Could you edit in a reprex?
Please see the FAQ: What's a reproducible example (`reprex`) and how do I do one? Using a reprex, complete with representative data will attract quicker and more answers.
For this
library(WHICH ONE?)
# GET PITCHER.ENV WHERE?
m <- lme(log10(nitrogen) ~ 1, random = ~ 1|site/plant, data=pitcher.env, na.action = na.omit)
d <- varcomp(m, TRUE, TRUE)
will help others to replicate the problem; otherwise, the only thing that can easily be offered is a tour of help(lme)'s signature and return value and working the examples.