[R-sig-ME] lme4 broken ?
Martin Maechler
maechler at stat.math.ethz.ch
Fri Apr 13 12:00:05 CEST 2012
As Matrix comes with R, could you try to just use the version
that comes with R 2.15.0, and *then* install lme4 ?
Or in any case, install lm4 after Matrix, as lme4 depends on
Matrix?
I agree that this is not "useful" behavior...
Martin
>>>>> lancelot <renaud.lancelot at cirad.fr>
>>>>> on Fri, 13 Apr 2012 11:49:20 +0200 writes:
> 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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