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From shiva...@apache.org
Subject spark git commit: [SPARK-16579][SPARKR] add install.spark function
Date Wed, 10 Aug 2016 18:18:25 GMT
Repository: spark
Updated Branches:
  refs/heads/master d4a912243 -> 214ba66a0


[SPARK-16579][SPARKR] add install.spark function

## What changes were proposed in this pull request?

Add an install_spark function to the SparkR package. User can run `install_spark()` to install
Spark to a local directory within R.

Updates:

Several changes have been made:

- `install.spark()`
    - check existence of tar file in the cache folder, and download only if not found
    - trial priority of mirror_url look-up: user-provided -> preferred mirror site from
apache website -> hardcoded backup option
    - use 2.0.0

- `sparkR.session()`
    - can install spark when not found in `SPARK_HOME`

## How was this patch tested?

Manual tests, running the check-cran.sh script added in #14173.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14258 from junyangq/SPARK-16579.


Project: http://git-wip-us.apache.org/repos/asf/spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/214ba66a
Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/214ba66a
Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/214ba66a

Branch: refs/heads/master
Commit: 214ba66a030bc3a718c567a742b0db44bf911d61
Parents: d4a9122
Author: Junyang Qian <junyangq@databricks.com>
Authored: Wed Aug 10 11:18:23 2016 -0700
Committer: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Committed: Wed Aug 10 11:18:23 2016 -0700

----------------------------------------------------------------------
 R/check-cran.sh                           |   2 +-
 R/pkg/DESCRIPTION                         |   3 +-
 R/pkg/NAMESPACE                           |   2 +
 R/pkg/R/install.R                         | 235 +++++++++++++++++++++++++
 R/pkg/R/sparkR.R                          |  17 ++
 R/pkg/R/utils.R                           |   8 +
 R/pkg/inst/tests/testthat/test_sparkSQL.R |   4 +-
 7 files changed, 267 insertions(+), 4 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/spark/blob/214ba66a/R/check-cran.sh
----------------------------------------------------------------------
diff --git a/R/check-cran.sh b/R/check-cran.sh
index b3a6860..5c90fd0 100755
--- a/R/check-cran.sh
+++ b/R/check-cran.sh
@@ -47,6 +47,6 @@ $FWDIR/create-docs.sh
 
 VERSION=`grep Version $FWDIR/pkg/DESCRIPTION | awk '{print $NF}'`
 
-"$R_SCRIPT_PATH/"R CMD check --as-cran --no-tests SparkR_"$VERSION".tar.gz 
+"$R_SCRIPT_PATH/"R CMD check --as-cran SparkR_"$VERSION".tar.gz
 
 popd > /dev/null

http://git-wip-us.apache.org/repos/asf/spark/blob/214ba66a/R/pkg/DESCRIPTION
----------------------------------------------------------------------
diff --git a/R/pkg/DESCRIPTION b/R/pkg/DESCRIPTION
index ac73d6c..357ab00 100644
--- a/R/pkg/DESCRIPTION
+++ b/R/pkg/DESCRIPTION
@@ -7,7 +7,7 @@ Author: The Apache Software Foundation
 Maintainer: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
 Depends:
     R (>= 3.0),
-    methods,
+    methods
 Suggests:
     testthat,
     e1071,
@@ -31,6 +31,7 @@ Collate:
     'context.R'
     'deserialize.R'
     'functions.R'
+    'install.R'
     'mllib.R'
     'serialize.R'
     'sparkR.R'

http://git-wip-us.apache.org/repos/asf/spark/blob/214ba66a/R/pkg/NAMESPACE
----------------------------------------------------------------------
diff --git a/R/pkg/NAMESPACE b/R/pkg/NAMESPACE
index 1d74c6d..aaab92f 100644
--- a/R/pkg/NAMESPACE
+++ b/R/pkg/NAMESPACE
@@ -352,3 +352,5 @@ S3method(structField, character)
 S3method(structField, jobj)
 S3method(structType, jobj)
 S3method(structType, structField)
+
+export("install.spark")

http://git-wip-us.apache.org/repos/asf/spark/blob/214ba66a/R/pkg/R/install.R
----------------------------------------------------------------------
diff --git a/R/pkg/R/install.R b/R/pkg/R/install.R
new file mode 100644
index 0000000..987bac7
--- /dev/null
+++ b/R/pkg/R/install.R
@@ -0,0 +1,235 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#    http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+# Functions to install Spark in case the user directly downloads SparkR
+# from CRAN.
+
+#' Download and Install Apache Spark to a Local Directory
+#'
+#' \code{install.spark} downloads and installs Spark to a local directory if
+#' it is not found. The Spark version we use is the same as the SparkR version.
+#' Users can specify a desired Hadoop version, the remote mirror site, and
+#' the directory where the package is installed locally.
+#'
+#' The full url of remote file is inferred from \code{mirrorUrl} and \code{hadoopVersion}.
+#' \code{mirrorUrl} specifies the remote path to a Spark folder. It is followed by a subfolder
+#' named after the Spark version (that corresponds to SparkR), and then the tar filename.
+#' The filename is composed of four parts, i.e. [Spark version]-bin-[Hadoop version].tgz.
+#' For example, the full path for a Spark 2.0.0 package for Hadoop 2.7 from
+#' \code{http://apache.osuosl.org} has path:
+#' \code{http://apache.osuosl.org/spark/spark-2.0.0/spark-2.0.0-bin-hadoop2.7.tgz}.
+#' For \code{hadoopVersion = "without"}, [Hadoop version] in the filename is then
+#' \code{without-hadoop}.
+#'
+#' @param hadoopVersion Version of Hadoop to install. Default is \code{"2.7"}. It can take
other
+#'                      version number in the format of "x.y" where x and y are integer.
+#'                      If \code{hadoopVersion = "without"}, "Hadoop free" build is installed.
+#'                      See
+#'                      \href{http://spark.apache.org/docs/latest/hadoop-provided.html}{
+#'                      "Hadoop Free" Build} for more information.
+#'                      Other patched version names can also be used, e.g. \code{"cdh4"}
+#' @param mirrorUrl base URL of the repositories to use. The directory layout should follow
+#'                  \href{http://www.apache.org/dyn/closer.lua/spark/}{Apache mirrors}.
+#' @param localDir a local directory where Spark is installed. The directory contains
+#'                 version-specific folders of Spark packages. Default is path to
+#'                 the cache directory:
+#'                 \itemize{
+#'                   \item Mac OS X: \file{~/Library/Caches/spark}
+#'                   \item Unix: \env{$XDG_CACHE_HOME} if defined, otherwise \file{~/.cache/spark}
+#'                   \item Windows: \file{\%LOCALAPPDATA\%\\spark\\spark\\Cache}. See
+#'                         \href{https://www.microsoft.com/security/portal/mmpc/shared/variables.aspx}{
+#'                         Windows Common Folder Variables} about \%LOCALAPPDATA\%
+#'                 }
+#' @param overwrite If \code{TRUE}, download and overwrite the existing tar file in localDir
+#'                  and force re-install Spark (in case the local directory or file is corrupted)
+#' @return \code{install.spark} returns the local directory where Spark is found or installed
+#' @rdname install.spark
+#' @name install.spark
+#' @aliases install.spark
+#' @export
+#' @examples
+#'\dontrun{
+#' install.spark()
+#'}
+#' @note install.spark since 2.1.0
+#' @seealso See available Hadoop versions:
+#'          \href{http://spark.apache.org/downloads.html}{Apache Spark}
+install.spark <- function(hadoopVersion = "2.7", mirrorUrl = NULL,
+                          localDir = NULL, overwrite = FALSE) {
+  version <- paste0("spark-", packageVersion("SparkR"))
+  hadoopVersion <- tolower(hadoopVersion)
+  hadoopVersionName <- hadoop_version_name(hadoopVersion)
+  packageName <- paste(version, "bin", hadoopVersionName, sep = "-")
+  localDir <- ifelse(is.null(localDir), spark_cache_path(),
+                     normalizePath(localDir, mustWork = FALSE))
+
+  if (is.na(file.info(localDir)$isdir)) {
+    dir.create(localDir, recursive = TRUE)
+  }
+
+  packageLocalDir <- file.path(localDir, packageName)
+
+  if (overwrite) {
+    message(paste0("Overwrite = TRUE: download and overwrite the tar file",
+                   "and Spark package directory if they exist."))
+  }
+
+  # can use dir.exists(packageLocalDir) under R 3.2.0 or later
+  if (!is.na(file.info(packageLocalDir)$isdir) && !overwrite) {
+    fmt <- "Spark %s for Hadoop %s is found, and SPARK_HOME set to %s"
+    msg <- sprintf(fmt, version, ifelse(hadoopVersion == "without", "Free build", hadoopVersion),
+                   packageLocalDir)
+    message(msg)
+    Sys.setenv(SPARK_HOME = packageLocalDir)
+    return(invisible(packageLocalDir))
+  }
+
+  packageLocalPath <- paste0(packageLocalDir, ".tgz")
+  tarExists <- file.exists(packageLocalPath)
