Merge branch 'dev'

.travis.yml

@@ -1,29 +1,22 @@
-language: c
+language: r
+sudo: false
+cache: packages
 
-before_install:
-  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
-  - chmod 755 ./travis-tool.sh
-  - ./travis-tool.sh bootstrap
+repos:
+  CRAN: https://cloud.r-project.org
 
 env: NOT_CRAN="true"
 
-install:
-  - ./travis-tool.sh install_deps
-  - Rscript -e 'install.packages("igraph", repos=c(CRAN="http:/cran.revolutionanalytics.com"))'
-
-script: ./travis-tool.sh run_tests
-
-after_failure:
-  - ./travis-tool.sh dump_logs
-
-notifications:
-  email:
-    on_success: change
-    on_failure: change
-
 branches:
   only:
     - master
     - release
     - dev
-    - update-repo
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
+
+
+

DESCRIPTION

@@ -14,10 +14,10 @@ Description: Makes it possible to create an internally consistent
     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: 0.2.5
+Version: 0.2.6
 URL: https://github.com/RevolutionAnalytics/miniCRAN
 BugReports: https://github.com/RevolutionAnalytics/miniCRAN/issues
-Date: 2016-04-12
+Date: 2016-06-26
 Imports:
     tools,
     XML,

NEWS

@@ -1,13 +1,24 @@
+miniCRAN v0.2-6 (Release date: 2016-06-26)
+==============
+
+* allow using `makeRepo()` to create a miniCRAN repo from an existing local miniCRAN, i.e. the repos contains file:/// prefix. This enables a use case in the AzureML package. (#76)
+* easily manage packages for all three Operating Systems (#24)
+* fix inconsistent use of Rversion in `addPackage()` (#42)
+
+
 miniCRAN v0.2-5 (Release date: 2016-04-12)
 ==============
 
 * plot.pkgDepGraph() now displays legend only for edges that are actually in graph
+* make consistent use of Rversion argument (#42)
+
 
 miniCRAN v0.2-4 (Release date: 2016-03-27)
 ==============
 
 * Changed copyright to Microsoft
 
+
 miniCRAN v0.2-2 (Release date: 2015-03-25)
 ==============
 

R/MRAN.R

@@ -1,5 +1,5 @@
 MRAN <- function(snapshot){
-  url <- "http://mran.microsoft.com"
+  url <- "https://mran.microsoft.com"
   if(missing("snapshot") || is.null(snapshot)){
   url
   } else {

R/addPackages.R

@@ -8,7 +8,7 @@
 #'
 #' @param type  character, indicating the type of package to download and install. See \code{\link{install.packages}}.
 #'
-#' @param Rversion numeric version of the R system for which to fetch packages. See \code{\link{R_system_version}}.
+#' @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}}
 #'
 #' @return Returns invisibly the filepaths to packages with multiple versions for removal.
 #'
@@ -46,11 +46,11 @@ checkVersions <- function(pkgs=NULL, path=NULL, type="source",
 #' @inheritParams makeRepo
 #' @inheritParams pkgDep
 #'
-#' @param Rversion numeric version of the R system for which to fetch packages. See \code{\link{R_system_version}}.
+#' @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 deps logical indicating whether the package dependencies should be added (default \code{TRUE}).
 #'
-#' @return Installs the packages, rebuilds the package index, and invisibly returns the number of packages writen to the index files.
+#' @return Installs the packages, rebuilds the package index, and invisibly returns the number of packages written to the index files.
 #'
 #' @importFrom tools write_PACKAGES
 #' @export
@@ -62,27 +62,32 @@ addPackage <- function(pkgs=NULL, path=NULL, repos=getOption("repos"),
                        type="source", Rversion=R.version,
                        writePACKAGES=TRUE, deps=TRUE, quiet=FALSE) {
   if (is.null(path) || is.null(pkgs)) stop("path and pkgs must both be specified.")
-  prev <- checkVersions(pkgs=pkgs, path=path, type=type, Rversion=Rversion)
-  prev.df <- getPkgVersFromFile(prev)
 
-  if (deps) pkgs <- pkgDep(pkgs, repos=repos, type=type)
+  lapply(type, function(t) {
+    prev <- checkVersions(pkgs=pkgs, path=path, type=t, Rversion=Rversion)
+    prev.df <- getPkgVersFromFile(prev)
 
-  makeRepo(pkgs=pkgs, path=path, repos=repos, type=type, Rversion=Rversion,
-           download=TRUE, writePACKAGES=FALSE, quiet=quiet)
+    if (deps) pkgs <- pkgDep(pkgs, repos = repos, type = t, Rversion = Rversion)
 
