Make recursion optional

DESCRIPTION

@@ -3,6 +3,7 @@ Version: 0.2.16.9000
 Authors@R: c(
     person("Andrie", "de Vries", role=c("aut", "cre", "cph"), email="[email protected]"),
     person("Alex", "Chubaty", role="ctb", email="[email protected]"),
+    person("Alexandre", "Courtiol", role="ctb", email="[email protected]"),
     person("Microsoft Corporation", role="cph")
     )
 License: GPL-2
@@ -41,7 +42,7 @@ Suggests:
 LazyData: true
 LazyLoad: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Language: en-US

NEWS

@@ -1,3 +1,9 @@
+miniCRAN v0.2.17
+================
+
+* `makeDepGraph()` and `pkgDep()` gain an argument `recursive` to control whether dependencies of dependencies are retrieved or not (default = TRUE for default behaviour identical to previous versions) (#149)
+
+
 miniCRAN v0.2.16
 ================
 
@@ -44,7 +50,7 @@ Minor changes:
 miniCRAN v0.2.12 (Release date: 2019-07-06)
 ================
 
-New features: 
+New features:
 * None
 
 Bug fixes:
@@ -65,7 +71,7 @@ Internal changes
 miniCRAN v0.2.11 (Release date: 2018-01-15)
 ================
 
-New features: 
+New features:
 * None
 
 Bug fixes:

R/makeDepGraph.R

@@ -42,9 +42,13 @@ addDepType <- function(p, type = c("Imports", "Depends", "LinkingTo", "Suggests"
 makeDepGraph <- function(
   pkg, availPkgs, repos = getOption("repos"), type = "source",
   suggests = TRUE, enhances = FALSE,
-  includeBasePkgs = FALSE, ...)
+  includeBasePkgs = FALSE,
+  recursive = TRUE, ...)
 {
 
+  if (is.character(recursive))
+    stop("The argument recursive must be a logicial (TRUE or FALSE).")
+
   if (missing(availPkgs)) {
     availPkgs <- pkgAvail(repos = repos, type = type)
   }
@@ -84,10 +88,15 @@ makeDepGraph <- function(
     ))
     pkg <- unique(c(p_enh, pkg))
   }
+
+  pkg2 <- pkg
+  if(!recursive)
+    pkg2 <- pkg_orig
+
   p_dep <- unique(unlist(
                   tools::package_dependencies(
-                    pkg, db = availPkgs,
-                    which = c("Imports", "Depends", "LinkingTo"), recursive = TRUE)
+                    pkg2, db = availPkgs,
+                    which = c("Imports", "Depends", "LinkingTo"), recursive = recursive)
   ))
   pkg <- unique(c(p_dep, pkg))
 
@@ -103,6 +112,9 @@ makeDepGraph <- function(
   if (nedges && !includeBasePkgs)
     edges <- edges[!(edges[["dep"]] %in% basePkgs()), ]
 
+  if (nedges && !recursive)
+    edges <- edges[(edges[["dep"]] %in% pkg), ]
+
   vert <- unique(c(pkg_orig, edges[["dep"]], edges[["package"]]))
   ret <- igraph::graph.data.frame(d = edges, directed = TRUE, vertices = vert)
   class(ret) <- c("pkgDepGraph", "igraph")

R/pkgDep.R

@@ -14,7 +14,7 @@ basePkgs <- function()names(which(installed.packages()[, "Priority"] == "base"))
 
