PLEASE USE R 2.12 OR A NEWER VERSION OF R, IF AVAILABLE.
IF YOU NEED gMCP FOR AN OLDER VERSION OF R, PLEASE CONTACT US!
(For R 2.8 compatibility see instructions below.)

If you have not R already installed, you can download it
bundled with gMCP and all dependencies from:

 http://www.algorithm-forge.com/gMCP/R_with_gMCP.zip 
 Unzipping it and a double click on the R.exe in folder bin to
 bring up an R console with an automatically started gMCP GUI.

If you run into any problems, please write us an email at:

help@small-projects.de

gMCP requires Java >= 5.0 - most likely it is already installed on 
your computer. If it is not, download and install it from: 
http://www.java.com/en/download/

The installation of gMCP via install.packages("gMCP") should be
unproblematic. However one of the packages gMCP depends on perhaps 
needs more attention (most likely on Unix systems):

rJava:
======

Follow the instructions of rJava.

Troubleshooting for Unix:

Most likely you will have to run the command "R CMD javareconf" with
root permissions to let R find your java compiler and headers.


General Troubleshooting:
========================

 * "Warning: unable to move temporary installation 'XYZ' to 'ZYX'"
If you get this warning while installing or updating packages,
most likely some other Windows program is accessing the newly installed 
files and prevents R to move them to the correct place.
Often simply trying to install the package a second time works.
Otherwise try to pause your antivirus programs or search indexing 
(like Google Desktop Search) while installing the packages.

 * If you run into a "MSVCR71.dll is missing" please try updating your
rJava installation (install.packages("rJava")) or add your JAVA_HOME
directory (something like "C:\Program Files\Java\jre6\bin\") to your
PATH.

 * If "rJava.dll" can not be loaded or the "jvm.dll" can not be found
try setting JAVA_HOME in R before loading rJava or gMCP:

Sys.setenv(JAVA_HOME="C:/Program Files/Java/jre6/")

(Please check that this is the correct path on your system for your 
Java 6 installation and adapt it otherwise.)

 * "Error in .jinit() : unable to find the basic String class"
It looks like you have an ancient Java version installed (Java 1.4 is 
from 2002!) that is used.
Please check that Java >= 1.5 is installed and try to tell rJava to use 
this newer version of Java by setting JAVA_HOME accordingly as described 
in the previous paragraph.

Package graph:
==============

To install the package graph for further graph analysis, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("graph")


Package Rgraphviz:
==================

For visualization the method renderGraph from package Rgraphviz can be
used, which uses the graphviz library.  Therefore you need to install
the libraries and headers necessary to link graphviz library routines
into the Rgraphviz package. For example on Debian/Ubuntu you need to
install the package libgraphviz-dev beforehand:

sudo apt-get install libgraphviz-dev

To install Rgraphviz, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz")


Compatibility for R 2.8.0
=========================

gMCP is still compatible with R 2.8.0 but not extensively tested.

To get a Windows build go to
http://algorithm-forge.com/gMCPforR28/ 
or (if it's not up-to-date on the site) build the current gMCP package from source for your system.  

If you run into any problems, please write us an email at:

help@small-projects.de
