R Version Compatibility

The R goose will work in R versions 2.4 and higher. However, in order to take advantage of a simplified installation process, and the newest Bioconductor packages, it is recommended that you install (or upgrade to) R 2.7 or higher.

Instructions for R 2.7 and higher -- All operating systems

1. Download and install R from a CRAN repository, for instance, FHCRC. Detailed platform specific instructions for installing R are on CRAN. If you already have R installed, you can skip this step.
2. Start your newly-installed R and and issue the following commands:

   
   	source ("http://www.bioconductor.org/biocLite.R")
   	biocLite()
   	biocLite('gaggle')
   	

   If you are using Mac OS 10.5 (Leopard), and wish to take advantage of your 64-bit processor, issue the following commands instead:

   
   	source ("http://www.bioconductor.org/biocLite.R")
   	biocLite(type="source")
   	biocLite('gaggle')
   	

3. Proceed to Startup.

Instructions for R 2.4, 2.5, and 2.6

1. Download and install R from a CRAN repository, for instance, FHCRC. Detailed platform specific instructions for installing R are on CRAN. If you already have R installed, you can skip this step.
2. Start your newly-installed R and and install essential packages from Bioconductor: (NOTE: if you have a previous version of the R goose installed, you can skip the first three lines below; just make sure you run the final line.)

   
   source ("http://www.bioconductor.org/biocLite.R")
   biocLite()
   biocLite('gaggle')
   install.packages('RUnit')
   

3. (That last step will prompt you to choose a CRAN mirror; pick a location close to you.)
4. Now install the gaggle package:

(You can redo this step every time you reinstall the gaggle package, as after a bug-fix release.)

Mac and Linux Instructions

To use the R goose, right-click on this link and save the resulting file to your machine.

Shut down R if it is running.

Using a command-line window navigate (using the "cd" command) to the directory where you saved the file and issue the command:

sudo R CMD INSTALL gaggle_1.2.0.tar.gz

Windows Instructions

Right-click on this link and save the resulting file to your machine.

Shut down R, the Boss, and any geese which are running.

Restart R from the Start Menu

From the Packages menu, choose the Install package(s) from local zip files... option.

In the Select Files dialog box, navigate to and choose the file you just downloaded: gaggle_1.2.0.zip.

You may need administrative privileges to do this command.

Bug and Workaround in Windows R Goose

Because of a bug third-party software, there is a problem using the R goose in the graphical version of R that is available for Windows. The goose works properly but does not display important messages, such as notifying you when it has received a broadcast. The way to work around this bug is to use the command-line version of R, not the graphical version that comes up by default from the Start Menu. To do this:

• Click the Start button
• Click Run...
• type

  \Program Files\R

  and press ENTER.
• Double-click on the folder named for your version of R, for example, R-2.5.1.
• Double-click on the bin folder.
• Double-click on R.exe (the .exe extension may not be visible depending on your settings).

CLASSPATH issue in Windows R Goose

If you are still having problems, make sure that your CLASSPATH does not have any directories with a space in them ("\Program Files" can be changed to "\PROGRA~1", etc.) Also make sure that "." is not an entry in the CLASSPATH. You may need to add to the CLASSPATH the R bin directory (again without spaces).
5. Proceed to Startup.