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

Bolker,Benjamin Michael bolker at ufl.edu
Mon Aug 3 20:41:23 CEST 2009

  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).

  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).


    >> 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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