* using log directory ‘/data/localhost/ripley/R/packages/tests-MKL/tern.Rcheck’ * using R Under development (unstable) (2026-10-30 r90795) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) GNU Fortran (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2) * running under: Fedora Linux 44 (Server Edition) * using session charset: UTF-8 * current time: 2026-10-30 11:00:37 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘tern/DESCRIPTION’ ... OK * this is package ‘tern’ version ‘0.9.13’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘tern’ can be installed ... [22s/29s] OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [40s/53s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [76s/194s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [247s/583s] [247s/584s] 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 Attaching package: 'formatters' The following object is masked from 'package:base': %||% 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 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 [1.6s] ✔ | 5 10 | abnormal_by_baseline [1.4s] ✔ | 3 4 | abnormal_by_marked [12.6s] ✔ | 2 3 | abnormal_by_worst_grade ✔ | 8 12 | abnormal_lab_worsen_by_baseline [3.0s] ✔ | 31 83 | analyze_variables [18.3s] ✔ | 7 19 | analyze_vars_in_cols [26.5s] ✔ | 35 | assert_proportion_data ✔ | 2 7 | bland-altman [1.9s] ✔ | 16 | combination_function ✔ | 9 20 | compare_variables [1.5s] ✔ | 1 3 | control_logistic ✔ | 1 4 | control_step ✔ | 3 11 | control_survival ✔ | 8 8 | count_cumulative [1.8s] ✔ | 4 4 | count_missed_doses Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd A.1.1.1.1 -> { dcd A.1.1.1.1, dcd A.1.1.1.1[2], dcd A.1.1.1.1[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd A.1.1.1.2 -> { dcd A.1.1.1.2, dcd A.1.1.1.2[2], dcd A.1.1.1.2[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd B.1.1.1.1 -> { dcd B.1.1.1.1, dcd B.1.1.1.1[2], dcd B.1.1.1.1[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd B.2.1.2.1 -> { dcd B.2.1.2.1, dcd B.2.1.2.1[2], dcd B.2.1.2.1[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd B.2.2.3.1 -> { dcd B.2.2.3.1, dcd B.2.2.3.1[2], dcd B.2.2.3.1[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd C.1.1.1.3 -> { dcd C.1.1.1.3, dcd C.1.1.1.3[2], dcd C.1.1.1.3[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd C.2.1.2.1 -> { dcd C.2.1.2.1, dcd C.2.1.2.1[2], dcd C.2.1.2.1[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd D.1.1.1.1 -> { dcd D.1.1.1.1, dcd D.1.1.1.1[2], dcd D.1.1.1.1[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd D.1.1.4.2 -> { dcd D.1.1.4.2, dcd D.1.1.4.2[2], dcd D.1.1.4.2[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [dcd D.2.1.5.3 -> { dcd D.2.1.5.3, dcd D.2.1.5.3[2], dcd D.2.1.5.3[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [LOW -> { LOW, LOW[2], LOW[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [MEDIUM -> { MEDIUM, MEDIUM[2], MEDIUM[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [HIGH -> { HIGH, HIGH[2], HIGH[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [LOW -> { LOW, LOW[2], LOW[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [MEDIUM -> { MEDIUM, MEDIUM[2], MEDIUM[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [HIGH -> { HIGH, HIGH[2], HIGH[3] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. ✔ | 8 20 | count_occurrences [7.7s] ✔ | 17 27 | count_occurrences_by_grade [9.3s] ✔ | 4 4 | count_patients_events_in_cols [1.2s] ✔ | 8 9 | count_patients_with_event [1.7s] ✔ | 11 18 | count_patients_with_flags [5.7s] ✔ | 11 17 | count_values [2.6s] skipping term strata(ecog.ps) ✔ | 5 15 | coxph ✔ | 24 50 | coxreg [3.4s] ✔ | 2 13 | decorate_grob [3.7s] ✔ | 5 5 | desctools_binom_diff ✔ | 5 26 | df_explicit_na ✔ | 3 7 | estimate_multinomial_rsp ✔ | 18 28 | estimate_proportion [2.4s] ✔ | 3 16 | fit_rsp_step [1.6s] ✔ | 3 12 | fit_survival_step [1.7s] ✔ | 21 40 | formatting_functions [1.4s] ✔ | 14 61 | g_forest [124.6s] ✔ | 9 20 | g_km [38.5s] ✔ | 8 17 | g_lineplot [26.8s] ✔ | 4 16 | g_step [1.5s] ✔ | 2 2 | g_waterfall [1.2s] ✔ | 14 | get_complete_cases ✔ | 5 1 | h_adsl_adlb_merge_using_worst_flag ✔ | 2 5 | h_biomarkers_subgroups ✔ | 1 2 | h_format_row ✔ | 5 5 | h_incidence_rate ✔ | 14 27 | h_km [2.2s] ✔ | 16 62 | h_logistic_regression [1.9s] ✔ | 7 7 | h_map_for_count_abnormal ✔ | 2 2 | h_pkparam_sort ✔ | 1 65 | h_prepare_rsp_table [1.1s] ✔ | 4 4 | h_response_biomarkers_subgroups ✔ | 14 15 | h_response_subgroups [1.3s] ✔ | 3 8 | h_stack_by_baskets ✔ | 8 62 | h_step [2.6s] ✔ | 3 6 | h_survival_biomarkers_subgroups ✔ | 16 20 | h_survival_duration_subgroups [2.2s] ✔ | 2 0 | imputation_rule ✔ | 8 12 | incidence_rate [1.6s] ✔ | 7 | individual_patient_plot [1.4s] ✖ | 6 6 16 | logistic_regression [12.7s] ──────────────────────────────────────────────────────────────────────────────── Failure ('test-logistic_regression.R:23:3'): fit_logistic works with default paramters Expected `result1` to be identical to `expected1`. Differences: actual | expected [1] 4.14313472639153257404 - 4.14313472639153701493 [1] [2] -1.60943791243410116998 - -1.60943791243410383451 [2] [3] 16.42293379401698061315 - 16.42293379401603203860 [3] [4] 1.00790526135793800933 - 1.00790526135793934159 [4] [5] 1.10984054338721538358 - 1.10984054338721604971 [5] [6] 2458.76012225123849930242 - 2458.76012225050408233074 [6] [7] 4.11063905035036647462 - 4.11063905035036558644 [7] [8] -1.45015238632580745204 - -1.45015238632580900635 [8] [9] 0.00667935584500213737 - 0.00667935584500374720 [9] [10] 0.00003945655841248552 - 0.00003945655841248567 [10] ... ... ... and 2 more ... Failure ('test-logistic_regression.R:27:3'): fit_logistic works with default paramters Expected `result2` to be identical to `expected2`. Differences: `actual$Chisq`: 16.8973534022653666 2.1029940605643676 `expected$Chisq`: 16.8973534022653595 2.1029940605643715 `actual$Pr(>Chisq)`: 0.00003945655841248546 0.34941427363094307301 `expected$Pr(>Chisq)`: 0.00003945655841248559 0.34941427363094235137 Failure ('test-logistic_regression.R:31:3'): fit_logistic works with default paramters Expected `result3` to be identical to `expected3`. Differences: actual | expected [1] 1.0158730158730134 - 1.0158730158730158 [1] [2] -1.0158730158730136 - -1.0158730158730156 [2] [3] -1.0158730158730138 - -1.0158730158730154 [3] [4] -1.0158730158730136 - -1.0158730158730156 [4] [5] 1.2317460317460294 - 1.2317460317460311 [5] [6] 1.0158730158730138 - 1.0158730158730149 [6] [7] -1.0158730158730138 - -1.0158730158730154 [7] [8] 1.0158730158730138 - 1.0158730158730149 [8] [9] 6045501.3387729255482554 - 6045501.3387693138793111 [9] Failure ('test-logistic_regression.R:49:3'): fit_logistic