+
+  if (tarExists && !overwrite) {
+    message("tar file found.")
+  } else {
+    robust_download_tar(mirrorUrl, version, hadoopVersion, packageName, packageLocalPath)
+  }
+
+  message(sprintf("Installing to %s", localDir))
+  untar(tarfile = packageLocalPath, exdir = localDir)
+  if (!tarExists || overwrite) {
+    unlink(packageLocalPath)
+  }
+  message("DONE.")
+  Sys.setenv(SPARK_HOME = packageLocalDir)
+  message(paste("SPARK_HOME set to", packageLocalDir))
+  invisible(packageLocalDir)
+}
+
+robust_download_tar <- function(mirrorUrl, version, hadoopVersion, packageName, packageLocalPath)
{
+  # step 1: use user-provided url
+  if (!is.null(mirrorUrl)) {
+    msg <- sprintf("Use user-provided mirror site: %s.", mirrorUrl)
+    message(msg)
+    success <- direct_download_tar(mirrorUrl, version, hadoopVersion,
+                                   packageName, packageLocalPath)
+    if (success) return()
+  } else {
+    message("Mirror site not provided.")
+  }
+
+  # step 2: use url suggested from apache website
+  message("Looking for site suggested from apache website...")
+  mirrorUrl <- get_preferred_mirror(version, packageName)
+  if (!is.null(mirrorUrl)) {
+    success <- direct_download_tar(mirrorUrl, version, hadoopVersion,
+                                   packageName, packageLocalPath)
+    if (success) return()
+  } else {
+    message("Unable to find suggested mirror site.")
+  }
+
+  # step 3: use backup option
+  message("To use backup site...")
+  mirrorUrl <- default_mirror_url()
+  success <- direct_download_tar(mirrorUrl, version, hadoopVersion,
+                                 packageName, packageLocalPath)
+  if (success) {
+    return(packageLocalPath)
+  } else {
+    msg <- sprintf(paste("Unable to download Spark %s for Hadoop %s.",
+                         "Please check network connection, Hadoop version,",
+                         "or provide other mirror sites."),
+                   version, ifelse(hadoopVersion == "without", "Free build", hadoopVersion))
+    stop(msg)
+  }
+}
+
+get_preferred_mirror <- function(version, packageName) {
+  jsonUrl <- paste0("http://www.apache.org/dyn/closer.cgi?path=",
+                        file.path("spark", version, packageName),
+                        ".tgz&as_json=1")
+  textLines <- readLines(jsonUrl, warn = FALSE)
+  rowNum <- grep("\"preferred\"", textLines)
+  linePreferred <- textLines[rowNum]
+  matchInfo <- regexpr("\"[A-Za-z][A-Za-z0-9+-.]*://.+\"", linePreferred)
+  if (matchInfo != -1) {
+    startPos <- matchInfo + 1
+    endPos <- matchInfo + attr(matchInfo, "match.length") - 2
+    mirrorPreferred <- base::substr(linePreferred, startPos, endPos)
+    mirrorPreferred <- paste0(mirrorPreferred, "spark")
+    message(sprintf("Preferred mirror site found: %s", mirrorPreferred))
+  } else {
+    mirrorPreferred <- NULL
+  }
+  mirrorPreferred
+}
+
+direct_download_tar <- function(mirrorUrl, version, hadoopVersion, packageName, packageLocalPath)
{
+  packageRemotePath <- paste0(
+    file.path(mirrorUrl, version, packageName), ".tgz")
+  fmt <- paste("Downloading Spark %s for Hadoop %s from:\n- %s")
+  msg <- sprintf(fmt, version, ifelse(hadoopVersion == "without", "Free build", hadoopVersion),
+                 packageRemotePath)
+  message(msg)
+
+  isFail <- tryCatch(download.file(packageRemotePath, packageLocalPath),
+                     error = function(e) {
+                       message(sprintf("Fetch failed from %s", mirrorUrl))
+                       print(e)
+                       TRUE
+                     })
+  !isFail
+}
+
+default_mirror_url <- function() {
+  "http://www-us.apache.org/dist/spark"
+}
+
+hadoop_version_name <- function(hadoopVersion) {
+  if (hadoopVersion == "without") {
+    "without-hadoop"
+  } else if (grepl("^[0-9]+\\.[0-9]+$", hadoopVersion, perl = TRUE)) {
+    paste0("hadoop", hadoopVersion)
+  } else {
+    hadoopVersion
+  }
+}
+
+# The implementation refers to appdirs package: https://pypi.python.org/pypi/appdirs and
+# adapt to Spark context
+spark_cache_path <- function() {
+  if (.Platform$OS.type == "windows") {
+    winAppPath <- Sys.getenv("%LOCALAPPDATA%", unset = NA)
+    if (is.na(winAppPath)) {
+      msg <- paste("%LOCALAPPDATA% not found.",
+                   "Please define the environment variable",
+                   "or restart and enter an installation path in localDir.")
+      stop(msg)
+    } else {
+      path <- file.path(winAppPath, "spark", "spark", "Cache")
+    }
+  } else if (.Platform$OS.type == "unix") {
+    if (Sys.info()["sysname"] == "Darwin") {
+      path <- file.path(Sys.getenv("HOME"), "Library/Caches", "spark")
+    } else {
+      path <- file.path(
+        Sys.getenv("XDG_CACHE_HOME", file.path(Sys.getenv("HOME"), ".cache")), "spark")
+    }
+  } else {
+    stop(sprintf("Unknown OS: %s", .Platform$OS.type))
+  }
+  normalizePath(path, mustWork = FALSE)
+}

