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

R/pkg/NAMESPACE

@@ -12,7 +12,8 @@ export("print.jobj")
 
 # MLlib integration
 exportMethods("glm",
-              "predict")
+              "predict",
+              "summary")
 
 # Job group lifecycle management methods
 export("setJobGroup",
@@ -26,7 +27,9 @@ exportMethods("arrange",
               "collect",
               "columns",
               "count",
+              "crosstab",
               "describe",
+              "dim",
               "distinct",
               "dropna",
               "dtypes",
@@ -43,11 +46,15 @@ exportMethods("arrange",
               "isLocal",
               "join",
               "limit",
+              "names",
+              "ncol",
+              "nrow",
               "orderBy",
               "mutate",
               "names",
               "persist",
               "printSchema",
+              "rbind",
               "registerTempTable",
               "rename",
               "repartition",
@@ -64,6 +71,7 @@ exportMethods("arrange",
               "summarize",
               "take",
               "unionAll",
+              "unique",
               "unpersist",
               "where",
               "withColumn",

R/pkg/R/DataFrame.R

@@ -255,6 +255,16 @@ setMethod("names",
             columns(x)
           })
 
+#' @rdname columns
+setMethod("names<-",
+          signature(x = "DataFrame"),
+          function(x, value) {
+            if (!is.null(value)) {
+              sdf <- callJMethod(x@sdf, "toDF", listToSeq(as.list(value)))
+              dataFrame(sdf)
+            }
+          })
+
 #' Register Temporary Table
 #'
 #' Registers a DataFrame as a Temporary Table in the SQLContext
@@ -473,6 +483,18 @@ setMethod("distinct",
             dataFrame(sdf)
           })
 
+#' @title Distinct rows in a DataFrame
+#
+#' @description Returns a new DataFrame containing distinct rows in this DataFrame
+#'
+#' @rdname unique
+#' @aliases unique
+setMethod("unique",
+          signature(x = "DataFrame"),
+          function(x) {
+            distinct(x)
+          })
+
 #' Sample
 #'
 #' Return a sampled subset of this DataFrame using a random seed.
@@ -534,6 +556,58 @@ setMethod("count",
             callJMethod(x@sdf, "count")
           })
 
+#' @title Number of rows for a DataFrame
+#' @description Returns number of rows in a DataFrames
+#'
+#' @name nrow
+#'
+#' @rdname nrow
+#' @aliases count
+setMethod("nrow",
+          signature(x = "DataFrame"),
+          function(x) {
+            count(x)
+          })
+
+#' Returns the number of columns in a DataFrame
+#'
+#' @param x a SparkSQL DataFrame
+#'
+#' @rdname ncol
+#' @export
+#' @examples
+#'\dontrun{
+#' sc <- sparkR.init()
+#' sqlContext <- sparkRSQL.init(sc)
+#' path <- "path/to/file.json"
+#' df <- jsonFile(sqlContext, path)
+#' ncol(df)
+#' }
+setMethod("ncol",
+          signature(x = "DataFrame"),
+          function(x) {
+            length(columns(x))
+          })
+
+#' Returns the dimentions (number of rows and columns) of a DataFrame
+#' @param x a SparkSQL DataFrame
+#'
+#' @rdname dim
+#' @export
+#' @examples
+#'\dontrun{
+#' sc <- sparkR.init()
+#' sqlContext <- sparkRSQL.init(sc)
+#' path <- "path/to/file.json"
+#' df <- jsonFile(sqlContext, path)
+#' dim(df)
+#' }
+setMethod("dim",
+          signature(x = "DataFrame"),
+          function(x) {
+            c(count(x), ncol(x))
+          })
+
 #' Collects all the elements of a Spark DataFrame and coerces them into an R data.frame.
 #'
 #' @param x A SparkSQL DataFrame
@@ -1231,6 +1305,22 @@ setMethod("unionAll",
             dataFrame(unioned)
           })
 