-  if (length(prev)) {
-    curr <- suppressWarnings(
-              checkVersions(pkgs=pkgs, path=path, type=type, Rversion=Rversion)
-            )
-    curr.df <- getPkgVersFromFile(curr)
+    makeRepo(pkgs = pkgs, path = path, repos = repos, type = t, Rversion = Rversion,
+             download = TRUE, writePACKAGES = FALSE, quiet = quiet)
 
-    dupes <- with(curr.df, package[duplicated(package)])
-    if (length(dupes)) {
-      old <- lapply(dupes, function(x) { grep(paste0("^", x), basename(prev)) } )
-      file.remove(prev[unlist(old)])
+    if (length(prev)) {
+      curr <- suppressWarnings(
+        checkVersions(pkgs=pkgs, path=path, type=t, Rversion=Rversion)
+      )
+      curr.df <- getPkgVersFromFile(curr)
+
+      dupes <- with(curr.df, package[duplicated(package)])
+      if (length(dupes)) {
+        old <- lapply(dupes, function(x) { grep(paste0("^", x), basename(prev)) } )
+        file.remove(prev[unlist(old)])
+      }
     }
-  }
-  if (writePACKAGES) invisible(updateRepoIndex(path=path, type=type, Rversion=Rversion))
+  })
+
+  n <- if (writePACKAGES) updateRepoIndex(path=path, type=type, Rversion=Rversion)
+  return(invisible(n))
 }
 
 
@@ -99,7 +104,7 @@ addPackage <- function(pkgs=NULL, path=NULL, repos=getOption("repos"),
 #'
 #' @param vers The package version to install.
 #'
-#' @return Installs the packages, rebuilds the package index, and invisibly returns the number of packages writen to the index files.
+#' @return Adds the packages, rebuilds the package index, and invisibly returns the number of packages written to the index files.
 #'
 #' @note Dependencies for old package versions cannot be determined automatically and must be specified by the user in \code{pkgs} and \code{vers}. Thus, \code{deps=FALSE} is the default for this function.
 #'
@@ -119,8 +124,8 @@ addOldPackage <- function(pkgs=NULL, path=NULL, vers=NULL,
   if (type!="source") stop("Older binary versions are not normally available on CRAN. ",
                            "You must build the binary versions from source.")
   if(deps) {
-    message("Unable to automatically determine dependency version information.")
-    message("Use pkgs and vers to identify which dependecies and their versions to download.")
+    message("Unable to automatically determine dependency version information.\n",
+            "Use pkgs and vers to identify which dependecies and their versions to download.")
   }
   vers <- as.character(vers)
   oldPkgs <- file.path(repos, repoPrefix(type, R.version), "Archive",
@@ -129,10 +134,8 @@ addOldPackage <- function(pkgs=NULL, path=NULL, vers=NULL,
   pkgPath <- repoBinPath(path=path, type=type, Rversion=Rversion)
   if(!file.exists(pkgPath)) dir.create(pkgPath, recursive=TRUE)
   sapply(oldPkgs, function(x) {
-    result <- download.file(x, destfile=file.path(pkgPath, basename(x)),
-                            method="auto",
-                            mode="wb",
-                            quiet=quiet)
+    result <- utils::download.file(x, destfile=file.path(pkgPath, basename(x)),
+                                   method="auto", mode="wb", quiet=quiet)
     if(result!=0) warning("error downloading file ", x)
   })
   if (writePACKAGES) invisible(updateRepoIndex(path=path, type=type, Rversion))

R/helpers.R

@@ -1,6 +1,6 @@
 #' Get the path to the repo directory containing the package files.
 #'
-#' @param Rversion numeric version of the R system for which to fetch packages. See \code{\link{R_system_version}}.
+#' @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 type  character, indicating the type of package to download and install. See \code{\link{install.packages}}.
 #'

