Helpful packages and their dependencies to install with a fresh install of R

packages.R

#' ---
#' title: "Helpful packages and their dependencies to install with a fresh install of R"
#' author: Tom Palmer
#' date: 2020-03-27
#' ---

#' Tested on Ubuntu 18.04
if (Sys.info()["sysname"] == "Linux"){
  system('sudo apt-get install -y libcurl4-openssl-dev')
  system('sudo apt-get install -y libssl-dev')
  system('sudo apt-get install -y libfreetype6-dev')
  system('sudo apt-get install -y libmagick++-dev')
  system('sudo apt-get install -y cargo')
  system('sudo apt-get install -y libxml2-dev')
  system('sudo apt-get install -y xorg')
  system('sudo apt-get install -y libx11-dev')
  system('sudo apt-get install -y libglu1-mesa-dev')
  system('sudo apt-get install -y libatlas-base-dev')
  system('sudo apt-get install -y gfortran')
  system('sudo apt-get install -y libblas-dev')
  system('sudo apt-get install -y liblapack-dev')
  system('sudo apt install -y python-autopep8')
  system('sudo apt install -y libftgl2 libcgal-dev')
  system('sudo apt-get install -y libclang-dev libpq5')
}

install.packages(c('knitr', 'rmarkdown', 'bookdown', 'tidyverse', 'devtools', 'tinytex', 'pkgdown', 'remotes', 'markdown'), dependencies = TRUE)

remotes::install_github("MRCIEU/TwoSampleMR")

tinytex::install_tinytex()
tinytex::tlmgr_install("fira")

remotes::install_github("Hemken/Statamarkdown")

Run with (on Ubuntu I launch R with sudo R)

source("packages.R", echo = TRUE)

• Installing the knitr dependencies, e.g. the png package, is helpful to avoid problems with html output and png figures.