+#' @title Union two or more DataFrames
+#
+#' @description Returns a new DataFrame containing rows of all parameters.
+#
+#' @rdname rbind
+#' @aliases unionAll
+setMethod("rbind",
+          signature(... = "DataFrame"),
+          function(x, ..., deparse.level = 1) {
+            if (nargs() == 3) {
+              unionAll(x, ...)
+            } else {
+              unionAll(x, Recall(..., deparse.level = 1))
+            }
+          })
+
 #' Intersect
 #'
 #' Return a new DataFrame containing rows only in both this DataFrame
@@ -1322,9 +1412,11 @@ setMethod("write.df",
                                     "org.apache.spark.sql.parquet")
             }
             allModes <- c("append", "overwrite", "error", "ignore")
+            # nolint start
             if (!(mode %in% allModes)) {
               stop('mode should be one of "append", "overwrite", "error", "ignore"')
             }
+            # nolint end
             jmode <- callJStatic("org.apache.spark.sql.api.r.SQLUtils", "saveMode", mode)
             options <- varargsToEnv(...)
             if (!is.null(path)) {
@@ -1384,9 +1476,11 @@ setMethod("saveAsTable",
                                     "org.apache.spark.sql.parquet")
             }
             allModes <- c("append", "overwrite", "error", "ignore")
+            # nolint start
             if (!(mode %in% allModes)) {
               stop('mode should be one of "append", "overwrite", "error", "ignore"')
             }
+            # nolint end
             jmode <- callJStatic("org.apache.spark.sql.api.r.SQLUtils", "saveMode", mode)
             options <- varargsToEnv(...)
             callJMethod(df@sdf, "saveAsTable", tableName, source, jmode, options)
@@ -1554,3 +1648,31 @@ setMethod("fillna",
             }
             dataFrame(sdf)
           })
+
+#' crosstab
+#'
+#' Computes a pair-wise frequency table of the given columns. Also known as a contingency
+#' table. The number of distinct values for each column should be less than 1e4. At most 1e6
+#' non-zero pair frequencies will be returned.
+#'
+#' @param col1 name of the first column. Distinct items will make the first item of each row.
+#' @param col2 name of the second column. Distinct items will make the column names of the output.
+#' @return a local R data.frame representing the contingency table. The first column of each row
+#'         will be the distinct values of `col1` and the column names will be the distinct values
+#'         of `col2`. The name of the first column will be `$col1_$col2`. Pairs that have no
+#'         occurrences will have zero as their counts.
+#'
+#' @rdname statfunctions
+#' @export
+#' @examples
+#' \dontrun{
+#' df <- jsonFile(sqlCtx, "/path/to/file.json")
+#' ct = crosstab(df, "title", "gender")
+#' }
+setMethod("crosstab",
+          signature(x = "DataFrame", col1 = "character", col2 = "character"),
+          function(x, col1, col2) {
+            statFunctions <- callJMethod(x@sdf, "stat")
+            sct <- callJMethod(statFunctions, "crosstab", col1, col2)
+            collect(dataFrame(sct))
+          })

R/pkg/R/RDD.R

@@ -85,7 +85,9 @@ setMethod("initialize", "PipelinedRDD", function(.Object, prev, func, jrdd_val)
 
   isPipelinable <- function(rdd) {
     e <- rdd@env
+    # nolint start
     !(e$isCached || e$isCheckpointed)
+    # nolint end
   }
 
   if (!inherits(prev, "PipelinedRDD") || !isPipelinable(prev)) {
@@ -97,7 +99,8 @@ setMethod("initialize", "PipelinedRDD", function(.Object, prev, func, jrdd_val)
     # prev_serializedMode is used during the delayed computation of JRDD in getJRDD
   } else {
     pipelinedFunc <- function(partIndex, part) {
-      func(partIndex, prev@func(partIndex, part))
+      f <- prev@func
+      func(partIndex, f(partIndex, part))
     }
     .Object@func <- cleanClosure(pipelinedFunc)
     .Object@prev_jrdd <- prev@prev_jrdd # maintain the pipeline
@@ -841,7 +844,7 @@ setMethod("sampleRDD",
                 if (withReplacement) {
                   count <- rpois(1, fraction)
                   if (count > 0) {
-                    res[(len + 1):(len + count)] <- rep(list(elem), count)
+                    res[ (len + 1) : (len + count) ] <- rep(list(elem), count)
                     len <- len + count
                   }
                 } else {
@@ -1261,12 +1264,12 @@ setMethod("pipeRDD",
           signature(x = "RDD", command = "character"),
           function(x, command, env = list()) {
             func <- function(part) {
-              trim.trailing.func <- function(x) {
+              trim_trailing_func <- function(x) {
                 sub("[\r\n]*$", "", toString(x))
               }
-              input <- unlist(lapply(part, trim.trailing.func))
+              input <- unlist(lapply(part, trim_trailing_func))
               res <- system2(command, stdout = TRUE, input = input, env = env)
-              lapply(res, trim.trailing.func)
+              lapply(res, trim_trailing_func)
             }
             lapplyPartition(x, func)
           })

