Package check result: OK Changes to worse in reverse depends: Package: coursekata Check: examples New result: ERROR Running examples in ‘coursekata-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: middle > ### Title: Find a percentage of a distribution > ### Aliases: middle tails outer lower upper > > ### ** Examples > > > upper(1:10, .1) [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE > lower(1:10, .2) [1] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE > middle(1:10, .5) [1] FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE > tails(1:10, .5) [1] TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE > > sampling_distribution <- do(1000) * mean(rnorm(100, 5, 10)) > sampling_distribution %>% + gf_histogram(~mean, data = sampling_distribution, fill = ~ middle(mean, .68)) %>% + gf_refine(scale_fill_manual(values = c("blue", "coral"))) Error: ! Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error in `as.data.frame.default()`: ! cannot coerce class ‘"function"’ to a data.frame Backtrace: ▆ 1. ├─base (local) ``(x) 2. ├─ggformula:::print.gf_ggplot(x) 3. ├─base::NextMethod() 4. ├─ggplot2 (local) `print.ggplot2::ggplot`(x) 5. │ ├─ggplot2::ggplot_build(x) 6. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x) 7. │ └─ggplot2:::by_layer(...) 8. │ ├─rlang::try_fetch(...) 9. │ │ ├─base::tryCatch(...) 10. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 11. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 13. │ │ └─base::withCallingHandlers(...) 14. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 15. │ └─l$compute_aesthetics(d, plot) 16. │ └─ggplot2 (local) compute_aesthetics(..., self = self) 17. │ └─ggplot2:::eval_aesthetics(aesthetics, data) 18. │ └─base::lapply(aesthetics, eval_tidy, data = data, env = env) 19. │ └─rlang (local) FUN(X[[i]], ...) 20. ├─coursekata::middle(mean, 0.68) 21. │ └─coursekata::upper(x, tail_prop, !greedy) 22. │ └─base::data.frame(x = x, original_pos = seq_along(x)) 23. │ ├─base::as.data.frame(x[[i]], optional = TRUE) 24. │ └─base::as.data.frame.default(x[[i]], optional = TRUE) 25. │ └─base::stop(...) 26. └─base::.handleSimpleError(...) 27. └─rlang (local) h(simpleError(msg, call)) 28. └─handlers[[1L]](cnd) 29. └─cli::cli_abort(...) 30. └─rlang::abort(...) Execution halted Package: coursekata Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘gf-squareplot.Rmd’ using rmarkdown Quitting from gf-squareplot.Rmd:106-114 [dgp] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `gf_squareplot()`: ! `x` must be numeric. --- Backtrace: ▆ 1. └─coursekata::gf_squareplot(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'gf-squareplot.Rmd' failed with diagnostics: `x` must be numeric. --- failed re-building ‘gf-squareplot.Rmd’ SUMMARY: processing the following file failed: ‘gf-squareplot.Rmd’ Error: Vignette re-building failed. Execution halted Package: DeclareDesign Check: tests New result: ERROR Running ‘testthat.R’ [94s/94s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(DeclareDesign) Loading required package: randomizr Loading required package: fabricatr Loading required package: estimatr > > library(AER) Loading required package: car Loading required package: carData Loading required package: lmtest Loading required package: zoo Attaching package: 'zoo' The following objects are masked from 'package:base': as.Date, as.Date.numeric Loading required package: sandwich Loading required package: survival > library(betareg) > library(biglm) Loading required package: DBI > library(coin) Attaching package: 'coin' The following object is masked from 'package:testthat': expectation > library(future.apply) Loading required package: future Attaching package: 'future' The following object is masked from 'package:survival': cluster The following object is masked from 'package:lmtest': reset > library(gam) Loading required package: splines Loading required package: foreach Loaded gam 1.22-7 > library(Matching) Loading required package: MASS ## ## Matching (Version 4.10-15, Build Date: 2024-10-14) ## See https://www.jsekhon.com for additional documentation. ## Please cite software as: ## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching ## Software with Automated