Merge pull request #61 from RevolutionAnalytics/master

Merge master into dev at v0.2.2

DESCRIPTION

@@ -4,23 +4,26 @@ Authors@R: c(person("Revolution Analytics", role="aut"), person("Andrie", "de
     person("Alex", "Chubaty", role="ctb", email="[email protected]"))
 License: GPL-2
 Copyright: Revolution Analytics
-Title: Create a mini Version of CRAN Containing Only Selected Packages
+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.
+    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: 0.2.2
 URL: https://github.com/RevolutionAnalytics/miniCRAN
 BugReports: https://github.com/RevolutionAnalytics/miniCRAN/issues
-Date: 2015-03-25
+Date: 2015-03-26
 Imports:
     tools,
     XML,
     httr,
-    methods
+    methods,
+    utils
 Suggests:
     testthat(>= 0.9),
     knitr,

NEWS

@@ -1,3 +1,9 @@
+miniCRAN v0.2-2 (Release date: 2015-03-25)
+==============
+
+Changes:
+* Additional vignettes and documentation
+
 miniCRAN v0.2-0 (Release date: 2014-12-16)
 ==============
 

R/makeRepo.R

@@ -66,9 +66,11 @@ makeRepo <- function(pkgs, path, repos=getOption("repos"), type="source",
     }
   }
 
-  pdb <- pkgAvail(repos = repos, type=type)
+  pdb <- pkgAvail(repos = repos, type=type, Rversion = Rversion)
 
-  if(download) download.packages(pkgs, destdir=pkgPath, available=pdb, repos=repos, type=type, quiet=quiet)
+  if(download) utils::download.packages(pkgs, destdir=pkgPath, available=pdb, repos=repos, 
+                                 contriburl = contribUrl(repos, type, Rversion),
+                                 type=type, quiet=quiet)
   if(writePACKAGES) updateRepoIndex(path=path, type=type, Rversion=Rversion)
 }
 

R/pkgDep.R

@@ -28,14 +28,15 @@ basePkgs <- function()names(which(installed.packages()[, "Priority"] == "base"))
 #' @param enhances If TRUE, retrieves Enhances dependencies (non-recursively)
 #' 
 #' @param includeBasePkgs If TRUE, include base R packages in results
+#' @param Rversion Version of R. Can be specified as a character string with the two digit R version, e.g. "3.1".  Defaults to \code{\link{R.version}}
 #' @param ... Other arguments passed to \code{\link{available.packages}}
 #'
 #' @export
 #' @family dependency functions
 #'
 #' @example /inst/examples/example_pkgDep.R
 
-pkgDep <- function(pkg, availPkgs, repos=getOption("repos"), type="source", depends=TRUE, suggests=TRUE, enhances=FALSE, includeBasePkgs=FALSE, ...){
+pkgDep <- function(pkg, availPkgs, repos=getOption("repos"), type="source", depends=TRUE, suggests=TRUE, enhances=FALSE, includeBasePkgs=FALSE, Rversion = R.version, ...){
   if(!depends & !suggests & !enhances) {
     warning("Returning nothing, since depends, suggests and enhances are all FALSE")
     return(character(0))
@@ -49,7 +50,7 @@ pkgDep <- function(pkg, availPkgs, repos=getOption("repos"), type="source", depe
       repos <- c(CRAN="http://cran.revolutionanalytics.com")
     }
     if(is.na(type)) type <- "source"
-    availPkgs <- pkgAvail(repos=repos, type=type, ...)
+    availPkgs <- pkgAvail(repos=repos, type=type, Rversion = Rversion, ...)
   }
   if(nrow(availPkgs) == 0){
     stop("Unable to retrieve available packages from CRAN")
@@ -125,14 +126,51 @@ print.pkgDep <- function(x, ...){
 #' @export
 #' @family create repo functions
 #' @seealso \code{\link{pkgDep}}
-pkgAvail <- function(repos=getOption("repos"), type="source"){
+pkgAvail <- function(repos=getOption("repos"), type="source", Rversion = R.version){
   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")
     }
   }
-  available.packages(contrib.url(repos, type=type), type=type, filters=list())
+  utils::available.packages(contribUrl(repos, type=type, Rversion = Rversion), type=type, filters=list())
 }
 
