Merge branch 'master' into python_import_reorg_plus_exec

.gitignore

@@ -42,6 +42,7 @@ dependency-reduced-pom.xml
 derby.log
 dev/create-release/*final
 dev/create-release/*txt
+dev/pr-deps/
 dist/
 docs/_site
 docs/api

.travis.yml

@@ -44,7 +44,7 @@ notifications:
 # 5. Run maven install before running lint-java.
 install:
   - export MAVEN_SKIP_RC=1
-  - build/mvn -T 4 -q -DskipTests -Pmesos -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install
+  - build/mvn -T 4 -q -DskipTests -Pmesos -Pyarn -Pkinesis-asl -Phive -Phive-thriftserver install
 
 # 6. Run lint-java.
 script:

R/check-cran.sh

@@ -20,25 +20,14 @@
 set -o pipefail
 set -e
 
-FWDIR="$(cd `dirname $0`; pwd)"
+FWDIR="$(cd `dirname "${BASH_SOURCE[0]}"`; pwd)"
 pushd $FWDIR > /dev/null
 
-if [ ! -z "$R_HOME" ]
-  then
-    R_SCRIPT_PATH="$R_HOME/bin"
-  else
-    # if system wide R_HOME is not found, then exit
-    if [ ! `command -v R` ]; then
-      echo "Cannot find 'R_HOME'. Please specify 'R_HOME' or make sure R is properly installed."
-      exit 1
-    fi
-    R_SCRIPT_PATH="$(dirname $(which R))"
-fi
-echo "Using R_SCRIPT_PATH = ${R_SCRIPT_PATH}"
+. $FWDIR/find-r.sh
 
 # Install the package (this is required for code in vignettes to run when building it later)
 # Build the latest docs, but not vignettes, which is built with the package next
-$FWDIR/create-docs.sh
+. $FWDIR/install-dev.sh
 
 # Build source package with vignettes
 SPARK_HOME="$(cd "${FWDIR}"/..; pwd)"
@@ -84,19 +73,4 @@ else
   SPARK_HOME="${SPARK_HOME}" "$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz
 fi
 
-# Install source package to get it to generate vignettes rds files, etc.
-if [ -n "$CLEAN_INSTALL" ]
-then
-  echo "Removing lib path and installing from source package"
-  LIB_DIR="$FWDIR/lib"
-  rm -rf $LIB_DIR
-  mkdir -p $LIB_DIR
-  "$R_SCRIPT_PATH/"R CMD INSTALL SparkR_"$VERSION".tar.gz --library=$LIB_DIR
-
-  # Zip the SparkR package so that it can be distributed to worker nodes on YARN
-  pushd $LIB_DIR > /dev/null
-  jar cfM "$LIB_DIR/sparkr.zip" SparkR
-  popd > /dev/null
-fi
-
 popd > /dev/null

R/create-docs.sh

@@ -29,26 +29,27 @@ set -o pipefail
 set -e
 
 # Figure out where the script is
-export FWDIR="$(cd "`dirname "$0"`"; pwd)"
-export SPARK_HOME="$(cd "`dirname "$0"`"/..; pwd)"
+export FWDIR="$(cd "`dirname "${BASH_SOURCE[0]}"`"; pwd)"
+export SPARK_HOME="$(cd "`dirname "${BASH_SOURCE[0]}"`"/..; pwd)"
 
 # Required for setting SPARK_SCALA_VERSION
 . "${SPARK_HOME}"/bin/load-spark-env.sh
 
 echo "Using Scala $SPARK_SCALA_VERSION"
 
-pushd $FWDIR
+pushd $FWDIR > /dev/null
+. $FWDIR/find-r.sh
 
 # Install the package (this will also generate the Rd files)
-./install-dev.sh
+. $FWDIR/install-dev.sh
 
 # Now create HTML files
 
 # knit_rd puts html in current working directory
 mkdir -p pkg/html
 pushd pkg/html
 
-Rscript -e 'libDir <- "../../lib"; library(SparkR, lib.loc=libDir); library(knitr); knit_rd("SparkR", links = tools::findHTMLlinks(paste(libDir, "SparkR", sep="/")))'
+"$R_SCRIPT_PATH/"Rscript -e 'libDir <- "../../lib"; library(SparkR, lib.loc=libDir); library(knitr); knit_rd("SparkR", links = tools::findHTMLlinks(paste(libDir, "SparkR", sep="/")))'
 
 popd
 

R/create-rd.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+#
+# 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.
+#
+
+# This scripts packages the SparkR source files (R and C files) and
+# creates a package that can be loaded in R. The package is by default installed to
+# $FWDIR/lib and the package can be loaded by using the following command in R:
+#
+#   library(SparkR, lib.loc="$FWDIR/lib")
+#
+# NOTE(shivaram): Right now we use $SPARK_HOME/R/lib to be the installation directory
+# to load the SparkR package on the worker nodes.
+
+set -o pipefail
+set -e
+
+FWDIR="$(cd `dirname "${BASH_SOURCE[0]}"`; pwd)"
+pushd $FWDIR > /dev/null
+. $FWDIR/find-r.sh
+
+# Generate Rd files if devtools is installed
+"$R_SCRIPT_PATH/"Rscript -e ' if("devtools" %in% rownames(installed.packages())) { library(devtools); devtools::document(pkg="./pkg", roclets=c("rd")) }'

R/find-r.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+#
+# 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.
+#
+
+if [ -z "$R_SCRIPT_PATH" ]
+then
+  if [ ! -z "$R_HOME" ]
+  then
+    R_SCRIPT_PATH="$R_HOME/bin"
+  else
+    # if system wide R_HOME is not found, then exit
+    if [ ! `command -v R` ]; then
+      echo "Cannot find 'R_HOME'. Please specify 'R_HOME' or make sure R is properly installed."
+      exit 1
+    fi
+    R_SCRIPT_PATH="$(dirname $(which R))"
+  fi
+  echo "Using R_SCRIPT_PATH = ${R_SCRIPT_PATH}"
+fi

R/install-dev.sh

@@ -29,27 +29,15 @@
 set -o pipefail
 set -e
 
-FWDIR="$(cd `dirname $0`; pwd)"
+FWDIR="$(cd `dirname "${BASH_SOURCE[0]}"`; pwd)"
 LIB_DIR="$FWDIR/lib"
 
 mkdir -p $LIB_DIR
 
 pushd $FWDIR > /dev/null
-if [ ! -z "$R_HOME" ]
-  then
-    R_SCRIPT_PATH="$R_HOME/bin"
-  else
-    # if system wide R_HOME is not found, then exit
-    if [ ! `command -v R` ]; then
-      echo "Cannot find 'R_HOME'. Please specify 'R_HOME' or make sure R is properly installed."
-      exit 1
-    fi
-    R_SCRIPT_PATH="$(dirname $(which R))"
-fi
-echo "Using R_SCRIPT_PATH = ${R_SCRIPT_PATH}"
-
-# Generate Rd files if devtools is installed
-"$R_SCRIPT_PATH/"Rscript -e ' if("devtools" %in% rownames(installed.packages())) { library(devtools); devtools::document(pkg="./pkg", roclets=c("rd")) }'
+. $FWDIR/find-r.sh
+
+. $FWDIR/create-rd.sh
 
 # Install SparkR to $LIB_DIR
 "$R_SCRIPT_PATH/"R CMD INSTALL --library=$LIB_DIR $FWDIR/pkg/

R/install-source-package.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+#
+# 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.
+#
+
+# This scripts packages the SparkR source files (R and C files) and
+# creates a package that can be loaded in R. The package is by default installed to
+# $FWDIR/lib and the package can be loaded by using the following command in R:
+#
+#   library(SparkR, lib.loc="$FWDIR/lib")
+#
+# NOTE(shivaram): Right now we use $SPARK_HOME/R/lib to be the installation directory
+# to load the SparkR package on the worker nodes.
+
+set -o pipefail
+set -e
+
+FWDIR="$(cd `dirname "${BASH_SOURCE[0]}"`; pwd)"
+pushd $FWDIR > /dev/null
+. $FWDIR/find-r.sh
+
+if [ -z "$VERSION" ]; then
+  VERSION=`grep Version $FWDIR/pkg/DESCRIPTION | awk '{print $NF}'`
+fi
+
+if [ ! -f "$FWDIR"/SparkR_"$VERSION".tar.gz ]; then
+  echo -e "R source package file $FWDIR/SparkR_$VERSION.tar.gz is not found."
+  echo -e "Please build R source package with check-cran.sh"
+  exit -1;
+fi
+
+echo "Removing lib path and installing from source package"
+LIB_DIR="$FWDIR/lib"
+rm -rf $LIB_DIR
+mkdir -p $LIB_DIR
+"$R_SCRIPT_PATH/"R CMD INSTALL SparkR_"$VERSION".tar.gz --library=$LIB_DIR
+
+# Zip the SparkR package so that it can be distributed to worker nodes on YARN
+pushd $LIB_DIR > /dev/null
+jar cfM "$LIB_DIR/sparkr.zip" SparkR
+popd > /dev/null
+
+popd

R/pkg/NAMESPACE

@@ -1,3 +1,20 @@
+#
+# 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.
+#
+
 # Imports from base R
 # Do not include stats:: "rpois", "runif" - causes error at runtime
 importFrom("methods", "setGeneric", "setMethod", "setOldClass")
@@ -47,7 +64,8 @@ exportMethods("glm",
               "spark.kstest",
               "spark.logit",
               "spark.randomForest",
-              "spark.gbt")
+              "spark.gbt",
+              "spark.bisectingKmeans")
 
 # Job group lifecycle management methods
 export("setJobGroup",
@@ -94,6 +112,7 @@ exportMethods("arrange",
               "freqItems",
               "gapply",
               "gapplyCollect",
+              "getNumPartitions",
               "group_by",
               "groupBy",
               "head",
@@ -306,6 +325,7 @@ exportMethods("%in%",
               "toDegrees",
               "toRadians",
               "to_date",
+              "to_timestamp",
               "to_utc_timestamp",
               "translate",
               "trim",