Balance Optimization: The Matching package for R.'' ## Journal of Statistical Software, 42(7): 1-52. ## > library(reshape2) > library(sf) Linking to GEOS 3.14.1, GDAL 3.12.3, PROJ 9.8.0; sf_use_s2() is TRUE > > test_check("DeclareDesign") Error : No estimates or inquiries were declared, so design cannot be simulated. Saving _problems/test-modify-design-25.R Saving _problems/test-modify-design-94.R Saving _problems/test-modify-design-106.R Saving _problems/test-modify-design-114.R Saving _problems/test-modify-design-121.R Saving _problems/test-name-steps-8.R Saving _problems/test-name-steps-12.R Saving _problems/test-names-and-labels-73.R Saving _problems/test-print-code-30.R [ FAIL 9 | WARN 0 | SKIP 7 | PASS 638 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-reshape-diagnosis.R:123:3' • test requires updated DesignLbrary (6): 'test-design-library.R:7:3', 'test-design-library.R:37:3', 'test-design-library.R:46:3', 'test-design-library.R:136:3', 'test-simulate-design.R:121:3', 'test-simulate-design.R:137:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-modify-design.R:25:3'): test modify declare design ────────── Expected `names(redesigned)` to equal `c("my_population", "my_potential_outcomes", "custom", "my_assignment_2")`. Differences: 2/4 mismatches x[1]: "model" y[1]: "my_population" x[2]: "potential_outcomes" y[2]: "my_potential_outcomes" ── Failure ('test-modify-design.R:91:3'): names are correct ──────────────────── Expected `names(neighbors_design)` to equal `c(...)`. Differences: 2/5 mismatches x[1]: "model" y[1]: "my_population" x[2]: "model_1" y[2]: "my_potential_outcomes" ── Failure ('test-modify-design.R:100:3'): names are correct ─────────────────── Expected `names(check0)` to equal `c(...)`. Differences: 2/6 mismatches x[1]: "model" y[1]: "my_population" x[2]: "model_1" y[2]: "my_potential_outcomes" ── Failure ('test-modify-design.R:108:3'): names are correct ─────────────────── Expected `names(check1)` to equal `c(...)`. Differences: 2/6 mismatches x[1]: "model" y[1]: "my_population" x[2]: "model_1" y[2]: "my_potential_outcomes" ── Failure ('test-modify-design.R:115:3'): names are correct ─────────────────── Expected `names(check2)` to equal `c(...)`. Differences: 2/7 mismatches x[1]: "model" y[1]: "my_population" x[2]: "model_1" y[2]: "my_potential_outcomes" ── Failure ('test-name-steps.R:8:3'): design steps are named appropriately when blank ── Expected `names(des)` to equal `c("pop", "model")`. Differences: 2/2 mismatches x[1]: "model" y[1]: "pop" x[2]: "model_1" y[2]: "model" ── Failure ('test-name-steps.R:12:3'): design steps are named appropriately when blank ── Expected `names(des)` to equal `c("model", "smp")`. Differences: 1/2 mismatches x[2]: "sampling" y[2]: "smp" ── Failure ('test-names-and-labels.R:73:3'): step name conflicts in design ───── Expected `names(pop + assign_1 + assign_1)` to equal `c("pop", "assign_1", "assign_1_1")`. Differences: 3/3 mismatches x[1]: "model" y[1]: "pop" x[2]: "assignment" y[2]: "assign_1" x[3]: "assignment_1" y[3]: "assign_1_1" ── Failure ('test-print-code.R:30:3'): print code works ──────────────────────── Expected output from `print_code(design)` to match regexp "my_population <- declare". Actual output: ✖ │ model <- declare_model(N = N, noise = rnorm(N)) │ │ potential_outcomes <- declare_potential_outcomes(Y_Z_0 = noise, Y_Z_1 = noise + rnorm(N, mean = 2, sd = 2)) │ │ sampling <- declare_sampling(S = complete_rs(N, n = 250)) │ │ ATE <- declare_inquiry(ATE = mean(Y_Z_1 - Y_Z_0)) │ │ custom <- declare_step(dplyr::mutate, q = 5) │ │ custom_1 <- declare_step(dplyr::mutate, q = 6) │ │ assignment <- declare_assignment(Z = complete_ra(N, m = 25)) │ │ measurement <- declare_measurement(Y = reveal_outcomes(Y ~ Z)) │ │ estimator <- declare_estimator(Y ~ Z, inquiry = my_inquiry) │ │ my_design <- construct_design(steps = steps) │ [ FAIL 9 | WARN 0 | SKIP 7 | PASS 638 ] Error: ! Test failures. Execution halted Package: ggplot2 Check: tests New result: ERROR Running ‘testthat.R’ [167s/169s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ggplot2) > > test_check("ggplot2") Saving _problems/test-plot-4.R [ FAIL 1 | WARN 0 | SKIP 269 | PASS 1781 ] ══ Skipped tests (269) ═════════════════════════════════════════════════════════ • .Platform$OS.type == "windows" is not TRUE (1): 'test-patterns.R:67:3' • On CRAN (267): 'test-aes-calculated.R:55:1', 'test-aes-calculated.R:75:1', 'test-aes-calculated.R:95:1', 'test-aes-setting.R:1:1', 'test-aes.R:47:1', 'test-aes.R:109:1', 'test-aes.R:122:1', 'test-aes.R:142:1', 'test-aes.R:162:1', 'test-aes.R:168:1', 'test-aes.R:173:1', 'test-aes.R:189:1', 'test-aes.R:198:1', 'test-aes.R:204:1', 'test-aes.R:221:1', 'test-annotate.R:19:1', 'test-annotate.R:51:1', 'test-annotate.R:66:1', 'test-annotate.R:71:1', 'test-annotate.R:75:1', 'test-annotate.R:79:1', 'test-annotate.R:83:1', 'test-annotate.R:118:1', 'test-autolayer.R:1:1', 'test-autoplot.R:1:1', 'test-coord-.R:1:1', 'test-coord-.R:43:1', 'test-coord-cartesian.R:17:1', 'test-coord-cartesian.R:25:1', 'test-coord-cartesian.R:41:1', 'test-coord-cartesian.R:52:1', 'test-coord-flip.R:1:1', 'test-coord-flip.R:16:1', 'test-coord-map.R:1:1', 'test-coord-map.R:14:1', 'test-coord-map.R:43:1', 'test-coord-map.R:51:1', 'test-coord-polar.R:101:1', 'test-coord-polar.R:107:1', 'test-coord-polar.R:158:1', 'test-coord-polar.R:184:1', 'test-coord-polar.R:222:1', 'test-coord-polar.R:281:1', 'test-coord-polar.R:335:1', 'test-coord-transform.R:1:1', 'test-coord-transform.R:100:1', 'test-coord-transform.R:109:1', 'test-coord-transform.R:127:1', 'test-coord-transform.R:135:1', 'test-coord_sf.R:1:1', 'test-coord_sf.R:20:1', 'test-coord_sf.R:33:1', 'test-coord_sf.R:70:1', 'test-coord_sf.R:235:1', 'test-coord_sf.R:358:1', 'test-coord_sf.R:382:1', 'test-coord_sf.R:391:1', 'test-coord_sf.R:410:3', 'test-draw-key.R:3:1', 'test-draw-key.R:23:1', 'test-draw-key.R:41:1', 'test-draw-key.R:75:1', 'test-empty-data.R:32:1', 'test-empty-data.R:44:1', 'test-empty-data.R:55:1', 'test-facet-.R:45:1', 'test-facet-.R:144:1', 'test-facet-.R:148:1', 'test-facet-.R:230:1', 'test-facet-.R:348:1', 'test-facet-.R:354:1', 'test-facet-.R:362:1', 'test-facet-.R:451:1', 'test-facet-.R:472:1', 'test-facet-.R:477:1', 'test-facet-.R:483:1', 'test-facet-.R:519:1', 'test-facet-labels.R:75:1', 'test-facet-labels.R:144:1', 'test-facet-labels.R:155:1', 'test-facet-layout.R:121:1', 'test-facet-layout.R:220:1', 'test-facet-layout.R:243:1', 'test-facet-layout.R:273:1', 'test-facet-strips.R:123:1', 'test-facet-strips.R:188:1', 'test-fortify.R:59:1', 'test-fortify.R:63:1', 'test-function-args.R:99:1', 'test-function-args.R:122:1', 'test-geom-.R:1:1', 'test-geom-bar.R:1:1', 'test-geom-boxplot.R:38:1', 'test-geom-boxplot.R:79:1', 'test-geom-boxplot.R:92:1', 'test-geom-col.R:1:1', 'test-geom-curve.R:1:1', 'test-geom-dotplot.R:1:1', 'test-geom-hex.R:24:1', 'test-geom-hex.R:32:1', 'test-geom-hline-vline-abline.R:4:1', 'test-geom-hline-vline-abline.R:28:1', 'test-geom-hline-vline-abline.R:66:1', 'test-geom-jitter.R:1:1', 'test-geom-label.R:1:1', 'test-geom-label.R:26:1', 'test-geom-linerange.R:1:1', 'test-geom-map.R:1:1', 'test-geom-map.R:6:1', 'test-geom-path.R:8:1', 'test-geom-path.R:36:1', 'test-geom-path.R:65:1', 'test-geom-path.R:90:1', 'test-geom-point.R:21:1', 'test-geom-polygon.R:5:1', 'test-geom-polygon.R:28:1', 'test-geom-raster.R:1:1', 'test-geom-raster.R:12:1', 'test-geom-raster.R:21:1', 'test-geom-rect.R:1:1', 'test-geom-ribbon.R:1:1', 'test-geom-ribbon.R:16:1', 'test-geom-rug.R:22:1', 'test-geom-rug.R:43:1', 'test-geom-sf.R:79:1', 'test-geom-sf.R:130:1', 'test-geom-sf.R:156:1', 'test-geom-sf.R:189:1', 'test-geom-sf.R:230:1', 'test-geom-sf.R:267:1', 'test-geom-sf.R:296:1', 'test-geom-smooth.R:30:3', 'test-geom-smooth.R:83:1', 'test-geom-smooth.R:114:1', 'test-geom-text.R:1:1', 'test-geom-text.R:5:1', 'test-geom-text.R:28:1', 'test-geom-text.R:36:1', 'test-geom-violin.R:50:1', 'test-geom-violin.R:82:1', 'test-ggproto.R:8:1', 'test-ggsave.R:12:1', 'test-ggsave.R:85:1', 'test-ggsave.R:98:1', 'test-ggsave.R:120:1', 'test-ggsave.R:133:1', 'test-ggsave.R:159:1', 'test-ggsave.R:163:1', 'test-guide-.R:1:1', 'test-guide-axis.R:1:1', 'test-guide-colorbar.R:1:1', 'test-guide-legend.R:1:1', 'test-guides.R:1:1', 'test-labellers.R:17:1', 'test-labellers.R:22:1', 'test-labels.R:101:1', 'test-labels.R:108:1', 'test-labels.R:112:1', 'test-labels.R:123:1', 'test-labels.R:312:1', 