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mllib_pmml_model_export_SPARK-1406

Conflicts:
	mllib/src/main/scala/org/apache/spark/mllib/clustering/KMeansModel.scala
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selvinsource committed Apr 19, 2015
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3 changes: 3 additions & 0 deletions .gitignore
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*.iml
*.iws
*.pyc
*.pyo
.idea/
.idea_modules/
build/*.jar
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rat-results.txt
scalastyle.txt
scalastyle-output.xml
R-unit-tests.log
R/unit-tests.out

# For Hive
metastore_db/
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target
cache
.gitignore
.gitattributes
.project
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spark-defaults.conf.template
log4j.properties
log4j.properties.template
metrics.properties
metrics.properties.template
slaves
slaves.template
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.*scalastyle-output.xml
.*dependency-reduced-pom.xml
known_translations
DESCRIPTION
NAMESPACE
16 changes: 16 additions & 0 deletions LICENSE
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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
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6 changes: 6 additions & 0 deletions R/.gitignore
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*.o
*.so
*.Rd
lib
pkg/man
pkg/html
12 changes: 12 additions & 0 deletions R/DOCUMENTATION.md
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# 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/
67 changes: 67 additions & 0 deletions R/README.md
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# 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
```
13 changes: 13 additions & 0 deletions R/WINDOWS.md
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## 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`
46 changes: 46 additions & 0 deletions R/create-docs.sh
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#!/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
27 changes: 27 additions & 0 deletions R/install-dev.bat
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@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\
36 changes: 36 additions & 0 deletions R/install-dev.sh
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#!/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/
28 changes: 28 additions & 0 deletions R/log4j.properties
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#
# 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
35 changes: 35 additions & 0 deletions R/pkg/DESCRIPTION
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Package: SparkR
Type: Package
Title: R frontend for Spark
Version: 1.4.0
Date: 2013-09-09
Author: The Apache Software Foundation
Maintainer: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Imports:
methods
Depends:
R (>= 3.0),
methods,
Suggests:
testthat
Description: R frontend for Spark
License: Apache License (== 2.0)
Collate:
'generics.R'
'jobj.R'
'RDD.R'
'pairRDD.R'
'schema.R'
'column.R'
'group.R'
'DataFrame.R'
'SQLContext.R'
'backend.R'
'broadcast.R'
'client.R'
'context.R'
'deserialize.R'
'serialize.R'
'sparkR.R'
'utils.R'
'zzz.R'
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