requirements-r-colab.txt

ubuntu_packages <- c("libudunits2-dev", "libgdal-dev", "libgeos-dev", "libproj-dev")

cli::cli_alert_info("Installing ubuntu packages")

system(paste("sudo apt install", paste(ubuntu_packages, collapse = " ")))

cli::cli_alert_info("Installing R packages on CRAN")

# To install by system binaries put as a name
# e.g. "sudo apt install r-cran-dplyr" = "dplyr"
req_packages <- c(
  "sudo apt install r-cran-terra" = "terra",
  "sudo apt install r-cran-sf" = "sf",
  "sudo apt install r-cran-tidyverse" = "tidyverse",
  "sudo apt install r-cran-devtools" = "devtools",
  "sudo apt install r-cran-robis" = "robis",
  "sudo apt install r-cran-arrow" = "arrow",
  "sudo apt install r-cran-sfarrow" = "sfarrow",
  "sudo apt install r-cran-stars" = "stars",
  "sudo apt install r-cran-patchwork" = "patchwork"
  #,"BiocManager"
)

#bioconductor_packages <- c("ggtree", "ggtreeExtra", "phyloseq")

# Needed packages on GitHub
git_packages <- c("obistools", "biooracler")
git_packages_source <- c(
  "iobis/obistools",
  "bio-oracle/biooracler"
)

# Create a function to check if is installed
is_package_installed <- function(pkg) {
  requireNamespace(pkg, quietly = TRUE)
}

# Check which ones are not installed and install if needed:
for (i in 1:length(req_packages)) {
  if (!is_package_installed(req_packages[i])) {
    if (names(req_packages)[i] == "") {
        cli::cli_alert_info("Installing {cli::bg_cyan(req_packages[i])} by install.packages")
        install.packages(req_packages[i])
    } else {
        cli::cli_alert_info("Installing {cli::bg_cyan(req_packages[i])} by Ubuntu binaries")
        system(names(req_packages)[i])
    }
  } else {
    cli::cli_alert_success("{cli::bg_cyan(req_packages[i])} already installed.")
  }
}

cli::cli_alert_info("Installing R packages on GitHub")

# Check github packages
for (i in 1:length(git_packages)) {
  if (!is_package_installed(git_packages[i])) {
    cli::cli_alert_info("Installing {cli::bg_cyan(git_packages_source[i])} by devtools")
    devtools::install_github(git_packages_source[i])
  } else {
    cli::cli_alert_success("{cli::bg_cyan(git_packages_source[i])} already installed.")
  }
}

# # Check bioconductor packages
# for (i in 1:length(bioconductor_packages)) {
#   if (!is_package_installed(bioconductor_packages[i])) {
#     BiocManager::install(bioconductor_packages[i])
#   }
# }