deps.R

#' Find all dependencies of a CRAN or dev package.
#'
#' Find all the dependencies of a package and determine whether they are ahead
#' or behind CRAN. A `print()` method identifies mismatches (if any)
#' between local and CRAN versions of each dependent package; an
#' `update()` method installs outdated or missing packages from CRAN.
#'
#' @param packages A character vector of package names.
#' @param pkgdir Path to a package directory, or to a package tarball.
#' @param dependencies Which dependencies do you want to check?
#'   Can be a character vector (selecting from "Depends", "Imports",
#'    "LinkingTo", "Suggests", or "Enhances"), or a logical vector.
#'
#'   `TRUE` is shorthand for "Depends", "Imports", "LinkingTo" and
#'   "Suggests". `NA` is shorthand for "Depends", "Imports" and "LinkingTo"
#'   and is the default. `FALSE` is shorthand for no dependencies (i.e.
#'   just check this package, not its dependencies).
#'
#'   The value "soft" means the same as `TRUE`, "hard" means the same as `NA`.
#'
#'   You can also specify dependencies from one or more additional fields,
#'   common ones include:
#'   - Config/Needs/website - for dependencies used in building the pkgdown site.
#'   - Config/Needs/coverage for dependencies used in calculating test coverage.
#' @param quiet If `TRUE`, suppress output.
#' @param upgrade Should package dependencies be upgraded? One of "default", "ask", "always", or "never". "default"
#'   respects the value of the `R_REMOTES_UPGRADE` environment variable if set,
#'   and falls back to "ask" if unset. "ask" prompts the user for which out of
#'   date packages to upgrade. For non-interactive sessions "ask" is equivalent
#'   to "always". `TRUE` and `FALSE` are also accepted and correspond to
#'   "always" and "never" respectively.
#' @param repos A character vector giving repositories to use.
#' @param type Type of package to `update`.
#' @param remote_precedence A logical flag specifying whether remote sources should take precedence over
#'   CRAN when both were found.
#' @param additional_repositories A logical flag specifying whether `Additional_repositories` should
#'   be extracted from the DESCRIPTION and appended to `repos`.
#' @param object A `package_deps` object.
#' @param ... Additional arguments passed to `install_packages`.
#' @inheritParams install_github
#'
#' @return
#'
#' A `data.frame` with columns:
#'
#' \tabular{ll}{
#' `package` \tab The dependent package's name,\cr
#' `installed` \tab The currently installed version,\cr
#' `available` \tab The version available on CRAN,\cr
#' `diff` \tab An integer denoting whether the locally installed version
#'   of the package is newer (1), the same (0) or older (-1) than the version
#'   currently available on CRAN.\cr
#' }
#'
#' @export
#' @examples
#' \dontrun{
#' package_deps("devtools")
#' # Use update to update any out-of-date dependencies
#' update(package_deps("devtools"))
#' }

package_deps <- function(packages, dependencies = NA,
                         repos = getOption("repos"),
                         type = getOption("pkgType")) {

  repos <- fix_repositories(repos)
  cran <- available_packages(repos, type)

  deps <- find_deps(packages, available = cran, top_dep = dependencies)

  # Remove base packages
  inst <- utils::installed.packages()
  base <- unname(inst[inst[, "Priority"] %in% c("base", "recommended"), "Package"])
  deps <- setdiff(deps, base)

  # get remote types
  remote <- structure(lapply(deps, package2remote, repos = repos, type = type), class = "remotes")

  inst_ver <- vapply(deps, local_sha, character(1))
  cran_ver <- vapply(remote, function(x) remote_sha(x), character(1))
  is_cran_remote <- vapply(remote, inherits, logical(1), "cran_remote")

  diff <- compare_versions(inst_ver, cran_ver, is_cran_remote)

  res <- structure(
    data.frame(
      package = deps,
      installed = inst_ver,
      available = cran_ver,
      diff = diff,
      is_cran = is_cran_remote,
      stringsAsFactors = FALSE
    ),
    class = c("package_deps", "data.frame")
  )

  res$remote <- remote

  res
}

#' `local_package_deps` extracts dependencies from a
#' local DESCRIPTION file.
#'
#' @export
#' @rdname package_deps

local_package_deps <- function(pkgdir = ".", dependencies = NA) {
  pkg <- load_pkg_description(pkgdir)

  dependencies <- tolower(standardise_dep(dependencies))
  dependencies <- intersect(dependencies, names(pkg))

  parsed <- lapply(pkg[tolower(dependencies)], parse_deps)
  unlist(lapply(parsed, `[[`, "name"), use.names = FALSE)
}

#' `dev_package_deps` lists the status of the dependencies
#' of a local package.
#'
#' @export
#' @rdname package_deps

dev_package_deps <- function(pkgdir = ".", dependencies = NA,
                             repos = getOption("repos"),
                             type = getOption("pkgType"),
                             remote_precedence = TRUE,
                             additional_repositories = TRUE) {

  pkg <- load_pkg_description(pkgdir)
  repos <- c(repos, if (additional_repositories) parse_additional_repositories(pkg))

  deps <- local_package_deps(pkgdir = pkgdir, dependencies = dependencies)

  if (is_bioconductor(pkg)) {
    bioc_repos <- bioc_install_repos()

    missing_repos <- setdiff(names(bioc_repos), names(repos))

    if (length(missing_repos) > 0)
      repos[missing_repos] <- bioc_repos[missing_repos]
  }

  cran_deps <- package_deps(deps, repos = repos, type = type)

  res <- combine_remote_deps(cran_deps, extra_deps(pkg, "remotes"), remote_precedence)

  res <- do.call(rbind, c(list(res), lapply(get_extra_deps(pkg, dependencies), extra_deps, pkg = pkg), stringsAsFactors = FALSE))

  res[is.na(res$package) | !duplicated(res$package, fromLast = TRUE), ]
}

combine_remote_deps <- function(cran_deps, remote_deps, remote_precedence) {
  # If there are no dependencies there will be no remote dependencies either,
  # so just return them (and don't force the remote_deps promise)
  if (nrow(cran_deps) == 0) {
    return(cran_deps)
  }

  # Only keep the remotes that are specified in the cran_deps or are NA
  remote_deps <- remote_deps[is.na(remote_deps$package) | remote_deps$package %in% cran_deps$package, ]

  # If there are remote deps remove the equivalent CRAN deps
  if (remote_precedence) {
    cran_deps <- cran_deps[!(cran_deps$package %in% remote_deps$package), ]
  # Otherwise remove remotes already covered by CRAN
  } else {
    remote_deps <- remote_deps[!(remote_deps$package %in% cran_deps$package), ]
  }
  

  rbind(remote_deps, cran_deps)
}

## -2 = not installed, but available on CRAN
## -1 = installed, but out of date
##  0 = installed, most recent version
##  1 = installed, version ahead of CRAN
##  2 = package not on CRAN

compare_versions <- function(inst, remote, is_cran) {
  stopifnot(length(inst) == length(remote) && length(inst) == length(is_cran))

  compare_var <- function(i, c, cran) {
    if (!cran) {
      if (identical(i, c)) {
        return(CURRENT)
      } else {
        return(BEHIND)
      }
    }
    if (is.na(c)) return(UNAVAILABLE)           # not on CRAN
    if (is.na(i)) return(UNINSTALLED)           # not installed, but on CRAN

    i <- package_version(i)
    c <- package_version(c)

    if (i < c) {
      BEHIND                               # out of date
    } else if (i > c) {
      AHEAD                                # ahead of CRAN
    } else {
      CURRENT                              # most recent CRAN version
    }
  }

  vapply(seq_along(inst),
    function(i) compare_var(inst[[i]], remote[[i]], is_cran[[i]]),
    integer(1))
}

has_extra_deps <- function(pkg, dependencies) {
  any(dependencies %in% names(pkg))
}

get_extra_deps <- function(pkg, dependencies) {
  dependencies <- tolower(dependencies)

  dependencies <- intersect(dependencies, names(pkg))

  #remove standard dependencies
  setdiff(dependencies, tolower(standardise_dep(c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"))))
}

#' @export
print.package_deps <- function(x, show_ok = FALSE, ...) {
  class(x) <- "data.frame"
  x$remote <-lapply(x$remote, format)

  ahead <- x$diff > 0L
  behind <- x$diff < 0L
  same_ver <- x$diff == 0L

  x$diff <- NULL
  x[] <- lapply(x, format_str, width = 12)

  if (any(behind)) {
    cat("Needs update -----------------------------\n")
    print(x[behind, , drop = FALSE], row.names = FALSE, right = FALSE)
  }

  if (any(ahead)) {
    cat("Not on CRAN ----------------------------\n")
    print(x[ahead, , drop = FALSE], row.names = FALSE, right = FALSE)
  }

  if (show_ok && any(same_ver)) {
    cat("OK ---------------------------------------\n")
    print(x[same_ver, , drop = FALSE], row.names = FALSE, right = FALSE)
  }
}

## -2 = not installed, but available on CRAN
## -1 = installed, but out of date
##  0 = installed, most recent version
##  1 = installed, version ahead of CRAN
##  2 = package not on CRAN

UNINSTALLED <- -2L
BEHIND <- -1L
CURRENT <- 0L
AHEAD <- 1L
UNAVAILABLE <- 2L

#' @export
#' @rdname package_deps
#' @importFrom stats update

update.package_deps <- function(object,
                           dependencies = NA,
                           upgrade = c("default", "ask", "always", "never"),
                           force = FALSE,
                           quiet = FALSE,
                           build = TRUE, build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"),
                           build_manual = FALSE, build_vignettes = FALSE,
                           repos = getOption("repos"),
                           type = getOption("pkgType"),
                           ...) {

  dependencies <- standardise_dep(dependencies)

  object <- upgradable_packages(object, upgrade, quiet)

  unavailable_on_cran <- object$diff == UNAVAILABLE & object$is_cran

  unknown_remotes <- (object$diff == UNAVAILABLE | object$diff == UNINSTALLED) & !object$is_cran

  if (any(unavailable_on_cran) && !quiet) {
    message("Skipping ", sum(unavailable_on_cran), " packages not available: ",
      paste(object$package[unavailable_on_cran], collapse = ", "))
  }

  if (any(unknown_remotes)) {
    install_remotes(object$remote[unknown_remotes],
                    dependencies = dependencies,
                    upgrade = upgrade,
                    force = force,
                    quiet = quiet,
                    build = build,
                    build_opts = build_opts,
                    build_manual = build_manual,
                    build_vignettes = build_vignettes,
                    repos = repos,
                    type = type,
                    ...)
  }

  ahead_of_cran <- object$diff == AHEAD & object$is_cran
  if (any(ahead_of_cran) && !quiet) {
    message("Skipping ", sum(ahead_of_cran), " packages ahead of CRAN: ",
      paste(object$package[ahead_of_cran], collapse = ", "))
  }

  ahead_remotes <- object$diff == AHEAD & !object$is_cran
  if (any(ahead_remotes)) {
    install_remotes(object$remote[ahead_remotes],
                    dependencies = dependencies,
                    upgrade = upgrade,
                    force = force,
                    quiet = quiet,
                    build = build,
                    build_opts = build_opts,
                    build_manual = build_manual,
                    build_vignettes = build_vignettes,
                    repos = repos,
                    type = type,
                    ...)
  }

  behind <- is.na(object$installed) | object$diff < CURRENT

  if (any(object$is_cran & !unavailable_on_cran & behind)) {
    # get the first cran-like remote and use its repos and pkg_type
    r <- object$remote[object$is_cran & behind][[1]]
    install_packages(object$package[object$is_cran & behind], repos = r$repos,
      type = r$pkg_type, dependencies = dependencies, quiet = quiet, ...)
  }

  install_remotes(object$remote[!object$is_cran & behind],
                  dependencies = dependencies,
                  upgrade = upgrade,
                  force = force,
                  quiet = quiet,
                  build = build,
                  build_opts = build_opts,
                  build_manual = build_manual,
                  build_vignettes = build_vignettes,
                  repos = repos,
                  type = type,
                  ...)

