Merge branch 'master' of github.com:apache/spark into fail_rule

Author: Davies Liu

R/README.md

@@ -40,7 +40,7 @@ To set other options like driver memory, executor memory etc. you can pass in th
 If you wish to use SparkR from RStudio or other R frontends you will need to set some environment variables which point SparkR to your Spark installation. For example 
 ```
 # Set this to where Spark is installed
-Sys.setenv(SPARK_HOME="/Users/shivaram/spark")
+Sys.setenv(SPARK_HOME="/Users/username/spark")
 # This line loads SparkR from the installed directory
 .libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
 library(SparkR)
@@ -51,7 +51,7 @@ sc <- sparkR.init(master="local")
 
 The [instructions](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark) for making contributions to Spark also apply to SparkR.
 If you only make R file changes (i.e. no Scala changes) then you can just re-install the R package using `R/install-dev.sh` and test your changes.
-Once you have made your changes, please include unit tests for them and run existing unit tests using the `run-tests.sh` script as described below. 
+Once you have made your changes, please include unit tests for them and run existing unit tests using the `R/run-tests.sh` script as described below.
 
 #### Generating documentation
 
@@ -60,17 +60,17 @@ The SparkR documentation (Rd files and HTML files) are not a part of the source
 ### Examples, Unit tests
 
 SparkR comes with several sample programs in the `examples/src/main/r` directory.
-To run one of them, use `./bin/sparkR <filename> <args>`. For example:
+To run one of them, use `./bin/spark-submit <filename> <args>`. For example:
 
-    ./bin/sparkR examples/src/main/r/dataframe.R
+    ./bin/spark-submit examples/src/main/r/dataframe.R
 
 You can also run the unit-tests for SparkR by running (you need to install the [testthat](http://cran.r-project.org/web/packages/testthat/index.html) package first):
 
     R -e 'install.packages("testthat", repos="http://cran.us.r-project.org")'
     ./R/run-tests.sh
 
 ### Running on YARN
-The `./bin/spark-submit` and `./bin/sparkR` can also be used to submit jobs to YARN clusters. You will need to set YARN conf dir before doing so. For example on CDH you can run
+The `./bin/spark-submit` can also be used to submit jobs to YARN clusters. You will need to set YARN conf dir before doing so. For example on CDH you can run
 ```
 export YARN_CONF_DIR=/etc/hadoop/conf
 ./bin/spark-submit --master yarn examples/src/main/r/dataframe.R

R/pkg/DESCRIPTION

@@ -11,7 +11,8 @@ Depends:
     R (>= 3.0),
     methods,
 Suggests:
-    testthat
+    testthat,
+    e1071
 Description: R frontend for Spark
 License: Apache License (== 2.0)
 Collate:

R/pkg/NAMESPACE

@@ -15,7 +15,8 @@ exportMethods("glm",
               "predict",
               "summary",
               "kmeans",
-              "fitted")
+              "fitted",
+              "naiveBayes")
 
 # Job group lifecycle management methods
 export("setJobGroup",

R/pkg/R/generics.R

@@ -1175,3 +1175,7 @@ setGeneric("kmeans")
 #' @rdname fitted
 #' @export
 setGeneric("fitted")
+
+#' @rdname naiveBayes
+#' @export
+setGeneric("naiveBayes", function(formula, data, ...) { standardGeneric("naiveBayes") })

R/pkg/R/mllib.R

@@ -22,6 +22,11 @@
 #' @export
 setClass("PipelineModel", representation(model = "jobj"))
 
+#' @title S4 class that represents a NaiveBayesModel
+#' @param jobj a Java object reference to the backing Scala NaiveBayesWrapper
+#' @export
+setClass("NaiveBayesModel", representation(jobj = "jobj"))
+
 #' Fits a generalized linear model
 #'
 #' Fits a generalized linear model, similarly to R's glm(). Also see the glmnet package.
@@ -42,7 +47,7 @@ setClass("PipelineModel", representation(model = "jobj"))
 #' @rdname glm
 #' @export
 #' @examples
-#'\dontrun{
+#' \dontrun{
 #' sc <- sparkR.init()
 #' sqlContext <- sparkRSQL.init(sc)
 #' data(iris)
@@ -71,7 +76,7 @@ setMethod("glm", signature(formula = "formula", family = "ANY", data = "DataFram
 #' @rdname predict
 #' @export
 #' @examples
-#'\dontrun{
+#' \dontrun{
 #' model <- glm(y ~ x, trainingData)
 #' predicted <- predict(model, testData)
 #' showDF(predicted)
@@ -81,6 +86,26 @@ setMethod("predict", signature(object = "PipelineModel"),
             return(dataFrame(callJMethod(object@model, "transform", newData@sdf)))
           })
 
