R Under development (unstable) (2024-09-21 r87186 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> pkg_name <- "tern"
> library(testthat)
> test_check(pkg_name, reporter = ParallelProgressReporter$new())
Loading required package: tern
Loading required package: rtables
Loading required package: formatters

Attaching package: 'formatters'

The following object is masked from 'package:base':

    %||%

Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not


Attaching package: 'rtables'

The following object is masked from 'package:utils':

    str

Registered S3 method overwritten by 'tern':
  method   from 
  tidy.glm broom

Attaching package: 'dplyr'

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

✔ | F W  S  OK | Context

⠋ [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] Starting up...                          
✔ |      7   7 | abnormal [1.5s]                                                

✔ |      5   8 | abnormal_by_baseline                                           

✔ |      3   4 | abnormal_by_marked [5.0s]                                      

✔ |      2   3 | abnormal_by_worst_grade                                        

✔ |      8  12 | abnormal_by_worst_grade_worsen [1.3s]                          

✔ |     31  47 | analyze_variables [4.9s]                                       

✔ |      7   8 | analyze_vars_in_cols [4.0s]                                    

✔ |      2   6 | bland-altman                                                   

✔ |         16 | combination_function                                           

✔ |      9  17 | compare_variables                                              

✔ |      1   3 | control_logistic                                               

✔ |      1   4 | control_step                                                   

✔ |      3  11 | control_survival                                               

✔ |      6   6 | count_cumulative                                               

✔ |      5   5 | count_missed_doses                                             

✔ |      8  15 | count_occurrences [1.5s]                                       

✔ |     13  15 | count_occurrences_by_grade [2.7s]                              

✔ |      4   4 | count_patients_events_in_cols                                  

✔ |      6   6 | count_patients_with_event                                      

✔ |      8   8 | count_patients_with_flags [1.2s]                               

✔ |     10  10 | count_values                                                   

✔ |      5  11 | coxph                                                          

✔ |     24  50 | coxreg [1.4s]                                                  

✔ |      2  13 | decorate_grob [1.5s]                                           

✔ |      5   5 | desctools_binom_diff                                           

✔ |      5  12 | df_explicit_na                                                 

✔ |      3   7 | estimate_multinom_rsp                                          

✔ |     17  17 | estimate_proportion                                            

✔ |      3  13 | fit_rsp_step                                                   

✔ |      3   9 | fit_survival_step                                              

✔ |     21  33 | formatting_functions                                           

✔ |      3  18 | g_forest [6.9s]                                                

✔ |      9  18 | g_km [9.1s]                                                    

✔ |      6  11 | g_lineplot [6.3s]                                              

✔ |      4  10 | g_step                                                         

✔ |      2   2 | g_waterfall                                                    

✔ |      5   1 | h_adsl_adlb_merge_using_worst_flag                             

✔ |      1   1 | h_format_row                                                   

✔ |      5   5 | h_incidence_rate                                               

✔ |     13  21 | h_km                                                           

✔ |     16  38 | h_logistic_regression                                          

✔ |      7   7 | h_map_for_count_abnormal                                       

✔ |      2   2 | h_pkparam_sort                                                 

✔ |      5   5 | h_response_biomarkers_subgroups                                

✔ |     14  15 | h_response_subgroups                                           

✔ |      3   5 | h_stack_by_baskets                                             

✔ |      8  43 | h_step                                                         

✔ |      4   8 | h_survival_biomarkers_subgroups                                

✔ |     16  17 | h_survival_duration_subgroups                                  

✔ |      2   0 | imputation_rule                                                

✔ |      8  12 | incidence_rate                                                 

✔ |          7 | individual_patient_plot                                        

✔ |      6  21 | logistic_regression [3.9s]                                     

✔ |      7  19 | make_afun                                                      

✔ |      7   8 | odds_ratio                                                     

✔ |     11  19 | prop_diff                                                      

✔ |      7  14 | prune_occurrences [3.5s]                                       

✔ |      6  10 | response_biomarkers_subgroups [2.8s]                           

✔ |     14  16 | response_subgroups [8.9s]                                      

✔ |      5   8 | rtables_access [3.1s]                                          

✔ |      5   8 | score_occurrences [1.8s]                                       

✔ |     15  19 | split_cols_by_groups [1.0s]                                    

✔ |      9  11 | stat                                                           

✔ |      5  11 | summarize_ancova [2.0s]                                        