R/makeRepo.R

@@ -36,42 +36,64 @@
 #' @note Internally makes use of \code{\link[utils]{download.packages}} and \code{\link{write_PACKAGES}}
 #'
 #' @inheritParams pkgDep
-#' 
+#'
 #' @param pkgs Character vector of packages to download
-#' 
+#'
 #' @param path Destination download path. This path is the root folder of your new repository.
-#' 
+#'
 #' @param Rversion List with two named elements: `major` and `minor`. If not supplied, defaults to system version of R, using \code{\link{R.version}}.  Only used if \code{type} is not "source"
-#' 
+#'
 #' @param download If TRUE downloads packages.
-#' 
+#'
 #' @param quiet If TRUE, suppress status messages (if any), and the progress bar during download.
-#' 
+#'
 #' @param writePACKAGES If TRUE, calls \code{\link{write_PACKAGES}} to update the repository PACKAGES file.
 #'
 #' @export
 #' @family update repo functions
-#' 
+#'
 #' @example /inst/examples/example_makeRepo.R
 makeRepo <- function(pkgs, path, repos=getOption("repos"), type="source",
                      Rversion=R.version, download=TRUE, writePACKAGES=TRUE, quiet=FALSE) {
   if(!file.exists(path)) stop("Download path does not exist")
-  pkgPath <- repoBinPath(path=path, type=type, Rversion=Rversion)
-  if(!file.exists(pkgPath)) {
-    result <- dir.create(pkgPath, recursive=TRUE, showWarnings = FALSE)
-    if(result) {
-      if(!quiet) message("Created new folder: ", pkgPath)
-    } else {
-      stop("Unable to create repo path: ", pkgPath)
+
+  downloaded <- lapply(type, function(type) {
+    pkgPath <- repoBinPath(path=path, type=type, Rversion=Rversion)
+    if(!file.exists(pkgPath)) {
+      result <- dir.create(pkgPath, recursive=TRUE, showWarnings = FALSE)
+      if(result) {
+        if(!quiet) message("Created new folder: ", pkgPath)
+      } else {
+        stop("Unable to create repo path: ", pkgPath)
+      }
+    }
+
+    pdb <- pkgAvail(repos = repos, type=type, Rversion = Rversion)
+
+    if(download) {
+      utils::download.packages(pkgs, destdir=pkgPath, available=pdb, repos=repos,
+                               contriburl = contribUrl(repos, type, Rversion),
+                               type=type, quiet=quiet)
+    }
+  })
+
+  if(download){
+
+    downloaded <- downloaded[[1]][, 2]
+
+    fromLocalRepos <- grepl("^file://", repos)
+    if(fromLocalRepos){
+      # need to copy files to correct folder
+      repoPath <- gsub("^file:///", "", repos)
+      repoPath <- normalizePath(repoPath, winslash = "/")
+      newPath  <- gsub(repoPath, normalizePath(path, winslash = "/"), downloaded)
+      file.copy(downloaded, newPath)
+      downloaded <- newPath
     }
   }
 
-  pdb <- pkgAvail(repos = repos, type=type, Rversion = Rversion)
-
-  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)
+  if(download) downloaded else character(0)
 }
 
 
@@ -80,11 +102,13 @@ makeRepo <- function(pkgs, path, repos=getOption("repos"), type="source",
 #' @rdname makeRepo
 #' @export
 updateRepoIndex <- function(path, type="source", Rversion=R.version) {
-  lapply(type, function(type){
+  n <- lapply(type, function(type){
     pkgPath <- repoBinPath(path=path, type=type, Rversion=Rversion)
     if(grepl("mac.binary", type)) type <- "mac.binary"
     tools::write_PACKAGES(dir=pkgPath, type=type)
   })
+  names(n) <- type
+  return(n)
 }
 
 
@@ -97,11 +121,11 @@ updateRepoIndex <- function(path, type="source", Rversion=R.version) {
 makeLibrary <- function(pkgs, path, type="source"){
   .Deprecated("makeRepo")
   NULL
-#   if(!file.exists(path)) stop("Download path does not exist")
-#   wd <- getwd()
-#   on.exit(setwd(wd))
-#   setwd(normalizePath(path))
-#   message(getwd())
-#   download.packages(pkgs, destdir=path, type=type)
+  #   if(!file.exists(path)) stop("Download path does not exist")
+  #   wd <- getwd()
+  #   on.exit(setwd(wd))
+  #   setwd(normalizePath(path))
+  #   message(getwd())
+  #   download.packages(pkgs, destdir=path, type=type)
 }
 

R/testthat_helpers.R

@@ -1,11 +1,24 @@
 # 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)
+is.online <- function(url = MRAN(), tryHttp = TRUE){
+  readFromUrl <- function(url){
+    z <- tryCatch(suppressWarnings(readLines(url, n = 1, warn = FALSE)),
+                  error = function(e)e
+    )
+    !inherits(z, "error")
+  }
+
+  if(!readFromUrl(url)){
+    if(grepl("^https://", url) && tryHttp){
+      url <- sub("^https://", "http://", url) # for older versions of R
+      if(!readFromUrl(url))
+        return(FALSE)
+    } else {
+      return(FALSE)
+    }
+  }
+
   TRUE
 }