+#' Make predictions from a naive Bayes model
+#'
+#' Makes predictions from a model produced by naiveBayes(), similarly to R package e1071's predict.
+#'
+#' @param object A fitted naive Bayes model
+#' @param newData DataFrame for testing
+#' @return DataFrame containing predicted labels in a column named "prediction"
+#' @rdname predict
+#' @export
+#' @examples
+#' \dontrun{
+#' model <- naiveBayes(y ~ x, trainingData)
+#' predicted <- predict(model, testData)
+#' showDF(predicted)
+#'}
+setMethod("predict", signature(object = "NaiveBayesModel"),
+          function(object, newData) {
+            return(dataFrame(callJMethod(object@jobj, "transform", newData@sdf)))
+          })
+
 #' Get the summary of a model
 #'
 #' Returns the summary of a model produced by glm(), similarly to R's summary().
@@ -97,7 +122,7 @@ setMethod("predict", signature(object = "PipelineModel"),
 #' @rdname summary
 #' @export
 #' @examples
-#'\dontrun{
+#' \dontrun{
 #' model <- glm(y ~ x, trainingData)
 #' summary(model)
 #'}
@@ -140,6 +165,35 @@ setMethod("summary", signature(object = "PipelineModel"),
             }
           })
 
+#' Get the summary of a naive Bayes model
+#'
+#' Returns the summary of a naive Bayes model produced by naiveBayes(), similarly to R's summary().
+#'
+#' @param object A fitted MLlib model
+#' @return a list containing 'apriori', the label distribution, and 'tables', conditional
+#          probabilities given the target label
+#' @rdname summary
+#' @export
+#' @examples
+#' \dontrun{
+#' model <- naiveBayes(y ~ x, trainingData)
+#' summary(model)
+#'}
+setMethod("summary", signature(object = "NaiveBayesModel"),
+          function(object, ...) {
+            jobj <- object@jobj
+            features <- callJMethod(jobj, "features")
+            labels <- callJMethod(jobj, "labels")
+            apriori <- callJMethod(jobj, "apriori")
+            apriori <- t(as.matrix(unlist(apriori)))
+            colnames(apriori) <- unlist(labels)
+            tables <- callJMethod(jobj, "tables")
+            tables <- matrix(tables, nrow = length(labels))
+            rownames(tables) <- unlist(labels)
+            colnames(tables) <- unlist(features)
+            return(list(apriori = apriori, tables = tables))
+          })
+
 #' Fit a k-means model
 #'
 #' Fit a k-means model, similarly to R's kmeans().
@@ -152,7 +206,7 @@ setMethod("summary", signature(object = "PipelineModel"),
 #' @rdname kmeans
 #' @export
 #' @examples
-#'\dontrun{
+#' \dontrun{
 #' model <- kmeans(x, centers = 2, algorithm="random")
 #'}
 setMethod("kmeans", signature(x = "DataFrame"),
@@ -173,7 +227,7 @@ setMethod("kmeans", signature(x = "DataFrame"),
 #' @rdname fitted
 #' @export
 #' @examples
-#'\dontrun{
+#' \dontrun{
 #' model <- kmeans(trainingData, 2)
 #' fitted.model <- fitted(model)
 #' showDF(fitted.model)
@@ -192,3 +246,30 @@ setMethod("fitted", signature(object = "PipelineModel"),
               stop(paste("Unsupported model", modelName, sep = " "))
             }
           })
+
+#' Fit a Bernoulli naive Bayes model
+#'
+#' Fit a Bernoulli naive Bayes model, similarly to R package e1071's naiveBayes() while only
+#' categorical features are supported. The input should be a DataFrame of observations instead of a
+#' contingency table.
+#'
+#' @param object A symbolic description of the model to be fitted. Currently only a few formula
+#'               operators are supported, including '~', '.', ':', '+', and '-'.
+#' @param data DataFrame for training
+#' @param laplace Smoothing parameter
+#' @return a fitted naive Bayes model
+#' @rdname naiveBayes
+#' @seealso e1071: \url{https://cran.r-project.org/web/packages/e1071/}
+#' @export
+#' @examples
+#' \dontrun{
+#' df <- createDataFrame(sqlContext, infert)
+#' model <- naiveBayes(education ~ ., df, laplace = 0)
+#'}
+setMethod("naiveBayes", signature(formula = "formula", data = "DataFrame"),
+          function(formula, data, laplace = 0, ...) {
+            formula <- paste(deparse(formula), collapse = "")
+            jobj <- callJStatic("org.apache.spark.ml.r.NaiveBayesWrapper", "fit",
+                                 formula, data@sdf, laplace)
+            return(new("NaiveBayesModel", jobj = jobj))
+          })