✔ |      4   4 | summarize_change                                               

✔ |      3   3 | summarize_colvars [1.1s]                                       

✔ |     13  15 | summarize_coxreg [6.0s]                                        

✔ |     17  25 | summarize_glm_count [3.0s]                                     

✔ |     16  16 | summarize_num_patients [2.2s]                                  

✔ |      9   9 | summarize_patients_exposure_in_cols [1.2s]                     

✔ |      7  10 | survival_biomarkers_subgroups [5.1s]                           

✔ |      8   9 | survival_coxph_pairwise                                        

✔ |     14  17 | survival_duration_subgroups [9.0s]                             

✔ |      7   9 | survival_time [1.0s]                                           

✔ |     10  11 | survival_timepoint [1.3s]                                      

✔ |     11  12 | test_proportion_diff                                           

✔ |     59  79 | utils [1.6s]                                                   

✔ |         42 | utils_checkmate                                                

✔ |      6  24 | utils_default_stats_formats_labels                             

✔ |     13  26 | utils_factor                                                   

✔ |      3   3 | utils_ggplot [2.1s]                                            

✔ |          8 | utils_grid                                                     

✔ |     19  24 | utils_rtables [7.0s]                                           

✔ |      6  13 | utils_split_fun [2.5s]                                         

                                                                                
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 141.5 s

── Skipped tests (682) ─────────────────────────────────────────────────────────
• On CRAN (682): 'test-abnormal.R:24:3', 'test-abnormal.R:51:3',
  'test-abnormal.R:80:3', 'test-abnormal.R:103:3', 'test-abnormal.R:134:3',
  'test-abnormal.R:160:3', 'test-abnormal.R:186:3',
  'test-abnormal_by_baseline.R:16:3', 'test-abnormal_by_baseline.R:46:3',
  'test-abnormal_by_baseline.R:80:3', 'test-abnormal_by_baseline.R:94:3',
  'test-abnormal_by_baseline.R:113:3', 'test-abnormal_by_marked.R:80:3',
  'test-abnormal_by_marked.R:135:3', 'test-abnormal_by_marked.R:254:3',
  'test-abnormal_by_worst_grade.R:43:3', 'test-abnormal_by_worst_grade.R:71:3',
  'test-abnormal_by_worst_grade_worsen.R:64:3',
  'test-abnormal_by_worst_grade_worsen.R:82:3',
  'test-abnormal_by_worst_grade_worsen.R:102:3',
  'test-abnormal_by_worst_grade_worsen.R:122:3',
  'test-abnormal_by_worst_grade_worsen.R:142:3',
  'test-abnormal_by_worst_grade_worsen.R:162:3',
  'test-abnormal_by_worst_grade_worsen.R:184:3',
  'test-abnormal_by_worst_grade_worsen.R:211:3',
  'test-analyze_variables.R:7:3', 'test-analyze_variables.R:17:3',
  'test-analyze_variables.R:31:3', 'test-analyze_variables.R:39:3',
  'test-analyze_variables.R:48:3', 'test-analyze_variables.R:62:3',
  'test-analyze_variables.R:72:3', 'test-analyze_variables.R:81:3',
  'test-analyze_variables.R:90:3', 'test-analyze_variables.R:113:3',
  'test-analyze_variables.R:127:3', 'test-analyze_variables.R:134:3',
  'test-analyze_variables.R:143:3', 'test-analyze_variables.R:152:3',
  'test-analyze_variables.R:171:3', 'test-analyze_variables.R:228:3',
  'test-analyze_variables.R:245:3', 'test-analyze_variables.R:275:3',
  'test-analyze_variables.R:295:3', 'test-analyze_variables.R:310:3',
  'test-analyze_variables.R:321:3', 'test-analyze_variables.R:332:3',
  'test-analyze_variables.R:343:3', 'test-analyze_variables.R:378:3',
  'test-analyze_variables.R:389:3', 'test-analyze_variables.R:437:3',
  'test-analyze_variables.R:448:3', 'test-analyze_variables.R:474:3',
  'test-analyze_variables.R:492:3', 'test-analyze_variables.R:502:3',
  'test-analyze_variables.R:521:3', 'test-analyze_vars_in_cols.R:11:3',
  'test-analyze_vars_in_cols.R:53:3', 'test-analyze_vars_in_cols.R:105:3',
  'test-analyze_vars_in_cols.R:180:3', 'test-analyze_vars_in_cols.R:251:3',
  'test-analyze_vars_in_cols.R:319:3', 'test-analyze_vars_in_cols.R:422:3',
  'test-bland-altman.R:79:3', 'test-bland-altman.R:103:3',
  'test-compare_variables.R:9:3', 'test-compare_variables.R:20:3',
  'test-compare_variables.R:29:3', 'test-compare_variables.R:47:3',
  'test-compare_variables.R:69:3', 'test-compare_variables.R:78:3',
  'test-compare_variables.R:100:3', 'test-compare_variables.R:115:3',
  'test-compare_variables.R:125:3', 'test-control_logistic.R:8:3',
  'test-control_step.R:5:3', 'test-control_survival.R:7:3',
  'test-control_survival.R:21:3', 'test-control_survival.R:36:3',
  'test-count_cumulative.R:12:3', 'test-count_cumulative.R:30:3',
  'test-count_cumulative.R:44:3', 'test-count_cumulative.R:62:3',
  'test-count_cumulative.R:81:3', 'test-count_cumulative.R:103:3',
  'test-count_missed_doses.R:8:3', 'test-count_missed_doses.R:17:3',
  'test-count_missed_doses.R:24:3', 'test-count_missed_doses.R:35:3',
  'test-count_missed_doses.R:55:3', 'test-count_occurrences.R:10:3',
  'test-count_occurrences.R:65:3', 'test-count_occurrences.R:109:3',
  'test-count_occurrences.R:135:3', 'test-count_occurrences.R:161:3',
  'test-count_occurrences.R:175:3', 'test-count_occurrences.R:230:3',
  'test-count_occurrences.R:245:3', 'test-count_occurrences_by_grade.R:26:3',
  'test-count_occurrences_by_grade.R:40:3',
  'test-count_occurrences_by_grade.R:48:3',
  'test-count_occurrences_by_grade.R:67:3',
  'test-count_occurrences_by_grade.R:84:3',
  'test-count_occurrences_by_grade.R:135:3',
  'test-count_occurrences_by_grade.R:149:3',
  'test-count_occurrences_by_grade.R:174:3',
  'test-count_occurrences_by_grade.R:200:3',
  'test-count_occurrences_by_grade.R:235:3',
  'test-count_occurrences_by_grade.R:282:3',
  'test-count_occurrences_by_grade.R:314:3',
  'test-count_occurrences_by_grade.R:397:3',
  'test-count_patients_events_in_cols.R:23:3',
  'test-count_patients_events_in_cols.R:39:3',
  'test-count_patients_events_in_cols.R:55:3',
  'test-count_patients_events_in_cols.R:75:3',
  'test-count_patients_with_event.R:14:3',
  'test-count_patients_with_event.R:31:3',
  'test-count_patients_with_event.R:63:3',
  'test-count_patients_with_event.R:101:3',
  'test-count_patients_with_event.R:121:3',
  'test-count_patients_with_event.R:137:3',
  'test-count_patients_with_flags.R:14:3',
  'test-count_patients_with_flags.R:31:3',
  'test-count_patients_with_flags.R:52:3',
  'test-count_patients_with_flags.R:130:3',
  'test-count_patients_with_flags.R:178:3',
  'test-count_patients_with_flags.R:217:3',
  'test-count_patients_with_flags.R:243:3',
  'test-count_patients_with_flags.R:320:3', 'test-count_values.R:8:3',
  'test-count_values.R:24:3', 'test-count_values.R:39:3',
  'test-count_values.R:47:3', 'test-count_values.R:55:3',
  'test-count_values.R:64:3', 'test-count_values.R:81:3',
  'test-count_values.R:91:3', 'test-count_values.R:101:3',
  'test-count_values.R:118:3', 'test-coxph.R:5:3', 'test-coxph.R:17:3',
  'test-coxph.R:41:3', 'test-coxph.R:56:3', 'test-coxph.R:108:3',
  'test-coxreg.R:44:3', 'test-coxreg.R:56:3', 'test-coxreg.R:67:3',
  'test-coxreg.R:80:3', 'test-coxreg.R:92:3', 'test-coxreg.R:124:3',
  'test-coxreg.R:136:3', 'test-coxreg.R:147:3', 'test-coxreg.R:158:3',
  'test-coxreg.R:170:3', 'test-coxreg.R:182:3', 'test-coxreg.R:193:3',
  'test-coxreg.R:204:3', 'test-coxreg.R:216:3', 'test-coxreg.R:225:3',
  'test-coxreg.R:248:3', 'test-coxreg.R:298:3', 'test-coxreg.R:309:3',
  'test-coxreg.R:320:3', 'test-coxreg.R:360:3', 'test-coxreg.R:374:3',
  'test-coxreg.R:388:3', 'test-coxreg.R:533:3', 'test-coxreg.R:585:3',
  'test-decorate_grob.R:55:3', 'test-decorate_grob.R:124:3',
  'test-desctools_binom_diff.R:18:3', 'test-desctools_binom_diff.R:33:3',
  'test-desctools_binom_diff.R:42:3', 'test-desctools_binom_diff.R:51:3',
  'test-desctools_binom_diff.R:63:3', 'test-df_explicit_na.R:22:3',
  'test-df_explicit_na.R:36:3', 'test-df_explicit_na.R:44:3',
  'test-df_explicit_na.R:57:3', 'test-df_explicit_na.R:70:3',
  'test-estimate_multinom_rsp.R:6:3', 'test-estimate_multinom_rsp.R:14:3',
  'test-estimate_multinom_rsp.R:48:3', 'test-estimate_proportion.R:9:3',
  'test-estimate_proportion.R:29:3', 'test-estimate_proportion.R:43:3',
  'test-estimate_proportion.R:78:3', 'test-estimate_proportion.R:106:3',
  'test-estimate_proportion.R:131:3', 'test-estimate_proportion.R:142:3',
  'test-estimate_proportion.R:154:3', 'test-estimate_proportion.R:170:3',
  'test-estimate_proportion.R:181:3', 'test-estimate_proportion.R:203:3',
  'test-estimate_proportion.R:210:3', 'test-estimate_proportion.R:223:3',
