R/packages.R

In DHatziioanou/simpleepi: Simplifying functions to improve the ease and speed of basic epidemiological analysis

#' For a list of packages install missing ones and load them all.
#'
#'
#' @param packages vector of required package names
#' @param repo repository path (optional)
#' @param lib library path (optional)
#'
#' @param quiet True or False
#' @param ... Other packages
#'
#' @return Named packages installed and loaded
#'
#' @examples
#'
#' # install_load("data.table")
#' # install_load("data.table", "dplyr", "tidyr", "ggplot2")
#'
#' @export
install_load <- function(packages, ..., repo, lib, quiet)  {
  packages <- c(packages, ...)

  if (missing(repo)) {
    repo <- 'http://cran.rstudio.com/'
  }

  if (missing(lib)) {
    lib <- .libPaths()[1]
  }

  if (missing(quiet)) {
    quiet <- T
  }


  # Packages needing installed
  missing <- packages[!(packages %in% rownames(utils::installed.packages()))]

  # Add dependencies
  depend <- tools::package_dependencies(packages = packages, db = NULL,
                                        which = c("Depends", "Imports", "LinkingTo"),
                                        recursive = T, reverse = F, verbose = getOption("verbose"))
  depend <- unique(unlist(depend))
  missing <- c(depend[!(depend %in% rownames(utils::installed.packages()))], missing)

  # Install missing packages
  if (length(missing)  > 0) {
    message(paste("Please wait while",length(missing),"packages are installed..."))

    if (sum("devtools" %in% packages) > 0 & !("pkgbuild" %in% rownames(utils::installed.packages()))) {
      missing <- c("pkgbuild", "ps", missing)
    }

    for (package in missing) {
      if (!is.null(utils::sessionInfo()$otherPkgs)) lapply(paste('package:' ,names(utils::sessionInfo()$otherPkgs), sep = ""), detach,character.only = TRUE, unload = TRUE)

      t <- try(utils::install.packages(package, type = "source", dependencies = T, quiet = quiet, repos = repo, lib = lib))
      t2 <- try(if(inherits(t, "try-error")){
        utils::install.packages(package, type = "binary", dependencies = T, quiet = quiet, repos = repo, lib = lib)
        })

      if (!(package %in% rownames(utils::installed.packages()))) {
        if (!is.null(utils::sessionInfo()$otherPkgs)) lapply(paste('package:' ,names(utils::sessionInfo()$otherPkgs), sep = ""), detach,character.only = TRUE, unload = TRUE)
        utils::install.packages(package, type = "binary", dependencies = T, quiet = quiet, repos = repo, lib = lib)
      }
      if (package %in% rownames(utils::installed.packages())) message(paste(package, "installed")) else message(paste(package, "not installed"))
    }
  }

  missing <- packages[!(packages %in% rownames(utils::installed.packages()))]
  if ( length(missing) > 0) {
    message(paste("Packages not installed:"))
    print(missing)
    message("Try installing manually")
  }

  # Load packages
  for (package in packages) {

    # if package is installed locally, load
    if (package %in% rownames(utils::installed.packages()))
      t <- try( do.call('library', list(suppressPackageStartupMessages(package))))
    if (inherits(t, "try-error")) {
      utils::install.packages(package, type = "binary", dependencies = T, quiet = quiet, repos = repo, lib = lib)
      do.call('library', list(suppressPackageStartupMessages(package)))
    }
  }
  loaded_packages <- (.packages())
  message(sum(unique(loaded_packages) %in% packages), " packages out of ",length(unique(packages)), " loaded.")
  if(length(loaded_packages[!(packages %in% loaded_packages)]) >0){
    message("Not loaded:")
    print(loaded_packages[!(packages %in% loaded_packages)])
  }
}



#' Package replacement with specified version of package
#'
#' @param package  name of package
#' @param version  version to install
#' @param repo  Optional repository. Default is CRAN.
#' @param force Optional force replacement if package version already installed. Default is FALSE
#' @param upgrade Optional should package dependencies be upgraded? One of "default", "ask", "always", or "never".
#' @param ... Optional parameters from package remotes
#'
#' @return installs the desired package version
#'
#' @examples
#' # package_replace(package = "roxygen2", "7.1.2", force = TRUE)
#'
#' @export
package_replace <- function(package, version, repo ="https://cloud.r-project.org", force = FALSE, upgrade ="default", ...){
  p <- utils::installed.packages()
  package_found <- p[which(p[, "Package"] == package),]
  if(!is.na(package_found["Package"])) {
    if(package_found["Built"] == version & force == FALSE) {
      stop("version already installed")
    } else {
      utils::remove.packages(package)
    }
  }
  remotes::install_version(package = package, version = version, repos = repo, force = TRUE, upgrade = upgrade, ...)

}