install_packages.R

cat("Installing packages...\n")
Sys.sleep(1)

install.packages("common")
req_file <- common::file.find(pattern = "req.txt")

# Read text file containing required packages
if(!file.exists(req_file)) {
  warning(req_file, "was not found. No packages installed or checked.")
  return()
}

req <- scan(req_file, character(), quiet = TRUE)

# Install missing packages
if (length(req) > 0) {
  missing_packages <- req[!(req %in% installed.packages()[,"Package"])]
  if (length(missing_packages) > 0) {
    cat("Number of packages to install: ", length(missing_packages), "\n")
    pak::pkg_install(missing_packages, ask = FALSE)
  }
}

# Load packages
suppressPackageStartupMessages(invisible(lapply(req, library, character.only = TRUE)))

# options
options(dplyr.summarise.inform = FALSE)

# special case for packages not on CRAN
if (!require("MALDIcellassay", character.only = TRUE)) {
  pak::pkg_install("CeMOS-Mannheim/MALDIcellassay")

  library(MALDIcellassay, character.only = TRUE)
}