  'test-estimate_proportion.R:247:3', 'test-estimate_proportion.R:281:3',
  'test-estimate_proportion.R:307:3', 'test-estimate_proportion.R:339:5',
  'test-fit_rsp_step.R:29:3', 'test-fit_rsp_step.R:58:3',
  'test-fit_rsp_step.R:85:3', 'test-fit_survival_step.R:34:3',
  'test-fit_survival_step.R:65:3', 'test-fit_survival_step.R:88:3',
  'test-formatting_functions.R:5:3', 'test-formatting_functions.R:12:3',
  'test-formatting_functions.R:19:3', 'test-formatting_functions.R:26:3',
  'test-formatting_functions.R:33:3', 'test-formatting_functions.R:40:3',
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  'test-formatting_functions.R:66:3', 'test-formatting_functions.R:73:3',
  'test-formatting_functions.R:82:3', 'test-formatting_functions.R:91:3',
  'test-formatting_functions.R:116:3', 'test-formatting_functions.R:125:3',
  'test-formatting_functions.R:134:3', 'test-formatting_functions.R:150:3',
  'test-formatting_functions.R:158:3', 'test-formatting_functions.R:172:3',
  'test-formatting_functions.R:181:3', 'test-formatting_functions.R:190:3',
  'test-formatting_functions.R:252:3', 'test-g_forest.R:23:3',
  'test-g_forest.R:58:3', 'test-g_forest.R:98:3', 'test-g_km.R:15:3',
  'test-g_km.R:28:3', 'test-g_km.R:40:3', 'test-g_km.R:62:3',
  'test-g_km.R:77:3', 'test-g_km.R:114:3', 'test-g_km.R:128:3',
  'test-g_km.R:147:3', 'test-g_km.R:162:3', 'test-g_lineplot.R:9:3',
  'test-g_lineplot.R:30:3', 'test-g_lineplot.R:50:3', 'test-g_lineplot.R:69:3',
  'test-g_lineplot.R:99:3', 'test-g_lineplot.R:112:3', 'test-g_step.R:18:3',
  'test-g_step.R:28:3', 'test-g_step.R:36:3', 'test-g_step.R:65:3',
  'test-g_waterfall.R:7:3', 'test-g_waterfall.R:29:3',
  'test-h_adsl_adlb_merge_using_worst_flag.R:11:3',
  'test-h_adsl_adlb_merge_using_worst_flag.R:25:3',
  'test-h_adsl_adlb_merge_using_worst_flag.R:39:3',
  'test-h_adsl_adlb_merge_using_worst_flag.R:55:5',
  'test-h_adsl_adlb_merge_using_worst_flag.R:68:3', 'test-h_format_row.R:11:3',
  'test-h_incidence_rate.R:5:3', 'test-h_incidence_rate.R:12:3',
  'test-h_incidence_rate.R:19:3', 'test-h_incidence_rate.R:26:3',
  'test-h_incidence_rate.R:37:3', 'test-h_km.R:11:3', 'test-h_km.R:18:3',
  'test-h_km.R:26:3', 'test-h_km.R:34:3', 'test-h_km.R:43:3',
  'test-h_km.R:58:3', 'test-h_km.R:68:3', 'test-h_km.R:77:3',
  'test-h_km.R:84:3', 'test-h_km.R:99:3', 'test-h_km.R:118:3',
  'test-h_km.R:131:3', 'test-h_km.R:143:3',
  'test-h_logistic_regression.R:28:3', 'test-h_logistic_regression.R:49:3',
  'test-h_logistic_regression.R:74:3', 'test-h_logistic_regression.R:107:3',
  'test-h_logistic_regression.R:146:5', 'test-h_logistic_regression.R:204:3',
  'test-h_logistic_regression.R:218:3', 'test-h_logistic_regression.R:230:3',
  'test-h_logistic_regression.R:247:3', 'test-h_logistic_regression.R:283:3',
  'test-h_logistic_regression.R:300:3', 'test-h_logistic_regression.R:317:3',
  'test-h_logistic_regression.R:336:3', 'test-h_logistic_regression.R:373:3',
  'test-h_logistic_regression.R:395:3', 'test-h_logistic_regression.R:442:3',
  'test-h_map_for_count_abnormal.R:27:3',
  'test-h_map_for_count_abnormal.R:49:3',
  'test-h_map_for_count_abnormal.R:71:5',
  'test-h_map_for_count_abnormal.R:98:5',
  'test-h_map_for_count_abnormal.R:125:5',
  'test-h_map_for_count_abnormal.R:154:5',
  'test-h_map_for_count_abnormal.R:182:5', 'test-h_pkparam_sort.R:6:3',
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  'test-h_response_biomarkers_subgroups.R:51:3',
  'test-h_response_biomarkers_subgroups.R:69:3',
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  'test-h_response_subgroups.R:108:3', 'test-h_response_subgroups.R:122:3',
  'test-h_response_subgroups.R:141:3', 'test-h_response_subgroups.R:155:3',
  'test-h_response_subgroups.R:167:3', 'test-h_response_subgroups.R:179:3',
  'test-h_response_subgroups.R:201:3', 'test-h_response_subgroups.R:224:3',
  'test-h_stack_by_baskets.R:9:3', 'test-h_stack_by_baskets.R:48:5',
  'test-h_stack_by_baskets.R:76:5', 'test-h_step.R:30:3', 'test-h_step.R:56:3',
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  'test-h_survival_biomarkers_subgroups.R:75:3',
  'test-h_survival_biomarkers_subgroups.R:103:3',
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  'test-h_survival_duration_subgroups.R:139:3',
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  'test-utils_split_fun.R:124:3'

