* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/insight.Rcheck’
* using R Under development (unstable) (2025-03-01 r87860)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘insight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘insight’ version ‘1.1.0’
* 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 ‘insight’ can be installed ... [61s/156s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/insight-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... 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 ... 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 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 ... [161s/472s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [41s/109s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [11m/12m] ERROR
Running ‘testthat.R’ [11m/12m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(insight)
> test_check("insight")
Starting 2 test processes
[ FAIL 27 | WARN 506 | SKIP 73 | PASS 3434 ]
â•â• Skipped tests (73) 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 (65): 'test-GLMMadaptive.R:1:1', 'test-averaging.R:3:1',
'test-bias_correction.R:1:1', 'test-brms.R:1:1', 'test-brms_aterms.R:1:1',
'test-brms_gr_random_effects.R:1:1', 'test-brms_missing.R:1:1',
'test-brms_von_mises.R:1:1', 'test-blmer.R:249:3',
'test-clean_names.R:103:3', 'test-clean_parameters.R:2:3',
'test-clean_parameters.R:35:3', 'test-clmm.R:165:3', 'test-cpglmm.R:145:3',
'test-export_table.R:4:3', 'test-export_table.R:8:3',
'test-export_table.R:106:3', 'test-export_table.R:133:3',
'test-export_table.R:164:3', 'test-export_table.R:193:3',
'test-export_table.R:205:3', 'test-export_table.R:233:3',
'test-find_random.R:27:3', 'test-format_table.R:1:1',
'test-format_table_ci.R:71:3', 'test-gam.R:1:1', 'test-find_smooth.R:31:3',
'test-get_data.R:385:1', 'test-get_loglikelihood.R:93:3',
'test-get_loglikelihood.R:158:3', 'test-get_predicted.R:2:1',
'test-get_priors.R:3:3', 'test-get_varcov.R:40:3',
'test-is_converged.R:28:1', 'test-lme.R:34:3', 'test-lme.R:210:3',
'test-glmmTMB.R:71:3', 'test-glmmTMB.R:755:3', 'test-glmmTMB.R:787:3',
'test-marginaleffects.R:1:1', 'test-mgcv.R:1:1', 'test-mipo.R:1:1',
'test-mvrstanarm.R:1:1', 'test-panelr-asym.R:142:3', 'test-panelr.R:272:3',
'test-phylolm.R:5:1', 'test-r2_nakagawa_bernoulli.R:1:1',
'test-r2_nakagawa_beta.R:1:1', 'test-r2_nakagawa_binomial.R:1:1',
'test-r2_nakagawa_gamma.R:1:1', 'test-r2_nakagawa_linear.R:1:1',
'test-r2_nakagawa_negbin.R:1:1', 'test-r2_nakagawa_negbin_zi.R:1:1',
'test-r2_nakagawa_ordered_beta.R:1:1', 'test-r2_nakagawa_poisson.R:1:1',
'test-r2_nakagawa_poisson_zi.R:1:1',
'test-r2_nakagawa_truncated_poisson.R:1:1', 'test-r2_nakagawa_tweedie.R:1:1',
'test-rlmer.R:259:3', 'test-rqss.R:1:1', 'test-rstanarm.R:1:1',
'test-spatial.R:1:1', 'test-svylme.R:1:1', 'test-vgam.R:1:1',
'test-weightit.R:1:1'
• On Linux (3): 'test-BayesFactorBF.R:1:1', 'test-MCMCglmm.R:1:1',
'test-get_data.R:150:3'
• Package `logistf` is loaded and breaks `mmrm::mmrm()` (1): 'test-mmrm.R:4:1'
• TRUE is TRUE (1): 'test-fixest.R:2:1'
• works interactively (2): 'test-coxph-panel.R:34:3', 'test-coxph.R:38:3'
• {bigglm} is not installed (1): 'test-model_info.R:24:3'
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-get_loglikelihood.R:216:3'): get_loglikelihood - gamm4 ───────
as.numeric(ll) (`actual`) not equal to -101.1107 (`expected`).