  invisible()
}

install_packages <- function(packages, repos = getOption("repos"),
                             type = getOption("pkgType"), ...,
                             dependencies = FALSE, quiet = NULL) {

  # We want to pass only args that exist in the downstream functions
  args_to_keep <-
    unique(
      names(
        c(
          formals(utils::install.packages),
          formals(utils::download.file)
        )
      )
    )

  args <- list(...)
  args <- args[names(args) %in% args_to_keep]

  if (is.null(quiet))
    quiet <- !identical(type, "source")

  message("Installing ", length(packages), " packages: ",
    paste(packages, collapse = ", "))

  do.call(
    safe_install_packages,
    c(list(
        packages,
        repos = repos,
        type = type,
        dependencies = dependencies,
        quiet = quiet
      ),
      args
    )
  )
}

find_deps <- function(packages, available = available_packages(),
                      top_dep = TRUE, rec_dep = NA, include_pkgs = TRUE) {
  if (length(packages) == 0 || identical(top_dep, FALSE))
    return(character())

  top_dep <- standardise_dep(top_dep)
  rec_dep <- standardise_dep(rec_dep)

  top <- tools::package_dependencies(packages, db = available, which = top_dep)
  top_flat <- unlist(top, use.names = FALSE)

  if (length(rec_dep) != 0 && length(top_flat) > 0) {
    rec <- tools::package_dependencies(top_flat, db = available, which = rec_dep,
      recursive = TRUE)
    rec_flat <- unlist(rec, use.names = FALSE)
  } else {
    rec_flat <- character()
  }

  # We need to return these in reverse order, so that the packages furthest
  # down in the tree are installed first.
  unique(rev(c(if (include_pkgs) packages, top_flat, rec_flat)))
}

#' Standardise dependencies using the same logical as [install.packages]
#'
#' @param x The dependencies to standardise.
#'   A character vector (selecting from "Depends", "Imports",
#'    "LinkingTo", "Suggests", or "Enhances"), or a logical vector.
#'
#'   `TRUE` is shorthand for "Depends", "Imports", "LinkingTo" and
#'   "Suggests". `NA` is shorthand for "Depends", "Imports" and "LinkingTo"
#'   and is the default. `FALSE` is shorthand for no dependencies.
#'
#'   The value "soft" means the same as `TRUE`, "hard" means the same as `NA`.
#'
#'   Any additional values that don't match one of the standard dependency
#'   types are filtered out.
#'
#' @seealso <https://r-pkgs.org/description.html> for
#' additional information on what each dependency type means.
#' @keywords internal
#' @export
standardise_dep <- function(x) {
  if (identical(x, NA)) {
    c("Depends", "Imports", "LinkingTo")
  } else if (isTRUE(x)) {
    c("Depends", "Imports", "LinkingTo", "Suggests")
  } else if (identical(x, FALSE)) {
    character(0)
  } else if (is.character(x)) {
    if (any(x == "hard")) {
      c("Depends", "Imports", "LinkingTo")
    } else if (any(x == "soft")) {
      c("Depends", "Imports", "LinkingTo", "Suggests")
    } else {
      intersect(x, c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"))
    }
  } else {
    stop("Dependencies must be a boolean or a character vector", call. = FALSE)
  }
}

#' Update packages that are missing or out-of-date.
#'
#' Works similarly to [utils::install.packages()] but doesn't install packages
#' that are already installed, and also upgrades out dated dependencies.
#'
#' @param packages Character vector of packages to update.
#' @param force Deprecated, this argument has no effect.
#' @inheritParams install_github
#' @seealso [package_deps()] to see which packages are out of date/
#'   missing.
#' @export
#' @examples
#' \dontrun{
#' update_packages("ggplot2")
#' update_packages(c("plyr", "ggplot2"))
#' }

update_packages <- function(packages = TRUE,
                            dependencies = NA,
                            upgrade = c("default", "ask", "always", "never"),
                            force = FALSE,
                            quiet = FALSE,
                            build = TRUE, build_opts = c("--no-resave-data", "--no-manual", "--no-build-vignettes"),
                            build_manual = FALSE, build_vignettes = FALSE,
                            repos = getOption("repos"),
                            type = getOption("pkgType"),
                            ...) {

  if (isTRUE(force)) {
    .Deprecated(msg = "`update_packages(force = TRUE)` is deprecated and has no effect.")
  }

  if (isTRUE(packages)) {
    packages <- utils::installed.packages()[, "Package"]
  }

  pkgs <- package_deps(packages, repos = repos, type = type)
  update(pkgs,
         dependencies = dependencies,
         upgrade = upgrade,
         force = FALSE,
         quiet = quiet,
         build = build,
         build_opts = build_opts,
         build_manual = build_manual,
         build_vignettes = build_vignettes,
         repos = repos,
         type = type,
         ...)
}

has_additional_repositories <- function(pkg) {
  "additional_repositories" %in% names(pkg)
}

parse_additional_repositories <- function(pkg) {
  if (has_additional_repositories(pkg)) {

    strsplit(trim_ws(pkg[["additional_repositories"]]), "[,[:space:]]+")[[1]]
  }
}

fix_repositories <- function(repos) {
  if (length(repos) == 0)
    repos <- character()

  # Override any existing default values with the cloud mirror
  # Reason: A "@CRAN@" value would open a GUI for choosing a mirror
  repos[repos == "@CRAN@"] <- download_url("cloud.r-project.org")
  repos
}

parse_one_extra <- function(x, ...) {
  pieces <- strsplit(x, "::", fixed = TRUE)[[1]]

  if (length(pieces) == 1) {
    if (!grepl("/", pieces)) {
      type <- "cran"
    } else {
      type <- "github"
    }
    repo <- pieces
  } else if (length(pieces) == 2) {
    type <- pieces[1]
    repo <- pieces[2]
  } else {
    stop("Malformed remote specification '", x, "'", call. = FALSE)
  }

  type = sub("^[.a-zA-Z0-9]+=", "", type)

  if (grepl("@", type)) {
    # Custom host
    tah <- strsplit(type, "@", fixed = TRUE)[[1]]
    type <- tah[1]
    host <- tah[2]
  } else {
    host <- NULL
  }

  tryCatch({
    # We need to use `environment(sys.function())` instead of
    # `asNamespace("remotes")` because when used as a script in
    # install-github.R there is no remotes namespace.

    fun <- get(paste0(tolower(type), "_remote"), mode = "function", inherits = TRUE)

    if (!is.null(host)) {
      res <- fun(repo, host = host, ...)
    } else {
      res <- fun(repo, ...)
    }
    }, error = function(e) stop("Unknown remote type: ", type, "\n  ", conditionMessage(e), call. = FALSE)
  )
  res
}

split_extra_deps <- function(x, name = "Remotes") {
  pkgs <- trim_ws(unlist(strsplit(x, ",[[:space:]]*")))
  if (any((res <- grep("[[:space:]]+", pkgs)) != -1)) {
    stop("Missing commas separating ", name, ": '", pkgs[res], "'", call. = FALSE)
  }
  pkgs
}


package_deps_new <- function(package = character(), installed = character(),
  available = character(), diff = logical(), is_cran = logical(),
  remote = list()) {

  res <- structure(
    data.frame(package = package, installed = installed, available = available, diff = diff, is_cran = is_cran, stringsAsFactors = FALSE),
    class = c("package_deps", "data.frame")
  )

  res$remote = structure(remote, class = "remotes")
  res
}

extra_deps <- function(pkg, field) {
  if (!has_extra_deps(pkg, field)) {
    return(package_deps_new())
  }
  dev_packages <- split_extra_deps(pkg[[field]])
  extra <- lapply(dev_packages, parse_one_extra)

  package <- vapply(extra, function(x) remote_package_name(x), character(1), USE.NAMES = FALSE)
  installed <- vapply(package, function(x) local_sha(x), character(1), USE.NAMES = FALSE)
  available <- vapply(extra, function(x) remote_sha(x), character(1), USE.NAMES = FALSE)
  diff <- installed == available
  diff <- ifelse(!is.na(diff) & diff, CURRENT, BEHIND)
  diff[is.na(installed)] <- UNINSTALLED
  is_cran_remote <- vapply(extra, inherits, logical(1), "cran_remote")

  package_deps_new(package, installed, available, diff, is_cran = is_cran_remote, extra)
}


# interactive is an argument to make testing easier.
resolve_upgrade <- function(upgrade, is_interactive = interactive()) {
  if (isTRUE(upgrade)) {
    upgrade <- "always"
  } else if (identical(upgrade, FALSE)) {
    upgrade <- "never"
  }

  upgrade <- match.arg(upgrade[[1]], c("default", "ask", "always", "never"))

  if (identical(upgrade, "default"))
    upgrade <- Sys.getenv("R_REMOTES_UPGRADE", unset = "ask")

  if (!is_interactive && identical(upgrade, "ask")) {
    upgrade <- "always"
  }

  upgrade
}

upgradable_packages <- function(x, upgrade, quiet, is_interactive = interactive()) {

  uninstalled <- x$diff == UNINSTALLED

  behind <- x$diff == BEHIND

  switch(resolve_upgrade(upgrade, is_interactive = is_interactive),

    always = {
      return(msg_upgrades(x, quiet))
    },

    never = return(x[uninstalled, ]),

    ask = {

      if (!any(behind)) {
        return(x)
      }

      pkgs <- format_upgrades(x[behind, ])

      choices <- pkgs
      if (length(choices) > 0) {
        choices <- c("All", "CRAN packages only", "None", choices)
      }

      res <- select_menu(choices, title = "These packages have more recent versions available.\nIt is recommended to update all of them.\nWhich would you like to update?")

      if ("None" %in% res || length(res) == 0) {
        return(x[uninstalled, ])
      }

      if ("All" %in% res) {
        wch <- seq_len(NROW(x))
      } else {

        if ("CRAN packages only" %in% res) {
          wch <- uninstalled | (behind & x$is_cran)
        } else {
          wch <- sort(c(which(uninstalled), which(behind)[pkgs %in% res]))
        }
      }

      msg_upgrades(x[wch, ], quiet)
    }
  )
}

select_menu <- function(choices, title = NULL, msg = "Enter one or more numbers, or an empty line to skip updates: ", width = getOption("width")) {
  if (!is.null(title)) {
    cat(title, "\n", sep = "")
  }

  nc <- length(choices)
  op <- paste0(format(seq_len(nc)), ": ", choices)
  fop <- format(op)
  cat("", fop, "", sep = "\n")
  repeat {
    answer <- readline(msg)
    answer <- strsplit(answer, "[ ,]+")[[1]]
    if (all(answer %in% seq_along(choices))) {
      return(choices[as.integer(answer)])
    }
  }
}


msg_upgrades <- function(x, quiet) {

  if (isTRUE(quiet) || nrow(x) == 0) {
    return(invisible(x))
  }

  cat(format_upgrades(x[x$diff <= BEHIND, ]), sep = "\n")

  invisible(x)
}

format_upgrades <- function(x) {

  if (nrow(x) == 0) {
    return(character(0))
  }

  remote_type <- lapply(x$remote, format)

  # This call trims widths to 12 characters
  x[] <- lapply(x, format_str, width = 12)

  # This call aligns the columns
  x[] <- lapply(x, format, trim = FALSE, justify = "left")

  pkgs <- paste0(x$package, " (", x$installed, " -> ", x$available, ") ", "[", remote_type, "]")
  pkgs
}