R: rJava package install failing

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When installing rJava using the install.packages("rJava") command I get the following error:

checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver    : '/usr/bin/jar'
compiler    : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../include -I/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/amd64/server -L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/lib/amd64 -L/usr/lib/jvm/java-6-sun-1.6.0.20/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’

I have the Java JDK installed and java -version returns the following:

$ java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)

When Googling around for the error I see that others are having the same issue but not finding a solution other than "install the whole JDK, not just the JRE" which I have done.

The other thing I read was to run sudo R CMD javareconf which runs quite happily with no errors.

Any ideas what my problem is?

[[EDIT]] It's been a few months since I had this problem. I had initially solved this by editing my Java paths, as illustrated in the answer I posted below. I recently ran into the same issue on a new Ubuntu install. I tried Dirk's recommendation to use apt-get to install the rJava package. It worked perfectly. What I failed to appreciate initially is that installing packages using the Ubuntu apt-get method is fundamentally different than just loading the same package using install.packages() inside of R. The Ubuntu packages solve some issues which I didn't realize or appreciate.

rjava r
18 Answers

That is how I make it work :

In Linux (Ubuntu 16.04 and 20.04 worked confirmed)

sudo apt-get install default-jre
sudo apt-get install default-jdk
sudo R CMD javareconf

in R:

install.packages("rJava")
user_71556840
user_31368690

I was facing the same problem while using Windows 10. I have solved the problem using the following procedure

  1. Download Java from https://java.com/en/download/windows-64bit.jsp for 64-bit windows\Install it
  2. Download Java development kit from https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html for 64-bit windows\Install it
  3. Then right click on “This PC” icon in desktop\Properties\Advanced system settings\Advanced\Environment Variables\Under System variables select Path\Click Edit\Click on New\Copy and paste paths “C:\Program Files\Java\jdk1.8.0_201\bin” and “C:\Program Files\Java\jre1.8.0_201\bin” (without quote) \OK\OK\OK

Note: jdk1.8.0_201 and jre1.8.0_201 will be changed depending on the version of Java development kit and Java

  1. In Environment Variables window go to User variables for User\Click on New\Put Variable name as “JAVA_HOME” and Variable value as “C:\Program Files\Java\jdk1.8.0_201\bin”\Press OK

To check the installation, open CMD\Type javac\Press Enter and Type java\press enter It will show enter image description here

In RStudio run 

Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jdk1.8.0_201")

Note: jdk1.8.0_201 will be changed depending on the version of Java development kit

Now you can install and load rJava package without any problem.

user_61238240

The problem was rJava wont install in RStudio (Version 1.0.136). The following worked for me (macOS Sierra version 10.12.6) (found here):

Step-1: Download and install javaforosx.dmg from here

Step-2: Next, run the command from inside RStudio:

install.packages("rJava", type = 'source')
user_60052060

On Arch Linux, I needed to install openjdk-src to get a JNI path working.

In other words, these are the packages I needed to install before sudo R CMD javareconf ran successfully:

local/jdk-openjdk 14.0.2.u12-1
    OpenJDK Java 14 development kit
local/jre-openjdk 14.0.2.u12-1
    OpenJDK Java 14 full runtime environment
local/jre-openjdk-headless 14.0.2.u12-1
    OpenJDK Java 14 headless runtime environment
local/openjdk-src 14.0.2.u12-1
    OpenJDK Java 14 sources
user_11692330

Assuming you have sudo privileges and not in Ubuntu where package manager makes this easier -- I tried variations of prior answers and found this gem on Databricks blog for nonUbuntu (https://kb.databricks.com/r/install-rjava-rjdbc-libraries.html)

  1. Installed JDK
sudo apt-get install openjdk-8-jdk
  1. Verify path to libjvm.so; for me-->
cd /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64 
grep -r libjvm

output:

Binary file server/libjvm.so matches <<<<<<<<
  1. Do java configure
    sudo R CMD javareconf

  1. Remove prior versions of the package and install 'rJava' from CRAN mirror in RStudio

  2. Restart RStudio

  3. In RStudio verify link to libjvm.so

    dyn.load('/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjvm.so')
    library('rJava')
user_94297380
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