R rJava package install failing

Question

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

User · Answer

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.

User · Answer

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

User · Answer

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

User · Answer

I was facing the same problem while using Windows 10  I have solved the problem using the following procedure   Download Java from https   java com en download windows-64bit jsp for 64-bit windows Install it Download Java development kit from https   www oracle com technetwork java javase downloads jdk8-downloads-2133151 html for 64-bit windows Install it 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   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   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 · Answer

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 · Answer

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 · Answer

That is how I make it work    In Linux  Ubuntu 16 04   sudo apt-get install default-jre sudo apt-get install default-jdk sudo R CMD javareconf   in R   install packages  rJava

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

Thanks - your suggestion about  JAVA HOME lead me to a similar solution   prompt  unset JAVA HOME   before invoking R

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

what I do is here    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

User · Answer

Wouldn t   apt-get install r-cran-rjava   have been easier  You could have asked me at useR

[r] R: rJava package install failing

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