Merge branch 'master' into SPARK-15288, and resolving conflicts

Author: Devaraj K

.github/PULL_REQUEST_TEMPLATE

@@ -2,11 +2,9 @@
 
 (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)
 
+Please review http://spark.apache.org/contributing.html before opening a pull request.

.gitignore

@@ -17,11 +17,14 @@
 .idea/
 .idea_modules/
 .project
+.pydevproject
 .scala_dependencies
 .settings
 /lib/
 R-unit-tests.log
 R/unit-tests.out
+R/cran-check.out
+R/pkg/vignettes/sparkr-vignettes.html
 build/*.jar
 build/apache-maven*
 build/scala*
@@ -54,6 +57,8 @@ project/plugins/project/build.properties
 project/plugins/src_managed/
 project/plugins/target/
 python/lib/pyspark.zip
+python/deps
+python/pyspark/python
 reports/
 scalastyle-on-compile.generated.xml
 scalastyle-output.xml
@@ -77,3 +82,8 @@ spark-warehouse/
 # For R session data
 .RData
 .RHistory
+.Rhistory
+*.Rproj
+*.Rproj.*
+
+.Rproj.user

.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 -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install
+  - build/mvn -T 4 -q -DskipTests -Pmesos -Pyarn -Phadoop-2.3 -Pkinesis-asl -Phive -Phive-thriftserver install
 
 # 6. Run lint-java.
 script:

CONTRIBUTING.md

@@ -1,12 +1,12 @@
 ## Contributing to Spark
 
 *Before opening a pull request*, review the 
-[Contributing to Spark wiki](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark). 
+[Contributing to Spark guide](http://spark.apache.org/contributing.html). 
 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 this a new feature that can stand alone as a [third party project](http://spark.apache.org/third-party-projects.html) ?
 - Is the change being proposed clearly explained and motivated?
 
 When you contribute code, you affirm that the contribution is your original work and that you 

LICENSE

@@ -263,7 +263,7 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
      (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:0.9.2 - http://py4j.sourceforge.net/)
+     (The New BSD License) Py4J (net.sf.py4j:py4j:0.10.4 - 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)
@@ -296,3 +296,4 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
      (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)
+     (MIT License) modernizr (https://github.com/Modernizr/Modernizr/blob/master/LICENSE)

NOTICE

@@ -1,5 +1,5 @@
 Apache Spark
-Copyright 2014 The Apache Software Foundation.
+Copyright 2014 and onwards The Apache Software Foundation.
 
 This product includes software developed at
 The Apache Software Foundation (http://www.apache.org/).
@@ -421,9 +421,6 @@ Copyright (c) 2011, Terrence Parr.
 This product includes/uses ASM (http://asm.ow2.org/),
 Copyright (c) 2000-2007 INRIA, France Telecom.
 
-This product includes/uses org.json (http://www.json.org/java/index.html),
-Copyright (c) 2002 JSON.org
-
 This product includes/uses JLine (http://jline.sourceforge.net/),
 Copyright (c) 2002-2006, Marc Prud'hommeaux <mwp1@cornell.edu>.
 

