[R-sig-ME] lme4 broken ?
lancelot
renaud.lancelot at cirad.fr
Fri Apr 13 12:26:00 CEST 2012
Dear Martin,
I just installed the patched version of R, and then re-installed from
source the CRAN version of lme4. It now works fine. The same for the
R-Forge version of lme4. Here is the session info for the latter case:
> sessionInfo()
R version 2.15.0 Patched (2012-04-09 r58947)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] 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_1.0-7 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
[6] tools_2.15.0
Thank you very much for your help.
Best regards,
Renaud
Le 13/04/2012 12:00, Martin Maechler a écrit :
> 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
>
--
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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