Install

• The best option is to use docker

Run

• Run docker: docker-compose up -d
• SSH to container to run R console: docker exec -ti dat246_rlang /bin/bash
• Run R statement from cmdline: Rscript -e 'sessionInfo()'
• Run R script from cmd line (inside directory scripts/): Rscript first.r
  • Hint: copy src/first.r and src/second.r to directory scripts/
• Run R console: R

Dockerize

• CD to directory scripts : cd /Users/ali/projects/uni/dat246/rlang

• docker run -ti -v $(pwd)/scripts:/app/scripts -w /app/scripts r-base /bin/bash

• apt update

• apt install software-properties-common -y

• apt install gpg-agent -y

• apt install python3-launchpadlib -y

• add-apt-repository ppa:marutter/rrutter4.0 -y

• add-apt-repository ppa:c2d4u.team/c2d4u4.0+ -y

• apt install libcurl4-openssl-dev -y

• apt install r-base r-base-dev libcurl4-openssl-dev -y

• apt install libxml2-dev -y

• apt install libharfbuzz-dev libfribidi-dev -y

• apt -y install libfontconfig1-dev -y

• apt install cmake -y

• apt install libgit2-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y

• apt install r-cran-rstan -y

• R

  Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1)
  install.packages("rstan")

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (!file.exists(M)) file.create(M)
cat("\nCXX17FLAGS=-O3 -march=native -mtune=native -fPIC",
    "CXX17=g++", # or clang++ but you may need a version postfix
    file = M, sep = "\n", append = TRUE)

Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1)
install.packages("V8")

• install.packages("xml2", dependencies = TRUE)
• install.packages(c("coda","mvtnorm","devtools","loo","dagitty","shape"))
• install.packages('BH')
• devtools::install_github("stan-dev/cmdstanr") -> 1
• cmdstanr::install_cmdstan()
• devtools::install_github("rmcelreath/rethinking")
• library(rethinking)
• library(rstan)
• sessionInfo()
• https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started#how-to-use-rstan
• https://www.datamentor.io/r-programming/saving-plot

Troubleshooting

• Error: List directory /var/lib/apt/lists/partial is missing. - Acquire (2: No such file or directory)
  • mkdir -p /var/lib/apt/lists/partial
• Error: install.packages('BH')
  • Install packege in R: install.packages('BH')
  • Relaunch R