[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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