http://git-wip-us.apache.org/repos/asf/spark/blob/214ba66a/R/pkg/R/sparkR.R
----------------------------------------------------------------------
diff --git a/R/pkg/R/sparkR.R b/R/pkg/R/sparkR.R
index 524f7c4..f8bdee7 100644
--- a/R/pkg/R/sparkR.R
+++ b/R/pkg/R/sparkR.R
@@ -365,6 +365,23 @@ sparkR.session <- function(
     }
     overrideEnvs(sparkConfigMap, paramMap)
   }
+  # do not download if it is run in the sparkR shell
+  if (!nzchar(master) || is_master_local(master)) {
+    if (!is_sparkR_shell()) {
+      if (is.na(file.info(sparkHome)$isdir)) {
+        msg <- paste0("Spark not found in SPARK_HOME: ",
+                      sparkHome,
+                      " .\nTo search in the cache directory. ",
+                      "Installation will start if not found.")
+        message(msg)
+        packageLocalDir <- install.spark()
+        sparkHome <- packageLocalDir
+      } else {
+        msg <- paste0("Spark package is found in SPARK_HOME: ", sparkHome)
+        message(msg)
+      }
+    }
+  }
 
   if (!exists(".sparkRjsc", envir = .sparkREnv)) {
     sparkExecutorEnvMap <- new.env()

http://git-wip-us.apache.org/repos/asf/spark/blob/214ba66a/R/pkg/R/utils.R
----------------------------------------------------------------------
diff --git a/R/pkg/R/utils.R b/R/pkg/R/utils.R
index 240b9f6..d78c0a7 100644
--- a/R/pkg/R/utils.R
+++ b/R/pkg/R/utils.R
@@ -689,3 +689,11 @@ getSparkContext <- function() {
   sc <- get(".sparkRjsc", envir = .sparkREnv)
   sc
 }
+
+is_master_local <- function(master) {
+  grepl("^local(\\[([0-9]+|\\*)\\])?$", master, perl = TRUE)
+}
+
+is_sparkR_shell <- function() {
+  grepl(".*shell\\.R$", Sys.getenv("R_PROFILE_USER"), perl = TRUE)
+}

http://git-wip-us.apache.org/repos/asf/spark/blob/214ba66a/R/pkg/inst/tests/testthat/test_sparkSQL.R
----------------------------------------------------------------------
diff --git a/R/pkg/inst/tests/testthat/test_sparkSQL.R b/R/pkg/inst/tests/testthat/test_sparkSQL.R
index 3f3cb76..39ed4fe 100644
--- a/R/pkg/inst/tests/testthat/test_sparkSQL.R
+++ b/R/pkg/inst/tests/testthat/test_sparkSQL.R
@@ -1824,11 +1824,11 @@ test_that("describe() and summarize() on a DataFrame", {
   expect_equal(collect(stats)[2, "age"], "24.5")
   expect_equal(collect(stats)[3, "age"], "7.7781745930520225")
   stats <- describe(df)
-  expect_equal(collect(stats)[4, "name"], "Andy")
+  expect_equal(collect(stats)[4, "summary"], "min")
   expect_equal(collect(stats)[5, "age"], "30")
 
   stats2 <- summary(df)
-  expect_equal(collect(stats2)[4, "name"], "Andy")
+  expect_equal(collect(stats2)[4, "summary"], "min")
   expect_equal(collect(stats2)[5, "age"], "30")
 
   # SPARK-16425: SparkR summary() fails on column of type logical


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