R/installed.R

In pkgcache: Cache 'CRAN'-Like Metadata and R Packages

# This is not actually used anywhere, we I'll leave it here.
# It might be useful for testing improvements for the more complicated
# parsers.

parse_description <- function(path) {
  path <- path.expand(path)
  path <- encode_path(path)
  ret <- .Call(pkgcache_parse_description, path)
  ret2 <- gsub("\r", "", ret, fixed = TRUE)

  # Fix encoding. If UTF-8 is declared, then we just mark it.
  # Otherwise we convert it to UTF-8. Conversion might throw an error.
  if ("Encoding" %in% names(ret2)) {
    enc <- trimws(ret2[["Encoding"]])
    if (enc == "UTF-8") {
      Encoding(ret2) <- "UTF-8"
    } else {
      trs <- iconv(ret2, enc, "UTF-8")
      ret2[] <- ifelse(is.na(trs), ret2, trs)
    }
  }
  ret2
}

fix_encodings <- function(lst, col = "Encoding") {
  if (! col %in% names(lst)) return(lst)
  utf8 <- which(!is.na(lst[[col]]) & lst[[col]] == "UTF-8")
  other <- which(!is.na(lst[[col]]) & lst[[col]] != "UTf-8")
  unq <- unique(lst[[col]][other])
  if (length(utf8)) {
    for (i in seq_along(lst)) {
      Encoding(lst[[i]][utf8]) <- "UTF-8"
    }
  }
  if (length(unq)) {
    for (u in unq) {
      wh <- which(!is.na(lst[[col]]) & lst[[col]] == u)
      for (i in seq_along(lst)) {
        tryCatch({
          trs <- iconv(lst[[i]][wh], u, "UTF-8")
          lst[[i]][wh] <- ifelse(is.na(trs), lst[[i]][wh], trs)
        }, error = function(e) NULL)
      }
    }
  }
  lst
}

#' Parse a repository metadata `PACAKGES*` file
#'
#' @details
#' Non-existent, unreadable or corrupt `PACKAGES` files with trigger an
#' error.
#'
#' `PACKAGES*` files do not usually declare an encoding, but nevertheless
#' `parse_packages()` works correctly if they do.
#'
#' # Note
#' `parse_packages()` cannot currently read files that have very many
#' different fields (many columns in the result data frame). The current
#' limit is 1000. Typical `PACKAGES` files contain less than 20 field
#' types.
#'
#' @param path Path to the `PACKAGES*` file.
#' @param type Type of the file. By default it is determined automatically.
#'   Types:
#'   * `uncompressed`,
#'   * `gzip` compressed,
#'   * `bzip2` compressed,
#'   * `xz` compressed.
#'   * `rds`, an RDS file, which will be read using [base::readRDS()].
#' @return A data frame, with all columns from the file at `path`.
#'
#' @export

parse_packages <- function(path, type = NULL) {
  stopifnot(
    "`path` must be a character scalar" = is_string(path),
    is.null(type) || (is_string(type) && type %in% packages_types)
  )
  path <- path.expand(path)
  path <- encode_path(path)

  type <- type %||% guess_packages_type(path)
  if (type == "rds") {
    tab <- readRDS(path)

  } else {
    cmp <- .Call(pkgcache_read_raw, path)[[1]]
    if (is.character(cmp)) {
      stop(cmp)
    }

    if (type == "gzip") {
      if (getRversion() >= "4.0.0") {
        bts <- memDecompress(cmp, type = "gzip")
      } else {
        bts <- gzip_decompress(cmp)     # nocov
      }
    } else if (type == "bzip2") {
      bts <- memDecompress(cmp, type = "bzip2")
    } else if (type == "xz") {
      bts <- memDecompress(cmp, type = "xz")
    } else {
      bts <- cmp
    }

    # Might still be an RDS we just uncompressed
    if (length(bts) >= 2 &&
        bts[1] %in% as.raw(c(0x58, 0x41, 0x42)) &&
        bts[2] == 0x0a) {
      tab <- unserialize(bts)

    } else {
      tab <- .Call(pkgcache_parse_packages_raw, bts)
      tab[] <- lapply(tab, function(x) {
        x <- gsub("\r", "", fixed = TRUE, x)
        empt <- is.na(x)
        miss <- x == ""
        x[empt] <- ""
        x[miss] <- NA_character_
        x
      })

      # this is rarely needed for PACKAGES files, included for completeness
      tab <- fix_encodings(tab)
    }
  }

  tbl <- as_data_frame(tab)

  tbl
}

packages_types <- c("uncompressed", "gzip", "bzip2", "xz", "rds")

# Note that compressed RDS will be reported as gzip, bzip2 or xz,
# depending on the compression

guess_packages_type <- function(path) {
  buf <- readBin(path, what = "raw", 6)

  if (length(buf) >= 3 &&
      buf[1] == 0x1f &&
      buf[2] == 0x8b &&
      buf[3] == 0x08) return("gzip")

  if (length(buf) >= 3 &&
      buf[1] == 0x42 &&
      buf[2] == 0x5a &&
      buf[3] == 0x68) return("bzip2")

  if (length(buf) >= 6 &&
      buf[1] == 0xFD &&
      buf[2] == 0x37 &&
      buf[3] == 0x7A &&
      buf[4] == 0x58 &&
      buf[5] == 0x5A &&
      buf[6] == 0x00) return("xz")

  if (length(buf) >= 2 &&
      buf[1] %in% as.raw(c(0x58, 0x41, 0x42)) &&
      buf[2] == 0x0a) return("rds")

  "uncompressed"
}

#' List metadata of installed packages
#'
#' This function is similar to [utils::installed.packages()].
#' See the differences below.
#'
#' @details
#' Differences with [utils::installed.packages()]:
#' * `parse_installed()` cannot subset the extracted fields. (But you can
#'   subset the result.)
#' * `parse_installed()` does not cache the results.
#' * `parse_installed()` handles errors better. See Section 'Errors' below.
#' #' * `parse_installed()` uses the `DESCRIPTION` files in the installed packages
#'   instead of the `Meta/package.rds` files. This should not matter,
#'   but because of a bug `Meta/package.rds` might contain the wrong
#'   `Archs` field on multi-arch platforms.
#' * `parse_installed()` reads _all_ fields from the `DESCRIPTION` files.
#'   [utils::installed.packages()] only reads the specified fields.
#' * `parse_installed()` converts its output to UTF-8 encoding, from the
#'   encodings declared in the `DESCRIPTION` files.
#' * `parse_installed()` is considerably faster.
#'
#' ## Encodings
#'
#' `parse_installed()` always returns its result in UTF-8 encoding.
#' It uses the `Encoding` fields in the `DESCRIPTION` files to learn their
#' encodings. `parse_installed()` does not check that an UTF-8 file has a
#' valid encoding. If it fails to convert a string to UTF-8 from another
#' declared encoding, then it leaves it as `"bytes"` encoded, without a
#' warning.
#'
#' ## Errors
#'
#' pkgcache silently ignores files and directories inside the library
#' directory.
#'
#' The result also omits broken package installations. These include
#'
#' * packages with invalid `DESCRIPTION` files, and
#' * packages the current user have no access to.
#'
#' These errors are reported via a condition with class
#' `pkgcache_broken_install`. The condition has an `errors` entry, which
#' is a data frame with columns
#'
#' * `file`: path to the `DESCRIPTION` file of the broken package,
#' * `error`: error message for this particular failure.
#'
#' If you intend to handle broken package installation, you need to catch
#' this condition with `withCallingHandlers()`.
#'
#' @param library Character vector of library paths.
#' @param priority If not `NULL` then it may be a `"base"` `"recommended"`
#'   `NA` or a vector of these to select _base_ packages, _recommended_
#'   packages or _other_ packages. (These are the official, CRAN supported
#'   package priorities, but you may introduce others in non-CRAN packages.)
#' @param lowercase Whether to convert keys in `DESCRIPTION` to lowercase.
#' @param reencode Whether to re-encode strings in UTF-8, from the
#'   encodings specified in the `DESCRIPTION` files. Re-encoding is
#'   somewhat costly, and sometimes it is not important (e.g. when you only
#'   want to extract the dependencies of the installed packages).
#' @param packages If not `NULL`, then it must be a character vector,
#'   and only these packages will be listed.
#'
#' @export

parse_installed <- function(library = .libPaths(), priority = NULL,
                            lowercase = FALSE, reencode = TRUE,
                            packages = NULL) {
  stopifnot(
    "`library` must be a character vector" = is.character(library),
    "`priority` must be `NULL` or a character vector" =
      is.null(priority) || is.character(priority) || identical(NA, priority),
    "`library` cannot have length zero" = length(library) > 0,
    "`lowercase` must be a boolean flag" = is_flag(lowercase),
    "`packages` must be `NULL` or a character vector" =
      is.null(packages) || is.character(packages)
  )

  # Merge multiple libraries
  if (length(library) > 1) {
    lsts <- lapply(
      library,
      parse_installed,
      priority = priority,
      lowercase = lowercase,
      reencode = reencode,
      packages = packages
    )
    return(rbind_expand(.list = lsts))
  }

  # Handle ~ in path name
  library <- path.expand(library)

  # NOTE: a package is a directory with `DESCRIPTION`, other
  #       files and directories are ignored.
  # TODO: replace dir() with something that errors if library does not
  #       exist or we cannot get the list of directories.
  packages <- packages %||% dir(library)
  dscs <- file.path(library, packages, "DESCRIPTION")
  dscs <- dscs[file.exists(dscs)]

  dscs <- encode_path(dscs)
  prs <- .Call(pkgcache_parse_descriptions, dscs, lowercase)
  tab <- prs[[1]]

  tab[] <- lapply(tab, function(x) {
    x <- gsub("\r", "", x, fixed = TRUE)
    empt <- is.na(x)
    miss <- x == ""
    x[empt] <- ""
    x[miss] <- NA_character_
    x
  })

  tbl <- as_data_frame(tab)
  if (lowercase) {
    tbl$libpath <- if (nrow(tbl)) library else character()
  } else {
    tbl$LibPath <- if (nrow(tbl)) library else character()
  }

  # Filter out errors
  if (prs[[3]]) {
    bad <- prs[[2]] != ""
    tbl <- tbl[!bad, ]
    cnd <- new_pkgcache_warning(
      "Cannot read DESCRIPTION files:\n", paste0("* ", prs[[2]][bad], "\n"),
      class = "pkgcache_broken_install",
      data = list(errors = data_frame(file = dscs[bad], error = prs[[2]][bad]))
    )
    withRestarts(
      muffleWarning = function() NULL,
      signalCondition(cnd)
    )
  }

  # filter for priority
  prname <- if (lowercase) "priority" else "Priority"
  if (!is.null(priority) && prname %in% names(tbl)) {
    keep <- if (anyNA(priority)) {
      is.na(tbl[[prname]])
    } else {
      FALSE
    }
    priority <- na_omit(priority)
    keep <- keep | tbl[[prname]] %in% priority
    tbl <- tbl[keep, ]
  }

  if (reencode) tbl <- fix_encodings(tbl)

  tbl
}