Merge branch 'dev'

DESCRIPTION

@@ -1,31 +1,35 @@
 Package: miniCRAN
 Authors@R: c(person("Revolution Analytics", role="aut"), person("Andrie", "de
-    Vries", role=c("aut", "cre"), email="andrie@revolutionanalytics.com"),
+    Vries", role=c("aut", "cre"), email="adevries@microsoft.com"),
     person("Alex", "Chubaty", role="ctb", email="[email protected]"))
 License: GPL-2
-Copyright: Revolution Analytics
+Copyright: Microsoft Corporation
 Title: Create a Mini Version of CRAN Containing Only Selected Packages
 LazyData: true
 LazyLoad: true
 Description: 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. The user can then install packages from this repository directly, 
-    rather than from CRAN.  This is useful in production settings, e.g. server 
+    subset. The user can then install packages from this repository directly,
+    rather than from CRAN.  This is useful in production settings, e.g. server
     behind a firewall, or remote locations with slow broadband access.
-Version: 0.2.4
+Version: 0.2.5
 URL: https://github.com/RevolutionAnalytics/miniCRAN
 BugReports: https://github.com/RevolutionAnalytics/miniCRAN/issues
-Date: 2015-03-26
+Date: 2016-04-12
 Imports:
     tools,
     XML,
     httr,
     methods,
-    utils
+    utils,
+    graphics,
+    stats
 Suggests:
     testthat(>= 0.9),
     knitr,
+    rmarkdown,
     igraph
 VignetteBuilder: knitr
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.0): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(plot,pkgDepGraph)
 S3method(print,pkgDep)
@@ -17,8 +17,19 @@ export(pkgDep)
 export(updatePackages)
 export(updateRepoIndex)
 import(XML)
+importFrom(graphics,legend)
+importFrom(graphics,par)
+importFrom(graphics,title)
 importFrom(httr,GET)
 importFrom(httr,content)
 importFrom(httr,stop_for_status)
 importFrom(methods,is)
+importFrom(stats,reshape)
+importFrom(stats,setNames)
 importFrom(tools,write_PACKAGES)
+importFrom(utils,chooseCRANmirror)
+importFrom(utils,compareVersion)
+importFrom(utils,download.file)
+importFrom(utils,flush.console)
+importFrom(utils,installed.packages)
+importFrom(utils,select.list)

R/MRAN.R

@@ -0,0 +1,9 @@
+MRAN <- function(snapshot){
+  url <- "http://mran.microsoft.com"
+  if(missing("snapshot") || is.null(snapshot)){
+  url
+  } else {
+    sprintf("%s/snapshot/%s", url, snapshot)
+  }
+}
+CRAN <- function()getOption("repos")[1]

R/getCranDescription.R

@@ -6,12 +6,20 @@
 #' @export
 #' 
 #' @example /inst/examples/example_getCranDescription.R
-getCranDescription <- function(pkg, repos=getOption("repos"), type="source", path, pkgs = pkgDep(pkg, repos=repos, type=type)){
+getCranDescription <- function(pkg, repos = getOption("repos"), 
+                               type = "source", 
+                               pkgs = pkgDep(pkg, repos=repos, type=type)){
 
   getOne <- function(package){
-    url <- sprintf("http://cran.r-project.org/web/packages/%s/index.html", package)
+    repos <- repos[[1]]
+    if(!grepl("/$", repos)) repos <- paste0(repos, "/")
+
+    url <- gsub("https://", "http://", 
+                sprintf("%sweb/packages/%s/index.html", repos, package)
+    )
     x <- tryCatch({
-      readHTMLTable(url, header=FALSE, which=1, stringsAsFactors=FALSE)
+      text <- paste(readLines(url), collapse = "\n")
+      XML::readHTMLTable(text, header=FALSE, which=1, stringsAsFactors=FALSE)
     }, error=function(e) e
     )
     if(inherits(x, "error")) {

R/github-functions.R

@@ -72,7 +72,8 @@ addPackageListing <- function(pdb=pkgAvail(), dcf, warnings=TRUE) {
 
 
 
-# from http://stackoverflow.com/questions/13163248/possible-to-override-the-blocking-of-a-packages-re-installation-after-it-has
+# from http://stackoverflow.com/questions/13163248
+# Possible to override the blocking of a package's (re-)installation after it has been required/loaded?
 
