Gaggle Components
Geese
Data Standards
Boss

Installing the Gaggle Package for R

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. Now install the gaggle package:
  3. (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_1.19.2.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_1.19.2.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, issue the following command before you input the startup commands described at the top of this page:

    Sys.unsetenv("CLASSPATH")

    This problem (and workaround) will go away in version 1.8.0 and greater of the R Goose, after September 24, 2008.

    PATH issue in Windows R Goose

    If you see the following message when attempting to load the Gaggle package:

    Loading required package: rJava
    Error in inDL(x, as.logical(local), as.logical(now), ...) : 
      unable to load shared library 'C:/PROGRA~1/R/R-28~1.1/library/rJava/libs/rJava.dll':
      LoadLibrary failure:  The specified module could not be found.
    
    
    In addition: Warning message:
    In fun(...) :
      *** WARNING: your Windows system seems to suffer from truncated PATH bug which will likely prevent rJava from loading.
          Either reduce your PATH or read http://support.microsoft.com/kb/906469 on how to fix your system.
    Error : .onLoad failed in 'loadNamespace' for 'rJava'
    Error: package 'rJava' could not be loaded
    
    
    

    ...you should install the recommended hotfix. Another workaround is to type the following before trying to load the Gaggle package:

    Sys.unsetenv("PATH")
    

    If you like, you can put this command in the .Rprofile file in your home directory, so you don't have to type it every time. To find your home directory, issue this command in R:

    Sys.getenv("R_USER")
    
  4. Proceed to Startup.
© 2006, Institute for Systems Biology, All Rights Reserved
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