R/get.dependencies.R

In groundhogR/groundhog: Version-Control for CRAN, GitHub, and GitLab Packages

#' Get dependencies for one package
#'
#' Get direct dependencies for one package `pkg`, for the version on CRAN at the
#' given `date`.
#'
#' @param pkg character. Name of the package to install
#' @param date date (in the format "%Y-%m-%d"), Required date for the package.
#' @param include.suggests Logical (defaults to `FALSE`. Should suggested
#'   packages be installed?
#' @return A character vector containing the package dependencies for `pkg`, for
#'   the version on CRAN at `date.`
#' @noRd
# @examples
# \dontrun{
# groundhog:::get.dependencies("magrittr", "2018-02-12", include.suggests = TRUE)
# }
#'
#' @seealso [get.all.dependencies()] for recursive (=indirect) dependencies
#'
#' @noRd

get.dependencies <- function(pkg, date, include.suggests = FALSE) {

  update_cran.toc_if.needed(date = date) #also loads the cran.toc if not yet loaded
  cran.toc <- .pkgenv[["cran.toc"]]

  
  #If a base R package, return empty character vector (cannot lookup in cran.toc.rds for it is not on cran)
    if (pkg %in% base_pkg()) {
      return(as.character())
    }
  
  # Get version from date
  vrs <- get.version(pkg, date)

  # Get dependencies if version exists
  row <- cran.toc[cran.toc$Package == pkg & cran.toc$Version == vrs, c("Imports", "Depends", "Suggests", "LinkingTo")]
  dep <- c(row$Imports, row$Depends, row$LinkingTo) # merge
  if (include.suggests) {
    dep <- c(dep, row$Suggests) # add 'Suggests' dependencies if requested
  }
  dep <- unlist(strsplit(dep, ","))  # turn to array
  #dep <- dep[!dep %in% base_pkg()]   # base dependencies from R
  dep <- unique(dep)                 # some dependencies can be listed both in Imports and LinkingTo, keep only one

  #Drop non-cran
  non.cran <- dep[!dep %in% cran.toc$Package]
  dep <- dep[!dep %in% non.cran]

  
  # These steps are normally taken care of server side but let's stay on the
  # safe side
  dep <- dep[dep != ""] # drop empty values
  dep <- dep[dep != "R"] # drop R as a dependency
  dep <- dep[!is.na(dep)] # drop NA

  return(dep)
} # End get.dependencies()

#' Get recursive dependencies
#'
#' Get all recursive (=indirect) dependencies for one package `pkg`, for the
#' version on CRAN at the given `date`.
#'
#'
#' @return a `data.frame` where the first column (`pkg`) contains non-terminal
#'   dependencies and the second column (`dep2` contains a dependencies of the
#'   package in column `pkg`.
#' @noRd
# @examples
# \dontrun{
# groundhog:::get.all.dependencies("magrittr", "2018-02-12", include.suggests = TRUE)
# }
#'
#seealso [get.dependencies()] for direct dependencies only

get.all.dependencies <- function(pkg, date, include.suggests = FALSE) {


  #1 If saved before, load it
        #Path to dep12
            dep12_dir <- paste0(get.groundhog.folder() , '/dep12' )
            
        #With and without suggests are different files
            if (include.suggests==FALSE) dep12_file <- paste0(pkg , "_" ,  gsub( "-", "_" , date) , '.rds')  
            if (include.suggests==TRUE)  dep12_file <- paste0(pkg , "_" ,  gsub( "-", "_" , date) , '_with_suggests.rds')  
        
            
        #Final path    
            dep12_path <- file.path(dep12_dir, dep12_file)
            
        #Create directory if it does not exist
            if (!file.exists(dep12_dir)) dir.create(dep12_dir,recursive=TRUE, showWarnings = FALSE)  
            
        #If dep12 has been saved, load and return it
            if (file.exists(dep12_path)) {
                dep12 <- readRDS(dep12_path)
                return(dep12)
              } 
            
  
      # 2. Populate the starting point with this package and its dependencies
      # [a] Vector with pending deps, for looping install
      pending <- get.dependencies(pkg, date, include.suggests = include.suggests) # include.suggests=TRUE means that suggested dependencies and their dependencies are installed.
    
      if (length(pending) == 0) {
        return(data.frame(pkg = character(), dep2 = character(),stringsAsFactors = FALSE))
      }
    
      # [b] dep12: data.frame with two columns, pkg-left, dependency-right, for snowball loading
      dep12 <- data.frame(pkg = pkg, dep2 = pending, stringsAsFactors = FALSE)
    
      # 5.2 Loop over pending, adding to dep12, and both adding and subtracting from pending till it's empty
      k <- 1
      while (length(pending) != 0) {
        # 5.3 Grab the first among the pending dependencies
        depk <- pending[1]
    
        # 5.4 Get its dependencies
        pendingk <- get.dependencies(pkg = depk, date = date, include.suggests = FALSE) # Note: never include suggested deps for deps
    
        # 5.5 Drop depk from pending
        pending <- pending[-match(depk, pending)]
        
        #5.6 Add new pairs to  dep12 
          if (length(pendingk) > 0) {
            dep12k <- data.frame(pkg = depk, dep2 = pendingk, stringsAsFactors=FALSE)
            dep12 <- rbind(dep12, dep12k)
            }
    
        #5.7 Add new dependencies to pending 
        if (length(pendingk) > 0) {
          already.processed <- pendingk %in% dep12[, 1] # identify in pending those already processed
          pendingk.net <- pendingk[!already.processed] # drop them
          pending <- unique(c(pending, pendingk.net)) # Unique so that if we add something already pending we don't add it
        } # End 5.5 if some new dependencies to add
        
        k <- k + 1
        if (k > 50000) break # In case the loop does not converge to a stable dataframe
      } # End while
      
      #Save copy
        saveRDS(dep12, dep12_path, version=2)
        
      return(dep12)
} # End function get.all.dependencies