 #' @importFrom httr GET stop_for_status content
 readDescriptionGithub <- function(repo, username, branch="master", quiet=TRUE){

R/minicran-package.R

@@ -68,8 +68,11 @@
 #' @name miniCRAN-package
 #' @aliases miniCRAN minicran
 #' @docType package
-#' @author Andrie de Vries \email{andrie@@revolutionanalytics.com} with contributions from Alex Chubaty \email{alex.chubaty@@gmail.com}
+#' @author Andrie de Vries \email{adevries@@microsoft.com} with contributions from Alex Chubaty \email{alex.chubaty@@gmail.com}
 #' @keywords package
+#' @importFrom  graphics legend par title
+#' @importFrom stats reshape setNames
+#' @importFrom utils chooseCRANmirror compareVersion download.file flush.console installed.packages select.list
 NULL
 
 

R/pkgDep.R

@@ -47,7 +47,7 @@ pkgDep <- function(pkg, availPkgs, repos=getOption("repos"), type="source", depe
   }
   if(missing(availPkgs)){
     if(!is.null(names(repos)) & repos["CRAN"] == "@CRAN@"){
-      repos <- c(CRAN="http://cran.revolutionanalytics.com")
+      repos <- MRAN()
     }
     if(is.na(type)) type <- "source"
     availPkgs <- pkgAvail(repos=repos, type=type, Rversion = Rversion, ...)
@@ -130,8 +130,8 @@ pkgAvail <- function(repos=getOption("repos"), type="source", Rversion = R.versi
   if(!grepl("^http://|file:///", repos[1]) && file.exists(repos[1])) {
      repos <- paste0("file:///", normalizePath(repos[1], mustWork = FALSE, winslash = "/"))
   } else {
-    if(!is.null(names(repos)) && repos["CRAN"] == "@CRAN@"){
-      repos <- c(CRAN="http://cran.revolutionanalytics.com")
+    if(!is.null(names(repos)) && isTRUE(unname(repos["CRAN"]) == "@CRAN@")){
+      repos <- MRAN()
     }
   }
   utils::available.packages(contribUrl(repos, type=type, Rversion = Rversion), type=type, filters=list())

R/pkgDepTools.R

@@ -1,13 +1,22 @@
-# This code is from package pkgDepTools
+# Code copied from the pkgDepTools project
+# Copyright (C) Seth Falcon
 # http://www.bioconductor.org/packages/release/bioc/html/pkgDepTools.html
-# Author: Seth Falcom
+# 
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License version 2
+# as published by the Free Software Foundation
 
 
 
+# Code copied from the pkgDepTools project
+# Copyright (C) Seth Falcon
+# http://www.bioconductor.org/packages/release/bioc/html/pkgDepTools.html
+
+
 # Copy of tools:::split_op_version.
 
-#' @rdname pkgDepTools
-#' @keywords internal
+# @rdname pkgDepTools
+# @keywords internal
 split_op_version <- function (x) {
   pat <- "^([^\\([:space:]]+)[[:space:]]*\\(([^\\)]+)\\).*"
   x1 <- sub(pat, "\\1", x)
@@ -25,8 +34,8 @@ split_op_version <- function (x) {
 
 # Copy of tools:::.split_dependencies.
 
-#' @rdname pkgDepTools
-#' @keywords internal
+# @rdname pkgDepTools
+# @keywords internal
 split_dependencies <- function (x) {
   if (!length(x)) 
     return(list())
@@ -38,12 +47,12 @@ split_dependencies <- function (x) {
 }
 
 
-#' Clean package fields.
-#' 
-#' Given the value from a field like 'Depends' in a package's DESCRIPTION file, return a character vector of package names with the version restrictions stripped and \R~removed.
-#' @param val Value from a field like 'Depends' in a package's DESCRIPTION file
-#' @rdname pkgDepTools
-#' @keywords internal
+# Clean package fields.
+# 
+# Given the value from a field like 'Depends' in a package's DESCRIPTION file, return a character vector of package names with the version restrictions stripped and \R~removed.
+# @param val Value from a field like 'Depends' in a package's DESCRIPTION file
+# @rdname pkgDepTools
+# @keywords internal
 cleanPkgField <- function(val) {
   if (is.na(val))
     return(character(0))

R/plot.pkgDepGraph.R

@@ -37,6 +37,10 @@ plot.pkgDepGraph <- function(
 
   edgeColor <- c(Imports="red", Depends="orange", Suggests="grey80", Enhances="blue", LinkingTo="black")
   eColor <- edgeColor[igraph::get.edge.attribute(x, "type")]
+
+  typesInGraph <- unique(igraph::get.edge.attribute(x, "type"))
+  edgeColor <- edgeColor[typesInGraph]
+  # eColor    <- eColor[typesInGraph]
 
   par(mai=rep(0.25, 4))
   # browser()

R/testSuiteFunctions.R

@@ -13,7 +13,7 @@
 
 # Create sample repo from MRAN snapshot
 .createSampleRepo <- function(MRAN, path, pkgs, Rversion="3.1"){
-  if(missing(MRAN)) MRAN <- c(CRAN="http://mran.revolutionanalytics.com/snapshot/2014-10-15")
+  if(missing(MRAN)) MRAN <- MRAN("2014-10-15")
   if(missing(path)) path <- file.path(tempdir(), "miniCRAN", Sys.Date())
   if(missing(pkgs)) pkgs <- c("chron", "adaptivetau")
 

R/testthat_helpers.R

@@ -0,0 +1,16 @@
+# helper functions for testing
+
+# Returns TRUE if a URL can be accessed
+is.online <- function(url = MRAN()){
+  z <- tryCatch(suppressWarnings(readLines(url, n = 10, warn = FALSE)),
+                error = function(e)e
+  )
+  if(inherits(z, "error")) return(FALSE)
+  TRUE
+}
+
+# Interrupt the test if url can not be reached
+skip_if_offline <- function(url = MRAN()){
+  if(!is.online(url)) testthat::skip("offline")
+}
+

inst/doc/miniCRAN-dependency-graph.rmd

@@ -1,13 +1,13 @@
 ---
 title:  "Using miniCRAN to identify package dependencies"
 author: "Andrie de Vries"
-date:   "March 26, 2015"
+date:   "`r as.character(format(Sys.Date(), format='%B %d, %Y'))`"
 output:
   html_document:
     self_contained: yes
     toc: yes
 vignette: >
-  %\VignetteEngine{knitr::knitr}
+  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Using miniCRAN to identify package dependencies}
   %\VignettePackage{miniCRAN}
   %\VignetteKeyword{miniCRAN}

inst/doc/miniCRAN-introduction.R

@@ -2,7 +2,7 @@
 library("miniCRAN")
 
 # use Revolution Analytics CRAN mirror
-revolution <- c(CRAN="http://cran.revolutionanalytics.com")
+revolution <- c(CRAN="http://cran.microsoft.com")
 