+
+# Modified copy of utils::contrib.url()
+contribUrl <- function (repos, type = getOption("pkgType"), Rversion = R.version) {
+  Rversion <- twodigitRversion(Rversion)
+  if (type == "both") 
+    type <- "source"
+  if (type == "binary") 
+    type <- .Platform$pkgType
+  if (is.null(repos)) 
+    return(NULL)
+  if ("@CRAN@" %in% repos && interactive()) {
+    cat(gettext("--- Please select a CRAN mirror for use in this session ---"), 
+        "\n", sep = "")
+    flush.console()
+    chooseCRANmirror()
+    m <- match("@CRAN@", repos)
+    nm <- names(repos)
+    repos[m] <- getOption("repos")["CRAN"]
+    if (is.null(nm)) 
+      nm <- rep("", length(repos))
+    nm[m] <- "CRAN"
+    names(repos) <- nm
+  }
+  if ("@CRAN@" %in% repos) 
+    stop("trying to use CRAN without setting a mirror")
+  ver <- Rversion
+  mac.path <- "macosx"
+  if (substr(type, 1L, 11L) == "mac.binary.") {
+    mac.path <- paste(mac.path, substring(type, 12L), sep = "/")
+    type <- "mac.binary"
+  }
+  res <- switch(type, 
+                source = paste(gsub("/$", "", repos), "src", "contrib", sep = "/"), 
+                mac.binary = paste(gsub("/$", "", repos), "bin", mac.path, "contrib", ver, sep = "/"), 
+                win.binary = paste(gsub("/$", "", repos), "bin", "windows", "contrib", ver, sep = "/"))
+  res
+}

R/testSuiteFunctions.R

@@ -11,37 +11,23 @@
 }
 
 
-# Use in unit tests to copy sample repo to path
-# .copySampleRepo <- function(path){
-#   file.copy(
-#     from = list.dirs(system.file("inst/sample-repo", package="miniCRAN"), recursive = FALSE),
-#     to = path,
-#     recursive = TRUE
-#   )
-#   updateRepoIndex(path=path, 
-#                   type=c("source", "win.binary", "mac.binary.mavericks"), 
-#                   Rversion=list(major=3, minor=1))
-#   invisible(NULL)
-# }
-
-
 # Create sample repo from MRAN snapshot
-.createSampleRepo <- function(MRAN, path, pkgs, Rversion=list(major=3, minor=1)){
+.createSampleRepo <- function(MRAN, path, pkgs, Rversion="3.1"){
   if(missing(MRAN)) MRAN <- c(CRAN="http://mran.revolutionanalytics.com/snapshot/2014-10-15")
   if(missing(path)) path <- file.path(tempdir(), "miniCRAN", Sys.Date())
   if(missing(pkgs)) pkgs <- c("chron", "adaptivetau")
 
-  pdb_source <- pkgAvail(repos=MRAN, type="source")
-  pdb_win    <- pkgAvail(repos=MRAN, type="win.binary")
-  pdb_mac    <- pkgAvail(repos=MRAN, type="mac.binary.mavericks")
+  pdb_source <- pkgAvail(repos=MRAN, type="source", Rversion = Rversion)
+  pdb_win    <- pkgAvail(repos=MRAN, type="win.binary", Rversion = Rversion)
+  pdb_mac    <- pkgAvail(repos=MRAN, type="mac.binary", Rversion = Rversion)
 
 
-  pkgList_source <- pkgDep(pkgs, availPkgs=pdb_source, repos=MRAN, type="source", suggests=FALSE)
-  makeRepo(pkgList_source, path=path, repos=MRAN, type="source", quiet=TRUE)
+  pkgList_source <- pkgDep(pkgs, availPkgs=pdb_source, repos=MRAN, type="source", suggests=FALSE, Rversion = Rversion)
+  makeRepo(pkgList_source, path=path, repos=MRAN, type="source", quiet=TRUE, Rversion = Rversion)
 
-  pkgList_win <- pkgDep(pkgs, availPkgs=pdb_win, repos=MRAN, type="win.binary", suggests=FALSE)
-  makeRepo(pkgList_win, path=path, repos=MRAN, type="win.binary", quiet=TRUE)
+  pkgList_win <- pkgDep(pkgs, availPkgs=pdb_win, repos=MRAN, type="win.binary", suggests=FALSE, Rversion = Rversion)
+  makeRepo(pkgList_win, path=path, repos=MRAN, type="win.binary", quiet=TRUE, Rversion = Rversion)
 
-  pkgList_mac <- pkgDep(pkgs, availPkgs=pdb_mac, repos=MRAN, type="mac.binary.mavericks", suggests=FALSE)
-  makeRepo(pkgList_mac, path=path, repos=MRAN, type="mac.binary.mavericks", quiet=TRUE)
+  pkgList_mac <- pkgDep(pkgs, availPkgs=pdb_mac, repos=MRAN, type="mac.binary", suggests=FALSE, Rversion = Rversion)
+  makeRepo(pkgList_mac, path=path, repos=MRAN, type="mac.binary", quiet=TRUE, Rversion = Rversion)
 }

R/updatePackages.R

@@ -22,10 +22,12 @@
 #'
 #' @example /inst/examples/example_updatePackages.R
 #'
-oldPackages <- function (path=NULL, repos=getOption("repos"),
-                         availPkgs=pkgAvail(repos=repos, type=type),
-                         method, availableLocal=pkgAvail(repos=path, type=type), type="source",
-                         Rversion=R.version) {
+oldPackages <- function (path = NULL, 
+                         repos = getOption("repos"),
+                         availPkgs = pkgAvail(repos=repos, type=type, Rversion=Rversion),
+                         method, 
+                         availableLocal = pkgAvail(repos=path, type=type, Rversion=Rversion), type="source",
+                         Rversion = R.version) {
   if (is.null(path)) stop("path to miniCRAN repo must be specified")
   if (!missing(availPkgs)) {
     if (!is.matrix(availPkgs) || !is.character(availPkgs[, "Package"]))
@@ -64,13 +66,14 @@ oldPackages <- function (path=NULL, repos=getOption("repos"),
 #' @export
 #'
 updatePackages <- function (path=NULL, repos=getOption("repos"),
-                            method, ask=TRUE, availPkgs=pkgAvail(repos=repos, type=type),
+                            method, ask=TRUE, 
+                            availPkgs=pkgAvail(repos=repos, type=type, Rversion=Rversion),
                             oldPkgs=NULL, type="source",
-                            Rversion=getRversion(),
+                            Rversion=R.version,
                             quiet=FALSE) {
   force(ask)
   simplifyRepos <- function(repos, type) {
-    tail <- substring(contrib.url("---", type), 4)
+    tail <- substring(contribUrl("---", type=type, Rversion=Rversion), 4)
     ind <- regexpr(tail, repos, fixed=TRUE)
     ind <- ifelse(ind > 0, ind-1, nchar(repos, type="c"))
     substr(repos, 1, ind)
@@ -129,6 +132,6 @@ updatePackages <- function (path=NULL, repos=getOption("repos"),
     oldPkgs
   }
   if (length(update[,"Package"])) {
-    addPackage(update[,"Package"], path=path, repos=repos, type=type, quiet=quiet, deps=FALSE)
+    addPackage(update[,"Package"], path=path, repos=repos, type=type, quiet=quiet, deps=FALSE, Rversion=Rversion)
   }
 }

inst/doc/miniCRAN-dependency-graph.R

@@ -1,5 +1,5 @@
 ## ----init----------------------------------------------------------------
-library(miniCRAN)
+library("miniCRAN")
 
 ## ----pkgdep--------------------------------------------------------------
 tags <- "chron"