Last updated on 2026-10-24 01:51:35 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.0 | 31.88 | 614.85 | 646.73 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 21.81 | 387.99 | 409.80 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 28.00 | 418.27 | 446.27 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 26.00 | 414.58 | 440.58 | OK | |
| r-devel-windows-x86_64 | 1.1.0 | 31.00 | 544.00 | 575.00 | OK | |
| r-patched-linux-x86_64 | 1.2.0 | 31.04 | 581.37 | 612.41 | OK | |
| r-release-linux-x86_64 | 1.1.0 | 25.71 | 574.73 | 600.44 | OK | |
| r-release-macos-arm64 | 1.2.0 | 8.00 | 125.00 | 133.00 | OK | |
| r-release-macos-x86_64 | 1.2.0 | 24.00 | 493.00 | 517.00 | OK | |
| r-release-windows-x86_64 | 1.2.0 | 39.00 | 516.00 | 555.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.0 | 10.00 | 155.00 | 165.00 | OK | |
| r-oldrel-macos-x86_64 | 1.2.0 | 23.00 | 803.00 | 826.00 | OK | |
| r-oldrel-windows-x86_64 | 1.2.0 | 56.00 | 699.00 | 755.00 | OK |
Version: 1.2.0
Check: examples
Result: ERROR
Running examples in ‘gtregression-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_cox_survival
> ### Title: Plot adjusted survival curves from a Cox model
> ### Aliases: plot_cox_survival
>
> ### ** Examples
>
> lung_data <- data_lungcancer
> lung_data$trt <- factor(lung_data$trt, levels = c(1, 2),
+ labels = c("Standard", "Test"))
> fit <- cox_reg(
+ lung_data, time, status,
+ exposures = c(trt, age, karno),
+ multivariable = TRUE
+ )
> plot_cox_survival(fit, by = trt)
Error: Could not calculate adjusted Cox curves: subscript out of bounds
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [91s/121s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(gtregression)
>
> test_check("gtregression")
Loading required package: shiny
Saving _problems/test-check_ph-16.R
Saving _problems/test-check_ph-57.R
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
Running stratified survival regression by: trt
> Stratum: trt = Standard treatment
> Stratum: trt = Test treatment
# A tibble: 2 x 7
Variable Type `Missing (%)` Unique Levels Compatibility Hint
<chr> <chr> <chr> <int> <chr> <chr> <chr>
1 x numeric 0% 3 - compatible Numeric variable c~
2 y factor 0% 2 a, b compatible Factor variable ca~
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `HG`: modelling the event 'High grade' (second level); reference level is 'Low grade'.
logistf::logistf(formula = formula, data = data)
Model fitted by Penalized ML
Coefficients:
coef se(coef) lower 0.95 upper 0.95 Chisq
(Intercept) 3.77455951 1.43900672 1.0825371 7.20928050 8.1980136
NVPresent 2.92927330 1.46497415 0.6097244 7.85463171 6.7984572
PI -0.03475175 0.03789237 -0.1244587 0.04045547 0.7468285
EH -2.60416387 0.75362838 -4.3651832 -1.23272106 17.7593175
p method
(Intercept) 4.193628e-03 2
NVPresent 9.123668e-03 2
PI 3.874822e-01 2
EH 2.506867e-05 2
Method: 1-Wald, 2-Profile penalized log-likelihood, 3-None
Likelihood ratio test=43.65582 on 3 df, p=1.78586e-09, n=79
Wald test = 21.66965 on 3 df, p = 7.641345e-05Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
select_models(): all candidate models are fitted to the same N = 32 complete cases.
Saving _problems/test-plot_cox_survival-12.R
Saving _problems/test-plot_cox_survival-31.R
select_models(): all candidate models are fitted to the same N = 189 complete cases.
select_models(): all candidate models are fitted to the same N = 189 complete cases.
select_models(): all candidate models are fitted to the same N = 189 complete cases.
select_models(): all candidate models are fitted to the same N = 189 complete cases.
select_models(): all candidate models are fitted to the same N = 189 complete cases.
select_models(): all candidate models are fitted to the same N = 32 complete cases.
select_models(): all candidate models are fitted to the same N = 146 complete cases.
select_models(): all candidate models are fitted to the same N = 146 complete cases.
select_models(): all candidate models are fitted to the same N = 137 complete cases.
select_models(): all candidate models are fitted to the same N = 137 complete cases.
select_models(): all candidate models are fitted to the same N = 137 complete cases.
select_models(): all candidate models are fitted to the same N = 32 complete cases.
select_models(): all candidate models are fitted to the same N = 32 complete cases.
select_models(): all candidate models are fitted to the same N = 32 complete cases.
Outcome `low`: modelling the event 'Low BW' (second level); reference level is 'Normal BW'.
