test failing with test-coxph

[shajoezhu]

• checking for unstated dependencies in ‘tests’ ... OK

• checking tests ...
  Running ‘testthat.R’
  ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:

  pkg_name <- "tern"
  library(testthat)
  test_check(pkg_name, reporter = ParallelProgressReporter$new())
  Loading required package: tern
  Loading required package: rtables
  Loading required package: formatters
  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...
  ✔ | 17 | abnormal_by_baseline [1.2s]

  ✔ | 7 | abnormal_by_marked [3.9s]

  ✔ | 20 | abnormal_by_worst_grade_worsen

  ✔ | 5 | abnormal_by_worst_grade

  ✔ | 14 | abnormal

  ✔ | 108 | analyze_variables [4.6s]

  ✔ | 32 | analyze_vars_in_cols [7.4s]

  ✔ | 1 7 | bland-altman

  ✔ | 16 | combination_function

  ✔ | 31 | compare_variables

  ✔ | 4 | control_logistic

  ✔ | 5 | control_step

  ✔ | 14 | control_survival

  ✔ | 14 | count_cumulative

  ✔ | 12 | count_missed_doses

  ✔ | 52 | count_occurrences_by_grade [3.6s]

  ✔ | 33 | count_occurrences [3.0s]

  ✔ | 8 | count_patients_events_in_cols

  ✔ | 18 | count_patients_with_event

  ✔ | 36 | count_patients_with_flags [1.9s]

  ✔ | 24 | count_values
  skipping term strata(ecog.ps)

  ✖ | 1 22 | coxph
  ────────────────────────────────────────────────────────────────────────────────
  Failure ('test-coxph.R:56:3'): try_car_anova works correctly
  Snapshot of code has changed:
  old vs new
  Code
  res
  Output

  • [1] 1.0000000 1.0000000 0.9678110 0.3970066 0.3252267 0.5286392
  • [1] 1.0000000 0.7521316 0.3858022
  • Run testthat::snapshot_accept('coxph') to accept the change.
  • Run testthat::snapshot_review('coxph') to interactively review the change.
    ────────────────────────────────────────────────────────────────────────────────

  ✔ | 74 | coxreg [1.4s]

  ✔ | 1 14 | decorate_grob [1.2s]

  ✔ | 10 | desctools_binom_diff

  ✔ | 19 | df_explicit_na

  ✔ | 10 | estimate_multinom_rsp

  ✔ | 41 | estimate_proportion [1.0s]

  ✔ | 22 | fit_rsp_step

  ✔ | 18 | fit_survival_step

  ✔ | 58 | formatting_functions [1.0s]

  ✔ | 3 18 | g_forest [4.3s]

  ✔ | 9 18 | g_km [5.0s]

  ✔ | 7 12 | g_lineplot [3.0s]

  ✔ | 2 20 | g_step

  ✔ | 2 2 | g_waterfall

  ✔ | 6 | h_adsl_adlb_merge_using_worst_flag

  ✔ | 4 | h_format_row

  ✔ | 10 | h_incidence_rate

  ✔ | 40 | h_km [1.2s]

  ✔ | 88 | h_logistic_regression [1.6s]

  ✔ | 14 | h_map_for_count_abnormal

  ✔ | 4 | h_pkparam_sort

  ✔ | 10 | h_response_biomarkers_subgroups

  ✔ | 29 | h_response_subgroups

  ✔ | 14 | h_stack_by_baskets

  ✔ | 82 | h_step [1.2s]

  ✔ | 12 | h_survival_biomarkers_subgroups

  ✔ | 38 | h_survival_duration_subgroups

  ✔ | 8 | imputation_rule

  ✔ | 20 | incidence_rate [1.0s]

  ✔ | 7 | individual_patient_plot

  ✔ | 28 | logistic_regression [3.1s]

  ✔ | 34 | make_afun

  ✔ | 21 | odds_ratio

  ✔ | 43 | prop_diff

  ✔ | 41 | prune_occurrences [3.2s]

  ✔ | 20 | response_biomarkers_subgroups [2.1s]

  ✔ | 34 | response_subgroups [7.1s]

  ✔ | 26 | rtables_access [2.4s]

  ✔ | 13 | score_occurrences [1.2s]

  ✔ | 34 | split_cols_by_groups [1.3s]

  ✔ | 84 | stat [1.6s]

  ✔ | 20 | summarize_ancova [2.3s]

  ✔ | 12 | summarize_change

  ✔ | 6 | summarize_colvars

  ✔ | 41 | summarize_coxreg [8.2s]

  ✔ | 44 | summarize_glm_count [2.5s]

  ✔ | 50 | summarize_num_patients [3.5s]

  ✔ | 18 | summarize_patients_exposure_in_cols [1.2s]

  ✔ | 19 | survival_biomarkers_subgroups [3.8s]

  ✔ | 17 | survival_coxph_pairwise

  ✔ | 37 | survival_duration_subgroups [7.9s]

  ✔ | 16 | survival_time

  ✔ | 21 | survival_timepoint [1.5s]

  ✔ | 23 | test_proportion_diff [1.1s]

  ✔ | 42 | utils_checkmate

  ✔ | 52 | utils_default_stats_formats_labels

  ✔ | 47 | utils_factor

  ✔ | 3 3 | utils_ggplot

  ✔ | 8 | utils_grid

  ✔ | 59 | utils_rtables [5.7s]

  ✔ | 19 | utils_split_fun [2.1s]

  ✔ | 140 | utils [2.3s]

  ══ Results ═════════════════════════════════════════════════════════════════════
  Duration: 132.7 s

  ── Skipped tests (28) ──────────────────────────────────────────────────────────
  • On CI (28): 'test-bland-altman.R:103:3', 'test-decorate_grob.R:124:3',
  'test-g_forest.R:23:3', 'test-g_forest.R:58:3', 'test-g_forest.R:98:3',
  'test-g_km.R:17:3', 'test-g_km.R:30:3', 'test-g_km.R:42:3',
  'test-g_km.R:64:3', 'test-g_km.R:79:3', 'test-g_km.R:116:3',
  'test-g_km.R:130:3', 'test-g_km.R:149:3', 'test-g_km.R:164:3',
  'test-g_lineplot.R:9:3', 'test-g_lineplot.R:32:3', 'test-g_lineplot.R:52:3',
  'test-g_lineplot.R:71:3', 'test-g_lineplot.R:101:3',
  'test-g_lineplot.R:114:3', 'test-g_lineplot.R:249:3', 'test-g_step.R:18:3',
  'test-g_step.R:28:3', 'test-g_waterfall.R:7:3', 'test-g_waterfall.R:29:3',
  'test-utils_ggplot.R:19:3', 'test-utils_ggplot.R:53:3',
  'test-utils_ggplot.R:59:3'

  ── Failed tests ────────────────────────────────────────────────────────────────
  Failure ('test-coxph.R:56:3'): try_car_anova works correctly
  Snapshot of code has changed:
  old vs new
  Code
  res
  Output

  • [1] 1.0000000 1.0000000 0.9678110 0.3970066 0.3252267 0.5286392
  • [1] 1.0000000 0.7521316 0.3858022
  • Run testthat::snapshot_accept('coxph') to accept the change.
  • Run testthat::snapshot_review('coxph') to interactively review the change.

  [ FAIL 1 | WARN 0 | SKIP 28 | PASS 2293 ]
  Error: Test failures
  Execution halted

• checking PDF version of manual ... OK

• DONE

Status: 1 ERROR
See
‘/builds/nest/automation/systems-integration-tests/tern.Rcheck/00check.log’
for details.