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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.
Mac os x mavericks installesd.dmg download. Steps have been modified to reflect problems (and it's solutions) reported here.

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)

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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.

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:

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

Exit from the script logging.

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Using RStudio.app or R.app

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) :

1 - Launching from the command line

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

What Is Rstudio 5.dmg Windows 10

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)

2 - Make a symlink to libjvm.dylib

What Is R Studio 5 Dmg Free

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

+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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System requirements: