[BioC] contrast matrix warning

scholz@Ag.arizona.edu scholz at Ag.arizona.edu
Tue Jan 10 08:22:01 CET 2006

Hi Seth,

Thanks for your response. Given my Cro-Magnon-level computing skills, though,
I'm not quite sure what this all means. You are correct that I'm using the
recent R-devel, and if I understand you correctly, I shouldn't worry about the



Hi Matt,

On  9 Jan 2006, scholz at ag.arizona.edu wrote:

> Hi all,
> I am getting a warning message when I create my contrast matrix (for
> a six-membered loop design experiment) that I can't find any
> previous threads about. The message reads:
> Warning message:
> use of NULL environment is deprecated

What version of R are you using?  My guess is a recent R-devel.  The
NEWS file says:

 o   Changed environment tree to be rooted in an empty environment,
    available as emptyenv().  baseenv() modified to return an
    environment with emptyenv() as parent, rather than NULL.

 o   Use of NULL as an environment is deprecated and gives a warning.

You will, at least, see this message any time you load an annotation
data package (that is, until we rebuilt the annotation packages with
the latest R-devel).

+ seth

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