add MRAN url as package option (close #72)

Note: use http instead of https for R < 3.2.2

R/MRAN.R

@@ -1,9 +1,9 @@
-MRAN <- function(snapshot){
-  url <- "https://mran.microsoft.com"
-  if(missing("snapshot") || is.null(snapshot)){
-  url
+MRAN <- function(snapshot) {
+  url <- getOption("minicran.mran")
+  if (missing("snapshot") || is.null(snapshot)) {
+    url
   } else {
     sprintf("%s/snapshot/%s", url, snapshot)
   }
 }
-CRAN <- function()getOption("repos")[1]
+CRAN <- function() getOption("repos")[1]

R/getCranDescription.R

@@ -1,13 +1,13 @@
 
 #' @importFrom XML readHTMLTable
-oldGetCranDescription <- function(pkg, repos = getOption("repos"), 
-                                  type = "source", 
+oldGetCranDescription <- function(pkg, repos = getOption("repos"),
+                                  type = "source",
                                   pkgs = pkgDep(pkg, repos = repos, type = type)){
   getOne <- function(package) {
     repos <- repos[[1]]
     if(!grepl("/$", repos)) repos <- paste0(repos, "/")
-    
-    url <- gsub("https://", "http://", 
+
+    url <- gsub("https://", "http://",
                 sprintf("%sweb/packages/%s/index.html", repos, package)
     )
     x <- tryCatch({
@@ -36,20 +36,18 @@ oldGetCranDescription <- function(pkg, repos = getOption("repos"),
 #'
 #' @inheritParams pkgDep
 #' @inheritParams makeRepo
-#' 
+#'
 #' @export
-#' 
+#'
 #' @example /inst/examples/example_getCranDescription.R
-getCranDescription <- function(pkg, repos = getOption("repos"), 
-                               type = "source", 
+getCranDescription <- function(pkg, repos = getOption("repos"),
+                               type = "source",
                                pkgs = pkgDep(pkg, repos = repos, type = type)){
-  
-  if(getRversion() >= "3.4.1"){
+
+  if (getRversion() >= "3.4.1"){
     pdb <- tools::CRAN_package_db()
     pdb[match(pkgs, pdb$Package), ]
   } else {
     oldGetCranDescription(pkg = pkg, repos = repos, type = type, pkgs = pkgs)
   }
 }
-
-

R/minicran-package.R

@@ -7,53 +7,58 @@
 #'
 #'@description
 #'
-#' At the end of 2014, CRAN consisted of more than 6,000 packages.  Many organisations need to maintain a private mirror of CRAN, but with only a subset of packages that are relevant to them.  
-#' 
-#' `miniCRAN` makes it possible to create an internally consistent repository consisting of selected packages from CRAN-like repositories.  The user specifies a set of desired packages, and miniCRAN recursively reads the dependency tree for these packages, then downloads only this subset.  
-#' 
-#' 
+#' At the end of 2014, CRAN consisted of more than 6,000 packages.  Many organisations need to maintain a private mirror of CRAN, but with only a subset of packages that are relevant to them.
+#'
+#' `miniCRAN` makes it possible to create an internally consistent repository consisting of selected packages from CRAN-like repositories.  The user specifies a set of desired packages, and miniCRAN recursively reads the dependency tree for these packages, then downloads only this subset.
+#'
+#'
 #' There are many reasons for not creating a complete mirror CRAN using `rsync`:
 #'
 #' * You may wish to mirror only a subset of CRAN, for security, legal compliance or any other in-house reason
 #' * You may wish to restrict internal package use to a subset of public packages, to minimize package duplication, or other reasons of coding standards
 #' * You may wish to make packages available from public repositories other than CRAN, e.g. BioConductor, r-forge, OmegaHat, etc.
 #' * You may wish to add custom in-house packages to your repository
-#' 
+#'
 #' The ambition of `miniCRAN` is to eventually satisfy all of these considerations.
-#' 
+#'
 #' @section Making a private repo:
-#' 
+#'
 #' * [pkgAvail()]: Read from a local (or remote) CRAN-like repository and determine available packages.
 #' * [pkgDep()]: Find (recursive) package dependencies.
 #' * [makeRepo()] : Make a mini CRAN repository, by downloading packages (and their dependencies) and creating the appropriate file structure for a repository.  This allows you to use functions like [utils::available.packages()] and [utils::install.packages()] on your local repository.
-#' 
+#'
 #' This subset will be internally consistent, i.e. the following functions will work as expected:
 #' * [utils::available.packages()]
 #' * [utils::install.packages()]
-#' 
+#'
 #' The main function is [makeRepo()] - this will download all the required packages, with their dependencies, into the appropriate repository file structure, and then create the repository index (PACKAGES) file.
-#' 
-#' 
-#' 
+#'
+#'
+#'
 #' @section Updating packages in a repo:
-#' 
+#'
 #' * [oldPackages()]: Indicates packages which have a (suitable) later version on the repositories
 #' * [updatePackages()]: Offers to download and install such packages
-#' 
-#' 
-#' 
+#'
+#'
+#'
 #' @section Creating dependencies:
-#' 
+#'
 #' To get a recursive list of dependencies as well as a plot, use [pkgDep()] followed by  [makeDepGraph()].
-#' 
+#'
 #' * [pkgDep()]: Find (recursive) package dependencies.
 #' * [makeDepGraph()]: Create graph of selected package dependencies.
 #' * [plot.pkgDepGraph()]: Create a visualization of the dependency graph
-#' 
-#' 
-#' 
-#' 
-#' 
+#'
+#'
+#'
+#' @section Package options:
+#'
+#' \describe{
+#'   \item{\code{minicran.mran}}{preferred MRAN URL. Defaults to \url{https://mran.microsoft.com}
+#'   for R versions 3.2.2 and greater. Versions earlier than 3.2.2 use HTTP instead of HTTPS.}
+#' }
+#'
 #' @name miniCRAN-package
 #' @aliases miniCRAN minicran
 #' @docType package
@@ -69,9 +74,9 @@ NULL
 # data documentation ------------------------------------------------------
 
