RGLM Installation Instructions

Installation of add-on packages downloaded from this site

This is a short description of the installation of the packages you can download from the main site. For more details, please take a look at the manuals provided by the R project.

Prerequisites

The RGLM package requires the following packages to be installed: “foreach”, “doParallel”.
The easiest
way to install them is to issue the following command at the R prompt:

install.packages(c( “foreach”, “doParallel”)
)
source(“http://bioconductor.org/biocLite.R”)
biocLite(“impute”)

Installation of the randomGLM package

Installation of the package is simple. Download the appropriate package file from the
download page and save it in a directory of your choice. Run an R session as a
user with sufficient privileges to install software (see below if you don’t have the requisite
privileges). At the prompt, type (replace path/to/file with the
directory and filename of the downloaded package):

install.packages(“path/to/file”, repos = NULL, lib=.Library)

For Mac users: if you are compiling and installing a source package, add the argument

 

type = “source”

to the install.packages command. The additional argument should not be supplied if you
are installing the pre-compiled binary bundle (.tgz file). The packages should be automatically unpacked and
installed. If you have trouble installing the package, make sure you have Apple Xcode Tools, available
from http://developer.apple.com, installed.
See the R documentation on http://cran.r-project.org, in particular
this
section for more details on installation of source packages on OS X.

If you do not have sufficient privileges, you can either (1) ask your system administrator to install the
packages for you, or (2) create your own personal R library. You may also wish to create a separate
R library to hold oder versions of these and/or other packages. To do that, create a directory on your
system where you want the library to reside. Then run an R session, and at the prompt type (replace
path/to/file with the
directory and filename of the downloaded package and path/to/library with your library directory)

install.packages(“path/to/file”, repos = NULL, lib = “path/to/library”)

Note that if you chose to go this route, you will need to specify your library location every time you
load the package, by using

library(package, lib.loc = “path/to/library”)

instead of the usual

library(package)

 

In particular, you will need to modify in this way the example scripts provided at the main page.

Troubleshooting

  • When downloading and saving the package file, make sure the file is saved without unpacking it. For
    example, Windows may automatically unzip the file randomGLM_0.10.zip, thus preventing R from installing it correctly. Similarly, Mac OS may automaticall unzip the source file randomGLM_0.10.tar.gz and turn it into randomGLM_0.10.tar, thus preventing R from being able to unpack it. Again, the downloaded package must be saved as is, without any changes to the file.
  • When installing the package on Mac OS, the following error message may appear at the end of package
    installation:

    cp: /Library/Frameworks/R.framework/Resources/library/R.css: fchmod failed: Operation not permitted

    As far as we can tell, this is a harmless error and the package will function normally.

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