rekhajoshm · rekhajoshm · Mar 18, 2016 · Mar 3, 2016 · Mar 3, 2016 · Mar 3, 2016
diff --git a/.github/PULL_REQUEST_TEMPLATE b/.github/PULL_REQUEST_TEMPLATE
@@ -0,0 +1,12 @@
+## What changes were proposed in this pull request?
+
+(Please fill in changes proposed in this fix)
+
+
+## How was this patch tested?
+
+(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)
+
+
+(If this patch involves UI changes, please attach a screenshot; otherwise, remove this)
+
diff --git a/.gitignore b/.gitignore
@@ -17,8 +17,6 @@ cache
 work/
 out/
 .DS_Store
-third_party/libmesos.so
-third_party/libmesos.dylib
 build/apache-maven*
 build/zinc*
 build/scala*
@@ -60,8 +58,6 @@ dev/create-release/*final
 spark-*-bin-*.tgz
 unit-tests.log
 /lib/
-ec2/lib/
-rat-results.txt
 scalastyle.txt
 scalastyle-output.xml
 R-unit-tests.log

diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,3 @@
-
                                  Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/
@@ -237,8 +236,7 @@ The following components are provided under a BSD-style license. See project lin
 The text of each license is also included at licenses/LICENSE-[project].txt.
 
      (BSD 3 Clause) netlib core (com.github.fommil.netlib:core:1.1.2 - https://github.com/fommil/netlib-java/core)
-     (BSD 3 Clause) JPMML-Model (org.jpmml:pmml-model:1.1.15 - https://github.com/jpmml/jpmml-model)
-     (BSD 3-clause style license) jblas (org.jblas:jblas:1.2.4 - http://jblas.org/)
+     (BSD 3 Clause) JPMML-Model (org.jpmml:pmml-model:1.2.7 - https://github.com/jpmml/jpmml-model)
      (BSD License) AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
      (BSD licence) ANTLR ST4 4.0.4 (org.antlr:ST4:4.0.4 - http://www.stringtemplate.org)
      (BSD licence) ANTLR StringTemplate (org.antlr:stringtemplate:3.2.1 - http://www.stringtemplate.org)
@@ -250,22 +248,22 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
         (Interpreter classes (all .scala files in repl/src/main/scala
         except for Main.Scala, SparkHelper.scala and ExecutorClassLoader.scala),
         and for SerializableMapWrapper in JavaUtils.scala)
-     (BSD-like) Scala Actors library (org.scala-lang:scala-actors:2.10.5 - http://www.scala-lang.org/)
-     (BSD-like) Scala Compiler (org.scala-lang:scala-compiler:2.10.5 - http://www.scala-lang.org/)
-     (BSD-like) Scala Compiler (org.scala-lang:scala-reflect:2.10.5 - http://www.scala-lang.org/)
-     (BSD-like) Scala Library (org.scala-lang:scala-library:2.10.5 - http://www.scala-lang.org/)
-     (BSD-like) Scalap (org.scala-lang:scalap:2.10.5 - http://www.scala-lang.org/)
-     (BSD-style) scalacheck (org.scalacheck:scalacheck_2.10:1.10.0 - http://www.scalacheck.org)
-     (BSD-style) spire (org.spire-math:spire_2.10:0.7.1 - http://spire-math.org)
-     (BSD-style) spire-macros (org.spire-math:spire-macros_2.10:0.7.1 - http://spire-math.org)
+     (BSD-like) Scala Actors library (org.scala-lang:scala-actors:2.11.7 - http://www.scala-lang.org/)
+     (BSD-like) Scala Compiler (org.scala-lang:scala-compiler:2.11.7 - http://www.scala-lang.org/)
+     (BSD-like) Scala Compiler (org.scala-lang:scala-reflect:2.11.7 - http://www.scala-lang.org/)
+     (BSD-like) Scala Library (org.scala-lang:scala-library:2.11.7 - http://www.scala-lang.org/)
+     (BSD-like) Scalap (org.scala-lang:scalap:2.11.7 - http://www.scala-lang.org/)
+     (BSD-style) scalacheck (org.scalacheck:scalacheck_2.11:1.10.0 - http://www.scalacheck.org)
+     (BSD-style) spire (org.spire-math:spire_2.11:0.7.1 - http://spire-math.org)
+     (BSD-style) spire-macros (org.spire-math:spire-macros_2.11:0.7.1 - http://spire-math.org)
      (New BSD License) Kryo (com.esotericsoftware.kryo:kryo:2.21 - http://code.google.com/p/kryo/)
      (New BSD License) MinLog (com.esotericsoftware.minlog:minlog:1.2 - http://code.google.com/p/minlog/)
      (New BSD License) ReflectASM (com.esotericsoftware.reflectasm:reflectasm:1.07 - http://code.google.com/p/reflectasm/)
      (New BSD license) Protocol Buffer Java API (com.google.protobuf:protobuf-java:2.5.0 - http://code.google.com/p/protobuf)
      (New BSD license) Protocol Buffer Java API (org.spark-project.protobuf:protobuf-java:2.4.1-shaded - http://code.google.com/p/protobuf)
      (The BSD License) Fortran to Java ARPACK (net.sourceforge.f2j:arpack_combined_all:0.1 - http://f2j.sourceforge.net)
      (The BSD License) xmlenc Library (xmlenc:xmlenc:0.52 - http://xmlenc.sourceforge.net)
-     (The New BSD License) Py4J (net.sf.py4j:py4j:0.9 - http://py4j.sourceforge.net/)
+     (The New BSD License) Py4J (net.sf.py4j:py4j:0.9.2 - http://py4j.sourceforge.net/)
      (Two-clause BSD-style license) JUnit-Interface (com.novocode:junit-interface:0.10 - http://github.com/szeiger/junit-interface/)
      (BSD licence) sbt and sbt-launch-lib.bash
      (BSD 3 Clause) d3.min.js (https://github.com/mbostock/d3/blob/master/LICENSE)
@@ -284,11 +282,17 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
      (MIT License) SLF4J API Module (org.slf4j:slf4j-api:1.7.5 - http://www.slf4j.org)
      (MIT License) SLF4J LOG4J-12 Binding (org.slf4j:slf4j-log4j12:1.7.5 - http://www.slf4j.org)
      (MIT License) pyrolite (org.spark-project:pyrolite:2.0.1 - http://pythonhosted.org/Pyro4/)
-     (MIT License) scopt (com.github.scopt:scopt_2.10:3.2.0 - https://github.com/scopt/scopt)
+     (MIT License) scopt (com.github.scopt:scopt_2.11:3.2.0 - https://github.com/scopt/scopt)
      (The MIT License) Mockito (org.mockito:mockito-core:1.9.5 - http://www.mockito.org)
      (MIT License) jquery (https://jquery.org/license/)
      (MIT License) AnchorJS (https://github.com/bryanbraun/anchorjs)
      (MIT License) graphlib-dot (https://github.com/cpettitt/graphlib-dot)
      (MIT License) dagre-d3 (https://github.com/cpettitt/dagre-d3)
      (MIT License) sorttable (https://github.com/stuartlangridge/sorttable)
      (MIT License) boto (https://github.com/boto/boto/blob/develop/LICENSE)
+     (MIT License) datatables (http://datatables.net/license)
+     (MIT License) mustache (https://github.com/mustache/mustache/blob/master/LICENSE)
+     (MIT License) cookies (http://code.google.com/p/cookies/wiki/License)
+     (MIT License) blockUI (http://jquery.malsup.com/block/)
+     (MIT License) RowsGroup (http://datatables.net/license/mit)
+     (MIT License) jsonFormatter (http://www.jqueryscript.net/other/jQuery-Plugin-For-Pretty-JSON-Formatting-jsonFormatter.html)
diff --git a/NOTICE b/NOTICE
@@ -606,4 +606,63 @@ Vis.js uses and redistributes the following third-party libraries:
 
 - keycharm
   https://github.com/AlexDM0/keycharm
-  The MIT License
+  The MIT License
+
+===============================================================================
+
+The CSS style for the navigation sidebar of the documentation was originally
+submitted by Óscar Nájera for the scikit-learn project. The scikit-learn project
+is distributed under the 3-Clause BSD license.
+===============================================================================
+
+For CSV functionality:
+
+/*
+ * Copyright 2014 Databricks
+ *
+ * Licensed 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.
+ */
+
+/*
+ * Copyright 2015 Ayasdi Inc
+ *
+ * Licensed 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.
+ */
+
+
+===============================================================================
+For dev/sparktestsupport/toposort.py:
+
+Copyright 2014 True Blade Systems, Inc.
+
+Licensed 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.
diff --git a/R/README.md b/R/README.md
@@ -1,6 +1,16 @@
 # R on Spark
 
 SparkR is an R package that provides a light-weight frontend to use Spark from R.
+### Installing sparkR
+
+Libraries of sparkR need to be created in `$SPARK_HOME/R/lib`. This can be done by running the script `$SPARK_HOME/R/install-dev.sh`.
+By default the above script uses the system wide installation of R. However, this can be changed to any user installed location of R by setting the environment variable `R_HOME` the full path of the base directory where R is installed, before running install-dev.sh script.
+Example: 
+```
+# where /home/username/R is where R is installed and /home/username/R/bin contains the files R and RScript
+export R_HOME=/home/username/R
+./install-dev.sh
+```
 
 ### SparkR development
 

diff --git a/R/install-dev.sh b/R/install-dev.sh
@@ -35,12 +35,19 @@ LIB_DIR="$FWDIR/lib"
 mkdir -p $LIB_DIR
 
 pushd $FWDIR > /dev/null
+if [ ! -z "$R_HOME" ]
+  then
+    R_SCRIPT_PATH="$R_HOME/bin"
+   else
+    R_SCRIPT_PATH="$(dirname $(which R))"
+fi
+echo "USING R_HOME = $R_HOME"
 
 # Generate Rd files if devtools is installed
-Rscript -e ' if("devtools" %in% rownames(installed.packages())) { library(devtools); devtools::document(pkg="./pkg", roclets=c("rd")) }'
+"$R_SCRIPT_PATH/"Rscript -e ' if("devtools" %in% rownames(installed.packages())) { library(devtools); devtools::document(pkg="./pkg", roclets=c("rd")) }'
 
 # Install SparkR to $LIB_DIR
-R CMD INSTALL --library=$LIB_DIR $FWDIR/pkg/
+"$R_SCRIPT_PATH/"R CMD INSTALL --library=$LIB_DIR $FWDIR/pkg/
 
 # Zip the SparkR package so that it can be distributed to worker nodes on YARN
 cd $LIB_DIR

diff --git a/R/pkg/DESCRIPTION b/R/pkg/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: SparkR
 Type: Package
 Title: R frontend for Spark
-Version: 1.6.0
+Version: 2.0.0
 Date: 2013-09-09
 Author: The Apache Software Foundation
 Maintainer: Shivaram Venkataraman <[email protected]>
@@ -18,10 +18,10 @@ Collate:
     'schema.R'
     'generics.R'
     'jobj.R'
-    'RDD.R'
-    'pairRDD.R'
     'column.R'
     'group.R'
+    'RDD.R'
+    'pairRDD.R'
     'DataFrame.R'
     'SQLContext.R'
     'backend.R'
@@ -36,3 +36,4 @@ Collate:
     'stats.R'
     'types.R'
     'utils.R'
+RoxygenNote: 5.0.1
diff --git a/R/pkg/NAMESPACE b/R/pkg/NAMESPACE
@@ -13,7 +13,9 @@ export("print.jobj")
 # MLlib integration
 exportMethods("glm",
               "predict",
-              "summary")
+              "summary",
+              "kmeans",
+              "fitted")
 
 # Job group lifecycle management methods
 export("setJobGroup",
@@ -27,15 +29,22 @@ exportMethods("arrange",
               "attach",
               "cache",
               "collect",
+              "colnames",
+              "colnames<-",
               "coltypes",
+              "coltypes<-",
               "columns",
               "count",
               "cov",
               "corr",
+              "covar_samp",
+              "covar_pop",
               "crosstab",
               "describe",
               "dim",
               "distinct",
+              "drop",
+              "dropDuplicates",
               "dropna",
               "dtypes",
               "except",
@@ -56,6 +65,7 @@ exportMethods("arrange",
               "mutate",
               "na.omit",
               "names",
+              "names<-",
               "ncol",
               "nrow",
               "orderBy",
@@ -88,7 +98,10 @@ exportMethods("arrange",
               "with",
               "withColumn",
               "withColumnRenamed",
-              "write.df")
+              "write.df",
+              "write.json",
+              "write.parquet",
+              "write.text")
 
 exportClasses("Column")
 
@@ -98,6 +111,7 @@ exportMethods("%in%",
               "add_months",
               "alias",
               "approxCountDistinct",
+              "approxQuantile",
               "array_contains",
               "asc",
               "ascii",
@@ -123,15 +137,18 @@ exportMethods("%in%",
               "count",
               "countDistinct",
               "crc32",
-              "cumeDist",
+              "hash",
+              "cume_dist",
               "date_add",
               "date_format",
               "date_sub",
               "datediff",
               "dayofmonth",
               "dayofyear",
-              "denseRank",
+              "decode",
+              "dense_rank",
               "desc",
+              "encode",
               "endsWith",
               "exp",
               "explode",
@@ -188,7 +205,7 @@ exportMethods("%in%",
               "next_day",
               "ntile",
               "otherwise",
-              "percentRank",
+              "percent_rank",
               "pmod",
               "quarter",
               "rand",
@@ -200,7 +217,7 @@ exportMethods("%in%",
               "rint",
               "rlike",
               "round",
-              "rowNumber",
+              "row_number",
               "rpad",
               "rtrim",
               "second",
@@ -221,6 +238,7 @@ exportMethods("%in%",
               "stddev",
               "stddev_pop",
               "stddev_samp",
+              "struct",
               "sqrt",
               "startsWith",
               "substr",
@@ -263,8 +281,12 @@ export("as.DataFrame",
        "loadDF",
        "parquetFile",
        "read.df",
+       "read.json",
+       "read.parquet",
+       "read.text",
        "sql",
-       "table",
+       "str",
+       "tableToDF",
        "tableNames",
        "tables",
        "uncacheTable")
@@ -276,4 +298,4 @@ export("structField",
        "structType",
        "structType.jobj",
        "structType.structField",
-       "print.structType")
+       "print.structType")