From Prof Brian Ripley <ripley@stats.ox.ac.uk>  Fri Feb 11 12:45:46 2000
From: Prof Brian Ripley <ripley@stats.ox.ac.uk> (Prof Brian Ripley)
Date: Fri, 11 Feb 2000 12:45:46 +0000 (GMT)
Subject: [Rd] R CMD check [nlme|MASS] fails (PR#431)
Message-ID: <200002111245.MAA24049@toucan.stats.ox.ac.uk>

> From: berwin@maths.uwa.edu.au
> Date: Fri, 11 Feb 2000 12:58:00 +0100 (MET)

To run CMD check on MASS you need to set R_NSIZE in the environment.
500k should do.  MASS passes here on Solaris, Linux and Windows, if one
is patient enough.  I will point out that information is in the on-line
R complements, page 11.

I have just tried nlme on linux and 0.99.0 and example(nlme.formula)
does fail there in CMD check, eventually.

What MASS does not do is make a PDF manual, and that is mainly due to 
problems with the definitions of what needs to be escaped in the 
.Rd files.  A new version will follow once that is resolved
(which may need 1.0.0).

> `R CMD check nlme' fails on my machine.  The final output in
> nlme-Ex.Rout is:
> 
> > library(nlme)
> > data(Soybean)
> > fm1 <- nlme(weight ~ SSlogis(Time, Asym, xmid, scal), data = Soybean,
> +             fixed = Asym + xmid + scal ~ 1, start = c(18, 52, 7.5),
> +             control = list(nlmStepMax = 1.0))
> Error in nlme.formula(weight ~ SSlogis(Time, Asym, xmid, scal), data = 
Soybean,  : 
> 	Maximum number of iterations reached without convergence
> Execution halted
> 
> I presume that `R CMD check MASS' fails for some similar reason.  The
> final output in MASS-Ex.Rout is:
> 
> > library(nlme)
> > fp2 <- deriv(~ 0.5 + 0.5/(1 + exp(-(x-L75)/2)), 
> +             "L75", function(x,L75) NULL)
> > OMEi.nls <- nlsList(Correct/Trials ~ fp2(Loud, L75) | UIDn,
> +    data = OMEi, start=list(L75=45), control = list(maxiter=100))
> Error in nls(formula = formula, data = data, start = start, control = control) 
: 
> 	maximum number of iterations exceeded
> 
> [above message repeated another 10 times]
> 
> Error in qr(attr(rhs, "gradient")) : NA/NaN/Inf in foreign function call (arg 
1)
> Error in nls(formula = formula, data = data, start = start, control = control) 
: 
> 	maximum number of iterations exceeded
> Error: cons memory (350000 cells) exhausted
>        See "help(Memory)" on how to increase the number of cons cells.

Um, looks like nlsList is not failing gracefully when memory is exhausted,
presumably because restart is in use.

> [above message repeated about another 45 times or so]
> 
> Execution halted
> > tmp <- sapply(OMEi.nls, function(X) 
> +               {if(is.null(X)) NA else as.vector(coef(X))})
> Error in as.list(X) : Object "OMEi.nls" not found
> Execution halted
> 
> Cheers,
> 
>         Berwin
> 
> --please do not edit the information below--
> 
> Version:
>  platform = i686-unknown-linux
>  arch = i686
>  os = linux
>  system = i686, linux
>  status = Patched
>  major = 0
>  minor = 99.0
>  year = 2000
>  month = February
>  day = 9
>  language = R
> 
> Search Path:
>  .GlobalEnv, Autoloads, package:base
> 
> 
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-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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[Rd] R CMD check [nlme|MASS] fails (PR#431)
Prof Brian Ripley