 #' Stored version of available.packages()
-#' 
+#'
 #' Copy of the result of [utils::available.packages()] on July 1, 2014.
-#' 
+#'
 #' @docType data
 #' @keywords datasets
 #' @name cranJuly2014

R/zzz.R

@@ -1,2 +1,20 @@
 # globals <- new.env(parent=emptyenv(), hash=TRUE)
 # globals$have_RCurl <- require("RCurl")
+
+.onLoad <- function(libname, pkgname) {
+  mran.url <- if (getRversion() >= "3.2.2") {
+    "https://mran.microsoft.com" ## use HTTPS
+  } else {
+    "http://mran.microsoft.com" ## use HTTP
+  }
+
+  ## set options using the approach used by devtools
+  opts <- options()
+  opts.miniCRAN <- list(
+    minicran.mran = mran.url
+  )
+  toset <- !(names(opts.miniCRAN) %in% names(opts))
+  if (any(toset)) options(opts.miniCRAN[toset])
+
+  invisible()
+}

inst/examples/example_addPackageListingGithub.R

@@ -2,16 +2,16 @@
 pdb <- cranJuly2014
 
 \dontrun{
-  pdb <- pkgAvail(repos = c(CRAN = "http://mran.microsoft.com"))
-  
+  pdb <- pkgAvail(repos = c(CRAN = getOption("minicran.mran")))
+
   # Overwrite pdb with development version of miniCRAN at github
   newpdb <- addPackageListingGithub(pdb = pdb, "andrie/miniCRAN")
   newpdb["miniCRAN", ]
-  
+
   # Add package from github that's not currently on CRAN
   newpdb <- addPackageListingGithub(pdb = pdb, repo = "RevolutionAnalytics/checkpoint")
   newpdb["checkpoint", ]
-  
+
   set.seed(1)
   plot(makeDepGraph("checkpoint", availPkgs = newpdb, suggests = TRUE))
 }

inst/examples/example_checkVersions.R

@@ -1,7 +1,7 @@
 ### `checkVersions` and `add.packages.miniCRAN` require an existing miniCRAN repo
 
 # Specify list of packages to download
-revolution <- c(CRAN = "http://mran.microsoft.com")
+revolution <- c(CRAN = getOption("miniCRAN.mran"))
 pkgs <- c("foreach")
 pkgTypes <- c("source", "win.binary")
 

inst/examples/example_getCranDescription.R

@@ -1,5 +1,5 @@
 \dontrun{
-getCranDescription(c("igraph", "ggplot2", "XML"), 
-  repos = c(CRAN = "http://mran.microsoft.com")
+getCranDescription(c("igraph", "ggplot2", "XML"),
+  repos = c(CRAN = getOption("minicran.mran"))
 )
 }

inst/examples/example_makeDepGraph.R

@@ -5,15 +5,15 @@ availPkgs <- cranJuly2014
 
 \dontrun{
 availPkgs <- pkgAvail(
-  repos = c(CRAN = "http://mran.microsoft.com"),
+  repos = c(CRAN = getOption("minicran.mran")),
   type = "source"
   )
 }
 