`actual`: -99.1
`expected`: -101.1
── Failure ('test-get_variance.R:49:3'): get_variance-1 ────────────────────────
v1$var.intercept (`actual`) not equal to c(Subject = 612.10016) (`expected`).
`actual`: 593.3
`expected`: 612.1
── Failure ('test-get_variance.R:53:3'): get_variance-1 ────────────────────────
v1$var.slope (`actual`) not equal to c(Subject.Days = 35.07171) (`expected`).
`actual`: 593.3
`expected`: 35.1
── Failure ('test-get_variance.R:60:3'): get_variance-2 ────────────────────────
v2$var.intercept (`actual`) not equal to c(Subject = 627.56905) (`expected`).
`actual`: 593.3
`expected`: 627.6
── Failure ('test-get_variance.R:64:3'): get_variance-2 ────────────────────────
v2$var.slope (`actual`) not equal to c(Subject.Days = 35.85838) (`expected`).
`actual`: 593.3
`expected`: 35.9
── Failure ('test-get_variance.R:71:3'): get_variance-3 ────────────────────────
v3$var.intercept (`actual`) not equal to c(subgrp.grp.1 = 0, Subject = 662.52047, grp.1 = 0) (`expected`).
`actual` is NULL
`expected` is a double vector (0, 662.52047, 0)
── Failure ('test-get_variance.R:79:3'): get_variance-3 ────────────────────────
v3$var.slope (`actual`) not equal to c(Subject.Days = 34.25771, subgrp.grp.Days = 7.88485, grp.Days = 0) (`expected`).
`actual` is NULL
`expected` is a double vector (34.25771, 7.88485, 0)
── Failure ('test-get_variance.R:91:3'): get_variance-4 ────────────────────────
v4$var.intercept (`actual`) not equal to c(Subject = 1378.17851) (`expected`).
`actual`: 811.1
`expected`: 1378.2
── Failure ('test-get_variance.R:99:3'): get_variance-5 ────────────────────────
v5$var.intercept (`actual`) not equal to c(`subgrp:grp` = 38.76069, Subject = 1377.50569, grp = 3.32031) (`expected`).
`actual`: 654.2 654.2 654.2
`expected`: 38.8 1377.5 3.3
── Failure ('test-get_variance.R:112:3'): get_variance-6 ───────────────────────
v6$var.intercept (`actual`) not equal to c(plate = 0.71691) (`expected`).
`actual`: 0.13
`expected`: 0.72
── Failure ('test-get_variance.R:113:3'): get_variance-6 ───────────────────────
v6$var.random (`actual`) not equal to 0.71691 (`expected`).
`actual`: 0.13
`expected`: 0.72
── Failure ('test-get_variance.R:124:3'): get_variance-7 ───────────────────────
`vmodel` (`actual`) not equal to list(...) (`expected`).
`actual$var.random`: 593.3
`expected$var.random`: 627.6
`actual$var.residual`: 593.3
`expected$var.residual`: 653.6
`actual$var.distribution`: 593.3
`expected$var.distribution`: 653.6
`actual$var.intercept`: 593.3
`expected$var.intercept`: 627.6
`actual$var.slope`: 593.3
`expected$var.slope`: 35.9
── Failure ('test-get_variance.R:144:3'): get_variance-8 ───────────────────────
`vmodel` (`actual`) not equal to list(...) (`expected`).
`actual$var.random`: 21856.9
`expected$var.random`: 1502.2
`actual$var.residual`: 766.9
`expected$var.residual`: 842.0
`actual$var.distribution`: 766.9
`expected$var.distribution`: 842.0
`actual$var.slope`: 766.9
`expected$var.slope`: 52.7
── Failure ('test-get_variance.R:169:3'): get_variance-9 ───────────────────────
`vmodel` (`actual`) not equal to list(...) (`expected`).
