Software

Installation guide for J/maanova

Follow the below steps to install J/maanova. I will not give details for each installation.
Please refer to softwares' installation guide if there is any question.

System requirements

This package was developed under the Windows 2000 operating system. The programs have been observed to work under Windows XP/NT/98/2000, Linux Redhat 8.0 and Macintosh OS X operating systems. The memory requirement depends on the size
of the input data but a minimum of 512Mb memory is recommended.

 J/maanova requires following softwares/platforms:

  • R
  • R/maanova
  • Rserve
  • Java Runtime Environment (JRE) 1.4.2 or higher

 
Installation

 

1. Download and install Java

The latest version of Java can be obtained from http://java.sun.com/javase/downloads/index.jsp. Some linux systems have Java installed. In that case you can skip this step.

Current J/maanova doesn't work well with the new JRE6. Sometimes you get an error log file named like this: hs_err_pidxxx.log and the starting portion of this file looks like this:

#
# An unexpected error has been detected by Java Runtime Environment:
#
#  EXCEPTION_FLT_STACK_CHECK (0xc0000092) at pc=0x00e3d0a9, pid=4020, tid=4092
#
# Java VM: Java HotSpot(TM) Client VM (1.6.0_02-b06 mixed mode)
# Problematic frame:
# v  ~RuntimeStub::resolve_virtual_call
#

The work around of this problem on Windows is as below.

Remove your current JRE6 and install the JRE5. Go to Start -> Control Panel -> Add/Remove Programs. Uninstall all versions of Java. Then get the older version of JRE from this link:

http://java.sun.com/javase/downloads/index_jdk5.jsp

You need "Java Runtime Environment (JRE) 5.0 Update 12". 

2. Download and install R

R is available in the Comprehensive R Archive Network (CRAN). Visit http://cran.r-project.org or a local mirror site. Source code is available for UNIX/LINUX, and binaries are available for Windows, MacOS, and many versions of Linux. 

The installation of R should be very straight forward. If you have R installed on your computer, skip this step.

3. Install R/maanova inside R

R/maanova is an add-on package for R. It is the work horse for J/maanova. Obtain R/maanova from here and follow the manual to install it.

4. Download and install Rserve

Rserve is a TCP/IP server which allows other programs to communicate to R. Obtain Rserve from http://stats.math.uni-augsburg.de/Rserve/. Both source codes and binaries are available for Windows, MacOS and linux.

For Windows system, you just need to download Rserve.exe (make sure to download the proper binary for your version of R) and copy it to the same directory where R.dll is located. If R.dll is in the system PATH, Rserve.exe can be started from anywhere.

For Linux sytem, follow the software's installation guide to install it.

5. Download J/maanova

Download the proper binary version for your operating system and save it to a directory such like c:\Jmaanova.

Starting J/maanova

First thing to mention is that Jmaanova will launch Rserve automatically so Rserve must be in the system PATH. You don't need to do anything on Linux or MacOSX. On Windows, the safest way is to put Rserve.exe and Jmaanova.exe in the same directory.

J/maanova executable can run directly. On Windows, you just need to double click the icon for Jmaanova.exe. On Linux or MacOSX, you first need to change the file mode to executable by doing "chmod +x Jmaanova", then type "./Jmaanova" to run it.