R/.gitignore

@@ -4,3 +4,5 @@
 lib
 pkg/man
 pkg/html
+SparkR.Rcheck/
+SparkR_*.tar.gz

R/CRAN_RELEASE.md

@@ -0,0 +1,91 @@
+# SparkR CRAN Release
+
+To release SparkR as a package to CRAN, we would use the `devtools` package. Please work with the
+`dev@spark.apache.org` community and R package maintainer on this.
+
+### Release
+
+First, check that the `Version:` field in the `pkg/DESCRIPTION` file is updated. Also, check for stale files not under source control.
+
+Note that while `run-tests.sh` runs `check-cran.sh` (which runs `R CMD check`), it is doing so with `--no-manual --no-vignettes`, which skips a few vignettes or PDF checks - therefore it will be preferred to run `R CMD check` on the source package built manually before uploading a release. Also note that for CRAN checks for pdf vignettes to success, `qpdf` tool must be there (to install it, eg. `yum -q -y install qpdf`).
+
+To upload a release, we would need to update the `cran-comments.md`. This should generally contain the results from running the `check-cran.sh` script along with comments on status of all `WARNING` (should not be any) or `NOTE`. As a part of `check-cran.sh` and the release process, the vignettes is build - make sure `SPARK_HOME` is set and Spark jars are accessible.
+
+Once everything is in place, run in R under the `SPARK_HOME/R` directory:
+
+```R
+paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::release(); .libPaths(paths)
+```
+
+For more information please refer to http://r-pkgs.had.co.nz/release.html#release-check
+
+### Testing: build package manually
+
+To build package manually such as to inspect the resulting `.tar.gz` file content, we would also use the `devtools` package.
+
+Source package is what get released to CRAN. CRAN would then build platform-specific binary packages from the source package.
+
+#### Build source package
+
+To build source package locally without releasing to CRAN, run in R under the `SPARK_HOME/R` directory:
+
+```R
+paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::build("pkg"); .libPaths(paths)
+```
+
+(http://r-pkgs.had.co.nz/vignettes.html#vignette-workflow-2)
+
+Similarly, the source package is also created by `check-cran.sh` with `R CMD build pkg`.
+
+For example, this should be the content of the source package:
+
+```sh
+DESCRIPTION	R		inst		tests
+NAMESPACE	build		man		vignettes
+
+inst/doc/
+sparkr-vignettes.html
+sparkr-vignettes.Rmd
+sparkr-vignettes.Rman
+
+build/
+vignette.rds
+
+man/
+ *.Rd files...
+
+vignettes/
+sparkr-vignettes.Rmd
+```
+
+#### Test source package
+
+To install, run this:
+
+```sh
+R CMD INSTALL SparkR_2.1.0.tar.gz
+```
+
+With "2.1.0" replaced with the version of SparkR.
+
+This command installs SparkR to the default libPaths. Once that is done, you should be able to start R and run:
+
+```R
+library(SparkR)
+vignette("sparkr-vignettes", package="SparkR")
+```
+
+#### Build binary package
+
+To build binary package locally, run in R under the `SPARK_HOME/R` directory:
+
+```R
+paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::build("pkg", binary = TRUE); .libPaths(paths)
+```
+
+For example, this should be the content of the binary package:
+
+```sh
+DESCRIPTION	Meta		R		html		tests
+INDEX		NAMESPACE	help		profile		worker
+```

R/DOCUMENTATION.md

@@ -1,12 +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,
+SparkR documentation is generated by using in-source comments and annotated by using
+[`roxygen2`](https://cran.r-project.org/web/packages/roxygen2/index.html). After making changes to the documentation and generating 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"))
-
+```R
+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

@@ -1,12 +1,13 @@
 # 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: 
-```
+Example:
+```bash
 # 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
@@ -17,8 +18,9 @@ export R_HOME=/home/username/R
 #### 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
+
+```bash
+build/mvn -DskipTests -Psparkr package
 ```
 
 #### Running sparkR
@@ -37,41 +39,43 @@ To set other options like driver memory, executor memory etc. you can pass in th
 
 #### 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 
-```
+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
+```R
 # Set this to where Spark is installed
 Sys.setenv(SPARK_HOME="/Users/username/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")
+sparkR.session()
 ```
 
 #### 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.
+The [instructions](http://spark.apache.org/contributing.html) 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 `R/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.
-    
+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. Also, you may need to install these [prerequisites](https://github.com/apache/spark/tree/master/docs#prerequisites). See also, `R/DOCUMENTATION.md`
+
 ### Examples, Unit tests
 
 SparkR comes with several sample programs in the `examples/src/main/r` directory.
 To run one of them, use `./bin/spark-submit <filename> <args>`. For example:
-
-    ./bin/spark-submit examples/src/main/r/dataframe.R
-
-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
+```bash
+./bin/spark-submit examples/src/main/r/dataframe.R
+```
+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:
+```bash
+R -e 'install.packages("testthat", repos="http://cran.us.r-project.org")'
+./R/run-tests.sh
+```
 
 ### Running on YARN
+
 The `./bin/spark-submit` 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
-```
+```bash
 export YARN_CONF_DIR=/etc/hadoop/conf
 ./bin/spark-submit --master yarn examples/src/main/r/dataframe.R
 ```