R: rJava package install failing

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?

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.

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最佳答案

Turns out my problem was an issue with my JAVA_HOME environment variable. Yes, shocking I know. My initial setting for PATH and JAVA_HOME looked like this:

export JAVA_HOME=/usr/lib/jvm/java-6-sun
export PATH=$PATH:$JAVA_HOME/bin

And I added /jre so it now looks like this:

export JAVA_HOME=/usr/lib/jvm/java-6-sun/jre
export PATH=$PATH:$JAVA_HOME/bin

Everything in Java seemed to work fine without the /jre but rJava would not. Odd.

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Wouldn't 

apt-get install r-cran-rjava

have been easier? You could have asked me at useR! :)

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Running R under Gentoo on an AMD64. I upgraded to R 2.12.0

R version 2.12.0 (2010-10-15) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) and those pesky messages went away.

Jan Vandermeer

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Thanks - your suggestion about $JAVA_HOME lead me to a similar solution:

unset JAVA_HOME

before invoking R.

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This worked for me on Ubuntu 12.04 and R version 3.0

cd /usr/lib/jvm/java-6-sun-1.6.0.26/include

this is the directory that has jni.h

Next create a soft link to another required header file (I'm too lazy to find out how to include more than one directory in the JAVA_CPPFLAGS option below):

sudo ln -s linux/jni_md.h .

Finally

sudo R CMD javareconf JAVA_CPPFLAGS=-I/usr/lib/jvm/java-6-sun-1.6.0.26/include
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what I do is here:

  1. in /etc/apt/sources.list, add:

    deb http://ftp.de.debian.org/debian sid main

Note:the rjava should be latest version

2 run: sudo apt-get update sudo apt-get install r-cran-rjava

Once update the old version of rjava, then can install rhdfs_1.0.8.

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I tried to install openjdk-7-* but still I had problems installing rJava. Turns out after I restarted my computer, then there was no problem at all.

so 

sudo apt-get install openjdk-7-*




RESTART after installing java, then try to install package "rJava" in R
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I came across the same issue, and it worked after running commands below.

export JAVA_LIBS="$JAVA_LIBS -ldl"
R CMD javareconf

See details at http://www-01.ibm.com/support/knowledgecenter/SSPT3X_3.0.0/com.ibm.swg.im.infosphere.biginsights.install.doc/doc/install_install_r.html

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below is one of my answers on another post - error: unable to load installed packages just now
(this is also relevant to this question)

For Linux(Ubuntu) users: If you have oracle-java (7/8) installed. It'll be at this location /usr/lib/jvm and sudo access is required.

Create the file /etc/ld.so.conf.d/java.conf with the following entries:

/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server

(Replace java-8-oracle with java-7-oracle depending on your java version)

Then:

sudo ldconfig

Restart RStudio and then install the rJava package.

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I've encountered similar problem on Ubuntu 16.04 and was able to solve it by creating a folder named "default-java" in /usr/lib/jvm and copying into it all the contents of the /usr/lib/jvm/java-8-oracle. I opted for this solution as correcting JAVA_HOME environment variable turned out to be of no use.

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I got it working by downloading : https://cran.r-project.org/src/contrib/rJava_0.9-8.tar.gz and running command R CMD install rJava_0.9-8.tar.gz

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The rJava package looks for the /usr/lib/jvm/default-java/ folder. But it's not available as default. This folder have a symlink for the default java configured for the system.

To activate the default java install the following packages:

sudo apt-get install default-jre default-jre-headless

Tested on ubuntu 17.04 with CRAN R 3.4.1

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What worked for me was changing JAVA_HOME from file /usr/lib/R/etc/javaconf

I first checked what was my version of Java enabled : sudo update-alternatives --config java. In my case, it was java-8-oracle

I opened the file /usr/lib/R/etc/javaconf and replaced default-java by java-8-oracle :

${JAVA_HOME=/usr/lib/jvm/default-java}

replaced by :

${JAVA_HOME=/usr/lib/jvm/java-8-oracle}

And then sudo R CMD javareconf

I restarted RStudio, and could then install rJava.

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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')
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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")
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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.

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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
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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')

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