R Under development (unstable) (2024-03-25 r86192 ucrt) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ## Test `gratia` using the `testthat` package > > ## Setup > library("testthat") > library("gratia") > > ## Runs the tests in tests/testthat > test_check("gratia") Loading required package: nlme This is mgcv 1.9-1. For overview type 'help("mgcv-package")'. Loading required package: Matrix Loading required package: lme4 Attaching package: 'lme4' The following object is masked from 'package:nlme': lmList This is gamm4 0.2-6 This is scam 1.2-16. Attaching package: 'dplyr' The following object is masked from 'package:nlme': collapse The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Random effect smooths not currently supported. Ignoring: [ FAIL 0 | WARN 0 | SKIP 229 | PASS 2169 ] ══ Skipped tests (229) ═════════════════════════════════════════════════════════ • On CRAN (213): 'test-add-functions.R:67:3', 'test-add-functions.R:200:3', 'test-add-functions.R:208:3', 'test-add-functions.R:216:3', 'test-add-functions.R:225:3', 'test-add-functions.R:234:3', 'test-bam-ar.R:11:3', 'test-bam-ar.R:18:3', 'test-basis.R:30:3', 'test-basis.R:71:3', 'test-basis.R:93:3', 'test-by-variables.R:7:3', 'test-by-variables.R:14:3', 'test-by-variables.R:61:3', 'test-compare-smooths.R:37:3', 'test-concurvity.R:16:3', 'test-concurvity.R:34:3', 'test-confint-methods.R:169:3', 'test-data-sim.R:17:3', 'test-data-sim.R:26:3', 'test-data-slice.R:257:3', 'test-data-slice.R:262:3', 'test-datagen.R:6:3', 'test-derivatives.R:400:3', 'test-derivatives.R:445:3', 'test-derivatives.R:481:3', 'test-diagnostic-plots.R:7:3', 'test-diagnostic-plots.R:55:3', 'test-diagnostic-plots.R:72:3', 'test-diagnostic-plots.R:89:3', 'test-diagnostic-plots.R:106:3', 'test-diagnostic-plots.R:123:3', 'test-diagnostic-plots.R:132:3', 'test-diagnostic-plots.R:142:3', 'test-difference-smooths.R:11:3', 'test-difference-smooths.R:25:3', 'test-difference-smooths.R:36:3', 'test-difference-smooths.R:47:3', 'test-difference-smooths.R:51:3', 'test-difference-smooths.R:65:3', 'test-difference-smooths.R:80:3', 'test-difference-smooths.R:111:3', 'test-difference-smooths.R:115:3', 'test-difference-smooths.R:139:3', 'test-draw-gam.R:7:3', 'test-draw-gam.R:13:3', 'test-draw-gam.R:22:3', 'test-draw-gam.R:28:3', 'test-draw-gam.R:34:3', 'test-draw-gam.R:40:3', 'test-draw-gam.R:45:3', 'test-draw-gam.R:53:3', 'test-draw-gam.R:59:3', 'test-draw-gam.R:65:3', 'test-draw-gam.R:71:3', 'test-draw-gam.R:77:3', 'test-draw-gam.R:83:3', 'test-draw-gam.R:92:3', 'test-draw-gam.R:98:3', 'test-draw-gam.R:104:3', 'test-draw-gam.R:110:3', 'test-draw-gam.R:116:3', 'test-draw-gam.R:128:3', 'test-draw-gam.R:140:3', 'test-draw-gam.R:147:3', 'test-draw-gam.R:154:3', 'test-draw-gam.R:160:3', 'test-draw-gam.R:166:3', 'test-draw-gam.R:176:3', 'test-draw-gam.R:186:3', 'test-draw-gam.R:236:3', 'test-draw-gam.R:243:3', 'test-draw-gam.R:252:3', 'test-draw-methods.R:7:3', 'test-draw-methods.R:36:3', 'test-draw-methods.R:49:3', 'test-draw-methods.R:58:3', 'test-draw-methods.R:72:3', 'test-draw-methods.R:100:3', 'test-draw-methods.R:112:3', 'test-draw-methods.R:121:3', 'test-draw-methods.R:139:3', 