R/pkg/inst/tests/testthat/test_mllib.R

@@ -141,3 +141,62 @@ test_that("kmeans", {
   cluster <- summary.model$cluster
   expect_equal(sort(collect(distinct(select(cluster, "prediction")))$prediction), c(0, 1))
 })
+
+test_that("naiveBayes", {
+  # R code to reproduce the result.
+  # We do not support instance weights yet. So we ignore the frequencies.
+  #
+  #' library(e1071)
+  #' t <- as.data.frame(Titanic)
+  #' t1 <- t[t$Freq > 0, -5]
+  #' m <- naiveBayes(Survived ~ ., data = t1)
+  #' m
+  #' predict(m, t1)
+  #
+  # -- output of 'm'
+  #
+  # A-priori probabilities:
+  # Y
+  #        No       Yes
+  # 0.4166667 0.5833333
+  #
+  # Conditional probabilities:
+  #      Class
+  # Y           1st       2nd       3rd      Crew
+  #   No  0.2000000 0.2000000 0.4000000 0.2000000
+  #   Yes 0.2857143 0.2857143 0.2857143 0.1428571
+  #
+  #      Sex
+  # Y     Male Female
+  #   No   0.5    0.5
+  #   Yes  0.5    0.5
+  #
+  #      Age
+  # Y         Child     Adult
+  #   No  0.2000000 0.8000000
+  #   Yes 0.4285714 0.5714286
+  #
+  # -- output of 'predict(m, t1)'
+  #
+  # Yes Yes Yes Yes No  No  Yes Yes No  No  Yes Yes Yes Yes Yes Yes Yes Yes No  No  Yes Yes No  No
+  #
+
+  t <- as.data.frame(Titanic)
+  t1 <- t[t$Freq > 0, -5]
+  df <- suppressWarnings(createDataFrame(sqlContext, t1))
+  m <- naiveBayes(Survived ~ ., data = df)
+  s <- summary(m)
+  expect_equal(as.double(s$apriori[1, "Yes"]), 0.5833333, tolerance = 1e-6)
+  expect_equal(sum(s$apriori), 1)
+  expect_equal(as.double(s$tables["Yes", "Age_Adult"]), 0.5714286, tolerance = 1e-6)
+  p <- collect(select(predict(m, df), "prediction"))
+  expect_equal(p$prediction, c("Yes", "Yes", "Yes", "Yes", "No", "No", "Yes", "Yes", "No", "No",
+                               "Yes", "Yes", "Yes", "Yes", "Yes", "Yes", "Yes", "Yes", "No", "No",
+                               "Yes", "Yes", "No", "No"))
+
+  # Test e1071::naiveBayes
+  if (requireNamespace("e1071", quietly = TRUE)) {
+    expect_that(m <- e1071::naiveBayes(Survived ~ ., data = t1), not(throws_error()))
+    expect_equal(as.character(predict(m, t1[1, ])), "Yes")
+  }
+})

common/network-common/src/main/java/org/apache/spark/network/TransportContext.java

@@ -43,7 +43,8 @@
 
 /**
  * Contains the context to create a {@link TransportServer}, {@link TransportClientFactory}, and to
- * setup Netty Channel pipelines with a {@link org.apache.spark.network.server.TransportChannelHandler}.
+ * setup Netty Channel pipelines with a
+ * {@link org.apache.spark.network.server.TransportChannelHandler}.
  *
  * There are two communication protocols that the TransportClient provides, control-plane RPCs and
  * data-plane "chunk fetching". The handling of the RPCs is performed outside of the scope of the

common/network-common/src/main/java/org/apache/spark/network/client/StreamCallback.java

@@ -21,9 +21,9 @@
 import java.nio.ByteBuffer;
 
 /**
- * Callback for streaming data. Stream data will be offered to the {@link #onData(String, ByteBuffer)}
- * method as it arrives. Once all the stream data is received, {@link #onComplete(String)} will be
- * called.
+ * Callback for streaming data. Stream data will be offered to the
+ * {@link #onData(String, ByteBuffer)} method as it arrives. Once all the stream data is received,
+ * {@link #onComplete(String)} will be called.
  * <p>
  * The network library guarantees that a single thread will call these methods at a time, but
  * different call may be made by different threads.

common/network-common/src/main/java/org/apache/spark/network/client/TransportClientFactory.java

@@ -64,7 +64,7 @@ private static class ClientPool {
     TransportClient[] clients;
     Object[] locks;
 
-    public ClientPool(int size) {
+    ClientPool(int size) {
       clients = new TransportClient[size];
       locks = new Object[size];
       for (int i = 0; i < size; i++) {

common/network-common/src/main/java/org/apache/spark/network/protocol/Message.java

@@ -33,15 +33,15 @@ public interface Message extends Encodable {
   boolean isBodyInFrame();
 
   /** Preceding every serialized Message is its type, which allows us to deserialize it. */
-  public static enum Type implements Encodable {
+  enum Type implements Encodable {
     ChunkFetchRequest(0), ChunkFetchSuccess(1), ChunkFetchFailure(2),
     RpcRequest(3), RpcResponse(4), RpcFailure(5),
     StreamRequest(6), StreamResponse(7), StreamFailure(8),
     OneWayMessage(9), User(-1);
 
     private final byte id;
 
-    private Type(int id) {
+    Type(int id) {
       assert id < 128 : "Cannot have more than 128 message types";
       this.id = (byte) id;
     }