Running stratified multivariable regression by: ht
> Stratum: ht = No
> Stratum: ht = Yes
Outcome `HG`: modelling the event 'High grade' (second level); reference level is 'Low grade'.
[ FAIL 4 | WARN 0 | SKIP 131 | PASS 1913 ]
══ Skipped tests (131) ═════════════════════════════════════════════════════════
• On CRAN (130): 'test-app-environment-data.R:3:1', 'test-app-history.R:30:3',
'test-app-history.R:91:3', 'test-app-history.R:109:3',
'test-app-reference-levels.R:2:3', 'test-app-reference-levels.R:23:3',
'test-app-reference-levels.R:40:3', 'test-app-role-safety.R:80:3',
'test-app-role-safety.R:92:3', 'test-app-role-safety.R:142:3',
'test-app-selection-continuity.R:115:3',
'test-app-selection-continuity.R:140:3',
'test-app-selection-continuity.R:188:3',
'test-app-selection-continuity.R:237:3',
'test-app-selection-continuity.R:290:3',
'test-app-selection-continuity.R:310:3', 'test-app-shared-shell.R:36:3',
'test-app-shared-shell.R:68:3', 'test-app-shared-shell.R:114:3',
'test-app-shared-shell.R:136:3', 'test-app-shared-shell.R:165:3',
'test-app-shared-shell.R:194:3', 'test-app-shared-shell.R:238:3',
'test-app-shared-shell.R:296:3', 'test-app-shared-shell.R:314:3',
'test-app-shared-shell.R:347:3', 'test-app-shared-shell.R:364:3',
'test-app-shared-shell.R:400:3', 'test-app-shared-shell.R:435:3',
'test-app-shared-shell.R:449:3', 'test-app-shared-shell.R:464:3',
'test-app-shared-shell.R:547:3', 'test-app-shared-shell.R:577:3',
'test-app-shared-shell.R:611:3', 'test-app-shared-shell.R:644:3',
'test-app-stress.R:51:3', 'test-app-structure.R:4:3',
'test-app-structure.R:67:3', 'test-app-trials.R:85:3',
'test-app-trials.R:110:3', 'test-app-trials.R:135:3',
'test-app-trials.R:160:3', 'test-app-trials.R:197:3',
'test-app-trials.R:216:3', 'test-app-trials.R:239:3',
'test-app-trials.R:265:3', 'test-app-workbench-components.R:27:3',
'test-app-workbench-components.R:45:3',
'test-app-workbench-components.R:66:3',
'test-app-workbench-components.R:113:3', 'test-app-workbench-safety.R:122:3',
'test-app-workbench-safety.R:192:3', 'test-app-workbench-safety.R:234:3',
'test-app-workbench-safety.R:260:3', 'test-check_collinearity.R:3:1',
'test-compare_models.R:3:1', 'test-data-prep-operations.R:2:3',
'test-data-prep-operations.R:43:3', 'test-data-prep-operations.R:105:3',
'test-data-prep-operations.R:134:3', 'test-data-prep-operations.R:170:3',
'test-data-prep-quick-starts.R:37:3', 'test-data-prep-quick-starts.R:63:3',
'test-data-prep-quick-starts.R:88:3', 'test-data-prep-quick-starts.R:102:3',
'test-data-prep-reproducibility.R:58:3',
'test-data-prep-reproducibility.R:77:3',
'test-data-prep-reproducibility.R:86:3',
'test-data-prep-reproducibility.R:111:3',
'test-data-prep-reproducibility.R:123:3',
'test-data-prep-reproducibility.R:141:3',
'test-data-prep-reproducibility.R:167:3',
'test-data-prep-reproducibility.R:188:3',
'test-data-prep-reproducibility.R:212:3',
'test-data-prep-reproducibility.R:234:3',
'test-data-prep-reproducibility.R:243:3',
'test-data-prep-reproducibility.R:257:3',
'test-data-prep-reproducibility.R:292:3',
'test-data-prep-reproducibility.R:335:3',
'test-data-prep-reproducibility.R:365:3',
'test-data-prep-reproducibility.R:379:3',
'test-data-prep-reproducibility.R:403:3', 'test-data-structure.R:20:3',
'test-data-structure.R:33:3', 'test-data-structure.R:46:3',
'test-data-structure.R:59:3', 'test-data-structure.R:73:3',
'test-data-structure.R:91:3', 'test-data-structure.R:99:3',
'test-fix-core-bare-names.R:3:1', 'test-fix-core-descriptive-import.R:3:1',
'test-fix-core-regression.R:3:1', 'test-fix-core-special.R:3:1',
'test-fix-integration.R:3:1', 'test-fix-output-forest-save.R:3:1',
'test-fix-output-merge.R:3:1', 'test-fix-output-modify.R:3:1',
'test-fix-output-plots.R:3:1', 'test-fix-survival-audit.R:3:1',
'test-forest-plot-special-models.R:3:1', 'test-forest_reg.R:3:1',
'test-gtregression_addin.R:3:1', 'test-gtregression_app.R:2:3',
'test-gtregression_app.R:11:3', 'test-gtregression_app.R:26:3',
'test-gtregression_app.R:47:3', 'test-gtregression_app.R:66:3',
'test-gtregression_app.R:90:3', 'test-gtregression_app.R:111:3',
'test-gtregression_app.R:134:3', 'test-gtregression_app.R:166:3',
'test-gtregression_app.R:199:3', 'test-gtregression_app.R:216:3',
'test-gtregression_app.R:232:3', 'test-gtregression_app.R:245:3',
'test-gtregression_app.R:258:3', 'test-gtregression_app.R:272:3',
'test-gtregression_app.R:283:3', 'test-gtregression_app.R:304:3',
