Problems installing R

Cathy,

In order to add the depository to sources.list, you need root access.
If you are the administrator, then all you need to do is:

sudo gedit /etc/apt/sources.list

If someone else is administering the machine, the simplest thing is to
request them to do it and install the latest versions R.

As for affy itslef, it is not in the cran repository since it is a
bioconductor package.  To install it under R you need root access and
I would do the following:

sudo R

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

This allowed me to install affy on jaunty, but it should work for
hardy as well.  It gave me a warning about the lib argument missing,
but it used the default.  If it doesn't work under hardy, I can look
into it some more.

Hope this helps,
Michael

On Mon, Jul 13, 2009 at 10:43 AM, Cathy

Hi,

I am new to Linux and have a linux machine running ubuntu (hardy heron). I
installed R 2.9.1 using the deb file provided on the R website. However I
can't install 'affy' - one of the R packages and apparently this is because
of the lib settings. I've tried to install R using the command line but I
can't add:

deb http://cran.uk.r-project.org/bin/linux/ubuntu hardy

to my /etc/apt/sources.list file because it says that the permission to do
so is denied. I don't know how to fix this problem or if this is the
problem. All I want to be able to do is run affy in R on my machine.

I would be very greatful if someone could help me.
Thank you.

Cathy

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Dr. Michael A. Rutter
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