 # Specify list of packages to download
 pkgs <- c("foreach")

inst/doc/miniCRAN-introduction.rmd

@@ -1,21 +1,19 @@
 ---
-title:  "Using miniCRAN to create a local CRAN repository"
+title: "Using miniCRAN to create a local CRAN repository"
 author: "Andrie de Vries and Alex Chubaty"
-date:   "March 26, 2015"
+date:   "`r as.character(format(Sys.Date(), format='%B %d, %Y'))`"
 output:
   html_document:
     self_contained: yes
     toc: yes
 vignette: >
-  %\VignetteEngine{knitr::knitr}
+  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Using miniCRAN to create and maintain a local CRAN repository}
   %\VignettePackage{miniCRAN}
   %\VignetteKeyword{miniCRAN}
   %\usepackage[utf8]{inputenc}
 ---
 
-# Creating a miniCRAN repository
-
 Start by creating the recursive dependency tree for your target packages.
 
 For example, imagine a scenario where you want to create a repository that consists of the package `foreach` and its dependencies.
@@ -26,7 +24,7 @@ Start by creating the dependency list:
 library("miniCRAN")
 
 # use Revolution Analytics CRAN mirror
-revolution <- c(CRAN="http://cran.revolutionanalytics.com")
+revolution <- c(CRAN="http://cran.microsoft.com")
 
 # Specify list of packages to download
 pkgs <- c("foreach")

inst/doc/miniCRAN-non-CRAN-repos.rmd

@@ -1,21 +1,19 @@
 ---
 title:  "Using repositories other than CRAN with miniCRAN"
 author: "Andrie de Vries"
-date:   "March 26, 2015"
+date:   "`r as.character(format(Sys.Date(), format='%B %d, %Y'))`"
 output:
   html_document:
     self_contained: yes
     toc: yes
 vignette: >
-  %\VignetteEngine{knitr::knitr}
+  %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Using repositories other than CRAN with miniCRAN}
   %\VignettePackage{miniCRAN}
   %\VignetteKeyword{miniCRAN}
   %\usepackage[utf8]{inputenc}
 ---
 
-# Using repositories other than CRAN with miniCRAN
-
 Although the package name `miniCRAN` seems to indicate you can only use CRAN as a repository, you can in fact use any CRAN-like repository.
 
 This vignette contains some examples of how to refer to different package repositories, including CRAN, alternative mirrors of CRAN, R-Forge as well as BioConductor.

inst/examples/example_addPackageListingGithub.R

@@ -2,7 +2,7 @@
 pdb <- cranJuly2014
 
 \dontrun{
-  pdb <- pkgAvail(repos=c(CRAN="http://cran.revolutionanalytics.com"))
+  pdb <- pkgAvail(repos = c(CRAN="http://mran.microsoft.com"))
 
 
   # Overwrite pdb with development version of miniCRAN at github

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://cran.revolutionanalytics.com")
+revolution <- c(CRAN = "http://mran.microsoft.com")
 pkgs <- c("foreach")
 
 pdb <- cranJuly2014

inst/examples/example_getCranDescription.R

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

inst/examples/example_makeDepGraph.R

@@ -5,7 +5,7 @@ availPkgs <- cranJuly2014
 
 \dontrun{
 availPkgs <- pkgAvail(
-  repos = c(CRAN="http://cran.revolutionanalytics.com"),
+  repos = c(CRAN="http://mran.microsoft.com"),
   type="source"
   )
 }
@@ -26,7 +26,7 @@ if(require(igraph)) plot(p)
 
   p <- makeDepGraph(
   c("ggplot2", "forecast"), 
-  repos = c(CRAN="http://cran.revolutionanalytics.com"), 
+  repos = c(CRAN = "http://mran.microsoft.com"), 
   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://cran.revolutionanalytics.com")
+revolution <- c(CRAN = "http://mran.microsoft.com")
 pkgs <- c("foreach")
 
 pdb <- cranJuly2014
 
 \dontrun{
   pdb <- pkgAvail(
-    repos = c(CRAN="http://cran.revolutionanalytics.com"),
+    repos = c(CRAN = "http://mran.microsoft.com"),
     type="source"
   )
 }

inst/examples/example_pkgDep.R

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