8a9110510c
## What changes were proposed in this pull request? changes in R/README.md - Make step of generating SparkR document more clear. - link R/DOCUMENTATION.md from R/README.md - turn on some code syntax highlight in R/README.md ## How was this patch tested? local test Author: Kai Jiang <jiangkai@gmail.com> Closes #13488 from vectorijk/R-Readme.
82 lines
3.7 KiB
Markdown
82 lines
3.7 KiB
Markdown
# 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:
|
|
```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
|
|
```
|
|
|
|
### 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
|
|
|
|
```bash
|
|
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
|
|
```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")
|
|
```
|
|
|
|
#### 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 `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. 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:
|
|
```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
|
|
```
|