[R-sig-ME] current r-forge version fails R CMD check ... ?

[Douglas Bates]

First, I apologize for my prolonged absence from the mailing list.  I
managed to get a bad cold at the end of my stay in Europe and still
had it when, shortly after returning home, we moved to a new home.  At
present I don't have internet access unless I go to the public library
or a coffee shop downstairs from where I now live.  Between unpacking
at the new home and fixing up our old home to get it ready to put on
the market, I have gone on hiatus from reading email.  I hope to have
an Internet connection by the end of this week, after which I can
start responding again.

On Mon, Aug 3, 2009 at 1:41 PM, Bolker,Benjamin Michael<bolker at ufl.edu> wrote:

>  Is there a simple way to determine the BLAS/LAPACK versions in use?
>  I believe at the moment I have the Debian binary installed, I can build
> a different version locally (although I'm not sure which BLAS/LAPACK versions
> it will pick up from my system).

I'll leave that to others to answer.  My netbook running Ubuntu is
upstairs and if I were to write out the instructions without checking
on the system I would likely get them wrong.

>  Is this going to be fixable/workable-around?

> ________________________________________
> From: r-sig-mixed-models-bounces at r-project.org [r-sig-mixed-models-bounces at r-project.org] On Behalf Of Martin Maechler [maechler at stat.math.ethz.ch]
> Sent: Monday, August 03, 2009 10:57 AM
> To: Fabian Scheipl
> Cc: r-sig-mixed-models at r-project.org
> Subject: Re: [R-sig-ME] current r-forge version fails R CMD check ... ?
>
>>>>>> "FS" == Fabian Scheipl <Fabian.Scheipl at stat.uni-muenchen.de>
>>>>>>     on Mon, 3 Aug 2009 16:36:24 +0200 writes:
>
>    FS> Comparison of m2 and m3 works for me.  I use R-2.9.0
>    FS> with lme4_0.999375-31, Matrix_0.999375-30 on Windoze XP
>    FS> Professional SP2.
>
>    FS> Code is below.
>
>    FS> Best, Fabian
>
> Thank you, Fabian (and Reinhold and Ben).
>
> I think the version of Matrix and lme4 do not matter here,
> really, but rather the compilers and libraries used to build
> *and* run R.
>
> Notably I have small suspicion that the case which show the
> buggy behavior are linked to an optimized version of BLAS and
> LAPACK, and these might be the culprit.
> My (self-compiled) versions of R always use the R-builtin
> non-optimized BLAS+LAPACK, so that would fit the picture that I
> never see the problem.
> Also, AFAIK, the Mac versions *do* use optimized libraries, and
> Ubuntu often does too (because Debian does).
>
> Martin
>
>    >> sessionInfo()
>    FS> R version 2.9.0 (2009-04-17) i386-pc-mingw32
>
>    FS> locale:
>    FS> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>
>    FS> attached base packages: [1] stats graphics grDevices
>    FS> utils datasets methods base
>
>    FS> other attached packages: [1] lme4_0.999375-31
>    FS> Matrix_0.999375-30 lattice_0.17-25
>
>    FS> loaded via a namespace (and not attached): [1]
>    FS> grid_2.9.0 tools_2.4.1
>
>    >> all(replicate(50, {
>    FS> + set.seed(1) + D <- data.frame(y= rnorm(20,10), ff =
>    FS> gl(4,5), + x1=rnorm(20,3), x2=rnorm(20,7), +
>    FS> x3=rnorm(20,1)) + m2 <- lmer(y ~ x1 + (x2|ff), data = D)
>    FS> + m3 <- lmer(y ~ (x2|ff) + x1, data = D) + +
>    FS> identical(ranef(m2), ranef(m3)) + })) [1] TRUE
>
>    >> set.seed(1) all(replicate(50, {
>    FS> + D <- data.frame(y= rnorm(20,10), ff = gl(4,5), +
>    FS> x1=rnorm(20,3), x2=rnorm(20,7), + x3=rnorm(20,1)) + m2
>    FS> <- lmer(y ~ x1 + (x2|ff), data = D) + m3 <- lmer(y ~
>    FS> (x2|ff) + x1, data = D) + + identical(ranef(m2),
>    FS> ranef(m3)) + })) [1] TRUE
>
>    FS>         [[alternative HTML version deleted]]
>
>    FS> _______________________________________________
>    FS> R-sig-mixed-models at r-project.org mailing list
>    FS> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
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