Running 'AAAtest-all.R' [227s]
  Running 'HSAURtrees.R' [4s]
  Running 'REMLdev.R' [4s]
  Running 'ST.R' [3s]
  Running 'agridat_gotway.R' [8s]
  Running 'bootMer.R' [17s]
  Running 'boundary.R' [15s]
  Running 'confint.R' [7s]
  Running 'devCritFun.R' [4s]
  Running 'devfunQ.R' [4s]
  Running 'drop.R' [6s]
  Running 'drop1contrasts.R' [5s]
  Running 'dynload.R' [1s]
  Running 'elston.R' [6s]
  Running 'evalCall.R' [5s]
  Running 'extras.R' [3s]
  Running 'falsezero_dorie.R' [3s]
  Running 'fewlevels.R' [26s]
  Running 'getME.R' [5s]
  Running 'glmer-1.R' [7s]
  Running 'glmerControlPass.R' [19s]
  Running 'glmerWarn.R' [6s]
Running the tests in 'tests/glmerWarn.R' failed.
Complete output:
  > library(lme4)
  Loading required package: Matrix
  > library(testthat)
  > 
  > ## [glmer(*, gaussian) warns to rather use lmer()]
  > m3 <- suppressWarnings(glmer(Reaction ~ Days + (Days|Subject), sleepstudy))
  > m4 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
  > m5 <- suppressWarnings(glmer(Reaction ~ Days + (Days|Subject), sleepstudy, family=gaussian))
  > expect_equal(fixef(m3),fixef(m5))
  > ## hack call -- comes out unimportantly different
  > m4@call[[1]] <- quote(lme4::lmer)
  > expect_equal(m3,m4)
  > expect_equal(m3,m5)
  > 
  > ## would like m3==m5 != m4 ??
  > (V4 <- VarCorr(m4))
   Groups   Name        Std.Dev. Corr 
   Subject  (Intercept) 24.7404       
            Days         5.9221  0.066
   Residual             25.5918       
  > V5 <- VarCorr(m5)
  > expect_equal(V4, V5, tolerance = 1e-14)
  > (th4 <- getME(m4,"theta"))
       Subject.(Intercept) Subject.Days.(Intercept)             Subject.Days 
                0.96673285               0.01516904               0.23090960 
  > expect_equal(th4, getME(m5,"theta"), tolerance = 1e-14)
  > 
  > ## glmer() - poly() + interaction
  > if (requireNamespace("mlmRev")) {
  +     data(Contraception, package="mlmRev")
  +     ## ch := with child
  +     Contraception <- within(Contraception, ch <- livch != "0")
  +     ## gmC1 <- glmer(use ~ poly(age,2) + ch + age:ch + urban + (1|district),
  +     ##               Contraception, binomial)
  + ### not a 'warning' per se {cannot suppressWarnings(.)}:
  + ###    fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
  + ### also printed with print(): labeled as  "fit warnings"
  + 
  +     ## ==> from ../R/modular.R  chkRank.drop.cols()
  +     ## --> Use   control = glmerControl(check.rankX = "ignore+drop.cols"))
  +     ## because further investigation shows "the problem" is really already
  +     ##     in model.matrix():
  +     dd <- data.frame(ch = c("Y","N")[1+rbinom(12, 1, 0.7)], age = rlnorm(12, 16))
  +     colnames(mm1 <- model.matrix( ~ poly(age,2) + ch + age:ch, dd))
  +     ## "(Int.)" "poly(age, 2)1" "poly(age, 2)2" "chY" "chN:age" "chY:age"      
  +     ## If we make the poly() columns to regular variables, can interact:
  +     d2 <- within(dd, { p2 <- poly(age,2); ageL <- p2[,1]; ageQ <- p2[,2]; rm(p2)})
  +     ## then, we can easily get what want
  +     (mm2 <- model.matrix( ~ ageL+ageQ + ch + ageL:ch, d2))
  +     ## actually even more compactly now ("drawback": 'ageQ' at end):
  +     (mm2. <- model.matrix( ~ ageL*ch + ageQ, d2))
  +     cn2 <- colnames(mm2)
  +     stopifnot(identical(mm2[,cn2], mm2.[,cn2]))
  + 
  + 
  + 
  + }
  Loading required namespace: mlmRev
  Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
    contrasts can be applied only to factors with 2 or more levels
  Calls: colnames ... model.matrix -> model.matrix.default -> contrasts<-
  Execution halted