install R package ubuntu.R

options("repos" = c("CRAN" = "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"))
install.packages("pak")

# List of R packages to install
to_install <- readLines("all-pkgs.txt")

# copy of purrrs safely function for system requirements. 
# this way we can capture errors associated with packages that
# wont be in paks database
capture_error <- function (code, otherwise = NULL, quiet = TRUE) {
  tryCatch(list(result = code, error = NULL), error = function(e) {
    if (!quiet) 
      message("Error: ", e$message)
    list(result = otherwise, error = e)
  }, interrupt = function(e) {
    stop("Terminated by user", call. = FALSE)
  })
}

safely <- function(.f, otherwise = NULL, quiet = TRUE) {
  function(...) capture_error(.f(...), otherwise, quiet) 
}

safe_sysreqs <- safely(pak::pkg_system_requirements)

# find package system requirements
sysreqs <- lapply(to_install, safe_sysreqs)
# find only the unique system requirements
sysreq_cmds <- unique(unlist(lapply(sysreqs, function(x) x[["result"]])))

# write to bash file
writeLines(c(
             "#!/bin/bash", # make executable
              # install build-essential first
              "sudo apt-get install build-essential", 
              sysreq_cmds, # then add the requirements
              ""), # add empty line at the end
           "install-sysreqs.sh")

# install sysdeps
system("./install-sysreqs.sh")

# install all packages
install.packages(to_install, dependencies = TRUE)