = TRUE)

There is a lot of packages, so the installation might take a bit of time…

When you are done, verify that the package is installed correctly :

library(CAIBIrnaseq)

If you do not encounter any errors, you’re DONE !

Hope this package will help you in your projects !!!

Issues

As there is a lot of packages, you could encounter some difficulties to install the package. Normally, the installation of devtools and BiocManager should be enough, but if you have missing packages, do not hesitate to install manually the missing ones.

You might have difficulties with DESeq2 and SummarizedExperiment packages. Just try running these command lines :

# Manual installation
BiocManager::install("DESeq2")
BiocManager::install("SummarizedExperiment")

If the errors persist, check that you have all system dependencies and write permissions in the folder where the libraries are installed.