Last updated on 2026-07-19 09:49:53 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0-1 | 85.08 | 789.19 | 874.27 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.0-6 | 62.76 | 488.52 | 551.28 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0-6 | 84.00 | 613.92 | 697.92 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.0-6 | 64.00 | 418.46 | 482.46 | OK | |
| r-devel-windows-x86_64 | 2.0-6 | 91.00 | 658.00 | 749.00 | OK | |
| r-patched-linux-x86_64 | 2.0-1 | 84.39 | 746.89 | 831.28 | ERROR | |
| r-release-linux-x86_64 | 2.0-6 | 86.36 | 664.85 | 751.21 | OK | |
| r-release-macos-arm64 | 2.0-6 | 18.00 | 158.00 | 176.00 | OK | |
| r-release-macos-x86_64 | 2.0-6 | 56.00 | 836.00 | 892.00 | OK | |
| r-release-windows-x86_64 | 2.0-6 | 95.00 | 573.00 | 668.00 | OK | |
| r-oldrel-macos-arm64 | 2.0-6 | 17.00 | 163.00 | 180.00 | OK | |
| r-oldrel-macos-x86_64 | 2.0-6 | 56.00 | 812.00 | 868.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0-6 | 89.00 | 640.00 | 729.00 | OK |
Version: 2.0-1
Check: R code for possible problems
Result: NOTE
Found calls to structure() using deprecated special names:
lme4/R/profile.R (.Names: 1)
lme4/tests/HSAURtrees.R (.Names: 1)
lme4/tests/agridat_gotway.R (.Names: 3)
lme4/tests/elston.R (.Names: 3)
lme4/tests/glmer-1.R (.Names: 3)
lme4/tests/glmmExt.R (.Dim: 1, .Dimnames: 1)
lme4/tests/lmer-1.R (.Names: 1)
lme4/tests/profile-tst.R (.Dim: 1, .Dimnames: 1)
lme4/tests/testcrab.R (.Names: 2)
lme4/tests/testthat/test-glmernb.R (.Names: 1)
lme4/tests/testthat/test-lmList.R (.Dim: 1, .Dimnames: 1, .Names: 1)
lme4/tests/testthat/test-predict.R (.Label: 1)
lme4/tests/testthat/test-ranef.R (.Label: 2)
'.Names' should be changed to 'names'.
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
'.Label' should be changed to 'levels'.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.0-1
Check: tests
Result: ERROR
Running ‘AAAtest-all.R’ [143s/168s]
Running ‘HSAURtrees.R’ [3s/5s]
Running ‘REMLdev.R’ [3s/4s]
Running ‘ST.R’ [3s/4s]
Running ‘agridat_gotway.R’ [5s/7s]
Running ‘bootMer.R’ [7s/19s]
Running ‘boundary.R’ [18s/23s]
Running ‘confint.R’ [5s/7s]
Running ‘devCritFun.R’ [3s/3s]
Running ‘drop.R’ [3s/4s]
Running ‘drop1contrasts.R’ [3s/4s]
Running ‘dynload.R’ [0s/1s]
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/5s]
Running ‘glmerControlPass.R’ [5s/6s]
Running ‘glmerWarn.R’ [4s/5s]
Running ‘glmmExt.R’ [7s/8s]
Running ‘glmmWeights.R’ [7s/9s]
Running ‘hatvalues.R’ [3s/4s]
Running ‘is.R’ [3s/4s]
Running ‘lmList-tst.R’ [3s/4s]
Running ‘lme4_nlme.R’ [3s/3s]
Running ‘lmer-0.R’ [3s/4s]
Running ‘lmer-1.R’ [2s/3s]
Running ‘lmer-conv.R’ [3s/3s]
Running ‘lmer2_ex.R’ [2s/3s]
Running ‘methods.R’ [4s/4s]
Running ‘minval.R’ [3s/4s]
Running ‘modFormula.R’ [4s/6s]
Running ‘nbinom.R’ [3s/3s]
Running ‘nlmer-conv.R’ [3s/3s]
Running ‘nlmer.R’ [3s/4s]
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/4s]
Running ‘priorWeights.R’ [6s/7s]
Running ‘priorWeightsModComp.R’ [4s/5s]
Running ‘profile-tst.R’ [3s/3s]
Running ‘refit.R’ [3s/3s]
Running ‘resids.R’ [3s/3s]
Running ‘respiratory.R’ [6s/7s]
Running ‘simulate.R’ [3s/3s]
Running ‘test-glmernbref.R’ [4s/6s]
Running ‘testOptControl.R’ [3s/3s]
Running ‘testcolonizer.R’ [3s/3s]
Running ‘testcrab.R’ [8s/10s]
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-covariance_structures-402.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:400:1'): (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:400:1
2. └─lme4::optimizeGlmer(...)
3. └─lme4:::optwrap(...)
4. └─lme4:::deriv12(fn, opt$par, fx = opt$value)
5. └─lme4 (local) fun(xaa, ...)
6. └─lme4 (local) pwrssUpdate(...)
[ FAIL 1 | WARN 0 | SKIP 6 | PASS 1673 ]
Error:
! Test failures.
Execution halted
Running the tests in ‘tests/glmerControlPass.R’ failed.
Complete output:
> if (.Platform$OS.type != "windows") {
+ ## test redirection from lmer to glmer (correct options passed,
+ ## specifically glmerControl -> tolPwrss
+
+ library("lme4")
+ library("testthat")
+ ## data("trees513", package = "multcomp")
+ load(system.file("testdata","trees513.RData",package="lme4"))
+
+
+ expect_is(mmod1 <- glmer(damage ~ species - 1 + (1 | lattice / plot),
+ data = trees513B, family = binomial()),"glmerMod")
+ if(FALSE) { ## Now (2019-05) defunct; was deprecated since 2013-06:
+ expect_warning(mmod2 <- lmer(damage ~ species - 1 + (1 | lattice / plot),
+ data = trees513B, family = binomial()),
+ "calling lmer with .* is deprecated")
+ mmod2@call <- mmod1@call ## hack calls to equality
+ expect_equal(mmod1,mmod2)
+ }
+ } ## skip on windows (for speed)
Loading required package: Matrix
Error: Downdated VtV is not positive definite
Execution halted
Running the tests in ‘tests/respiratory.R’ failed.
Complete output:
> ## Data originally from Davis 1991 Stat. Med., as packaged in geepack
> ## and transformed (center, id -> factor, idctr created, levels labeled)
> library(lme4)
Loading required package: Matrix
>
> if (.Platform$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
Flavor: r-patched-linux-x86_64