document.r

document <- function(pkg = NULL, clean = FALSE, roclets = c("collate", "namespace", "rd")) {
  require("roxygen2")
  man_path <- file.path(pkg$path)
  if (!file.path(pkg$path)) dir.create(man_path)

  message("Updating ", pkg$package, " documentation")
  
  pkg <- as.package(pkg)
  if (clean) {
    clear_caches()
    file.remove(dir(file.path(pkg$path, "man"), full.names = TRUE))
    load_all(pkg, reset = TRUE)
  } else {
    load_all(pkg)
  }
  
  # Could avoid this duplication if load_all returned a list combining
  # the results of all the individual load functions
  r_files <- find_code(pkg$path)

  env <- pkg_env(pkg)
  env_hash <- suppressWarnings(digest(env))
  
  parsed <- lapply(paths, parse.file, env = env, env_hash = env_hash), 
    recursive = FALSE)
  
  roclets <- str_c(roclets, "_roclet", sep = "")
  for (roclet in roclets) {
    roc <- match.fun(roclet)()
    results <- roc_process(roc, parsed, roxygen.dir)
    roc_output(roc, results, roxygen.dir)
  }
  
  invisible()
}

load-code.r

load_code <- function(pkg = NULL, env = pkg_env(pkg)) {
  pkg <- as.package(pkg)

  r_files <- find_code(pkg)
  paths <- changed_files(r_files)

  tryCatch(
    lapply(paths, sys.source, envir = env, chdir = TRUE, 
      keep.source = TRUE), 
    error = function(e) {
      clear_cache()
      stop(e)
    }
  )
  
  # Load .onLoad if it's defined
  if (exists(".onLoad", env, inherits = FALSE) && 
     !exists("__loaded", env, inherits = FALSE)) {
    env$.onLoad()
    env$`__loaded` <- TRUE
  }
  
  invisible(paths)
}


#' Parse collate string into vector of function names.
#' @keywords internal
parse_collate <- function(string) {
  con <- textConnection(string)
  on.exit(close(con))
  scan(con, "character", sep = " ", quiet = TRUE)
}

#' Find all R files in given directory.
#' @keywords internal
find_code <- function(pkg) {
  path_r <- file.path(pkg$path, "R")
  
  code_paths <- dir(path_r, "\\.[Rrq]$", full.names = TRUE)  
  r_files <- with_collate("C", sort(code_paths))
  
  if (!is.null(pkg$collate)) {
    collate <- file.path(path_r, parse_collate(pkg$collate))
    
    missing <- setdiff(collate, r_files)
    files <- function(x) paste(basename(x), collapse = ", ")
    if (length(missing) > 0) {
      message("Skipping missing files: ", files(missing))
    }
    
    extra <- setdiff(r_files, collate)
    if (length(extra) > 0) {
      message("Adding files missing in collate: ", files(extra))
    }
    
    r_files <- union(collate, r_files)
  }
  r_files
}