From 8a9110510c9e4cbbcb0dede62cb4b9dd1c6bc8cc Mon Sep 17 00:00:00 2001
From: Kai Jiang <jiangkai@gmail.com>
Date: Sun, 5 Jun 2016 13:03:02 -0700
Subject: [PATCH] [MINOR][R][DOC] Fix R documentation generation instruction.
## 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.
---
R/DOCUMENTATION.md | 12 ++++++------
R/README.md | 30 ++++++++++++++----------------
2 files changed, 20 insertions(+), 22 deletions(-)
diff --git a/R/DOCUMENTATION.md b/R/DOCUMENTATION.md
index 931d01549b..7314a1fccc 100644
--- a/R/DOCUMENTATION.md
+++ b/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/
diff --git a/R/README.md b/R/README.md
index 044f95312a..932d5272d0 100644
--- a/R/README.md
+++ b/R/README.md
@@ -7,8 +7,7 @@ SparkR is an R package that provides a light-weight frontend to use Spark from R
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
@@ -20,8 +19,8 @@ export R_HOME=/home/username/R
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
@@ -40,9 +39,8 @@ 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
@@ -59,25 +57,25 @@ Once you have made your changes, please include unit tests for them and run exis
#### 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
-
+```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:
-
- R -e 'install.packages("testthat", repos="http://cran.us.r-project.org")'
- ./R/run-tests.sh
+```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
```
--
GitLab