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Library Rjava Error Mac

27.05.2020
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  • Problem with XLConnect/rJava on macOS. I've got Java JDK installed and ran javareconf to no avail. I have an issue with XLConnect/rJava which seems to be fairly common, but I've tried all the suggested fixes, and can't seem to get rJava to load.

The R script uses rJava and RJDBC packages to load tables from database. In Mac OS X, to correctly load this packages
requires the following steps borrowed from https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X.
Steps have been modified to reflect problems (and it's solutions) reported here.

Sep 21, 2016  I was trying to reinstall RDAVIDWebService after upgrading to R-3.3.1 on El Capitan and I followed the steps from my previous blog post. Now you dont have to fix the ssl issue, but you still have t.

Overview

This is the list of software downloads needed in order to connect R via RJDBC to a database:

  • Xcode Command Line Tools
  • Java 6
  • Java 8
  • R
  • rJava source package
  • Database JDBC jar file
  • RStudio (optional)

If you have any of this software already installed, you can skip that section.

Open Terminal.app

We'll change to the Downloads directory as we'll have to download some packages from the internet.

Just to make debugging easier if something does not go as planned, log all output.

Xcode Command Line Tools

We need Xcode Command Line Tools, by running this command we will invoke the downloader if not installed, otherwise it will report it is already installed.

Java 6

Install the legacy Java 6 runtime which is needed despite us not going to use Java 6.

Now walk through the install to complete.

Java 8

Install Java 8. Note: newer versions may be available.

Now walk through the install to complete.

We'll run these two commands to output Java installations and what the current command defaults to. They are informative only.

Library(rjava) Error Mac

You should see something like this:

R for OS X

Download and install the R package for OS X.

Now walk through the install to complete.

Now we need to tell R to use our Java 8 as it's JAVA_HOME

You should see output similar to

Now install rJava from source and compile it against the Java 8 JDK.The 'unset JAVA_HOME' takes care of:

Library Java Error Mac Os

Now let's check that rJava can be loaded correctly and returns the correct JDK version.This command should return the string 1.8.0_111-b14 (or whatever Java 8 version you installed).

Finish

Rjava Image Not Found

Exit from the script logging.

Using RStudio.app or R.app

Rjava Package

A common error when trying to load rJava in RStudio is:

There are three ways to get around this problem and use rJava with RStudio or R console (R.app) :

Rjava Error Mac

1 - Launching from the command line

Library Java Error Mac Firefox

Library

You can launch it from the command line in Terminal.app like such:

This is a known limitation with RStudio on OS X. See this link for more details:[https://support.rstudio.com/hc/communities/public/questions/200650933-rJava-fails-to-load-in-RStudio-Desktop-OS-X](https://support.rstudio.com/hc/communities/public/questions/200650933-rJava-fails-to-load-in-RStudio-Desktop-OS-X)

Library Java Error Mac Pro

2 - Make a symlink to libjvm.dylib

This is an alternate solution to loading RStudio, but must be updated any time you upgrade Java

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+Based on this Stack Overflow thread, one can use the following to work around the libjvm.dylib loading issues.

3 - Load the library in the script (which is the used approach in the CohortEx R script)

Just a bit of code in your R script:

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