doc/rjava.md

In richelbilderbeek/rbeast2: Control 'BEAST2'

rJava questions

How to install rJava under different operating systems

• Installation
• Troubleshooting

Installation

Mac OS

On Travis, I do:

R CMD javareconf
R --quiet -e 'install.packages("rJava", type="source", repos="http://cran.us.r-project.org")'

May work for you as well.

Ubuntu 14.5 (Trusty Tahr)

The .travis.yml file shows a Trusty install:

 - sudo apt-get install -qq oracle-java8-installer # Java 8
 - sudo apt-get install oracle-java8-set-default

So I assume the same can be achieved with:

sudo add-apt-repository -y ppa:webupd8team/java 
sudo apt-get update -qq
sudo apt-get install oracle-java8-installer
sudo apt-get install oracle-java8-set-default

Ubuntu 17.10 (Artful Aardvark)

sudo apt-get install r-cran-rjava openjdk-8-jdk
R CMD javareconf

Do not use openjdk-9-jdk.

Ubuntu 18.4 (Bionic Beaver)

The .travis.yml file shows a Trusty install:

# - sudo apt install -qq oracle-java8-installer # Java 8
# - sudo apt install oracle-java8-set-default

On Bionic, I achieved the same with approx:

sudo add-apt-repository ppa:marutter/c2d4u3.5
sudo apt update
sudo apt grade
sudo apt install r-cran-rjava
sudo apt-get install openjdk-11-jdk
sudo R CMD javareconf

#sudo add-apt-repository -y ppa:webupd8team/java 
#sudo apt-get update -qq
#sudo apt-get install oracle-java8-installer
#sudo apt-get install oracle-java8-set-default

Troubleshooting

Error: libjvm.so: cannot open shared object file: No such file or directory

Random solution 1

Sometimes works:

For me, this Stack Overflow post helped me out:

sudo mousepad /etc/ld.so.conf.d/java.conf

In that file put:

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

Save, close, restart R studio, fixed!

Random solution 2

Random notes:

Else this Stack Overflow post may be helpful:

Ruthlessly install all JDK stuff:

sudo apt-get install jdk-*

sudo R CMD javareconf

sudo R CMD javareconf -e
export LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH
sudo apt-get install r-cran-rjava

BEAST2 cannot find Java

Download the Oracle Java SDK:

Open the Oracle Java SDK with the package installer:

Install the Oracle Java SDK with the package installer:

Pick the right java:

sudo update-alternatives --config java

I picked:

There are 5 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-9-openjdk-amd64/bin/java       1091      auto mode
  1            /usr/bin/gij-4.8                                 1048      manual mode
  2            /usr/bin/gij-5                                   1050      manual mode
* 3            /usr/bin/gij-6                                   1060      manual mode
  4            /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java   1081      manual mode
  5            /usr/lib/jvm/java-9-openjdk-amd64/bin/java       1091      manual mode

Press <enter> to keep the current choice[*], or type selection number: 

Reconfig:

sudo R CMD javareconf

richelbilderbeek/rbeast2 documentation built on Sept. 30, 2023, 9:39 a.m.