`actual$var.random`: 1264.6
`expected$var.random`: 1711.4
`actual$var.residual`: 790.4
`expected$var.residual`: 748.8
`actual$var.distribution`: 790.4
`expected$var.distribution`: 748.8
`actual$var.intercept`: 790.4
`expected$var.intercept`: 663.3
`actual$var.slope`: 790.4 790.4
`expected$var.slope`: 882.4 1415.7
actual$cor.slope_intercept vs expected$cor.slope_intercept
[,1]
- actual$cor.slope_intercept[1, ] 0.0000000
+ expected$cor.slope_intercept[1, ] 0.3611731
- actual$cor.slope_intercept[2, ] 0.0000000
+ expected$cor.slope_intercept[2, ] 0.3318785
`actual$cor.slopes`: 0.00
`expected$cor.slopes`: 0.85
── Failure ('test-get_variance.R:198:3'): get_variance-10 ──────────────────────
`vmodel` (`actual`) not equal to list(...) (`expected`).
`actual` is length 8
`expected` is length 7
names(actual) | names(expected)
[1] "var.fixed" | "var.fixed" [1]
[2] "var.random" -
[3] "var.residual" | "var.residual" [2]
[4] "var.distribution" | "var.distribution" [3]
[5] "var.dispersion" | "var.dispersion" [4]
`actual$var.random` is a double vector (739.145250002286)
`expected$var.random` is absent
names(actual$var.slope) | names(expected$var.slope)
[1] "Subject.1.Days2(3,6]" -
[2] "Subject.1.Days2(6,10]" -
[3] "Subject.Days2(-1,3]" | "Subject.Days2(-1,3]" [1]
[4] "Subject.Days2(3,6]" | "Subject.Days2(3,6]" [2]
[5] "Subject.Days2(6,10]" | "Subject.Days2(6,10]" [3]
actual$var.slope | expected$var.slope
[1] 739.145250002286 - 0 [1]
[2] 739.145250002286 - 994.015865559888 [2]
[3] 739.145250002286 - 1545.72576115283 [3]
[4] 739.145250002286 -
[5] 739.145250002286 -
names(actual$cor.slopes) | names(expected$cor.slopes)
[1] "Subject.1.Days2(-1,3]-Days2(3,6]" -
[2] "Subject.1.Days2(-1,3]-Days2(6,10]" -
[3] "Subject.1.Days2(3,6]-Days2(6,10]" | "Subject.1.Days2(3,6]-Days2(6,10]" [1]
`actual$cor.slopes`: 0 0 0
`expected$cor.slopes`: 0.859480774219098
── Failure ('test-get_variance.R:222:3'): get_variance-11 ──────────────────────
`vmodel` (`actual`) not equal to list(...) (`expected`).
`actual$var.random`: 589.0
`expected$var.random`: 1446.1
`actual$var.residual`: 981.6
`expected$var.residual`: 748.8
`actual$var.distribution`: 981.6
`expected$var.distribution`: 748.8
`actual$var.slope`: 981.6 981.6 981.6
`expected$var.slope`: 663.3 2098.2 2722.2
`actual$cor.slopes`: 0.00 0.00 0.00
`expected$cor.slopes`: 0.80 0.73 0.92
── Failure ('test-get_variance.R:250:3'): get_variance-12 ──────────────────────
`vmodel` (`actual`) not equal to list(...) (`expected`).
`actual$var.random`: 589.0
`expected$var.random`: 1446.1
`actual$var.residual`: 981.6
`expected$var.residual`: 748.8
`actual$var.distribution`: 981.6
`expected$var.distribution`: 748.8
`actual$var.slope`: 981.6 981.6 981.6
`expected$var.slope`: 663.3 2098.2 2722.2
`actual$cor.slopes`: 0.00 0.00 0.00
`expected$cor.slopes`: 0.80 0.73 0.92
── Failure ('test-get_variance.R:283:3'): get_variance-cat_random_slope ────────
vc$cor.slopes (`actual`) not equal to c(...) (`expected`).
