Documentation for JIRA 4.0. Documentation for other versions of JIRA is available too.

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Some linux distributions (notably Debian and Ubuntu) come with a free version of Java called GIJ (from the GCJ project) pre-installed:

jturner:~$ java -version
java version "1.4.2"
gij (GNU libgcj) version 4.1.2 (Ubuntu 4.1.2-0ubuntu5)

Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
jturner:~$ 

Unfortunately GCJ is incomplete, and unable to run Atlassian Java applications without problems.

The solution is to install Sun's version of Java:

jturner:~$ sudo apt-get install sun-java6-jdk 
Password:
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  java-common libltdl3 odbcinst1debian1 sun-java6-bin sun-java6-jre unixodbc
Suggested packages:
  equivs sun-java6-demo sun-java6-doc sun-java6-source sun-java6-plugin ia32-sun-java6-plugin sun-java6-fonts
  ttf-sazanami-gothic ttf-sazanami-mincho libmyodbc odbc-postgresql libct1
Recommended packages:
  gsfonts-x11
The following NEW packages will be installed:
  java-common libltdl3 odbcinst1debian1 sun-java6-bin sun-java6-jdk sun-java6-jre unixodbc
0 upgraded, 7 newly installed, 0 to remove and 3 not upgraded.
Need to get 42.6MB of archives.
After unpacking 127MB of additional disk space will be used.
Do you want to continue [Y/n]? y

....

Setting up java-common (0.25ubuntu2) ...

Setting up libltdl3 (1.5.22-4) ...

Setting up odbcinst1debian1 (2.2.11-13) ...

Setting up unixodbc (2.2.11-13) ...

Setting up sun-java6-bin (6-00-2ubuntu2) ...

Setting up sun-java6-jre (6-00-2ubuntu2) ...

Setting up sun-java6-jdk (6-00-2ubuntu2) ...

jturner:~$

After doing this, make sure the correct version of Java is in use by running java -version:

jturner:~$ java -version
java version "1.6.0"
Java(TM) SE Runtime Environment (build 1.6.0-b105)
Java HotSpot(TM) Server VM (build 1.6.0-b105, mixed mode)
jturner:~$ 

If the GCJ Java is still being used, you will need to explicitly set Sun's Java as the default:

jturner:~$ sudo update-alternatives --config java

There are 2 alternatives which provide `java'.

  Selection    Alternative
-----------------------------------------------
*         1    /usr/bin/gij-wrapper-4.1
 +        2    /usr/lib/jvm/java-6-sun/jre/bin/java

Press enter to keep the default[*], or type selection number: 2
Using `/usr/lib/jvm/java-6-sun/jre/bin/java' to provide `java'.
jturner:~$ 

Setting JAVA_HOME

Some programs like Tomcat (bundled with most Atlassian products) need a JAVA_HOME variable set, so they know where Java is installed. This can be set system-wide in /etc/profile:

jturner:~$ sudo su -
Password:
root:~# cat >> /etc/profile
JAVA_HOME=/usr/lib/jvm/java-6-sun
export JAVA_HOME
root:~# 

The variable will be set for new terminals:

jturner:~$ echo $JAVA_HOME
/usr/lib/jvm/java-6-sun
jturner:~$
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