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Quick Start Guide: Java Setup for ‘R’ Projects

Source: vignettes/rJavaEnv.qmd

This guide will walk you through downloading, installing, and managing Java environments for your R projects using the rJavaEnv package. We’ll cover setting up the environment, un-setting it, managing distributions, installing Java, and checking Java versions. For more advanced use refer to the vignettes on step-by-step fine-grained procedure to download, unpack, install and linke Java and vignette on using rJavaEnv with the targets and callr packages to manage multiple Java environments

1. Quickly Download and Install Java

Install rJavaEnv

Install rJavaEnv from CRAN:

install.packages("rJavaEnv")

Or install the latest version of rJavaEnv from R universe:

install.packages('rJavaEnv',
  repos = c('https://e-kotov.r-universe.dev', 'https://cloud.r-project.org')
)

Quick Install Java JDK

Assume your project directory is currently in a temporary directory. Feel free to skip that, if you are already working in a desired project directory where you would like to install Java. In the example outputs below you will see paths that point to a temporary directory, but in a real project you would see your project directory instead.

project_dir <- tempdir()
setwd(project_dir)

The first time you run any function that requires writing into your home space, you will be provided with a prompt warning you that the package may write to the package cache folder in your home directory, to your current project directory, as well as to the .Rprofile file in your project directory (or any directory you specify).

To quickly install Java JDK 21 (which is also default, if not specified) in your current project directory and set the environment:

On first run, you will be asked for consent to change your environment variables and .Rprofile file in the current working/project directory. This only happens once.

The command above:

  • Downloads the Java distribution compatible with your OS and architecture.

  • Installs Java in a cache directory.

  • Sets the JAVA_HOME and PATH environment variables for the current session and project/working directory, so that any Java/rJava dependent R package can use this requested Java version.

Example expected output (on a Windows machine):

Consent has been granted and recorded.
Detected platform: windows
Detected architecture: x64
You can change the platform and architecture by specifying the `platform` and `arch` arguments.
Downloading Java 21 (Corretto) for windows x64 to C:\Users\user_name\AppData\Local/R/cache/R/rJavaEnv/distrib/amazon-corretto-21-x64-windows-jdk.zip
 [100%] Downloaded 201696048 bytes...
Download completed.
MD5 checksum verified.
v Current R Session: JAVA_HOME and PATH set to C:\Users\user_name\AppData\Local/R/cache/R/rJavaEnv/installed/windows/x64/21
v Current R Project/Working Directory: JAVA_HOME and PATH set to 'C:\Users\user_name\AppData\Local/R/cache/R/rJavaEnv/installed/windows/x64/21' in .Rprofile at 'C:/Users/user_name/AppData/Local/Temp/75/
RtmpuoG3xJ'
Java 21 (amazon-corretto-21-x64-windows-jdk.zip) for windows x64 installed at C:\Users\user_name\AppData\Local/R/cache/R/rJavaEnv/installed/windows/x64/21 and symlinked to
C:/Users/user_name/AppData/Local/Temp/75/RtmpuoG3xJ/rjavaenv/windows/x64/21

That is it. You can now use your Java/rJava-dependent R package.

2. Check Java installation

You can check if the newly installed Java will be correctly picked up by the Java/rJava-dependent R package that you are going to use with.

For R packages that use Java via rJava-dependency (e.g. r5r), you can use the following command:

Example expected output (on a Windows machine):

Using current session's JAVA_HOME: C:\Users\user_name\AppData\Local/R/cache/R/rJavaEnv/installed/windows/x64/21
With the user-specified JAVA_HOME rJava and other rJava/Java-based packages will use Java version: "21.0.4"
[1] TRUE

For R packages that use Java from command line (e.g. opentripplanner), you can use the following command:

Example expected output (on a Windows machine):

java_check_version_cmd()
JAVA_HOME: C:\Users\user_name\AppData\Local/R/cache/R/rJavaEnv/installed/windows/x64/21
Java path: /c/Users/user_name/AppData/Local/R/cache/R/rJavaEnv/installed/windows/x64/21/bin/java
Java version: "openjdk version \"21.0.4\" 2024-07-16 LTS OpenJDK Runtime Environment Corretto-21.0.4.7.1 (build 21.0.4+7-LTS) OpenJDK 64-Bit Server VM Corretto-21.0.4.7.1 (build 21.0.4+7-LTS,
mixed mode, sharing)"
[1] TRUE

Note for Linux users

Note: if you are on a Linux system that did not have any Java version previoulsy installed and you are not using pre-build R package binaries (for example from ‘Posit Package Manager’) and instead install all R packages from source, after this step you may have to quit R, follow these steps to set configure Java for R, and only then install rJava, as otherwise rJava cannot be built from source.*

3. Return things to their original state

Unset Java

Run the following code to unset the Java for the current working directory:

Example expected output (on a Windows machine):

Removed JAVA_HOME settings from .Rprofile in 'C:/Users/user_name/AppData/Local/Temp/75/RtmpuoG3xJ/.Rprofile'

Delete Java from the project directory

The line below clears all Java installations in the project directory:

java_clear("project", delete_all = TRUE)

Example expected output:

All Java symlinks in the project have been cleared.

Now restart the current R session so that R picks up the system Java (or no Java, if it is not installed in the system).

4. Complete Cleanup

If you do not want to use rJavaEnv anymore, please clear the cache folders before removing the package:

java_clear("project", delete_all = TRUE)
java_clear("installed", delete_all = TRUE)
java_clear("distrib", delete_all = TRUE)

Also, clear the .Rprofile file in the projects there you used the package:

Now you can remove the package and restart the current R session so that R picks up the system Java (or no Java, if it is not installed in the system).