Merge pull request #66 from Microsoft/richcala/R-3.5.0Update

Changes for MRO 3.5.0

additionalPackages/RevoIOQ/DESCRIPTION

@@ -1,5 +1,5 @@
 Package: RevoIOQ
-Version: 8.0.10
+Version: 10.0.0
 Date: 2018-03-28
 Title: Microsoft R Services Test Suite
 Author: Microsoft Corporation
@@ -9,4 +9,5 @@ Suggests: RevoUtils
 Description: Test suite for Microsoft R Services.
 License: GPL-2
 Copyright: Copyright Microsoft Corporation
-BuildID: 9.4.1.0077
+BuildID: 10.0.0.5
+

additionalPackages/RevoIOQ/R/RevoIOQ.R

@@ -488,9 +488,10 @@ runRevoTestSuite <- function(testSuites, useOwnErrorHandler=TRUE, runTestFileInO
         save(.testLogger, testFile, testSuite, file=storefile)
         testscript <- gsub("\\\\", "/", tempfile(pattern="RevoIOQTest"))
         cat("library(RevoIOQ)\n",
-            if (length(grep("RevoScaleR", testFile)) > 0) "require(RevoScaleR)\n",
+            if (length(grep("RevoScaleR", testFile)) > 0) "require(RevoScaleR)\n",		
 			"Sys.setlocale('LC_COLLATE', 'C')\n",
             paste("load('", storefile, "', envir=.GlobalEnv)\n", sep=""),
+			"RUnitEnv <- .GlobalEnv\n",
             "RNGkind(kind=testSuite$rngKind, normal.kind=testSuite$rngNormalKind)\n",
              paste("RUnit:::.sourceTestFile('", testFile,"', '", testSuite$testFuncRegexp, "')\n",sep=""),
 		 paste("save(.testLogger, file='", storefile, "')\n",sep=""), "q('no')\n",

additionalPackages/RevoIOQ/inst/unitTests/R/common/runit-errormsgs.R

@@ -136,7 +136,9 @@ options(error=expression())
     checkException(delayedAssign(pi, "foo"))
     checkException(on.exit(ls(), add=NA_real_))
     checkException(on.exit(ls(), add=NA))
-    checkException(on.exit(1,2,3))
+	if (compareVersion(paste(R.version$major, R.version$minor, sep="."), "3.5.0") < 0) {
+		checkException(on.exit(1,2,3))
+	}
     (x <- new.env())
     (parent.env(x) <- emptyenv())
     checkException(parent.env(x) <- pi)

additionalPackages/RevoIOQ/inst/unitTests/Revo/common/runit.revo.common.version.R

@@ -18,28 +18,28 @@ if (!identical(system.file(package="RevoScaleR") , "")) {
     "test.revor.RevoUtilsMath.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoUtilsMath", ver = "10.0.1"))
 }
 if (!identical(system.file(package="foreach") , "")) {
-    "test.revoparallelr.foreach.version" <- function() checkTrue("checkPackageVersion"(pkg = "foreach", ver = "1.4.5"))
-    "test.revoparallelr.iterators.version" <- function() checkTrue("checkPackageVersion"(pkg = "iterators", ver = "1.0.9"))
+    "test.revoparallelr.foreach.version" <- function() checkTrue("checkPackageVersion"(pkg = "foreach", ver = "1.5.0"))
+    "test.revoparallelr.iterators.version" <- function() checkTrue("checkPackageVersion"(pkg = "iterators", ver = "1.0.10"))
 }
 if (!identical(system.file(package="RevoMods"), ""))
 {
     "test.revor.RevoIOQ.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoIOQ", ver = revover))
     "test.revor.RUnit.version" <- function() checkTrue("checkPackageVersion"(pkg = "RUnit", ver = "0.4.26"))
-    "test.revoparallelr.doParallel.version" <- function() checkTrue("checkPackageVersion"(pkg = "doParallel", ver = "1.0.12"))
-    "test.revor.RevoUtils.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoUtils", ver = "10.0.9"))
+    "test.revoparallelr.doParallel.version" <- function() checkTrue("checkPackageVersion"(pkg = "doParallel", ver = "1.0.13"))
+    "test.revor.RevoUtils.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoUtils", ver = "11.0.0"))
     "test.revor.RevoMods.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoMods", ver = "11.0.0"))
 } else
 {
     if (!identical(system.file(package="RevoUtilsMath"),""))
 	{
-        "test.revor.RevoUtilsMath.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoUtilsMath", ver = "10.0.1"))   
+        "test.revor.RevoUtilsMath.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoUtilsMath", ver = "11.0.0"))   
     } 
 	if (!identical(system.file(package="RevoUtils"),""))
 	{
-		"test.revor.RevoUtils.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoUtils", ver = "10.0.7"))
+		"test.revor.RevoUtils.version" <- function() checkTrue("checkPackageVersion"(pkg = "RevoUtils", ver = "11.0.0"))
 	}
     if (!identical(system.file(package="doParallel"),""))
 	{
-        "test.revoparallelr.doParallel.version" <- function() checkTrue("checkPackageVersion"(pkg = "doParallel", ver = "1.0.12"))
+        "test.revoparallelr.doParallel.version" <- function() checkTrue("checkPackageVersion"(pkg = "doParallel", ver = "1.0.13"))
 	}
 }

