Running ‘AAAtest-all.R’ [222s/252s]
  Running ‘HSAURtrees.R’
  Running ‘REMLdev.R’
  Running ‘ST.R’
  Running ‘agridat_gotway.R’
  Running ‘bootMer.R’ [12s/21s]
  Running ‘boundary.R’ [17s/21s]
  Running ‘condVar.R’
  Running ‘confint.R’
  Running ‘devCritFun.R’
  Running ‘devfunQ.R’
  Running ‘drop.R’
  Running ‘drop1contrasts.R’
  Running ‘dynload.R’
  Running ‘elston.R’
  Running ‘evalCall.R’
  Running ‘extras.R’
  Running ‘falsezero_dorie.R’
  Running ‘fewlevels.R’ [20s/24s]
  Running ‘getME.R’
  Running ‘glmer-1.R’ [8s/11s]
  Running ‘glmerControlPass.R’ [14s/17s]
  Running ‘glmerWarn.R’
  Running ‘glmmExt.R’ [14s/17s]
  Running ‘glmmWeights.R’ [13s/14s]
  Running ‘hatvalues.R’
  Running ‘is.R’
  Running ‘lmList-tst.R’
  Running ‘lme4_nlme.R’
  Running ‘lmer-0.R’
  Running ‘lmer-1.R’
  Comparing ‘lmer-1.Rout’ to ‘lmer-1.Rout.save’ ... OK
  Running ‘lmer-conv.R’
  Running ‘lmer2_ex.R’
  Running ‘methods.R’
  Running ‘minval.R’
  Running ‘modFormula.R’
  Running ‘nbinom.R’
  Running ‘nlmer-conv.R’
  Running ‘nlmer.R’
  Comparing ‘nlmer.Rout’ to ‘nlmer.Rout.save’ ... OK
  Running ‘offset.R’ [8s/10s]
  Running ‘optimizer.R’ [12s/15s]
  Running ‘polytomous.R’
  Running ‘prLogistic.R’
  Running ‘predict.R’
  Running ‘predict_basis.R’
  Running ‘predsim.R’
  Running ‘priorWeights.R’ [13s/16s]
  Running ‘priorWeightsModComp.R’
  Running ‘profile-tst.R’ [59s/84s]
  Running ‘refit.R’ [33s/38s]
  Running ‘resids.R’
  Running ‘respiratory.R’ [15s/17s]
  Running ‘simulate.R’ [11s/13s]
  Running ‘testOptControl.R’
  Running ‘test_times.R’
  Running ‘testcolonizer.R’
  Running ‘testcrab.R’ [15s/18s]
  Running ‘throw.R’ [10s/13s]
  Running ‘utils.R’
  Running ‘varcorr.R’
  Running ‘vcov-etc.R’
Running the tests in ‘tests/lme4_nlme.R’ failed.
Complete output:
  > ## testing whether lme4 and nlme play nicely.  Only known issue
  > ## is lmList-masking ...
  > library("lme4")
  Loading required package: Matrix
  > library("nlme")
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:lme4':
  
      lmList
  
  > fm1_lmer <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
  > fm1_lme <- lme(Reaction ~ Days, random=~Days|Subject, sleepstudy)
  > ## variance-covariance matrices: annoyingly different structures
  > vc_lmer <- VarCorr(fm1_lmer)
  > vc_lmerx <- c(diag(vc_lmer[[1]]),attr(vc_lmer[[1]],"correlation")[1,2])
  > vc_lme <- VarCorr(fm1_lme)
  > suppressWarnings(storage.mode(vc_lme) <- "numeric")
  > vc_lmex <- c(vc_lme[1:2,1],vc_lme[2,3])
  Error in vc_lme[2, 3] : subscript out of bounds
  Execution halted