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lme4.0 log file (check_x86_64_linux)

Sat Jul  5 20:16:01 2014: Checking package lme4.0 (SVN revision 1890) ...
* using log directory ‘/mnt/building/build_2014-07-05-20-04/RF_PKG_CHECK/PKGS/lme4.0.Rcheck’
* using R version 3.1.1 RC (2014-07-04 r66073)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘lme4.0/DESCRIPTION’ ... OK
* this is package ‘lme4.0’ version ‘0.999999-4’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Ben Bolker ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘lme4.0’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
'LinkingTo' for ‘stats’ is unused as it has no 'include' directory
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘00_chng_2_lme4’
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘lme4.0-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getME
> ### Title: Extract or Get Generalize Components from a Fitted Mixed Effects
> ###   Model
> ### Aliases: getME isREML isLMM isGLMM isNLMM
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## shows many methods you should consider *before* getME():
> showMethods(class = "mer")

Function ".DollarNames":
 
Function: VarCorr (package lme4.0)
x="mer"

Function: all.equal (package base)
target="mer", current="mer"
    (inherited from: target="ANY", current="ANY")

Function: anova (package stats)
object="mer"

Function: coef (package stats)
object="mer"

Function: coerce (package methods)
from="mer", to="dtCMatrix"
from="summary.mer", to="mer"

Function: coerce<- (package methods)
from="summary.mer", to="mer"


Function "complete":
 
Function: deviance (package stats)
object="mer"

Function: expand (package Matrix)
x="mer"

Function: fitted (package stats)
object="mer"

Function: fixef (package nlme)
object="mer"


Function "formals<-":
 
Function: formula (package stats)
x="mer"


Function "functions":
 

Function "getL":
 
Function: initialize (package methods)
.Object="mer"
    (inherited from: .Object="ANY")

Function: length (package base)

Function: logLik (package stats)
object="mer"

Function: mcmcsamp (package lme4.0)
object="mer"

Function: model.frame (package stats)
formula="mer"

Function: model.matrix (package stats)
object="mer"


Function "nobs":
 

Function "predict":
 
Function: print (package base)
x="mer"


Function "profile":
 

Function "prompt":
 
Function: ranef (package nlme)
object="mer"

Function: refit (package lme4.0)
object="mer", newresp="data.frame"
object="mer", newresp="matrix"
object="mer", newresp="numeric"

Function: resid (package stats)
object="mer"

Function: residuals (package stats)
object="mer"

Function: show (package methods)
object="mer"

Function: sigma (package lme4.0)
object="mer"

Function: simulate (package stats)
object="mer"

Function: summary (package base)
object="mer"

Function: terms (package stats)
x="mer"


Function "traceplot":
 
Function: update (package stats)
object="mer"

Function: vcov (package stats)
object="mer"

Function: with (package base)
data="mer"

> 
> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
Linear mixed model fit by REML 
Formula: Reaction ~ Days + (Days | Subject) 
   Data: sleepstudy 
  AIC  BIC logLik deviance REMLdev
 1756 1775 -871.8     1752    1744
Random effects:
 Groups   Name        Variance Std.Dev. Corr  
 Subject  (Intercept) 612.092  24.7405        
          Days         35.072   5.9221  0.066 
 Residual             654.941  25.5918        
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
> gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
+               data = cbpp, family = binomial)
Warning in mer_finalize(ans) : singular convergence (7)
> nm1 <- nlmer(circumference ~ SSlogis(age, Asym, xmid, scal) ~ Asym|Tree,
+               Orange, start = c(Asym = 200, xmid = 725, scal = 350))
> 
> Z <- getME(fm1, "Z")
> stopifnot(is(Z, "CsparseMatrix"),
+           c(180,36) == dim(Z),
+ 	  all.equal(fixef(fm1), getME(fm1, "beta"),
+ 		    check.attr=FALSE, tol = 0))
Error: all.equal(fixef(fm1), getME(fm1, "beta"), check.attr = FALSE,  .... is not TRUE
Execution halted
Run time: 110.69 seconds.