[R-sig-ME] lme4 broken ?
lancelot
renaud.lancelot at cirad.fr
Fri Apr 13 11:49:20 CEST 2012
Dear Martin and all,
Thank you very much for your time. However:
> remove.packages("lme4")
Elimination de(s) package(s) de ‘C:/R/RLIBS’
(car ‘lib’ n'est pas spécifié)
> install.packages("lme4")
Installation d(es) package(s) dans ‘C:/R/RLIBS’
(car ‘lib’ n'est pas spécifié)
essai de l'URL
'http://cran.r-project.org/bin/windows/contrib/2.15/lme4_0.999375-42.zip'
Content type 'application/zip' length 1300772 bytes (1.2 Mb)
URL ouverte
downloaded 1.2 Mb
le package ‘lme4’ a été décompressé et les sommes MD5 ont été vérifiées
avec succés
Les packages binaires téléchargés sont dans
C:\Temp\RtmpsnSVf7\downloaded_packages
> update.packages(checkBuilt = TRUE)
Matrix :
Version 1.0-5 installed in C:/R/RLIBS built under R 2.15.0
Version 1.0-7 available at http://R-Forge.R-project.org
Update (y/N/c)? y
essai de l'URL
'http://R-Forge.R-project.org/bin/windows/contrib/2.15/Matrix_1.0-7.zip'
Content type 'application/zip' length 3252028 bytes (3.1 Mb)
URL ouverte
downloaded 3.1 Mb
le package ‘Matrix’ a été décompressé et les sommes MD5 ont été
vérifiées avec succés
Les packages binaires téléchargés sont dans
C:\Temp\RtmpCGB7op\downloaded_packages
> library(lme4)
Le chargement a nécessité le package : lattice
Le chargement a nécessité le package : Matrix
> example(lmer)
lmer> ## linear mixed models - reference values from older code
lmer> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
Erreur dans diag(val) :
7 arguments passed to .Internal(identical) which requires 6
Renaud
Le 13/04/2012 09:19, Martin Maechler a écrit :
>>>>>> "l" == lancelot<renaud.lancelot at cirad.fr>
>>>>>> on Fri, 13 Apr 2012 08:55:24 +0200 writes:
>
> > I re-installed the previous version of Matrix (Matrix_1.0-5.tar.gz
> > available on CRAN) from source, and it now works (see below).
>
> > I confirm there is a problem - at least on Windows - between lme4
> > and R-Forge present versions) and the present version of
> > Matrix 1.0-6.
>
> Hmm, I very much doubt this, at it least in this generality.
> Other people have seen similar problems (not involving lme4 at
> all), on R-help or R-devel, and the solution has been to
> re-install packages (or R!) only.
>
> The mismatch of number of arguments of .Internal(identical)
> is really from using packages that were *built* with one version
> of R, in a different version of *R*.
>
> So, in principle
>
> update.packages(checkBuilt = TRUE)
>
> should get you there.
>
> Regards,
> Martin Maechler
>
>
> > All the best,
>
> > Renaud
>
> >> sessionInfo()
> > R version 2.15.0 (2012-03-30)
> > Platform: i386-pc-mingw32/i386 (32-bit)
>
> > locale:
> > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
> > LC_MONETARY=French_France.1252 LC_NUMERIC=C
> > LC_TIME=French_France.1252
>
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
>
> > other attached packages:
> > [1] lme4_0.999902344-0 Matrix_1.0-5 lattice_0.20-6
>
> > loaded via a namespace (and not attached):
> > [1] grid_2.15.0 MASS_7.3-17 minqa_1.2.0 nlme_3.1-103
> > splines_2.15.0 tools_2.15.0
>
>
> >> library(lme4)
> > Le chargement a nécessité le package : lattice
> > Le chargement a nécessité le package : Matrix
> >> example(lmer)
>
> lmer> ## linear mixed models - reference values from older code
> lmer> (fm1<- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
> > Linear mixed model fit by REML ['lmerMod']
> > Formula: Reaction ~ Days + (Days | Subject)
> > Data: sleepstudy
>
> > REML criterion at convergence: 1743.628
>
> > Random effects:
> > Groups Name Variance Std.Dev. Corr
> > Subject (Intercept) 612.10 24.741
> > Days 35.07 5.922 0.066
> > Residual 654.94 25.592
> > Number of obs: 180, groups: Subject, 18
>
> > Fixed effects:
> > Estimate Std. Error t value
> > (Intercept) 251.405 6.825 36.84
> > Days 10.467 1.546 6.77
>
> > Correlation of Fixed Effects:
> > (Intr)
> > Days -0.138
>
> lmer> (fm2<- lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject),
> > sleepstudy))
> > Linear mixed model fit by REML ['lmerMod']
> > Formula: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject)
> > Data: sleepstudy
>
> > REML criterion at convergence: 1743.669
>
> > Random effects:
> > Groups Name Variance Std.Dev.
> > Subject (Intercept) 627.58 25.052
> > Subject Days 35.86 5.988
> > Residual 653.58 25.565
> > Number of obs: 180, groups: Subject, 18
>
> > Fixed effects:
> > Estimate Std. Error t value
> > (Intercept) 251.405 6.885 36.51
> > Days 10.467 1.560 6.71
>
> > Correlation of Fixed Effects:
> > (Intr)
> > Days -0.184
>
> lmer> anova(fm1, fm2)
> > Data: sleepstudy
> > Models:
> > fm2: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject)
> > fm1: Reaction ~ Days + (Days | Subject)
> > Df AIC BIC logLik deviance Chisq Chi Df Pr(>Chisq)
> > fm2 5 1762.0 1778.0 -876.00 1752.0
> > fm1 6 1763.9 1783.1 -875.97 1751.9 0.0639 1 0.8004
>
>
>
> > Le 12/04/2012 20:11, Joehanes, Roby (NIH/NHLBI) [F] a écrit :
> >> Hi Renaud,
> >>
> >> It works okay in my computer (Linux). Maybe you want to update all
> >> underlying libraries?
> >>
> >> Hope this helps, Roby
> >>
> >> (fm1<- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
> >>
> >> _______________________________________________
> >> R-sig-mixed-models at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >>
>
> > --
> > Renaud Lancelot
> > EDENext Project, coordinator: http://www.edenext.eu/
>
> > CIRAD, UMR15, Campus International de Baillarguet TA A-DIR / B
> > F34398 Montpellier
>
> > Tel. +33 4 67 59 37 17 - Fax +33 4 67 59 37 98
> > Secr. +33 4 67 59 37 37 - Cell. +33 6 77 52 08 69
>
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
--
Renaud Lancelot
EDENext Project, coordinator: http://www.edenext.eu/
CIRAD, UMR15, Campus International de Baillarguet TA A-DIR / B
F34398 Montpellier
Tel. +33 4 67 59 37 17 - Fax +33 4 67 59 37 98
Secr. +33 4 67 59 37 37 - Cell. +33 6 77 52 08 69
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