 #' Retrieves package dependencies.
 #'
-#' Performs recursive retrieve for `Depends`, `Imports` and `LinkLibrary`.
+#' Performs recursive or non-recursive retrieve for `Depends`, `Imports` and `LinkLibrary`.
 #' Performs non-recursive retrieve for `Suggests`.
 #'
 #'
@@ -33,37 +33,42 @@ basePkgs <- function()names(which(installed.packages()[, "Priority"] == "base"))
 #'
 #' @param depends If TRUE, retrieves `Depends`, `Imports` and `LinkingTo` dependencies
 #'   (non-recursively)
-#'   
+#'
 #' @param suggests If TRUE, retrieves Suggests dependencies (non-recursively)
-#' 
+#'
 #' @param enhances If TRUE, retrieves Enhances dependencies (non-recursively)
-#' 
+#'
 #' @param quiet If TRUE, suppresses warnings
 #'
 #' @param includeBasePkgs If TRUE, include base R packages in results
-#' 
+#'
+#' @param recursive If TRUE, (reverse) dependencies of (reverse) dependencies (and so on) should be included
+#'
 #' @template Rversion
-#' 
+#'
 #' @param ... Other arguments passed to [available.packages()]
 #'
 #' @export
 #' @family dependency functions
-#' 
+#'
 #' @return character vector of package names
 #'
 #' @example /inst/examples/example_pkgDep.R
-#'   
+#'
 pkgDep <- function(pkg, availPkgs, repos = getOption("repos"), type = "source",
                    depends = TRUE, suggests = TRUE, enhances = FALSE,
-                   includeBasePkgs = FALSE, Rversion = R.version, quiet = FALSE, ...) 
+                   includeBasePkgs = FALSE, recursive = TRUE,
+                   Rversion = R.version, quiet = FALSE, ...)
 {
   assert_that(is_package(pkg))
 
+  if (is.character(recursive))
+    stop("The argument recursive must be a logicial (TRUE or FALSE).")
+
   if (!depends & !suggests & !enhances) {
     warning("Returning nothing, since depends, suggests and enhances are all FALSE")
     return(character(0))
   }
-
 
   if (missing(availPkgs)) {
     if (!is.null(names(repos)) & repos["CRAN"] == "@CRAN@") {
@@ -73,7 +78,7 @@ pkgDep <- function(pkg, availPkgs, repos = getOption("repos"), type = "source",
     availPkgs <- pkgAvail(repos = repos, type = type, Rversion = Rversion,
                           quiet = quiet, ...)
   }
-  
+
   assert_that(nrow(availPkgs) > 0, msg = "Unable to retrieve available packages from CRAN")
 
 
@@ -107,9 +112,13 @@ pkgDep <- function(pkg, availPkgs, repos = getOption("repos"), type = "source",
   }
 
   # Depends, Imports and LinkingTo
-  p_dep <- tools::package_dependencies(n_req_all, availPkgs,
+  pkg2 <- n_req_all
+  if (!recursive)
+    pkg2 <- n_req
+
+  p_dep <- tools::package_dependencies(pkg2, availPkgs,
                                        which = c("Depends", "Imports", "LinkingTo"),
-                                       recursive = TRUE)
+                                       recursive = recursive)
   n_dep <- unique(unname(unlist(p_dep)))
 
   p_all <- p_dep
@@ -149,13 +158,13 @@ print.pkgDep <- function(x, ...) {
 #' @export
 #' @family create repo functions
 #' @seealso [pkgDep()]
-pkgAvail <- function(repos = getOption("repos"), 
-                     type = "source", 
+pkgAvail <- function(repos = getOption("repos"),
+                     type = "source",
                      Rversion = R.version, quiet = FALSE) {
   assert_that(is_repos(repos))
   if (!grepl("^https*://|file:///", repos[1]) && file.exists(repos[1])) {
      repos <- paste0("file:///", normalizePath(repos[1],
-                                               mustWork = FALSE, 
+                                               mustWork = FALSE,
                                                winslash = "/"))
   } else {
     if (!is.null(names(repos)) && isTRUE(unname(repos["CRAN"]) == "@CRAN@")) {
@@ -165,19 +174,19 @@ pkgAvail <- function(repos = getOption("repos"),
   ap <- function() {
     if (getRversion() >= "3.3.0") {
     utils::available.packages(
-      contribUrl(repos, 
-                 type = type, 
-                 Rversion = Rversion), 
-      type = type, 
+      contribUrl(repos,
+                 type = type,
+                 Rversion = Rversion),
+      type = type,
       filters = list(),
       repos = repos
     )
     } else {
       utils::available.packages(
-        contribUrl(repos, 
-                   type = type, 
-                   Rversion = Rversion), 
-        type = type, 
+        contribUrl(repos,
+                   type = type,
+                   Rversion = Rversion),
+        type = type,
         filters = list()
       )
     }
@@ -188,46 +197,46 @@ pkgAvail <- function(repos = getOption("repos"),
 