'test-layer.R:3:1', 'test-layer.R:23:1', 'test-layer.R:27:1', 'test-layer.R:31:1', 'test-layer.R:36:1', 'test-layer.R:57:1', 'test-layer.R:69:1', 'test-layer.R:80:1', 'test-layer.R:126:1', 'test-layer.R:141:1', 'test-layer.R:149:1', 'test-layer.R:216:1', 'test-legend-draw.R:2:1', 'test-limits.R:1:1', 'test-patterns.R:1:1', 'test-performance.R:14:1', 'test-plot.R:1:1', 'test-plot.R:7:1', 'test-position-collide.R:1:1', 'test-position-stack.R:77:1', 'test-position_dodge.R:56:1', 'test-prohibited-functions.R:60:3', 'test-prohibited-functions.R:96:1', 'test-qplot.R:58:1', 'test-scale-binned.R:1:1', 'test-scale-colour.R:1:1', 'test-scale-date.R:86:1', 'test-scale-discrete.R:135:1', 'test-scale-discrete.R:145:1', 'test-scale-discrete.R:152:1', 'test-scale-discrete.R:188:1', 'test-scale-expansion.R:6:1', 'test-scale-gradient.R:13:1', 'test-scale-hue.R:1:1', 'test-scale-manual.R:1:1', 'test-scale-manual.R:53:1', 'test-scale-manual.R:115:1', 'test-scale_date.R:19:1', 'test-scales-breaks-labels.R:9:1', 'test-scales-breaks-labels.R:145:1', 'test-scales-breaks-labels.R:149:1', 'test-scales-breaks-labels.R:287:1', 'test-scales-breaks-labels.R:345:1', 'test-scales-breaks-labels.R:368:1', 'test-scales.R:103:1', 'test-scales.R:199:1', 'test-scales.R:209:1', 'test-scales.R:233:1', 'test-scales.R:316:1', 'test-scales.R:431:1', 'test-scales.R:460:1', 'test-scales.R:645:1', 'test-scales.R:672:1', 'test-scales.R:694:1', 'test-sec-axis.R:7:1', 'test-sec-axis.R:62:1', 'test-sec-axis.R:139:1', 'test-sec-axis.R:187:1', 'test-sec-axis.R:211:1', 'test-sec-axis.R:258:1', 'test-sec-axis.R:329:1', 'test-sec-axis.R:345:1', 'test-stat-align.R:1:1', 'test-stat-align.R:11:1', 'test-stat-align.R:21:1', 'test-stat-bin.R:1:1', 'test-stat-bin.R:173:1', 'test-stat-bin.R:203:1', 'test-stat-bin.R:229:1', 'test-stat-bin.R:235:1', 'test-stat-bin2d.R:1:1', 'test-stat-boxplot.R:1:1', 'test-stat-boxplot.R:23:1', 'test-stat-connect.R:53:1', 'test-stat-contour.R:1:1', 'test-stat-contour.R:10:1', 'test-stat-contour.R:84:1', 'test-stat-count.R:1:1', 'test-stat-density.R:79:1', 'test-stat-density.R:104:1', 'test-stat-density.R:121:1', 'test-stat-density.R:129:1', 'test-stat-density2d.R:19:1', 'test-stat-density2d.R:99:1', 'test-stat-ecdf.R:1:1', 'test-stat-ecdf.R:45:1', 'test-stat-function.R:133:1', 'test-stat-qq.R:1:1', 'test-stat-sum.R:46:1', 'test-stat-ydensity.R:1:1', 'test-stat-ydensity.R:7:1', 'test-stats.R:1:1', 'test-stats.R:14:1', 'test-stats.R:19:1', 'test-summarise-plot.R:1:1', 'test-theme.R:1:1', 'test-utilities-break.R:1:1', 'test-utilities-checks.R:2:1', 'test-utilities-checks.R:44:1', 'test-utilities.R:93:1', 'test-utilities.R:103:1', 'test-utilities.R:107:1', 'test-utilities.R:113:1', 'test-utilities.R:118:1', 'test-utilities.R:122:1', 'test-utilities.R:127:1', 'test-utilities.R:211:3' • {sp} is not installed (1): 'test-fortify.R:3:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-plot.R:4:3'): ggplot() throws informative errors ───────────── `ggplot(foobar = "nonsense")` did not generate warning ── Snapshots ─────────────────────────────────────────────────────────────────── To review and process snapshots locally: * Locate check directory. * Copy 'tests/testthat/_snaps' to local package. * Run `testthat::snapshot_accept()` to accept all changes. * Run `testthat::snapshot_review()` to review all changes. [ FAIL 1 | WARN 0 | SKIP 269 | PASS 1781 ] Deleting unused snapshots: 'geom-dotplot/2-na-values-bin-along-y-stack-center.svg', 'geom-dotplot/2-na-values-dot-density-binning-binwidth-4.svg', 'geom-dotplot/3-stackgroups-bin-y-histodot.svg', 'geom-dotplot/3-stackgroups-dot-density-with-aligned-bins.svg', 'geom-dotplot/3-stackgroups-histodot.svg', 'geom-dotplot/basic-dotplot-with-dot-density-binning-binwidth-4.svg', 'geom-dotplot/bin-along-y-stack-center.svg', 'geom-dotplot/bin-along-y-stack-centerwhole-histodot.svg', 'geom-dotplot/bin-along-y-stack-centerwhole.svg', 'geom-dotplot/bin-x-three-y-groups-stack-centerwhole.svg', 'geom-dotplot/bin-y-continous-x-axis-grouping-by-x.svg', 'geom-dotplot/bin-y-continous-x-axis-single-x-group.svg', 'geom-dotplot/bin-y-dodged-coord-flip.svg', 'geom-dotplot/bin-y-dodged.svg', 'geom-dotplot/bin-y-dodging-3-stackgroups-histodot.svg', 'geom-dotplot/bin-y-three-x-groups-bins-aligned-across-groups.svg', 'geom-dotplot/bin-y-three-x-groups-bins-aligned-coord-flip.svg', 'geom-dotplot/bin-y-three-x-groups-fill-and-dodge.svg', …, 'theme/vertical-legends-placed-apart.svg', and 'theme/width-is-3-times-height.svg' Error: ! Test failures. Execution halted Package: mosaic Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Resampling.Rmd’ using rmarkdown Quitting from Resampling.Rmd:271-274 [hist] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error: ! Aesthetics are not valid data columns. ✖ The following aesthetics are invalid: • `x = mean` ℹ Did you mistype the name of a data column or forget to add `after_stat()`? --- Backtrace: ▆ 1. ├─base::withVisible(knit_print(x, ...)) 2. ├─knitr::knit_print(x, ...) 3. └─knitr:::knit_print.default(x, ...) 4. └─knitr::normal_print(x) 5. ├─base::print(x) 6. ├─ggformula:::print.gf_ggplot(x) 7. ├─base::NextMethod() 8. └─ggplot2 (local) `print.ggplot2::ggplot`(x) 9. ├─ggplot2::ggplot_build(x) 10. └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x) 11. └─ggplot2:::by_layer(...) 12. ├─rlang::try_fetch(...) 13. │ ├─base::tryCatch(...) 14. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 15. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 16. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 17. │ └─base::withCallingHandlers(...) 18. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) 19. └─l$compute_aesthetics(d, plot) 20. └─ggplot2 (local) compute_aesthetics(..., self = self) 21. └─ggplot2:::check_nondata_cols(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Resampling.Rmd' failed with diagnostics: Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error: ! Aesthetics are not valid data columns. ✖ The following aesthetics are invalid: • `x = mean` ℹ Did you mistype the name of a data column or forget to add `after_stat()`? --- failed re-building ‘Resampling.Rmd’ --- re-building ‘mosaic-resources.Rmd’ using rmarkdown --- finished re-building ‘mosaic-resources.Rmd’ --- re-building ‘MinimalRgg.Rnw’ using knitr --- finished re-building ‘MinimalRgg.Rnw’ SUMMARY: processing the following file failed: ‘Resampling.Rmd’ Error: Vignette re-building failed. Execution halted Package: mosaic Check: tests New result: ERROR Running ‘testthat.R’ [31s/32s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(mosaic) Registered S3 method overwritten by 'mosaic': method from fortify.SpatialPolygonsDataFrame ggplot2 The 'mosaic' package masks several functions from core packages in order to add additional features. The original behavior of these functions should not be affected by this. Attaching package: 'mosaic' The following objects are masked from 'package:dplyr': count, do, tally The following object is masked from 'package:Matrix': mean The following object is masked from 'package:ggplot2': stat The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test, quantile, sd, t.test, var The following objects are masked from 'package:base': max, mean, min, prod, range, sample, sum > > test_check("mosaic") Saving _problems/test-do-5.R Saving _problems/test-do-6.R Mapping API still under development and may change in future releases. `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' `geom_smooth()` using formula = 'y ~ x' Reading data with read.csv() Null distribution appears to be asymmetric. (p = 0) Test statistic applied to sample data = 18 Quantiles of test statistic applied to random data: 50% 90% 95% 99% 16 19 20 22 Of the 1000 samples (1 original + 999 random), 131 ( 13.1 % ) had test stats = 18 297 ( 29.7 % ) had test stats >= 18 Null distribution appears to be asymmetric. (p = 2.28e-06) Test statistic applied to sample data = 18 Quantiles of test statistic applied to random data: 50% 90% 95% 99% 10.00000 26.00000 31.33333 48.69333 Of the 1000 samples (1 original + 999 random), 33 ( 3.3 % ) had test stats = 18 240 ( 24 % ) had test stats >= 18 Null distribution appears to be asymmetric. (p = 0) Test statistic applied to sample data = 18 Quantiles of test statistic applied to random data: 50% 90% 95% 99% 16 19 20 22 Of the 1000 samples (1 original + 999 random), 131 ( 13.1 % ) had test stats = 18 297 ( 29.7 % ) had test stats >= 18 Loading required package: manipulate If X ~ N(500, 100), then P(X <= 650) = P(Z <= 1.5) = 0.9332 P(X > 650) = P(Z > 1.5) = 0.06681 [1] 0.9331928 If X ~ N(500, 100), then P(X <= 567.449) = 0.75 P(X > 567.449) = 0.25 [1] 567.449 [ FAIL 2 | WARN 3 | SKIP 18 | PASS 246 ] ══ Skipped tests (18) ══════════════════════════════════════════════════════════ • On CRAN (18): 'test-ashplots.R:4:1', 'test-bargraph.R:2:1', 'test-clustering.R:2:1', 'test-dotplot.R:3:1', 'test-fitspline.R:3:1', 'test-frequencyPolygon.R:3:1', 'test-ladd.R:3:1', 'test-ladd.R:15:1', 'test-ladd.R:30:1', 'test-maps2.R:29:1', 'test-mplot.R:3:1', 'test-plotCumfreq.R:3:1', 'test-plotDist.R:3:1', 'test-plotModel.R:3:1', 'test-plotPoints.R:3:1', 'test-rfun.R:3:1', 'test-statTally.R:39:1', 'test-xpnorm.R:3:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-do.R:5:3'): naming as expected ─────────────────────────────── Expected `names(do(2) * mean(~cesd, data = mosaicData::HELPrct))` to equal "mean". Differences: `actual`: "result" `expected`: "mean" ── Failure ('test-do.R:6:3'): naming as expected ─────────────────────────────── Expected `names(do(2) * var(~cesd, data = mosaicData::HELPrct))` to equal "var". Differences: `actual`: "result" `expected`: "var" [ FAIL 2 | WARN 3 | SKIP 18 | PASS 246 ] Error: ! Test failures. Execution halted Package: openairmaps Check: Rd cross-references New result: WARNING Missing link(s) in Rd file 'windroseMap.Rd': ‘[openair:drawOpenKey]{drawOpenKey()}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Package: pipr Check: examples New result: ERROR Running examples in ‘pipr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: call_aux > ### Title: call a table from .pip env > ### Aliases: call_aux > > ### ** Examples > > # call one table > > get_aux("gdp", assign_tb = TRUE, replace = TRUE) # PR 63 Pruning cache Error in `httr2::req_perform()`: ! HTTP 502 Bad Gateway. ℹ Bad Gateway Backtrace: ▆ 1. └─pipr::get_aux("gdp", assign_tb = TRUE, replace = TRUE) 2. └─httr2::req_perform(req) 3. └─httr2:::handle_resp(req, resp, error_call = error_call) 4. └─httr2:::resp_failure_cnd(req, resp, error_call = error_call) 5. ├─rlang::catch_cnd(...) 6. │ ├─rlang::eval_bare(...) 7. │ ├─base::tryCatch(...) 8. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 9. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 11. │ └─base::force(expr) 12. └─rlang::abort(...) Execution halted Package: pkggraph Check: whether package can be installed New result: WARNING Found the following significant warnings: Warning: replacing previous import ‘checkmate::check_data_frame’ by ‘rlang::check_data_frame’ when loading ‘pkggraph’ Warning: replacing previous import ‘checkmate::check_string’ by ‘rlang::check_string’ when loading ‘pkggraph’ Package: rgph Check: examples New result: ERROR Running examples in ‘rgph-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: reeb_graph > ### Title: An S3 class and constructors for Reeb graphs > ### Aliases: reeb_graph print.reeb_graph format.reeb_graph read_reeb_graph > > ### ** Examples > > x <- reeb_graph( + values = c(a = 0, b = .4, c = .6, d = 1), + edgelist = rbind( c(1,2), c(1,3), c(2,4), c(3,4)) + ) > print(x) Reeb graph with 4 vertices and 4 edges on [0,1]: 1[a] (0.0) -- 2[b] (0.4) 1[a] (0.0) -- 3[c] (0.6) 2[b] (0.4) -- 4[d] (1.0) 3[c] (0.6) -- 4[d] (1.0) > > t10 <- system.file("extdata", "10_tree_iterations.txt", package = "rgph") > ( y <- read_reeb_graph(t10) ) Reeb graph with 41 vertices and 40 edges on [0,152.2565]: 1 ( 0.000000) -- 2 ( 1.386294) 1 ( 0.000000) -- 14 (36.946803) 2 ( 1.386294) -- 3 ( 3.295837) 3 ( 3.295837) -- 4 ( 5.545177) 3 ( 3.295837) -- 5 ( 8.047190) 4 ( 5.545177) -- 6 (10.750557) 6 (10.750557) -- 7 (13.621371) 7 (13.621371) -- 9 (19.775021) 7 (13.621371) -- 8 (16.635532) 8 (16.635532) -- 18 (52.026692) 9 (19.775021) -- 10 (23.025851) 10 (23.025851) -- 11 (26.376848) ... > > reeb_graph_pairs(x, method = "multi_pass") Error in .jnew(pairing_java_object) : java.lang.UnsupportedClassVersionError: usf/saav/cmd/MergePairingCLI has been compiled by a more recent version of the Java Runtime (class file version 69.0), this version of the Java Runtime only recognizes class file versions up to 65.0 Calls: reeb_graph_pairs -> reeb_graph_pairs.reeb_graph -> .jnew Execution halted Package: rgph Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘benchmark.Rmd’ using rmarkdown Quitting from benchmark.Rmd:32-38 [example calculation] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `.jnew()`: ! java.lang.UnsupportedClassVersionError: usf/saav/cmd/MergePairingCLI has been compiled by a more recent version of the Java Runtime (class file version 69.0), this version of the Java Runtime only recognizes class file versions up to 65.0 --- Backtrace: ▆ 1. ├─rgph::reeb_graph_pairs(ex_reeb, method = "multi_pass") 2. └─rgph:::reeb_graph_pairs.reeb_graph(ex_reeb, method = "multi_pass") 3. └─rJava::.jnew(pairing_java_object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'benchmark.Rmd' failed with diagnostics: java.lang.UnsupportedClassVersionError: usf/saav/cmd/MergePairingCLI has been compiled by a more recent version of the Java Runtime (class file version 69.0), this version of the Java Runtime only recognizes class file versions up to 65.0 --- failed re-building ‘benchmark.Rmd’ SUMMARY: processing the following file failed: ‘benchmark.Rmd’ Error: Vignette re-building failed. Execution halted Package: rgph Check: tests New result: ERROR Running ‘tinytest.R’ [1s/1s] Running the tests in ‘tests/tinytest.R’ failed. Complete output: > if (requireNamespace("tinytest", quietly = TRUE)) { + tinytest::test_package("rgph") + } Loading required package: rJava Loading required package: phutil test-as-reeb-graph.R.......... 2 tests OK test-as-reeb-graph.R.......... 4 tests OK test-as-reeb-graph.R.......... 6 tests OK test-as-reeb-graph.R.......... 9 tests OK test-as-reeb-graph.R.......... 12 tests OK test-as-reeb-graph.R.......... 12 tests OK test-as-reeb-graph.R.......... 12 tests OK test-as-reeb-graph.R.......... 12 tests OK test-as-reeb-graph.R.......... 16 tests OK test-as-reeb-graph.R.......... 20 tests OK 0.5s Error in .jnew(pairing_java_object) : java.lang.UnsupportedClassVersionError: usf/saav/cmd/PPPairingCLI has been compiled by a more recent version of the Java Runtime (class file version 69.0), this version of the Java Runtime only recognizes class file versions up to 65.0 Calls: ... reeb_graph_pairs -> reeb_graph_pairs.reeb_graph -> .jnew Execution halted Package: rsimsum Check: whether package can be installed New result: WARNING Found the following significant warnings: Warning: replacing previous import ‘checkmate::check_data_frame’ by ‘rlang::check_data_frame’ when loading ‘rsimsum’ Warning: replacing previous import ‘checkmate::check_string’ by ‘rlang::check_string’ when loading ‘rsimsum’ Package: shinyOAuth Check: tests New result: ERROR Running ‘testthat.R’ [72s/79s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard devtools workflow. > # See `?devtools::test()` for more information. > > library(testthat) > library(shiny) > library(shinyOAuth) > > test_check("shinyOAuth") [ FAIL 1 | WARN 0 | SKIP 83 | PASS 1999 ] ══ Skipped tests (83) ══════════════════════════════════════════════════════════ • On CRAN (83): 'test-async-serialization.R:105:3', 'test-async-serialization.R:172:3', 'test-audit-async-options.R:2:3', 'test-audit-async-options.R:201:3', 'test-audit-async-options.R:260:3', 'test-audit-async-options.R:345:3', 'test-audit-async-options.R:405:3', 'test-audit-async-options.R:480:3', 'test-audit-async-options.R:544:3', 'test-audit-async-options.R:629:3', 'test-audit-async-session-context.R:2:3', 'test-constant-time-compare.R:53:3', 'test-discovery-auth-methods.R:3:3', 'test-discovery-auth-methods.R:31:3', 'test-discovery-auth-methods.R:55:3', 'test-discovery-auth-methods.R:86:3', 'test-discovery-auth-methods.R:120:3', 'test-discovery-auth-methods.R:153:3', 'test-discovery-auth-methods.R:181:3', 'test-discovery-hardened.R:3:3', 'test-discovery-hardened.R:72:3', 'test-discovery-hardened.R:100:3', 'test-discovery-hardened.R:126:3', 'test-discovery-hardened.R:142:3', 'test-discovery-hardened.R:166:3', 'test-discovery-hardened.R:192:3', 'test-discovery-hardened.R:216:3', 'test-discovery-hardened.R:239:3', 'test-introspect-token.R:117:3', 'test-jwks-cache-host-policy.R:119:3', 'test-jwks-malformed-and-pinning.R:3:3', 'test-jwks-malformed-and-pinning.R:96:3', 'test-mirai-utils.R:10:3', 'test-mirai-utils.R:20:3', 'test-mirai-utils.R:29:3', 'test-mirai-utils.R:44:3', 'test-mirai-utils.R:56:3', 'test-mirai-utils.R:69:3', 'test-mirai-utils.R:174:3', 'test-mirai-utils.R:191:3', 'test-mirai-utils.R:207:3', 'test-mirai-utils.R:228:3', 'test-mirai-utils.R:246:3', 'test-mirai-utils.R:256:3', 'test-mirai-utils.R:281:3', 'test-module-server-async.R:2:3', 'test-module-server-async.R:65:3', 'test-module-server-async.R:180:3', 'test-module-server-async.R:243:3', 'test-module-server-async.R:268:3', 'test-module-server-async.R:302:3', 'test-module-server.R:191:3', 'test-module-server.R:241:3', 'test-redirect-following-disabled.R:50:3', 'test-redirect-following-disabled.R:126:3', 'test-redirect-following-disabled.R:195:3', 'test-redirect-following-disabled.R:249:3', 'test-redirect-following-disabled.R:312:3', 'test-redirect-following-disabled.R:377:3', 'test-redirect-following-disabled.R:414:3', 'test-redirect-following-disabled.R:479:3', 'test-refresh-races.R:2:3', 'test-refresh-races.R:109:3', 'test-revoke-on-session-end.R:63:3', 'test-revoke-token.R:80:3', 'test-state-fail-delay.R:3:3', 'test-state-store-concurrent-replay.R:54:3', 'test-state-store-concurrent-replay.R:117:3', 'test-state-store-concurrent-replay.R:172:3', 'test-state-store-concurrent-replay.R:206:3', 'test-state-store-concurrent-replay.R:243:3', 'test-state-store-concurrent-replay.R:309:3', 'test-state-store-concurrent-replay.R:356:3', 'test-state-store-concurrent-replay.R:404:3', 'test-utils-http-helpers.R:200:3', 'test-utils-http-helpers.R:242:3', 'test-utils-http-helpers.R:279:3', 'test-utils-http-helpers.R:323:3', 'test_chromote_cookie.R:106:3', 'test_chromote_cookie.R:149:3', 'test_chromote_cookie.R:183:3', 'test_state_store_single_use.R:2:3', 'test_state_store_single_use.R:38:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-jwt-auth-time.R:146:5'): validate_id_token accepts auth_time at exact boundary (max_age + leeway) ── Error in `err_abort(msg, class = "shinyOAuth_id_token_error", context = context)`: [shinyOAuth] - ID token error x Authentication too old (auth_time exceeded max_age) i auth_time=1775215162, now=1775215468, elapsed=306s, max_age=300s, leeway=5s i Trace ID: -9hRfpN49KeT Backtrace: ▆ 1. ├─withr::with_options(...) at test-jwt-auth-time.R:145:3 2. │ └─base::force(code) 3. ├─testthat::expect_silent(...) at test-jwt-auth-time.R:146:5 4. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 5. │ ├─testthat (local) .capture(...) 6. │ │ ├─withr::with_output_sink(...) 7. │ │ │ └─base::force(code) 8. │ │ ├─base::withCallingHandlers(...) 9. │ │ └─base::withVisible(code) 10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 11. └─shinyOAuth:::validate_id_token(client, jwt, max_age = 300) 12. └─shinyOAuth:::err_id_token(...) 13. └─shinyOAuth:::err_abort(msg, class = "shinyOAuth_id_token_error", context = context) 14. └─rlang::abort(...) [ FAIL 1 | WARN 0 | SKIP 83 | PASS 1999 ] Error: ! Test failures. Execution halted Package: tf Check: whether package can be installed New result: WARNING Found the following significant warnings: Warning: replacing previous import ‘checkmate::check_data_frame’ by ‘rlang::check_data_frame’ when loading ‘tf’ Warning: replacing previous import ‘checkmate::check_string’ by ‘rlang::check_string’ when loading ‘tf’ Package: tidynorm Check: whether package can be installed New result: WARNING Found the following significant warnings: Warning: replacing previous import ‘checkmate::check_data_frame’ by ‘rlang::check_data_frame’ when loading ‘tidynorm’ Warning: replacing previous import ‘checkmate::check_string’ by ‘rlang::check_string’ when loading ‘tidynorm’ See ‘/home/hornik/tmp/CRAN_recheck/tidynorm.Rcheck/00install.out’ for details. Used C++ compiler: ‘g++-15 (Debian 15.2.0-16) 15.2.0’ Package: uteals Check: whether package can be installed New result: WARNING Found the following significant warnings: Warning: replacing previous import ‘checkmate::check_data_frame’ by ‘rlang::check_data_frame’ when loading ‘uteals’ Warning: replacing previous import ‘checkmate::check_string’ by ‘rlang::check_string’ when loading ‘uteals’