'test-gtregression_app.R:326:3', 'test-identify_confounder.R:3:1',
'test-merge_tables.R:3:1', 'test-modify_table.R:3:1', 'test-plot_reg.R:3:1',
'test-plot_reg_combine.R:3:1', 'test-risk_difference-ecosystem.R:3:1',
'test-save_functions.R:3:1', 'test-stratified_uni_reg.R:3:1',
'test-surv_reg.R:3:1', 'test-variable_labels.R:3:1'
• package sources are not available (1): 'test-compat-null-default.R:17:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-check_ph.R:16:3'): check_ph works with direct coxph models ─────
Error: Could not compute proportional hazards test for model 'cox_model': subscript out of bounds
Backtrace:
▆
1. └─gtregression::check_ph(fit, format = tibble) at test-check_ph.R:16:3
2. └─base::lapply(...)
3. └─gtregression (local) FUN(X[[i]], ...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
── Error ('test-check_ph.R:57:3'): check_ph returns formatted tables ───────────
Error: Could not compute proportional hazards test for model 'cox_model': subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_s3_class(check_ph(fit), "flextable") at test-check_ph.R:57:3
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─gtregression::check_ph(fit)
5. └─base::lapply(...)
6. └─gtregression (local) FUN(X[[i]], ...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─value[[3L]](cond)
── Error ('test-plot_cox_survival.R:12:3'): plot_cox_survival builds adjusted curves from cox_reg ──
Error: Could not calculate adjusted Cox curves: subscript out of bounds
Backtrace:
▆
1. └─gtregression::plot_cox_survival(fit, by = trt) at test-plot_cox_survival.R:12:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
── Error ('test-plot_cox_survival.R:31:3'): plot_cox_survival accepts explicit profiles and model selection ──
Error: Could not calculate adjusted Cox curves: subscript out of bounds
Backtrace:
▆
1. └─gtregression::plot_cox_survival(fit, model_name = "age", newdata = profiles) at test-plot_cox_survival.R:31:3
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
[ FAIL 4 | WARN 0 | SKIP 131 | PASS 1913 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘causal-mediation.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘causal-mediation.Rmd’
--- re-building ‘choose-model.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘choose-model.Rmd’
--- re-building ‘confounding-interaction.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘confounding-interaction.Rmd’
--- re-building ‘customize-export.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘customize-export.Rmd’
--- re-building ‘descriptive-tables.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘descriptive-tables.Rmd’
--- re-building ‘diagnostics-selection.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘diagnostics-selection.Rmd’
--- re-building ‘function-options.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘function-options.Rmd’
--- re-building ‘gtregression-app.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘gtregression-app.Rmd’
--- re-building ‘gtregression-intro.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘gtregression-intro.Rmd’
--- re-building ‘merge-tables.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘merge-tables.Rmd’
--- re-building ‘regression-tables.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘regression-tables.Rmd’
--- re-building ‘risk-difference.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘risk-difference.Rmd’
--- re-building ‘special-models.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘special-models.Rmd’
--- re-building ‘stratified-analysis.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘stratified-analysis.Rmd’
--- re-building ‘survival-analysis.Rmd’ using rmarkdown
Quitting from survival-analysis.Rmd:226-228 [surv-cox-adjusted-curves]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Could not calculate adjusted Cox curves: subscript out of bounds
---
Backtrace:
▆
1. └─gtregression::plot_cox_survival(...)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'survival-analysis.Rmd' failed with diagnostics:
Could not calculate adjusted Cox curves: subscript out of bounds
--- failed re-building ‘survival-analysis.Rmd’
--- re-building ‘visualise-results.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘visualise-results.Rmd’
SUMMARY: processing the following file failed:
‘survival-analysis.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc