[BioC] making a cdf environment

[Moore, Stephen]

Dear All,

I have been attempting to create a cdf environment that I can use in conjunction with the Affy package in R.  I downloaded the makecdfenv package and installed it.  I have tried this package in two ways:

First I tried creating a cdf environment - myname = make.cdf.env("cdf file name.cdf")

This seemed to work O.K. however, when in the same session I loaded the Affy package it couldn't locate this environment.  I though that perhaps because I had renamed the actual cdf file name with one of my own that this was the problem, so I used the 'cat' argument (perhaps wrongly?) as follows:

>cat ("proper cdf file name is", cleancdfname("my cdf name"), "\n")

and got the response "proper cdf file name is my cdf file name".  Again I loaded the affy package and again it failed to find the environment.  Exasperated I tried creating a cdf package which I am still in the process of doing as follows:

>make.cdf.package("cdf filename.cdf")

This again seems to have worked O.K. and has created a subdirectory in my working directory with the cdf file name (as required).  However, I have created this on a windows environment and it says in the vignette that I need the source package installation files and Perl.  This is where I have come unstuck!  Can anyone give me any ideas as to how I might carry on with this, or alternatively how I might work with the environment rather that create the package?

Many Thanks for your time and patience, any help is greatly appreciated.

Stephen.

Dr. Stephen Moore
ArraDx Ltd.
Craigavon
N. Ireland.


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