 
 # Create dependency graph using stored database of available packages
 p <- makeDepGraph(
-  c("ggplot2", "forecast"), 
+  c("ggplot2", "forecast"),
   availPkgs = availPkgs
 )
 
@@ -23,10 +23,10 @@ if(require(igraph)) plot(p)
 
 \dontrun{
   # Create dependency graph using newly retrieved database from CRAN
-  
+
   p <- makeDepGraph(
-  c("ggplot2", "forecast"), 
-  repos = c(CRAN = "http://mran.microsoft.com"), 
+  c("ggplot2", "forecast"),
+  repos = c(CRAN = getOption("minicran.mran")),
   type = "source"
 )
 if(require(igraph)) plot(p)

inst/examples/example_makeRepo.R

@@ -1,13 +1,13 @@
 
 # Specify list of packages to download
-revolution <- c(CRAN = "http://mran.microsoft.com")
+revolution <- c(CRAN = getOption("minicran.mran"))
 pkgs <- c("foreach")
 
 pdb <- cranJuly2014
 
 \dontrun{
   pdb <- pkgAvail(
-    repos = c(CRAN = "http://mran.microsoft.com"),
+    repos = c(CRAN = getOption("minicran.mran")),
     type = "source"
   )
 }

inst/examples/example_pkgDep.R

@@ -1,13 +1,13 @@
 
 \dontrun{
-pkgDep(pkg = c("ggplot2", "plyr", "reshape2"), 
-       repos = c(CRAN = "http://mran.microsoft.com")
+pkgDep(pkg = c("ggplot2", "plyr", "reshape2"),
+       repos = c(CRAN = getOption("minicran.mran"))
 )
 }
 
 pdb <- cranJuly2014
 \dontrun{
-pdb <- pkgAvail(repos = c(CRAN = "http://mran.microsoft.com"))
+pdb <- pkgAvail(repos = c(CRAN = getOption("minicran.mran")))
 }
 
 pkgDep(pkg = c("ggplot2", "plyr", "reshape2"), pdb)

inst/examples/example_plot.pkgDepGraph.R

@@ -5,27 +5,27 @@ pdb <- cranJuly2014
 
 \dontrun{
   pdb <- pkgAvail(
-    repos = c(CRAN = "http://mran.microsoft.com"),
+    repos = c(CRAN = getOption("minicran.mran")),
     type = "source"
   )
 }
 
 dg <- makeDepGraph(tags, availPkgs = pdb  , includeBasePkgs = FALSE,
                    suggests = TRUE, enhances = TRUE)
 
-set.seed(42); 
+set.seed(42);
 plot(dg)
 
 # Move edge legend to top left
-set.seed(42); 
+set.seed(42);
 plot(dg, legendPosition = c(-1, 1))
 
 # Change font size and shape size
-set.seed(42); 
+set.seed(42);
 plot(dg, legendPosition = c(-1, 1), vertex.size = 20,  cex = 0.5)
 
 
 # Move vertex legend to top right
-set.seed(42); 
+set.seed(42);
 plot(dg, legendPosition = c(1, 1), vertex.size = 20,  cex = 0.5)
 

inst/examples/example_rsynctools.R

@@ -1,4 +1,4 @@
 \dontrun{
   pkgs <- c("ggplot2", "plyr", "reshape2")
-  makeRsyncInclude(pkgs, type = "source", repos = c(CRAN = "http://mran.microsoft.com"))
+  makeRsyncInclude(pkgs, type = "source", repos = c(CRAN = getOption("minicran.mran")))
 }

inst/examples/example_updatePackages.R

@@ -1,7 +1,7 @@
 ### `oldPackages` and `updatePackages` require an existing miniCRAN repo
 
 # Specify list of packages to download
-revolution <- c(CRAN = "http://mran.microsoft.com")
+revolution <- c(CRAN = getOption("minicran.mran"))
 pkgs <- c("foreach")
 
 pdb <- cranJuly2014