`actual`: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
`expected`: 1.0 1.0 1.0 1.0 1.0 1.0 -1.0 -1.0 -1.0 -1.0
── Failure ('test-get_variance.R:326:3'): random effects CIs, simple slope ─────
`vc` (`actual`) not equal to list(...) (`expected`).
`actual[[1]]`: 935.7
`expected[[1]]`: 921.9
`actual[[2]]`: 17808.7
`expected[[2]]`: 1068.0
`actual[[3]]`: 624.9
`expected[[3]]`: 764.5
`actual[[4]]`: 624.9
`expected[[4]]`: 764.5
`actual[[6]]`: 624.9 624.9
`expected[[6]]`: 37.5 27.6
`actual[[7]]`: 0.00
`expected[[7]]`: 0.46
── Failure ('test-get_variance.R:353:3'): random effects CIs, poly slope ───────
vc$cor.slopes (`actual`) not equal to c(`replicate.poly(temp, 2)1-poly(temp, 2)2` = 0.940016422944175) (`expected`).
`actual`: 0.00
`expected`: 0.94
── Failure ('test-is_converged.R:23:3'): is_converged ──────────────────────────
is_converged(model) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-lmer.R:60:3'): get_df ────────────────────────────────────────
get_df(m1, type = "satterthwaite") (`actual`) not equal to c(`(Intercept)` = 16.99973, Days = 16.99998) (`expected`).
`actual`: 18.1 115.7
`expected`: 17.0 17.0
── Failure ('test-lmer.R:334:3'): get_variance ─────────────────────────────────
get_variance(m1) (`actual`) not equal to list(...) (`expected`).
`actual$var.random`: 17503.7
`expected$var.random`: 1698.1
`actual$var.slope`: 593.3
`expected$var.slope`: 35.1
── Failure ('test-lmer.R:353:3'): get_variance ─────────────────────────────────
get_variance_random(m1) (`actual`) not equal to c(var.random = 1698.084) (`expected`).
`actual`: 17503.7
`expected`: 1698.1
── Failure ('test-lmer.R:377:3'): get_variance ─────────────────────────────────
get_variance_slope(m1) (`actual`) not equal to c(var.slope.Subject.Days = 35.07171) (`expected`).
`actual`: 593.3
`expected`: 35.1
── Failure ('test-lmer.R:388:3'): get_variance ─────────────────────────────────
suppressWarnings(get_variance(m2)) (`actual`) not equal to list(...) (`expected`).
`actual` is length 6
`expected` is length 5
names(actual) | names(expected)
[1] "var.fixed" | "var.fixed" [1]
[2] "var.random" -
[3] "var.residual" | "var.residual" [2]
[4] "var.distribution" | "var.distribution" [3]
[5] "var.dispersion" | "var.dispersion" [4]
`actual$var.random` is a double vector (2058.53584626217)
`expected$var.random` is absent
`actual$var.residual`: 686.2
`expected$var.residual`: 941.8
`actual$var.distribution`: 686.2
`expected$var.distribution`: 941.8
`actual$var.intercept`: 686.2 686.2 686.2
`expected$var.intercept`: 0.0 1357.4 24.4
── Failure ('test-lmer.R:558:3'): get_predicted_ci: warning when model matrix and varcovmat do not match ──
head(data.frame(p)$Predicted) (`actual`) not equal to known$Predicted (`expected`).
`actual`: 37.586 47.556 56.800 65.318 73.111 80.177
`expected`: 37.534 47.957 58.789 70.029 81.677 93.735
[ FAIL 27 | WARN 506 | SKIP 73 | PASS 3434 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/29s] OK
* checking PDF version of manual ... [17s/25s] OK
* checking HTML version of manual ... [12s/18s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR