R help - Dec 2007 - Problem of lmer under FreeBSD

I encounter such problem with lmer under FreeBSD, but not under
Windows. Anyone knows why? Thanks.
> example(lmer)
lmer> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
Error in UseMethod("as.logical") : no applicable method for
"as.logical"
> traceback()
9: as.logical(EMverbose)
8: as.logical(EMverbose)
7: lmerControl()
6: do.call("lmerControl", control)
5: lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
4: eval.with.vis(expr, envir, enclos)
3: eval.with.vis(ei, envir)
2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix,
       getOption("prompt"), sep = ""), continue.echo =
paste(prompt.prefix,
       getOption("continue"), sep = ""), verbose = verbose,
max.deparse.length = Inf,
       encoding = encoding, skip.echo = skips)
1: example(lmer)
>
> sessionInfo()
R version 2.6.0 (2007-10-03)
i386-portbld-freebsd6.3

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lme4_0.99875-9    Matrix_0.999375-2 lattice_0.16-5

loaded via a namespace (and not attached):
[1] grid_2.6.0      rcompgen_0.1-15 tools_2.6.0

-- 
Ronggui Huang

Department of Sociology, Fudan University, Shanghai, China

Department of Public and Social Administration, CityU, HK

Hello Ronggui Huang,

I am working with FreeBSD 8.0-CURRENT (i386) and R-2.6.1 (not built from 
ports). After loading version 0.99875-9 of lme4 and then executing the 
example

   library(lme4)
   example(lmer)

all works fine for me.


On 27.12.2007 09:19 (UTC+1), Ronggui wrote:
> I encounter such problem with lmer under FreeBSD, but not under
> Windows. Anyone knows why? Thanks.
Assuming, that your R installation is correct (from math/R ?), you 
should consider to reinstall lme4 and its dependencies. It is possible 
that these package have been built on a prior version of R.

For installing the package 'Matrix' on FreeBSD you have to use
gmake instead of make. The following example will do it

setenv MAKE gmake
R CMD INSTALL Matrix_0.999375-3.tar.gz
unsetenv MAKE

If reinstalling packages not solves your problem, please try if 
reinstalling R does. (Under FreeBSD the R sources build and install 
fine, so there is no need to use the port at math/R ...)

Hope this helps,
Rainer

>> example(lmer)
> 
> lmer> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
> Error in UseMethod("as.logical") : no applicable method for
"as.logical"
>> traceback()
> 9: as.logical(EMverbose)
> 8: as.logical(EMverbose)
> 7: lmerControl()
> 6: do.call("lmerControl", control)
> 5: lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
> 4: eval.with.vis(expr, envir, enclos)
> 3: eval.with.vis(ei, envir)
> 2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix,
>        getOption("prompt"), sep = ""), continue.echo =
paste(prompt.prefix,
>        getOption("continue"), sep = ""), verbose =
verbose,
> max.deparse.length = Inf,
>        encoding = encoding, skip.echo = skips)
> 1: example(lmer)
> 
>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-portbld-freebsd6.3
> 
> locale:
> C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] lme4_0.99875-9    Matrix_0.999375-2 lattice_0.16-5
> 
> loaded via a namespace (and not attached):
> [1] grid_2.6.0      rcompgen_0.1-15 tools_2.6.0

On Thu, 27 Dec 2007, ronggui wrote:
> I encounter such problem with lmer under FreeBSD, but not under
> Windows. Anyone knows why? Thanks.
Most likely you have a mixed-up system, with some packages installed under 
an earlier version of R.  Please use update.packages(checkBuilt=TRUE) to 
fix this.  (The culprit is probably Matrix.)

Searching the archives just after the releases of R 2.6.0 will find
quite a few postings from people who had made the same mistake.
>
>> example(lmer)
>
> lmer> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
> Error in UseMethod("as.logical") : no applicable method for
"as.logical"
>> traceback()
> 9: as.logical(EMverbose)
> 8: as.logical(EMverbose)
> 7: lmerControl()
> 6: do.call("lmerControl", control)
> 5: lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
> 4: eval.with.vis(expr, envir, enclos)
> 3: eval.with.vis(ei, envir)
> 2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix,
>       getOption("prompt"), sep = ""), continue.echo =
paste(prompt.prefix,
>       getOption("continue"), sep = ""), verbose =
verbose,
> max.deparse.length = Inf,
>       encoding = encoding, skip.echo = skips)
> 1: example(lmer)
>>
>
>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-portbld-freebsd6.3
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] lme4_0.99875-9    Matrix_0.999375-2 lattice_0.16-5
>
> loaded via a namespace (and not attached):
> [1] grid_2.6.0      rcompgen_0.1-15 tools_2.6.0
>
>
-- 
Brian D. Ripley,                  ripley at 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 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595