* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/broom.mixed.Rcheck’ * using R Under development (unstable) (2025-02-26 r87830) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3) * running under: Fedora Linux 40 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘broom.mixed/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘broom.mixed’ version ‘0.2.9.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘glmmADMB’ * 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 ‘broom.mixed’ can be installed ... [14s/48s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/broom.mixed-00install.html' for details. * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: ‘glmm_tidiers.R’ ‘rstanarm_tidiers.Rd’ * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... [24s/59s] OK * checking Rd files ... 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [32s/45s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [106s/138s] ERROR Running ‘test-all.R’ [106s/137s] Running the tests in ‘tests/test-all.R’ failed. Complete output: > Sys.setenv("R_TESTS" = "") > library(testthat) > test_check("broom.mixed") Loading required package: broom.mixed GAMLSS-RS iteration 1: Global Deviance = 4771.925 GAMLSS-CG iteration 1: Global Deviance = 4771.013 GAMLSS-CG iteration 2: Global Deviance = 4770.994 GAMLSS-CG iteration 3: Global Deviance = 4770.994 [ FAIL 6 | WARN 1219 | SKIP 1 | PASS 282 ] â•â• Skipped tests (1) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• • On CRAN (1): 'test-rstanarm.R:36:5' â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── Failure ('test-lme4.R:199:5'): effects='ran_pars' + conf.int works ────────── as.data.frame(tt0) not equal to as.data.frame(tt). Component "conf.low": 'is.NA' value mismatch: 2 in current 0 in target Component "conf.high": 'is.NA' value mismatch: 2 in current 0 in target ── Failure ('test-lme4.R:213:5'): conf intervals for ranef in correct order ──── cor_vals$conf.low > (-1) && cor_vals$conf.high < 1 is not TRUE `actual`: <NA> `expected`: TRUE ── Failure ('test-lmertest.R:8:5'): testing lmerTest p-values ────────────────── td$df not equal to c(17, 17). 2/2 mismatches (average diff: 49.9) [1] 18.1 - 17 == 1.15 [2] 115.7 - 17 == 98.69 ── Failure ('test-lmertest.R:34:7'): Wald t intervals ────────────────────────── tmpf("Satterthwaite") not equal to c(231.320558648089, 271.015491535434). 2/2 mismatches (average diff: 3.81) [1] 235 - 231 == 4.01 [2] 267 - 271 == -3.61 ── Failure ('test-lmertest.R:35:7'): Wald t intervals ────────────────────────── tmpf("lme4") not equal to c(232.327411469392, 270.008638714131). 2/2 mismatches (average diff: 3.17) [1] 236 - 232 == 3.37 [2] 267 - 270 == -2.97 ── Failure ('test-lmertest.R:36:7'): Wald t intervals ────────────────────────── tmpf("Kenward-Roger") not equal to c(231.331769141079, 271.004281042444). 2/2 mismatches (average diff: 3.5) [1] 235 - 231 == 3.70 [2] 268 - 271 == -3.31 [ FAIL 6 | WARN 1219 | SKIP 1 | PASS 282 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [29s/31s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE