- using R version 4.6.1 (2026-06-24)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-16 (Debian 16.1.0-2) 16.1.0
GNU Fortran (Debian 16.1.0-2) 16.1.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-07-11 14:57:38 UTC
- checking for file ‘lme4/DESCRIPTION’ ... OK
- this is package ‘lme4’ version ‘2.0-1’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- 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’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-16 (Debian 16.1.0-2) 16.1.0’
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
- checking loading without being on the library search path ... [2s/3s] OK
- checking whether startup messages can be suppressed ... [2s/3s] OK
- checking use of S3 registration ... 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 ... [46s/56s] OK
- checking Rd files ... [2s/3s] 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 ... [0s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking R/sysdata.rda ... 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 GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... 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 ... [11s/15s] ERROR
Running examples in ‘lme4-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glmer
> ### Title: Fitting Generalized Linear Mixed-Effects Models
> ### Aliases: glmer
> ### Keywords: models
>
> ### ** Examples
>
> ## generalized linear mixed model
> library(lattice)
> xyplot(incidence/size ~ period|herd, cbpp, type=c('g','p','l'),
+ layout=c(3,5), index.cond = function(x,y)max(y))
> (gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
+ data = cbpp, family = binomial))
Error: Downdated VtV is not positive definite
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [354s/450s] ERROR
Running ‘AAAtest-all.R’ [144s/184s]
Running ‘HSAURtrees.R’ [3s/3s]
Running ‘REMLdev.R’ [3s/4s]
Running ‘ST.R’ [3s/3s]
Running ‘agridat_gotway.R’ [4s/5s]
Running ‘bootMer.R’ [7s/18s]
Running ‘boundary.R’ [18s/23s]
Running ‘confint.R’ [5s/6s]
Running ‘devCritFun.R’ [3s/3s]
Running ‘drop.R’ [3s/4s]
Running ‘drop1contrasts.R’ [3s/4s]
Running ‘dynload.R’ [0s/0s]
Running ‘elston.R’ [3s/4s]
Running ‘evalCall.R’ [3s/3s]
Running ‘extras.R’ [3s/3s]
Running ‘falsezero_dorie.R’ [3s/3s]
Running ‘fewlevels.R’ [0s/0s]
Running ‘getME.R’ [3s/4s]
Running ‘glmer-1.R’ [5s/6s]
Running ‘glmerControlPass.R’ [5s/6s]
Running ‘glmerWarn.R’ [4s/4s]
Running ‘glmmExt.R’ [7s/9s]
Running ‘glmmWeights.R’ [7s/8s]
Running ‘hatvalues.R’ [3s/3s]
Running ‘is.R’ [3s/4s]
Running ‘lmList-tst.R’ [3s/3s]
Running ‘lme4_nlme.R’ [3s/3s]
Running ‘lmer-0.R’ [3s/4s]
Running ‘lmer-1.R’ [3s/3s]
Running ‘lmer-conv.R’ [3s/4s]
Running ‘lmer2_ex.R’ [3s/3s]
Running ‘methods.R’ [4s/4s]
Running ‘minval.R’ [3s/3s]
Running ‘modFormula.R’ [4s/5s]
Running ‘nbinom.R’ [3s/3s]
Running ‘nlmer-conv.R’ [2s/3s]
Running ‘nlmer.R’ [3s/3s]
Running ‘offset.R’ [4s/4s]
Running ‘optimizer.R’ [5s/7s]
Running ‘polytomous.R’ [2s/3s]
Running ‘prLogistic.R’ [2s/3s]
Running ‘predict_basis.R’ [3s/4s]
Running ‘predsim.R’ [4s/5s]
Running ‘priorWeights.R’ [6s/7s]
Running ‘priorWeightsModComp.R’ [4s/6s]
Running ‘profile-tst.R’ [2s/3s]
Running ‘refit.R’ [2s/3s]
Running ‘resids.R’ [3s/3s]
Running ‘respiratory.R’ [3s/4s]
Running ‘simulate.R’ [3s/3s]
Running ‘test-glmernbref.R’ [4s/4s]
Running ‘testOptControl.R’ [3s/3s]
Running ‘testcolonizer.R’ [3s/4s]
Running ‘testcrab.R’ [9s/11s]
Running ‘throw.R’ [4s/5s]
Running ‘varcorr.R’ [3s/4s]
Running ‘vcov-etc.R’ [3s/3s]
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-isSingular-97.R
[ FAIL 1 | WARN 0 | SKIP 6 | PASS 1768 ]
══ 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-isSingular.R:96:3'): checking singular fit for merMod ──────────
<Rcpp::exception/C++Error/error/condition>
Error: Downdated VtV is not positive definite
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-isSingular.R:96:3
2. │ └─base::withCallingHandlers(...)
3. └─lme4::glmer(form, family = poisson(link = "log"), data = dat)
4. └─lme4::optimizeGlmer(...)
5. └─lme4:::optwrap(...)
6. ├─base::withCallingHandlers(...)
7. ├─base::do.call(optfun, arglist)
8. └─lme4 (local) `<fn>`(...)
9. ├─nM$newf(fn(nM$xeval()))
10. │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
11. └─lme4 (local) fn(nM$xeval())
12. └─lme4 (local) pwrssUpdate(...)
[ FAIL 1 | WARN 0 | SKIP 6 | PASS 1768 ]
Error:
! Test failures.
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
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [212s/262s] OK
- checking PDF version of manual ... [14s/18s] OK
- checking HTML version of manual ... [14s/20s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs