Running ‘AAAtest-all.R’ [202s/208s]
  Running ‘HSAURtrees.R’
  Running ‘REMLdev.R’
  Running ‘ST.R’
  Running ‘agridat_gotway.R’
  Running ‘bootMer.R’ [10s/17s]
  Running ‘boundary.R’ [16s/16s]
  Running ‘confint.R’
  Running ‘devCritFun.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’
  Running ‘getME.R’
  Running ‘glmer-1.R’
  Running ‘glmerControlPass.R’
  Running ‘glmerWarn.R’
  Running ‘glmmExt.R’
  Running ‘glmmWeights.R’
  Running ‘hatvalues.R’
  Running ‘is.R’
  Running ‘lmList-tst.R’
  Running ‘lme4_nlme.R’
  Running ‘lmer-0.R’
  Running ‘lmer-1.R’
  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’
  Running ‘offset.R’
  Running ‘optimizer.R’
  Running ‘polytomous.R’
  Running ‘prLogistic.R’
  Running ‘predict_basis.R’
  Running ‘predsim.R’
  Running ‘priorWeights.R’
  Running ‘priorWeightsModComp.R’
  Running ‘profile-tst.R’
  Running ‘refit.R’
  Running ‘resids.R’
  Running ‘respiratory.R’
  Running ‘simulate.R’
  Running ‘test-glmernbref.R’
  Running ‘testOptControl.R’
  Running ‘testcolonizer.R’
  Running ‘testcrab.R’
  Running ‘throw.R’
  Running ‘varcorr.R’
  Running ‘vcov-etc.R’
Running the tests in ‘tests/AAAtest-all.R’ failed.
Complete output:
  > if (base::require("testthat", quietly = TRUE)) {
  +     pkg   <- "lme4"
  +     require(pkg, character.only=TRUE, quietly=TRUE)
  +     if(getRversion() < "3.5.0") { withAutoprint <- identity ; prt <- print } else { prt <- identity }
  +     if(Sys.getenv("USER") %in% c("maechler", "bbolker")) withAutoprint({
  +         ## for developers' sake:
  +         lP <- .libPaths() # ---- .libPaths() : ----
  +         prt(lP)
  +         ## ---- Entries in .libPaths()[1] : ----
  +         prt(list.files(lP[1], include.dirs=TRUE))
  +         prt(sessionInfo())
  +         prt(packageDescription("Matrix"))
  +         ## 'lme4' from packageDescription "file" :
  +         prt(attr(packageDescription("lme4"), "file"))
  +     })
  +     test_check(pkg)
  +     ##======== ^^^
  +     print(warnings()) # TODO? catch most of these by expect_warning(..)
  + } else {
  +     cat( "package 'testthat' not available, cannot run unit tests\n" )
  + }
  Saving _problems/test-covariance_structures-398.R
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 1673 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-eval.R:2:1'
  • Skipping (1): 'test-covariance_nlmer.R:22:3'
  • empty test (3): , ,
  • testLevel < 2 is TRUE (1): 'test-predict.R:689:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-covariance_structures.R:396:1'): (code run outside of `test_that()`) ──
  <Rcpp::exception/C++Error/error/condition>
  Error: Downdated VtV is not positive definite
  Backtrace:
       ▆
    1. └─lme4::glmer(...) at test-covariance_structures.R:396:1
    2.   └─lme4::optimizeGlmer(...)
    3.     └─lme4:::optwrap(...)
    4.       ├─base::withCallingHandlers(...)
    5.       ├─base::do.call(optfun, arglist)
    6.       └─lme4 (local) `<fn>`(...)
    7.         ├─nM$newf(fn(nM$xeval()))
    8.         │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
    9.         └─lme4 (local) fn(nM$xeval())
   10.           └─lme4 (local) pwrssUpdate(...)
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 1673 ]
  Error:
  ! Test failures.
  Execution halted
Running the tests in ‘tests/optimizer.R’ failed.
Complete output:
  > library(lme4)
  Loading required package: Matrix
  > source(system.file("test-tools-1.R", package = "Matrix"), keep.source = FALSE)
  Loading required package: tools
  > ## N.B. is.all.equal4() and assert.EQ() use 'tol', not 'tolerance' 
  > 
  > 
  > ## should be able to run any example with any bounds-constrained optimizer ...
  > ##  Nelder_Mead, bobyqa built in; optimx/nlminb, optimx/L-BFGS-B
  > ##  optimx/Rcgmin will require a bit more wrapping/interface work (requires gradient)
  > 
  > if (.Platform$OS.type != "windows") {
  + fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)  ## Nelder_Mead
  + fm1B <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy,
  +              control=lmerControl(optimizer="bobyqa"))
  + stopifnot(all.equal(fixef(fm1),fixef(fm1B)))
  + require(optimx)
  + lmerCtrl.optx <- function(method, ...)
  +     lmerControl(optimizer="optimx", ..., optCtrl=list(method=method))
  + glmerCtrl.optx <- function(method, ...)
  +     glmerControl(optimizer="optimx", ..., optCtrl=list(method=method))
  + 
  + (testLevel <- lme4:::testLevel())
  + 
  + ## FAILS on Windows (on r-forge only, not win-builder)... 'function is infeasible at initial parameters'
  + ## (can we test whether we are on r-forge??)
  + if (.Platform$OS.type != "windows") {
  +     fm1C <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy,
  +                  control=lmerCtrl.optx(method="nlminb"))
  +     fm1D <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy,
  +                  control=lmerCtrl.optx(method="L-BFGS-B"))
  +     stopifnot(is.all.equal4(fixef(fm1),fixef(fm1B),fixef(fm1C),fixef(fm1D)))
  + 
  +     fm1E <- update(fm1,control=lmerCtrl.optx(method=c("nlminb","L-BFGS-B")))
  +     ## hack equivalence of call and optinfo
  +     fm1E@call <- fm1C@call
  +     fm1E@optinfo <- fm1C@optinfo
  +     assert.EQ(fm1C,fm1E, tol=1e-5, giveRE=TRUE)# prints unless tolerance=0--equality
  + }
  + 
  + gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
  +              data = cbpp, family = binomial,
  +              control=glmerControl(tolPwrss=1e-13))
  + gm1B <- update(gm1, control=glmerControl  (tolPwrss=1e-13, optimizer="bobyqa"))
  + gm1C <- update(gm1, control=glmerCtrl.optx(tolPwrss=1e-13, method="nlminb"))
  + gm1D <- update(gm1, control=glmerCtrl.optx(tolPwrss=1e-13, method="L-BFGS-B"))
  + stopifnot(is.all.equal4(fixef(gm1),fixef(gm1B),fixef(gm1C),fixef(gm1D),
  +                         tol=1e-5))
  + 
  + if (testLevel > 1) {
  +     gm1E <- update(gm1, control=
  + 		   glmerCtrl.optx(tolPwrss=1e-13, method=c("nlminb","L-BFGS-B")))
  +     ## hack equivalence of call and optinfo
  +     gm1E@call <- gm1C@call
  +     gm1E@optinfo <- gm1C@optinfo
  +     assert.EQ(gm1E,gm1C, tol=1e-5, giveRE=TRUE)# prints unless tol=0--equality
  + }
  + } ## skip on windows (for speed)
  Loading required package: optimx
  Error in eval(call, envir = pf) : Downdated VtV is not positive definite
  Calls: update ... optimizeGlmer -> optwrap -> deriv12 -> fun -> pwrssUpdate
  In addition: Warning messages:
  1: In optimx.run(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
    Gradient not computable after method nlminb
  2: In optimx.run(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
    Gradient not computable after method nlminb
  3: In optimx.run(par, optcfg$ufn, optcfg$ugr, optcfg$uhess, lower,  :
    Gradient not computable after method nlminb
  Execution halted
Running the tests in ‘tests/respiratory.R’ failed.
Complete output:
  > ## Data originally from Davis 1991 Stat. Med., as packaged in geepack
  > ## and transformed (center, id -> factor, idctr created, levels labeled)
  > library(lme4)
  Loading required package: Matrix
  > 
  > if (.Platform$OS.type != "windows") {
  + load(system.file("testdata","respiratory.RData",package="lme4"))
  + m_glmer_4.L <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr),
  +                      family=binomial,data=respiratory)
  + 
  + m_glmer_4.GHQ5 <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr),
  +                         family=binomial,data=respiratory,nAGQ=5)
  + 
  + m_glmer_4.GHQ8 <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr),
  +                         family=binomial,data=respiratory,nAGQ=8)
  + 
  + m_glmer_4.GHQ16 <- glmer(outcome~center+treat+sex+age+baseline+(1|idctr),
  +                         family=binomial,data=respiratory,nAGQ=16)
  + } ## skip on windows (for speed)
  Error: Downdated VtV is not positive definite
  Execution halted