R/pkg/R/backend.R

@@ -110,6 +110,8 @@ invokeJava <- function(isStatic, objId, methodName, ...) {
 
   # TODO: check the status code to output error information
   returnStatus <- readInt(conn)
-  stopifnot(returnStatus == 0)
+  if (returnStatus != 0) {
+    stop(readString(conn))
+  }
   readObject(conn)
 }

R/pkg/R/client.R

@@ -48,7 +48,7 @@ generateSparkSubmitArgs <- function(args, sparkHome, jars, sparkSubmitOpts, pack
     jars <- paste("--jars", jars)
   }
 
-  if (packages != "") {
+  if (!identical(packages, "")) {
     packages <- paste("--packages", packages)
   }
 

R/pkg/R/column.R

@@ -65,7 +65,7 @@ functions <- c("min", "max", "sum", "avg", "mean", "count", "abs", "sqrt",
                "acos", "asin", "atan", "cbrt", "ceiling", "cos", "cosh", "exp",
                "expm1", "floor", "log", "log10", "log1p", "rint", "sign",
                "sin", "sinh", "tan", "tanh", "toDegrees", "toRadians")
-binary_mathfunctions<- c("atan2", "hypot")
+binary_mathfunctions <- c("atan2", "hypot")
 
 createOperator <- function(op) {
   setMethod(op,

R/pkg/R/context.R

@@ -121,7 +121,7 @@ parallelize <- function(sc, coll, numSlices = 1) {
     numSlices <- length(coll)
 
   sliceLen <- ceiling(length(coll) / numSlices)
-  slices <- split(coll, rep(1:(numSlices + 1), each = sliceLen)[1:length(coll)])
+  slices <- split(coll, rep(1: (numSlices + 1), each = sliceLen)[1:length(coll)])
 
   # Serialize each slice: obtain a list of raws, or a list of lists (slices) of
   # 2-tuples of raws

R/pkg/R/deserialize.R

@@ -102,11 +102,11 @@ readList <- function(con) {
 
 readRaw <- function(con) {
   dataLen <- readInt(con)
-  data <- readBin(con, raw(), as.integer(dataLen), endian = "big")
+  readBin(con, raw(), as.integer(dataLen), endian = "big")
 }
 
 readRawLen <- function(con, dataLen) {
-  data <- readBin(con, raw(), as.integer(dataLen), endian = "big")
+  readBin(con, raw(), as.integer(dataLen), endian = "big")
 }
 
 readDeserialize <- function(con) {

R/pkg/R/generics.R

@@ -59,6 +59,10 @@ setGeneric("count", function(x) { standardGeneric("count") })
 # @export
 setGeneric("countByValue", function(x) { standardGeneric("countByValue") })
 
+# @rdname statfunctions
+# @export
+setGeneric("crosstab", function(x, col1, col2) { standardGeneric("crosstab") })
+
 # @rdname distinct
 # @export
 setGeneric("distinct", function(x, numPartitions = 1) { standardGeneric("distinct") })
@@ -250,8 +254,10 @@ setGeneric("flatMapValues", function(X, FUN) { standardGeneric("flatMapValues")
 
 # @rdname intersection
 # @export
-setGeneric("intersection", function(x, other, numPartitions = 1) {
-  standardGeneric("intersection") })
+setGeneric("intersection",
+           function(x, other, numPartitions = 1) {
+             standardGeneric("intersection")
+           })
 
 # @rdname keys
 # @export
@@ -485,9 +491,7 @@ setGeneric("sample",
 #' @rdname sample
 #' @export
 setGeneric("sample_frac",
-           function(x, withReplacement, fraction, seed) {
-             standardGeneric("sample_frac")
-           })
+           function(x, withReplacement, fraction, seed) { standardGeneric("sample_frac") })
 
 #' @rdname saveAsParquetFile
 #' @export
@@ -549,8 +553,8 @@ setGeneric("withColumn", function(x, colName, col) { standardGeneric("withColumn
 
 #' @rdname withColumnRenamed
 #' @export
-setGeneric("withColumnRenamed", function(x, existingCol, newCol) {
-  standardGeneric("withColumnRenamed") })
+setGeneric("withColumnRenamed",
+           function(x, existingCol, newCol) { standardGeneric("withColumnRenamed") })
 
 
 ###################### Column Methods ##########################
@@ -665,3 +669,7 @@ setGeneric("upper", function(x) { standardGeneric("upper") })
 #' @rdname glm
 #' @export
 setGeneric("glm")
+
+#' @rdname rbind
+#' @export
+setGeneric("rbind", signature = "...")