works with covariates and interaction Expected `result1` to be identical to `expected1`. Differences: actual | expected [1] -1.341430970099093178 - -1.341430970099083630 [1] [2] -1.421604342788868491 - -1.421604342788867159 [2] [3] 17.536992014031721254 - 17.536992014088145453 [3] [4] 0.161642775722026594 - 0.161642775722026316 [4] [5] 17.825911177600463731 - 17.825911177184245560 [5] [6] 17.202548227956594218 - 17.202548220013873959 [6] [7] 1.018377569273993144 - 1.018377569773041280 [7] [8] -17.926334391418663472 - -17.926334391043805994 [8] [9] -18.105066978493642438 - -18.105066970550925731 [9] [10] -17.102940713284723984 - -17.102940705987148107 [10] ... ... ... and 30 more ... Failure ('test-logistic_regression.R:53:3'): fit_logistic works with covariates and interaction Expected `result2` to be identical to `expected2`. Differences: actual$Chisq | expected$Chisq [1] 0.2081491526896038 - 0.2081491526896005 [1] [2] 1.3718717877957138 - 1.3718717877957043 [2] [3] 2.8678464248651334 - 2.8678464248651174 [3] [4] 0.0000103670008907 - 0.0000103670009894 [4] [5] 0.0000079602555232 - 0.0000079602556304 [5] actual$Pr(>Chisq) | expected$Pr(>Chisq) [1] 0.64822196288278811 - 0.64822196288279077 [1] [2] 0.50361867530179993 - 0.50361867530180227 [2] [3] 0.09036571573813373 - 0.09036571573813448 [3] [4] 0.99999481651298905 - 0.99999481651293953 [4] [5] 0.99999999999207922 - 0.99999999999207934 [5] Failure ('test-logistic_regression.R:57:3'): fit_logistic works with covariates and interaction Expected `result3` to be identical to `expected3`. Differences: actual vs expected [, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [,10] - actual[1, ] 8.64494054 -0.37928337 -5.752307e-01 -0.263196437 -1.176739e+00 -2.981765e-01 6.514350e-01 7.990481e-01 2.723385e-02 -6.081502e-01 + expected[1, ] 8.64494054 -0.37928337 -5.752307e-01 -0.263196437 -1.176739e+00 -2.981765e-01 6.514350e-01 7.990481e-01 2.723382e-02 -6.081502e-01 actual[2, ] -0.37928337 1.47315338 1.082248e+00 -0.022927433 1.029849e+00 1.106382e+00 -1.449446e+00 -1.062751e+00 -1.503821e+00 -1.185334e+00 actual[3, ] -0.57523068 1.08224781 2.727056e+07 -0.016144524 1.033332e+00 1.087224e+00 -1.065554e+00 -2.727056e+07 -1.103844e+00 -2.727056e+07 actual[4, ] -0.26319644 -0.02292743 -1.614452e-02 0.009110804 4.677293e-03 -2.573503e-02 1.350664e-02 8.396864e-03 3.511398e-02 5.710842e-02 actual[5, ] -1.17673939 1.02984949 1.033332e+00 0.004677293 5.176236e+07 1.028407e+00 -5.176236e+07 -5.176236e+07 -1.023592e+00 -1.012301e+00 - actual[6, ] -0.29817653 1.10638240 1.087224e+00 -0.025735027 1.028407e+00 6.999040e+07 -1.079772e+00 -1.065339e+00 -6.999040e+07 -6.999040e+07 + expected[6, ] -0.29817651 1.10638241 1.087224e+00 -0.025735027 1.028407e+00 6.999040e+07 -1.079772e+00 -1.065339e+00 -6.999040e+07 -6.999040e+07 actual[7, ] 0.65143502 -1.44944584 -1.065554e+00 0.013506636 -5.176236e+07 -1.079772e+00 1.084750e+08 5.176236e+07 1.467512e+00 1.126282e+00 actual[8, ] 0.79904809 -1.06275074 -2.727056e+07 0.008396864 -5.176236e+07 -1.065339e+00 5.176236e+07 1.402499e+08 1.073983e+00 2.727056e+07 - actual[9, ] 0.02723385 -1.50382093 -1.103844e+00 0.035113975 -1.023592e+00 -6.999040e+07 1.467512e+00 1.073983e+00 6.999040e+07 6.999040e+07 + expected[9, ] 0.02723382 -1.50382094 -1.103844e+00 