'test-draw-methods.R:146:3', 'test-draw-methods.R:152:3', 'test-draw-methods.R:160:3', 'test-draw-methods.R:169:3', 'test-draw-methods.R:194:3', 'test-draw-methods.R:205:3', 'test-draw-methods.R:274:3', 'test-draw-methods.R:283:3', 'test-draw-methods.R:294:3', 'test-draw-methods.R:300:3', 'test-draw-methods.R:313:3', 'test-draw-methods.R:336:3', 'test-draw-methods.R:344:3', 'test-draw-methods.R:367:3', 'test-draw-methods.R:371:3', 'test-draw-methods.R:381:3', 'test-draw-methods.R:395:3', 'test-draw-methods.R:402:3', 'test-draw-methods.R:406:3', 'test-draw-methods.R:432:3', 'test-draw-methods.R:480:3', 'test-draw-methods.R:499:3', 'test-draw-methods.R:525:3', 'test-draw-methods.R:529:3', 'test-draw-methods.R:570:3', 'test-draw-parametric-effects.R:14:3', 'test-draw-parametric-effects.R:28:3', 'test-draw-parametric-effects.R:39:3', 'test-draw-parametric-effects.R:50:3', 'test-draw-parametric-effects.R:64:3', 'test-draw-parametric-effects.R:68:3', 'test-draw-parametric-effects.R:161:3', 'test-draw-smooth-estimates.R:5:3', 'test-draw-smooth-estimates.R:16:3', 'test-draw-smooth-estimates.R:24:3', 'test-draw-smooth-estimates.R:29:3', 'test-draw-smooth-estimates.R:40:3', 'test-draw-smooth-estimates.R:47:3', 'test-draw-smooth-estimates.R:54:3', 'test-draw-smooth-estimates.R:61:3', 'test-draw-smooth-estimates.R:85:3', 'test-draw-smooth-estimates.R:181:3', 'test-draw-smooth-estimates.R:207:3', 'test-draw-smooth-estimates.R:237:3', 'test-draw-smooth-estimates.R:262:3', 'test-draw-smooth-estimates.R:292:3', 'test-draw-smooth-estimates.R:316:3', 'test-draw-smooth-estimates.R:326:3', 'test-draw-smooth-estimates.R:336:3', 'test-draw-smooth-estimates.R:352:3', 'test-edf.R:11:3', 'test-edf.R:20:3', 'test-edf.R:34:3', 'test-edf.R:43:3', 'test-edf.R:61:3', 'test-edf.R:70:3', 'test-edf.R:79:3', 'test-edf.R:88:3', 'test-edf.R:97:3', 'test-fderiv.R:6:3', 'test-gjrm-methods.R:7:3', 'test-hgam-paper.R:39:3', 'test-hgam-paper.R:54:3', 'test-hgam-paper.R:73:3', 'test-hgam-paper.R:89:3', 'test-hgam-paper.R:104:3', 'test-hgam-paper.R:123:3', 'test-hgam-paper.R:139:3', 'test-hgam-paper.R:162:3', 'test-hgam-paper.R:183:3', 'test-hgam-paper.R:203:3', 'test-hgam-paper.R:220:3', 'test-hgam-paper.R:240:3', 'test-lp-matrix.R:26:3', 'test-overview.R:22:3', 'test-overview.R:31:3', 'test-overview.R:40:3', 'test-parametric-effects.R:107:3', 'test-penalty.R:45:3', 'test-penalty.R:58:3', 'test-penalty.R:69:3', 'test-penalty.R:99:3', 'test-penalty.R:118:3', 'test-posterior-samples.R:16:3', 'test-posterior-samples.R:33:3', 'test-posterior-samples.R:50:3', 'test-posterior-samples.R:268:3', 'test-posterior-samples.R:277:3', 'test-posterior-samples.R:311:3', 'test-posterior-samples.R:358:3', 'test-posterior-samples.R:382:3', 'test-posterior-samples.R:387:3', 'test-posterior-samples.R:431:3', 'test-qq-plot.R:22:3', 'test-qq-plot.R:30:3', 'test-qq-plot.R:38:3', 'test-qq-plot.R:46:3', 'test-qq-plot.R:56:3', 'test-qq-plot.R:63:3', 'test-qq-plot.R:71:3', 'test-qq-plot.R:81:3', 'test-qq-plot.R:91:3', 'test-response-derivatives.R:5:3', 'test-response-derivatives.R:39:3', 'test-rootograms.R:4:3', 'test-rootograms.R:15:3', 'test-rootograms.R:19:3', 'test-rootograms.R:32:3', 'test-simulate-methods.R:76:3', 'test-smooth-coefs.R:55:3', 'test-smooth-estimates.R:286:3', 'test-smooth-estimates.R:293:3', 'test-smooth-estimates.R:300:3', 'test-soap-films.R:7:3', 'test-soap-films.R:22:3', 'test-soap-films.R:31:3', 'test-utilities.R:376:3', 'test-variance-components.R:14:3', 'test-variance-components.R:26:3', 'test-variance-components.R:38:3', 'test-variance-components.R:50:3', 'test-variance-components.R:62:3', 'test-worm-plot.R:25:3', 'test-worm-plot.R:32:3', 'test-worm-plot.R:42:3', 'test-worm-plot.R:53:3', 'test-worm-plot.R:60:3', 'test-worm-plot.R:70:3', 'test-worm-plot.R:81:3', 'test-worm-plot.R:91:3', 'test-worm-plot.R:101:3' • On Windows (15): 'test-draw-gam.R:190:3', 'test-draw-gam.R:198:3', 'test-draw-methods.R:127:3', 'test-draw-methods.R:470:3', 'test-draw-methods.R:543:3', 'test-draw-smooth-estimates.R:66:3', 'test-draw-smooth-estimates.R:74:3', 'test-draw-smooth-estimates.R:89:3', 'test-draw-smooth-estimates.R:101:3', 'test-draw-smooth-estimates.R:113:3', 'test-draw-smooth-estimates.R:125:3', 'test-draw-smooth-estimates.R:137:3', 'test-draw-smooth-estimates.R:149:3', 'test-draw-smooth-estimates.R:161:3', 'test-draw-smooth-estimates.R:171:3' • This needs fixing as something in scam changed (1): 'test-basis.R:46:3' [ FAIL 0 | WARN 0 | SKIP 229 | PASS 2169 ] Deleting unused snapshots: • basis/draw-basis-works-with-a-bivariate-te-contour.svg • basis/draw-basis-works-with-a-bivariate-te.svg • basis/draw-basis-works-with-a-bivariate-tprs-contour.svg • basis/draw-basis-works-with-a-bivariate-tprs.svg • basis/draw-basis-works-with-a-gam-single-smooth.svg • compare-smooths/compare-smooths-bottom-legend.svg • compare-smooths/compare-smooths-set-nrow-ncol.svg • derivatives/draw-issue-47-derivatives-for-complex-factor-by.svg • derivatives/draw-issue-47-derivatives-for-factor-by.svg • derivatives/draw-issue-47-derivatives-for-gamm-factor-by.svg • derivatives/draw-issue-47-derivs-for-ordered-factor-by.svg • derivatives/draw-issue-57-derivatives-for-factor-by.svg • diagnostic-plots/qq-plot-glm-normal.svg • diagnostic-plots/qq-plot-glm-simulate.svg • diagnostic-plots/qq-plot-lm-normal.svg • diagnostic-plots/qq-plot-lm-simulate.svg • diagnostic-plots/worm-plot-gam-normal.svg • diagnostic-plots/worm-plot-gam-simulate.svg • diagnostic-plots/worm-plot-glm-normal.svg • diagnostic-plots/worm-plot-glm-simulate.svg • diagnostic-plots/worm-plot-lm-normal.svg • diagnostic-plots/worm-plot-lm-simulate.svg • difference-smooths/draw-difference-smooths-bam.svg • difference-smooths/draw-difference-smooths-bivariate-gam-contours.svg • difference-smooths/draw-difference-smooths-bivariate-gam.svg • difference-smooths/draw-difference-smooths-gamm.svg • difference-smooths/draw-difference-smooths-gamm4.svg • draw-gam/draw-gam-m-gamm4.svg • draw-gam/draw-gam-quadvar-te.svg • draw-gam/draw-gam-trivar-te.svg • draw-gam/draw-gam-univariate-t2-smooth.svg • draw-gam/draw-gam-univariate-te-smooth.svg • draw-gam/draw-gam-univariate-ti-smooth.svg • draw-gam/ordered-grouped-by-gam.svg • draw-methods/draw-2d-smooth-with-spectral-palette.svg • draw-methods/draw-am-with-2d-smooth.svg • draw-methods/draw-basic-tprs-basis-rotated.svg • draw-methods/draw-basic-tprs-basis.svg • draw-methods/draw-by-factor-basis.svg • draw-methods/draw-derivatives-for-a-gam-rotated-labels.svg • draw-methods/draw-derivatives-for-a-gam-with-default-change.svg • draw-methods/draw-derivatives-for-a-gam-with-fixed-scales-rotated.svg • draw-methods/draw-derivatives-for-a-gam-with-fixed-scales.svg • draw-methods/draw-derivatives-for-a-gam-with-sizer-change.svg • draw-methods/draw-factor-by-variable-smooth-with-fixed-scales.svg • draw-methods/draw-fs-smooth-with-discrete-plasma-palette.svg • draw-methods/draw-gam-smooth-for-two-selected-smooths-character.svg • draw-methods/draw-gam-smooth-for-two-selected-smooths-numeric.svg • draw-methods/draw-gam-with-factor-parametric-term.svg • draw-methods/draw-gam-with-linear-parametric-term.svg • draw-methods/draw-gam-with-select-and-parametric-is-false.svg • draw-methods/draw-gam-with-select-and-parametric-is-true.svg • draw-methods/draw-gam-without-select-and-parametric-is-false.svg • draw-methods/draw-gam-without-select-and-parametric-is-true.svg • draw-methods/draw-model-with-fs-smooth-fixed-scales.svg • draw-methods/draw-model-with-ranef-smooth-fixed-scales.svg • draw-methods/draw-partial-derivatives-for-a-gam-with-fixed-scales.svg • draw-methods/draw-partial-derivatives-for-gam-fixed-scales-rotated.svg • draw-methods/draw-partial-derivatives-for-gam-rotated-labels.svg • draw-methods/draw-selected-factor-by-smooth-samples-for-gam-m3.svg • draw-methods/draw-selected-smooth-samples-for-gam-m3.svg • draw-methods/draw-simple-multi-smooth-am-with-fixed-scales.svg • draw-methods/draw-simple-partial-residuals-with-fixed-scales.svg • draw-methods/draw-smooth-samples-for-bivariate-gam-contours.svg • draw-methods/draw-smooth-samples-for-gam-m1-rotated.svg • draw-methods/draw-smooth-samples-for-gam-m1.svg • draw-methods/draw-smooth-samples-for-gam-m2-rotated.svg • draw-methods/draw-smooth-samples-for-gam-m2.svg • draw-methods/draw-smooth-samples-for-gam-m3-fixed-scales-rotated.svg • draw-methods/draw-smooth-samples-for-gam-m3-fixed-scales.svg • draw-methods/draw-smooth-samples-for-gam-m3-rotated.svg • draw-methods/draw-smooth-samples-for-gam-m3.svg • draw-methods/draw-smooth-samples-for-gam-n-samples.svg • draw-methods/draw-smooth-samples-for-m1-n-samples.svg • draw-methods/draw-smooth-samples-for-m2-n-samples.svg • draw-methods/draw-with-ranef-smooth-factor-by-fixed-scales.svg • draw-methods/draw-works-for-sos-smooths.svg • draw-methods/issue-73-draw-uses-fixed-scales-if-asked-for-them.svg • draw-parametric-effects/issue-219-parametric-effects.svg • draw-parametric-effects/ziplss-with-both-parametric-not-plotted.svg • draw-parametric-effects/ziplss-with-both-parametric-plotted.svg • draw-parametric-effects/ziplss-with-factor-para-not-plotted.svg • draw-parametric-effects/ziplss-with-factor-para-plotted.svg • draw-parametric-effects/ziplss-with-numeric-para-not-plotted.svg • draw-parametric-effects/ziplss-with-numeric-para-plotted.svg • draw-smooth-estimates/draw-gam-for-su-m-quadvar-t22.svg • draw-smooth-estimates/draw-gam-for-su-m-quadvar-te2.svg • draw-smooth-estimates/draw-gam-for-su-m-trivar-t22.svg • draw-smooth-estimates/draw-gam-for-su-m-trivar-te2.svg • draw-smooth-estimates/draw-gam-sos-chlorophyll-with-crs.svg • draw-smooth-estimates/draw-gam-sos-chlorophyll.svg • draw-smooth-estimates/draw-sm-est-grouped-by-true-ordered.svg • draw-smooth-estimates/draw-sm-est-grouped-by-true.svg • draw-smooth-estimates/draw-smooth-est-works-with-change-indicators.svg • draw-smooth-estimates/draw-smooth-est-works-with-sizer-indicators.svg • draw-smooth-estimates/draw-smooth-estimates-m-1-smooth.svg • draw-smooth-estimates/draw-smooth-estimates-m-gamm4.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-bivar-te.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-bivar.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar-t2.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar-t22.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar-te.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar-te2.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-quadvar.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-trivar-t2.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-trivar-t22.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-trivar-te.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-trivar-te2.svg • draw-smooth-estimates/draw-smooth-estimates-su-m-trivar.svg • draw-smooth-estimates/draw-smooth-estimates-sz-factor-smooth.svg • draw-smooth-estimates/draw-smooth-estimates-sz-two-factor-smooth.svg • draw-smooth-estimates/draw-smooth-estimates-univariate-t2-smooth.svg • draw-smooth-estimates/draw-smooth-estimates-univariate-te-smooth.svg • draw-smooth-estimates/draw-smooth-estimates-univariate-ti-smooth.svg • draw-smooth-estimates/draw-subtitle-ordered-by-smooths.svg • gjrm-methods/draw-simple-gjrm-gamlss.svg • hgam-paper/hgam-paper-bird-move-model-1.svg • hgam-paper/hgam-paper-bird-move-model-2.svg • hgam-paper/hgam-paper-bird-move-model-3.svg • hgam-paper/hgam-paper-bird-move-model-4.svg • hgam-paper/hgam-paper-bird-move-model-5.svg • hgam-paper/hgam-paper-co2-model-1.svg • hgam-paper/hgam-paper-co2-model-2.svg • hgam-paper/hgam-paper-co2-model-3.svg • hgam-paper/hgam-paper-co2-model-4.svg • hgam-paper/hgam-paper-co2-model-5.svg • hgam-paper/hgam-paper-zoop-model-4.svg • hgam-paper/hgam-paper-zoop-model-5.svg • parametric-effects/testing-issue-212.svg • penalty/draw-penalty-df-as-matrix-false.svg • penalty/draw-penalty-df-as-matrix-true.svg • penalty/draw-penalty-df-issue-95-label-order.svg • penalty/draw-penalty-df-with-multiple-smooths-normalized.svg • penalty/draw-penalty-df-with-multiple-smooths.svg • penalty/draw-penalty-df-with-single-smooths-normalized.svg • penalty/draw-penalty-df-with-single-smooths.svg • penalty/draw-penalty-multiple-smooths-user-continuous-fill.svg • penalty/draw-penalty-single-smooths-user-continuous-fill.svg • rootograms/draw-gaussian-rootogram.svg • rootograms/draw-neg-bin-rootogram.svg • rootograms/draw-neg-bin-sqrt-rootogram.svg • rootograms/draw-neg-bin-standing-rootogram.svg • rootograms/draw-neg-bin-suspended-rootogram.svg • soap-films/draw-gam-so-soap-film.svg • soap-films/draw-smooth-estimates-so-soap-film.svg > > proc.time() user system elapsed 112.21 6.12 118.34