Merge pull request #1 from apache/master

Pulling functionality from apache spark

.gitignore

@@ -6,6 +6,7 @@
 *.iml
 *.iws
 *.pyc
+*.pyo
 .idea/
 .idea_modules/
 build/*.jar
@@ -62,6 +63,8 @@ ec2/lib/
 rat-results.txt
 scalastyle.txt
 scalastyle-output.xml
+R-unit-tests.log
+R/unit-tests.out
 
 # For Hive
 metastore_db/

.rat-excludes

@@ -1,4 +1,5 @@
 target
+cache
 .gitignore
 .gitattributes
 .project
@@ -14,10 +15,12 @@ TAGS
 RELEASE
 control
 docs
+docker.properties.template
 fairscheduler.xml.template
 spark-defaults.conf.template
 log4j.properties
 log4j.properties.template
+metrics.properties
 metrics.properties.template
 slaves
 slaves.template
@@ -27,7 +30,13 @@ spark-env.sh.template
 log4j-defaults.properties
 bootstrap-tooltip.js
 jquery-1.11.1.min.js
+d3.min.js
+dagre-d3.min.js
+graphlib-dot.min.js
 sorttable.js
+vis.min.js
+vis.min.css
+vis.map
 .*avsc
 .*txt
 .*json
@@ -65,3 +74,12 @@ logs
 .*scalastyle-output.xml
 .*dependency-reduced-pom.xml
 known_translations
+json_expectation
+local-1422981759269/*
+local-1422981780767/*
+local-1425081759269/*
+local-1426533911241/*
+local-1426633911242/*
+local-1427397477963/*
+DESCRIPTION
+NAMESPACE

CONTRIBUTING.md

@@ -1,12 +1,16 @@
 ## Contributing to Spark
 
-Contributions via GitHub pull requests are gladly accepted from their original
-author. Along with any pull requests, please state that the contribution is
-your original work and that you license the work to the project under the
-project's open source license. Whether or not you state this explicitly, by
-submitting any copyrighted material via pull request, email, or other means
-you agree to license the material under the project's open source license and
-warrant that you have the legal authority to do so.
+*Before opening a pull request*, review the 
+[Contributing to Spark wiki](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark). 
+It lists steps that are required before creating a PR. In particular, consider:
+
+- Is the change important and ready enough to ask the community to spend time reviewing?
+- Have you searched for existing, related JIRAs and pull requests?
+- Is this a new feature that can stand alone as a package on http://spark-packages.org ?
+- Is the change being proposed clearly explained and motivated?
 
-Please see the [Contributing to Spark wiki page](https://cwiki.apache.org/SPARK/Contributing+to+Spark)
-for more information.
+When you contribute code, you affirm that the contribution is your original work and that you 
+license the work to the project under the project's open source license. Whether or not you 
+state this explicitly, by submitting any copyrighted material via pull request, email, or 
+other means you agree to license the material under the project's open source license and 
+warrant that you have the legal authority to do so.

LICENSE

@@ -643,6 +643,36 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
 
+========================================================================
+For d3 (core/src/main/resources/org/apache/spark/ui/static/d3.min.js):
+========================================================================
+
+Copyright (c) 2010-2015, Michael Bostock
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* The name Michael Bostock may not be used to endorse or promote products
+  derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL MICHAEL BOSTOCK BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ========================================================================
 For Scala Interpreter classes (all .scala files in repl/src/main/scala
@@ -771,6 +801,22 @@ 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 TestTimSort (core/src/test/java/org/apache/spark/util/collection/TestTimSort.java):
+========================================================================
+Copyright (C) 2015 Stijn de Gouw
+
+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 LimitedInputStream
@@ -798,6 +844,7 @@ BSD-style licenses
 The following components are provided under a BSD-style license. See project link for details.
 
      (BSD 3 Clause) 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:1.2.3 - http://jblas.org/)
      (BSD License) AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
      (BSD License) Javolution (javolution:javolution:5.5.1 - http://javolution.org)

R/.gitignore

@@ -0,0 +1,6 @@
+*.o
+*.so
+*.Rd
+lib
+pkg/man
+pkg/html

R/DOCUMENTATION.md

@@ -0,0 +1,12 @@
+# SparkR Documentation
+
+SparkR documentation is generated using in-source comments annotated using using
+`roxygen2`. After making changes to the documentation, to generate man pages,
+you can run the following from an R console in the SparkR home directory
+
+    library(devtools)
+    devtools::document(pkg="./pkg", roclets=c("rd"))
+
+You can verify if your changes are good by running
+
+    R CMD check pkg/

R/README.md

@@ -0,0 +1,67 @@
+# R on Spark
+
+SparkR is an R package that provides a light-weight frontend to use Spark from R.
+
+### SparkR development
+
+#### Build Spark
+
+Build Spark with [Maven](http://spark.apache.org/docs/latest/building-spark.html#building-with-buildmvn) and include the `-PsparkR` profile to build the R package. For example to use the default Hadoop versions you can run
+```
+  build/mvn -DskipTests -Psparkr package
+```
+
+#### Running sparkR
+
+You can start using SparkR by launching the SparkR shell with
+
+    ./bin/sparkR
+
+The `sparkR` script automatically creates a SparkContext with Spark by default in
+local mode. To specify the Spark master of a cluster for the automatically created
+SparkContext, you can run
+
+    ./bin/sparkR --master "local[2]"
+
+To set other options like driver memory, executor memory etc. you can pass in the [spark-submit](http://spark.apache.org/docs/latest/submitting-applications.html) arguments to `./bin/sparkR`
+
+#### Using SparkR from RStudio
+
+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")
+# This line loads SparkR from the installed directory
+.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
+library(SparkR)
+sc <- sparkR.init(master="local")
+```
+
+#### Making changes to SparkR
+
+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. 
+
+#### Generating documentation
+
+The SparkR documentation (Rd files and HTML files) are not a part of the source repository. To generate them you can run the script `R/create-docs.sh`. This script uses `devtools` and `knitr` to generate the docs and these packages need to be installed on the machine before using the script.
+
+### 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:
+
+    ./bin/sparkR examples/src/main/r/pi.R local[2]
+
+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
+```
+export YARN_CONF_DIR=/etc/hadoop/conf
+./bin/spark-submit --master yarn examples/src/main/r/pi.R 4
+```

R/WINDOWS.md

@@ -0,0 +1,13 @@
+## Building SparkR on Windows
+
+To build SparkR on Windows, the following steps are required
+
+1. Install R (>= 3.1) and [Rtools](http://cran.r-project.org/bin/windows/Rtools/). Make sure to
+include Rtools and R in `PATH`.
+2. Install
+[JDK7](http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html) and set
+`JAVA_HOME` in the system environment variables.
+3. Download and install [Maven](http://maven.apache.org/download.html). Also include the `bin`
+directory in Maven in `PATH`.
+4. Set `MAVEN_OPTS` as described in [Building Spark](http://spark.apache.org/docs/latest/building-spark.html).
+5. Open a command shell (`cmd`) in the Spark directory and run `mvn -DskipTests -Psparkr package`

R/create-docs.sh

@@ -0,0 +1,46 @@
+#!/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.
+#
+
+# Script to create API docs for SparkR
+# This requires `devtools` and `knitr` to be installed on the machine.
+
+# After running this script the html docs can be found in 
+# $SPARK_HOME/R/pkg/html
+
+# Figure out where the script is
+export FWDIR="$(cd "`dirname "$0"`"; pwd)"
+pushd $FWDIR
+
+# Generate Rd file
+Rscript -e 'library(devtools); devtools::document(pkg="./pkg", roclets=c("rd"))'
+
+# Install the package
+./install-dev.sh
+
+# Now create HTML files
+
+# knit_rd puts html in current working directory
+mkdir -p pkg/html
+pushd pkg/html
+
+Rscript -e 'library(SparkR, lib.loc="../../lib"); library(knitr); knit_rd("SparkR")'
+
+popd
+
+popd

R/install-dev.bat

@@ -0,0 +1,27 @@
+@echo off
+
+rem
+rem Licensed to the Apache Software Foundation (ASF) under one or more
+rem contributor license agreements.  See the NOTICE file distributed with
+rem this work for additional information regarding copyright ownership.
+rem The ASF licenses this file to You under the Apache License, Version 2.0
+rem (the "License"); you may not use this file except in compliance with
+rem the License.  You may obtain a copy of the License at
+rem
+rem    http://www.apache.org/licenses/LICENSE-2.0
+rem
+rem Unless required by applicable law or agreed to in writing, software
+rem distributed under the License is distributed on an "AS IS" BASIS,
+rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+rem See the License for the specific language governing permissions and
+rem limitations under the License.
+rem
+
+rem Install development version of SparkR
+rem
+
+set SPARK_HOME=%~dp0..
+
+MKDIR %SPARK_HOME%\R\lib
+
+R.exe CMD INSTALL --library="%SPARK_HOME%\R\lib"  %SPARK_HOME%\R\pkg\

R/install-dev.sh

@@ -0,0 +1,36 @@
+#!/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 $SPARK_HOME/R/lib to be the installation directory
+# to load the SparkR package on the worker nodes.
+
+
+FWDIR="$(cd `dirname $0`; pwd)"
+LIB_DIR="$FWDIR/lib"
+
+mkdir -p $LIB_DIR
+
+# Install R
+R CMD INSTALL --library=$LIB_DIR $FWDIR/pkg/

R/log4j.properties

@@ -0,0 +1,28 @@
+#
+# 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.
+#
+
+# Set everything to be logged to the file target/unit-tests.log
+log4j.rootCategory=INFO, file
+log4j.appender.file=org.apache.log4j.FileAppender
+log4j.appender.file.append=true
+log4j.appender.file.file=R-unit-tests.log
+log4j.appender.file.layout=org.apache.log4j.PatternLayout
+log4j.appender.file.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss.SSS} %t %p %c{1}: %m%n
+
+# Ignore messages below warning level from Jetty, because it's a bit verbose
+log4j.logger.org.eclipse.jetty=WARN
+org.eclipse.jetty.LEVEL=WARN