nmds -- "Error in class(S) ...", package conflict between vegan and ??

2 messages · Kim MILFERSTEDT, Jari Oksanen

Wed, May 26, 2010 1:44 AM #

Hello,

I am attempting to use nonmetric dimensional scaling (metaMDS) in vegan 
(1.17.2).

My data are 105 samples in rows and 1271 variables (peak positions for 
community fingerprinting) in columns.

When starting metaMDS in the default settings, the analysis goes past 
Run 0 but after Run 1, I get the error message:

Error in class(S) <- "scores" : attempt to set an attribute on NULL

I tried several other dissimilarity indices (e.g. euclidean) and the 
analysis goes through various runs but eventually always crashes with 
the same error message.

I have also tried the example from ?metaMDS which also failed. This made 
me think that there may be some kind of conflict between packages. And 
voil?, after closing and restarting R, just using vegan and MASS, the 
example worked fine.

For aligning the community fingerprints, I use StatFingerprints which 
depends on a ton of other packages.

Does anybody know how to read the error message? What is it pointing at 
and how could I find out which package is causing me trouble?

Thanks a lot in advance for any help,

Kim


Package: vegan
Title: Community Ecology Package
Version: 1.17-2

R version 2.10.0 (2009-10-26)

________________________________________________
Kim Milferstedt, PhD
Postdoctoral Researcher
INRA
Laboratoire de Biotechnologie de l'Environnement
Avenue des Etangs
F-11100 Narbonne
France

phone: (+33) 04 68 42 51 87
fax: (+33) 04 68 42 51 60
email: milferst at supagro.inra.fr

Jari Oksanen

Wed, May 26, 2010 1:54 AM #

On Wed, 2010-05-26 at 10:44 +0200, Kim MILFERSTEDT wrote:

Kim,

After the crash, say 

traceback()

and send the output to me.

I have never used StatFingerprints, nor have I installed the package in
my system. This means that probably I cannot reproduce the problem.
However, the traceback can help me to focus on the problem. 

My guess is that that StatFingerprints (or some other package) has
function called scores() that is used instead of the one in vegan. Which
one of the competing versions of scores() is used depends on the order
they are loaded and attached, and how the different scores() are located
in the search path. -- If scores() is the problem.

Cheers, Jari Oksanen