[BioC] contrasts.fit Error

[Matt McCall]

When I try to run the following line of code:
cln.fit2 <- contrasts.fit(cln.fit, cln.cm)
where cln.fit comes from:
cln.fit <- lmFit(colon$M, cln.mm)
where colon is a limma object and cln.mm is the model matrix.
also cln.cm is the contrast matrix from:
cln.cm <- makeContrasts(MSLiver-MSLung, MSLiver-MSLiverLung, 
MSLung-MSLiverLung, levels=cln.mm)

I get the error:
Error in o %*% RUC^2 : non-conformable arguments

Can anyone tell me what I'm doing wrong?

I'm running:
Package: limma
Version: 1.7.0
Date: 2004/06/27
Title: Linear Models for Microarray Data
Author: Gordon Smyth <smyth at wehi.edu.au>, Matt Ritchie 
<mritchie at wehi.edu.au>, James Wettenhall <wettenhall at wehi.edu.au>, 
Natalie Thorne
                 <thorne at wehi.edu.au>
Maintainer: Gordon Smyth <smyth at wehi.edu.au>
Depends: R (>= 1.7.1), MASS, splines, statmod (>= 1.0.6), sma
Description: Data analysis, linear models and differential expression 
for microarray data.
License: LGPL
URL: http://bioinf.wehi.edu.au/limma/
Packaged: Tue Jun 29 21:38:42 2004; madman
Built: R 2.0.0; ; 2004-06-30 13:15:39; windows

platform powerpc-apple-darwin6.8
arch     powerpc
os       darwin6.8
system   powerpc, darwin6.8
status
major    1
minor    9.1
year     2004
month    06
day      21
language R