additionalPackages/RevoUtils/DESCRIPTION

@@ -1,12 +1,12 @@
 Package: RevoUtils
-Version: 10.0.9
-Date: 2018-04-15
-RevoBuildID: 10.0.9.0125
+Version: 11.0.0
+Date: 2018-06-07
+RevoBuildID: {11.0.0.6}
 Title: Microsoft R Utility Package
 Author: Microsoft Corporation
 Maintainer: Microsoft Corporation <mrspack@microsoft.com>
 SystemRequirements: R (>= 3.0.0)
 Description: Utility functions for Microsoft R
 License: GPL-2
 Copyright: Microsoft Corporation
-MRANDate: 2018-04-01
+MRANDate: 2018-06-01

additionalPackages/checkpoint/.Renviron

@@ -0,0 +1 @@
+NOT_CRAN="true"

additionalPackages/checkpoint/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: checkpoint
 Title: Install Packages from Snapshots on the Checkpoint Server for
-        Reproducibility
+    Reproducibility
 Description: The goal of checkpoint is to solve the problem of package
     reproducibility in R. Specifically, checkpoint allows you to install packages
     as they existed on CRAN on a specific snapshot date as if you had a CRAN time
@@ -15,10 +15,10 @@ Description: The goal of checkpoint is to solve the problem of package
     server (<https://mran.microsoft.com/>). Immediately after completion
     of the rsync mirror process, the process takes a snapshot, thus creating the
     archive. Snapshot archives exist starting from 2014-09-17.
-Version: 0.4.0
-Date: 2017-04-10
+Version: 0.4.4
+Date: 2018-04-09
 Author: Microsoft Corporation
-Maintainer: Andrie de Vries <adevries@microsoft.com>
+Maintainer: Rich Calaway <richcala@microsoft.com>
 Copyright: Microsoft
 License: GPL-2
 URL: https://github.com/RevolutionAnalytics/checkpoint
@@ -31,7 +31,10 @@ Suggests:
     knitr,
     rmarkdown,
     testthat(>= 0.9),
-    MASS
+    MASS,
+    darts,
+    mockery,
+    cli
 VignetteBuilder: knitr
 RoxygenNote: 6.0.1
 Roxygen: list(markdown = TRUE)

additionalPackages/checkpoint/NAMESPACE

@@ -6,6 +6,7 @@ export(checkpointRemove)
 export(getAccessDate)
 export(getValidSnapshots)
 export(mranUrl)
+export(scanForPackages)
 export(setSnapshot)
 export(unCheckpoint)
 importFrom(utils,Stangle)

additionalPackages/checkpoint/R/checkpoint.R

@@ -114,11 +114,11 @@ checkpoint <- function(snapshotDate, project = getwd(),
     }
   }
 
-  authorizeFileSystemUse(checkpointLocation)
-
   fixRstudioBug()
 
+
   # Create checkpoint folders
+  authorizeFileSystemUse(checkpointLocation)
   if(!createFolders(snapshotDate = snapshotDate, 
                     checkpointLocation = checkpointLocation))
     stop("Unable to create checkpoint folders at checkpointLocation = \"",
@@ -152,9 +152,10 @@ checkpoint <- function(snapshotDate, project = getwd(),
   if(isTRUE(scanForPackages)){
     mssg(verbose, "Scanning for packages used in this project")
     pkgs <- scanForPackages(project, use.knitr = use.knitr, 
-                                scan.rnw.with.knitr = scan.rnw.with.knitr,
-                                auto.install.knitr = auto.install.knitr
-                                )
+                            scan.rnw.with.knitr = scan.rnw.with.knitr,
+                            auto.install.knitr = auto.install.knitr,
+                            verbose = verbose
+    )
     packages.detected <- pkgs[["pkgs"]]
     mssg(verbose, "- Discovered ", length(packages.detected), " packages")
 

additionalPackages/checkpoint/R/checkpoint_internals.R

@@ -2,7 +2,9 @@
 setMranMirror <- function(
   snapshotDate, 
   snapshotUrl = checkpoint:::getSnapshotUrl(snapshotDate)){
-  options(repos = snapshotUrl)}
+  options(repos = snapshotUrl)
+}
+
 
 setLibPaths <- function(checkpointLocation, libPath){
   newLoc <- c(libPath, 

additionalPackages/checkpoint/R/checkpoint_log.R

@@ -42,4 +42,4 @@ checkpoint_log <- function(log, snapshotDate, pkg, file = NULL){
       )
     }
   }
-}  
+}

additionalPackages/checkpoint/R/checkpoint_paths.R

@@ -47,14 +47,19 @@ file.path <- function(...){
 
 # If the folder doesn't exists, ask user permission to create it
 # The argument interactive is purely for testing purposes
-authorizeFileSystemUse <- function(checkpointLocation, interactive = interactive()) {
+authorizeFileSystemUse <- function(checkpointLocation = "~/", 
+                                   interactive) {
+  if (missing(interactive)){
+	isInteractive <- base::interactive()
+	interactive <- isInteractive
+  }
   checkpointRoot = file.path(checkpointLocation, ".checkpoint")
   if(file.exists(checkpointRoot)) {
     if(!file.info(checkpointRoot)$isdir)
       stop("Can't use a non-directory as checkpoint root")}
   else {
     if(interactive) {
-      message("Can I create directory", checkpointRoot, "for internal checkpoint use?\n")
+      message("Can I create directory ", checkpointRoot, " for internal checkpoint use?\n")
       answer = readline("Continue (y/n)? ")
       if(tolower(answer) != "y")
         stop("Cannot proceed without access to checkpoint directory")}

additionalPackages/checkpoint/R/scanRepoPackages.R

@@ -5,10 +5,18 @@ projectScanPackages <- function(...){
   scanForPackages(...)
 }
 
+#' Scans a project (or folder) for references to packages.
+#' 
+#' @inheritParams checkpoint
+#' @return A list with two elements:
+#' * pkgs: a character vector with the names of identified packages
+#' * error: a character vector with information about files that could not be parsed
+#' @export
 scanForPackages <- function(project = getwd(), verbose = TRUE, 
-                                use.knitr = FALSE, 
-                                auto.install.knitr = FALSE, 
-                                scan.rnw.with.knitr = FALSE){
+                            use.knitr = FALSE, 
+                            auto.install.knitr = FALSE, 
+                            scan.rnw.with.knitr = FALSE
+                          ){
   # detect all package dependencies for a project
   dir <- normalizePath(project, winslash='/', mustWork=FALSE)
   pattern <- if(!use.knitr) "\\.[rR]$|\\.[rR]nw$" else

additionalPackages/checkpoint/tests/test-all.R

@@ -1,3 +1,4 @@
+library(cli)
 library(testthat)
 old.env <- Sys.getenv("checkpoint.mock.install")
 Sys.setenv("checkpoint.mock.install" = TRUE)

additionalPackages/checkpoint/tests/testthat/test-0-is-404.R

@@ -1,31 +1,53 @@
 if(interactive()) library(testthat)
+library(mockery)
 
 context("is.404")
 