[ FAIL 0 | WARN 0 | SKIP 682 | PASS 1154 ]
Deleting unused snapshots:
• estimate_incidence_rate.md
• g_forest/g_forest_custom_2.new.svg
• g_forest/g_forest_custom_2.svg
• g_forest/g_forest_custom_3.new.svg
• g_forest/g_forest_custom_3.svg
• g_forest/g_forest_or.new.svg
• g_forest/g_forest_or.svg
• g_forest/g_forest_plot_only.new.svg
• g_forest/g_forest_plot_only.svg
• g_km/g_km_crop_ylim_failure.new.svg
• g_km/g_km_crop_ylim_failure.svg
• g_km/g_km_custom_ylim.new.svg
• g_km/g_km_custom_ylim.svg
• g_km/g_km_table_only.new.svg
• g_km/g_km_table_only.svg
• g_lineplot/g_lineplot_xlim_ylim.svg
• g_lineplot/g_lineplot_xticks.svg
• utils_ggplot/df2gg_cw.svg
• utils_ggplot/df2gg_fs.svg
• utils_ggplot/rtable2gg_cw.svg
• utils_ggplot/rtable2gg_fs.svg
• utils_ggplot/rtable2gg_lblpad.svg
> 
> proc.time()
   user  system elapsed 
 151.32    6.84  158.64