From bates@stat.wisc.edu  Tue Mar  7 14:43:35 2000
From: bates@stat.wisc.edu (Douglas Bates)
Date: 07 Mar 2000 08:43:35 -0600
Subject: [Rd] Problems with nlme (PR#471)
In-Reply-To: berwin@maths.uwa.edu.au's message of "Tue, 7 Mar 2000 08:27:59 +0100 (MET)"
References: <200003070727.IAA11450@pubhealth.ku.dk>
Message-ID: <6rwvnelu20.fsf@franz.stat.wisc.edu>

berwin@maths.uwa.edu.au writes:

> bossiaea:/opt/R$ R CMD check -c nlme 
> Checking package `nlme' ...
>  Massaging examples into `nlme-Ex.R' ...
>  Running examples in package `nlme' ...
>  ERROR
> 
> The end of nlme-Ex.Rout is:
> 
> > rm(list = ls(all = TRUE)); .Random.seed <- c(0,rep(7654,3))
> > ###--- >>> `anova.gls' <<<----- Compare Likelihoods of Fitted Objects
> > 
> > 	## alias	 help(anova.gls)
> > 
> > ##___ Examples ___:
> > 
> > library(nlme)
> > data(Ovary)
> > # AR(1) errors within each Mare
> > fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
> +            correlation = corAR1(form = ~ 1 | Mare))
> Warning message: 
> NA/Inf replaced by maximum positive value 
> > anova(fm1)
> Denom. DF: 305 
>                    numDF  F-value p-value
> (Intercept)            1 354.7375  <.0001
> sin(2 * pi * Time)     1  18.5035  <.0001
> cos(2 * pi * Time)     1   1.6633  0.1981
> > # variance changes with a power of the absolute fitted values?
> > fm2 <- update(fm1, weights = varPower())
> Error in update.gls(fm1, weights = varPower()) : 
> 	subscript out of bounds
> Execution halted
> 
> 
> (R CMD check MASS is also failing on an example that uses update.gls.)
> 
> On my machine at home I run into troubles even faster when running `R
> CMD check nlme'.  One of the early examples chokes on the line:
> > data(Orthodont)
> 
> I had done a "clean install" on that machine, i.e., I first blew away
> the older installation of R.  It seems that the datasets Orthodont and
> Pixel have been distributed with the nls library in earlier R versions
> but not so in R 1.0.0.  But they are not distributed with the current
> version of nlme either.

Ah, it appears that I need to update the nlme library.  I probably
won't be able to do that until tomorrow at the earliest.
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[Rd] Problems with nlme (PR#471)
Douglas Bates