 
 # Modified copy of utils::contrib.url()
-contribUrl <- function (repos = getOption("repos"), 
-                        type = getOption("pkgType"), 
+contribUrl <- function (repos = getOption("repos"),
+                        type = getOption("pkgType"),
                         Rversion = R.version) {
   Rversion <- twodigitRversion(Rversion)
-  if (type == "both") 
+  if (type == "both")
     type <- "source"
-  if (type == "binary") 
+  if (type == "binary")
     type <- .Platform$pkgType
   if (is.null(repos)) return(NULL)
-  
+
   if ("@CRAN@" %in% repos && interactive()) {
-    cat(gettext("--- Please select a CRAN mirror for use in this session ---"), 
+    cat(gettext("--- Please select a CRAN mirror for use in this session ---"),
         "\n", sep = "")
     flush.console()
     chooseCRANmirror()
     m <- match("@CRAN@", repos)
     nm <- names(repos)
     repos[m] <- getOption("repos")["CRAN"]
-    if (is.null(nm)) 
+    if (is.null(nm))
       nm <- rep("", length(repos))
     nm[m] <- "CRAN"
     names(repos) <- nm
   }
-  if ("@CRAN@" %in% repos) 
+  if ("@CRAN@" %in% repos)
     stop("trying to use CRAN without setting a mirror")
   ver <- Rversion
   mac.path <- "macosx"
   if (substr(type, 1L, 11L) == "mac.binary.") {
     mac.path <- paste(mac.path, substring(type, 12L), sep = "/")
     type <- "mac.binary"
   }
-  res <- switch(type, 
-                source = paste(gsub("/$", "", repos), 
-                               "src", "contrib", 
-                               sep = "/"), 
-                mac.binary = paste(gsub("/$", "", repos), 
-                                   "bin", mac.path, "contrib", 
-                                   ver, sep = "/"), 
-                win.binary = paste(gsub("/$", "", repos), 
-                                   "bin", "windows", "contrib", 
+  res <- switch(type,
+                source = paste(gsub("/$", "", repos),
+                               "src", "contrib",
+                               sep = "/"),
+                mac.binary = paste(gsub("/$", "", repos),
+                                   "bin", mac.path, "contrib",
+                                   ver, sep = "/"),
+                win.binary = paste(gsub("/$", "", repos),
+                                   "bin", "windows", "contrib",
                                    ver, sep = "/"))
   res
 }

inst/examples/example_makeDepGraph.R

@@ -1,32 +1,56 @@
 
 if (interactive()) {
   availPkgs <- cranJuly2014
-  
+
   availPkgs <- pkgAvail(
     repos = c(CRAN = "https://cloud.r-project.org"),
     type = "source"
   )
-  
-  
+
+
   # Create dependency graph using stored database of available packages
   p <- makeDepGraph(
     c("ggplot2", "forecast"),
     availPkgs = availPkgs
   )
-  
+
   if(require(igraph)) plot(p)
 
   # Create dependency graph using newly retrieved database from CRAN
-  
+
   p <- makeDepGraph(
     c("ggplot2", "forecast"),
     repos = c(CRAN = getOption("minicran.mran")),
     type = "source"
   )
+
+  if(require(igraph)) plot(p)
+
+  # Same thing without suggests
+
+  p <- makeDepGraph(
+    c("ggplot2", "forecast"),
+    repos = c(CRAN = getOption("minicran.mran")),
+    type = "source",
+    suggests = FALSE
+  )
+
+  if(require(igraph)) plot(p)
+
+
+  # Same thing without suggests and recursive dependencies
+
+  p <- makeDepGraph(
+    c("ggplot2", "forecast"),
+    repos = c(CRAN = getOption("minicran.mran")),
+    type = "source",
+    suggests = FALSE,
+    recursive = FALSE
+  )
+
   if(requireNamespace("igraph", quietly = TRUE)) {
     plot(p)
   } else {
     message("install package `igraph` to view dependency graph")
   }
-
 }