[BioC] making a cdf environment

Moore, Stephen Stephen.Moore at arradx-almac.com
Mon Jul 4 17:29:04 CEST 2005

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.


Dr. Stephen Moore
ArraDx Ltd.
N. Ireland.

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