From berwin@maths.uwa.edu.au  Tue Mar  7 07:27:59 2000
From: berwin@maths.uwa.edu.au (berwin@maths.uwa.edu.au)
Date: Tue, 7 Mar 2000 08:27:59 +0100 (MET)
Subject: [Rd] Problems with nlme (PR#471)
Message-ID: <200003070727.IAA11450@pubhealth.ku.dk>

Dear R developers,

first of all let me join the chorus of congratulations for the release
of R 1.0.0.  Well, done!

Unfortunately, I find it necessary to e-mail in a bug report regarding
the `nlme' package.  On my office machine I experience the following
trouble:

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.

Cheers,

        Berwin

--please do not edit the information below--

Version:
 platform = i686-unknown-linux
 arch = i686
 os = linux
 system = i686, linux
 status = 
 major = 1
 minor = 0.0
 year = 2000
 month = February
 day = 29
 language = R

Search Path:
 .GlobalEnv, Autoloads, package:base

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[Rd] Problems with nlme (PR#471)
berwin@maths.uwa.edu.au