 test_that("is.404", {
   skip_if_offline()
-  expect_true(is.404("http://mran.microsoft.com/snapshot/1972-01-01", warn = FALSE))
-  expect_false(is.404("http://mran.microsoft.com/snapshot"))
-  expect_false(is.404("http://mran.microsoft.com/snapshot/2015-05-01"))
+  skip_on_cran()
+  expect_true(
+    is.404("http://mran.microsoft.com/snapshot/1972-01-01", warn = FALSE)
+  )
+  expect_false(
+    is.404("http://mran.microsoft.com/snapshot")
+  )
+  expect_false(
+    is.404("http://mran.microsoft.com/snapshot/2015-05-01")
+  )
 })
 
 test_that("is.404 works with https", {
 
   if(!httpsSupported()) skip("https not supported")
-  expect_true(suppressWarnings(is.404("https://mran.microsoft.com/snapshot/1972-01-01")))
-  expect_false(is.404("https://mran.microsoft.com/snapshot"))
-  expect_false(is.404("https://mran.microsoft.com/snapshot/2015-05-01"))
+  expect_true(
+    suppressWarnings(is.404("https://mran.microsoft.com/snapshot/1972-01-01"))
+  )
+  expect_false(
+    is.404("https://mran.microsoft.com/snapshot")
+  )
+  expect_false(
+    is.404("https://mran.microsoft.com/snapshot/2015-05-01")
+  )
 
 })
 
 test_that("is.404 gracefully deals with https URLs when https not supported", {
 
-  with_mock(`checkpoint:::httpsSupported` = function(mran) FALSE, {
-    # if(!httpsSupported()) skip("https not supported")
-    expect_true(is.404("https://mran.microsoft.com/snapshot/1972-01-01", warn = FALSE))
-    expect_true(is.404("https://mran.microsoft.com/snapshot", warn = FALSE))
-    expect_true(is.404("https://mran.microsoft.com/snapshot/2015-05-01", warn = FALSE))
-  })
+  stub(is.404, "httpsSupported", function(mran) FALSE)
+  expect_true(
+    is.404("https://mran.microsoft.com/snapshot/1972-01-01", warn = FALSE)
+  )
+
+  # stub(is.404, "httpsSupported", function(mran) FALSE)
+  expect_true(
+    is.404("https://mran.microsoft.com/snapshot", warn = FALSE)
+  )
+
+  # stub(is.404, "httpsSupported", function(mran) FALSE)
+  expect_true(
+    is.404("https://mran.microsoft.com/snapshot/2015-05-01", warn = FALSE)
+  )
 
 })
 

additionalPackages/checkpoint/tests/testthat/test-2-snapshot-dates.R

@@ -1,4 +1,5 @@
 if(interactive()) library("testthat")
+library(mockery)
 context("getValidSnapshots finds valid dates")
 
 
@@ -26,16 +27,17 @@ test_that("suggests a reasonable alternative", {
 })
 
 test_that("works with no network connection", {
-  with_mock(`getValidSnapshots` = function(...){x <- character(0); class(x) = "error"; x}, {
-    expect_message(stopIfInvalidDate("2015-06-05"),
-                   "Unable to connect to MRAN. Skipping some date validations."
-    )
-    with_mock(`getValidSnapshots` = function(...){x <- character(0); class(x) = "error"; x}, {
-      expect_message(stopIfInvalidDate("2015-06-05"),
-                     "Unable to connect to MRAN. Skipping some date validations."
-      )
-    })
-  })
+  stub(stopIfInvalidDate, "getValidSnapshots", 
+       function(...){x <- character(0); class(x) = "error"; x}
+  )
+  expect_message(
+    stopIfInvalidDate("2015-06-05"),
+    "Unable to connect to MRAN. Skipping some date validations."
+  )
+  expect_message(
+    stopIfInvalidDate("2015-06-05"),
+    "Unable to connect to MRAN. Skipping some date validations."
+  )
 })
 
 test_that("works on local file", {

additionalPackages/checkpoint/tests/testthat/test-3-checkpoint.R

@@ -11,7 +11,8 @@ test.start <- switch(current.R,
                      "3.1" = "2014-10-01",
                      "3.2" = "2015-05-01",
                      "3.3" = "2016-04-01",
-                     "2016-04-01"
+                     "3.4" = "2017-04-24",
+                     "2017-04-24"
 )
 
 MRAN.default = test.start[1] # ensure only a single value