1169db44bc
## What changes were proposed in this pull request?
SparkR tests, `R/run-tests.sh`, succeeds only once because `test_sparkSQL.R` does not clean up the test table, `people`.
As a result, the rows in `people` table are accumulated at every run and the test cases fail.
The following is the failure result for the second run.
```r
Failed -------------------------------------------------------------------------
1. Failure: create DataFrame from RDD (test_sparkSQL.R#204) -------------------
collect(sql("SELECT age from people WHERE name = 'Bob'"))$age not equal to c(16).
Lengths differ: 2 vs 1
2. Failure: create DataFrame from RDD (test_sparkSQL.R#206) -------------------
collect(sql("SELECT height from people WHERE name ='Bob'"))$height not equal to c(176.5).
Lengths differ: 2 vs 1
```
## How was this patch tested?
Manual. Run `run-tests.sh` twice and check if it passes without failures.
Author: Dongjoon Hyun <dongjoon@apache.org>
Closes #16310 from dongjoon-hyun/SPARK-18897.
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| .. | ||
| pkg | ||
| .gitignore | ||
| check-cran.sh | ||
| CRAN_RELEASE.md | ||
| create-docs.sh | ||
| DOCUMENTATION.md | ||
| install-dev.bat | ||
| install-dev.sh | ||
| log4j.properties | ||
| README.md | ||
| run-tests.sh | ||
| WINDOWS.md | ||
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
Build Spark
Build Spark with Maven 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 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/username/spark")
# This line loads SparkR from the installed directory
.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
library(SparkR)
sparkR.session()
Making changes to SparkR
The instructions 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. 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 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 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/dataframe.R