0.035113975 -1.023592e+00 -6.999040e+07 1.467512e+00 1.073983e+00 6.999040e+07 6.999040e+07 - actual[10, ] -0.60815015 -1.18533387 -2.727056e+07 0.057108418 -1.012301e+00 -6.999040e+07 1.126282e+00 2.727056e+07 6.999040e+07 1.622024e+08 + expected[10, ] -0.60815018 -1.18533387 -2.727056e+07 0.057108419 -1.012301e+00 -6.999040e+07 1.126282e+00 2.727056e+07 6.999040e+07 1.622024e+08 ──────────────────────────────────────────────────────────────────────────────── ✔ | 7 23 | make_afun ✔ | 64 | mantel_fleiss_crit ✔ | 8 12 | odds_ratio [1.0s] ✔ | 31 101 | prop_diff [5.1s] ✔ | 7 33 | prune_occurrences [10.0s] Modifying subtable (or row) names to ensure uniqueness among direct siblings [root -> { root, root[2] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [biomarker_label -> { biomarker_label, biomarker_label[2] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [root -> { root, root[2] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. ✔ | 6 13 | response_biomarkers_subgroups [8.4s] ✔ | 14 19 | response_subgroups [23.4s] ✔ | 5 15 | rtables_access [12.1s] ✔ | 5 8 | score_occurrences [3.8s] ✔ | 15 19 | split_cols_by_groups [1.9s] ✔ | 9 43 | stat [1.5s] ✔ | 5 35 | summarize_ancova [7.6s] ✔ | 5 7 | summarize_change [1.3s] ✔ | 3 3 | summarize_colvars [1.8s] ✔ | 13 23 | summarize_coxreg [20.5s] ✔ | 17 27 | summarize_glm_count [4.3s] ✔ | 17 27 | summarize_num_patients [3.6s] ✔ | 9 9 | summarize_patients_exposure_in_cols [2.6s] Modifying subtable (or row) names to ensure uniqueness among direct siblings [root -> { root, root[2] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [biomarker_label -> { biomarker_label, biomarker_label[2] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [root -> { root, root[2] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. Modifying subtable (or row) names to ensure uniqueness among direct siblings [root -> { root, root[2] }] To control table names use split_rows_by*(, parent_name =.) or analyze(., table_names = .) when analyzing a single variable, or analyze(., parent_name = .) when analyzing multiple variables in a single call. ✔ | 7 11 | survival_biomarkers_subgroups [8.3s] ✔ | 10 18 | survival_coxph_pairwise [4.4s] ✔ | 14 21 | survival_duration_subgroups [28.8s] ✔ | 7 17 | survival_time [3.4s] ✔ | 10 11 | survival_timepoint [2.4s] ✔ | 19 55 | test_proportion_diff [4.1s] ✔ | 59 86 | utils [4.0s] ✔ | 82 | utils_checkmate [1.5s] ✔ | 6 47 | utils_default_stats_formats_labels ✔ | 13 32 | utils_factor ✔ | 3 10 | utils_ggplot [10.5s] ✔ | 8 | utils_grid [1.0s] ✔ | 19 34 | utils_rtables [15.4s] ✔ | 6 13 | utils_split_fun [7.4s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 543.3 s ── Skipped tests (742) ───────────────────────────────────────────────────────── • On CRAN (742): 'test-abnormal.R:1:1', 'test-abnormal.R:27:1', 'test-abnormal.R:54:1', 'test-abnormal.R:83:1', 'test-abnormal.R:106:1', 'test-abnormal.R:137:1', 'test-abnormal.R:163:1', 'test-abnormal_by_baseline.R:1:1', 'test-abnormal_by_baseline.R:28:1', 'test-abnormal_by_baseline.R:59:1', 'test-abnormal_by_baseline.R:83:1', 'test-abnormal_by_baseline.R:97:1', 'test-abnormal_by_marked.R:28:1', 'test-abnormal_by_marked.R:83:1', 'test-abnormal_by_marked.R:192:1', 'test-abnormal_by_worst_grade.R:19:1', 'test-abnormal_by_worst_grade.R:46:1', 'test-abnormal_lab_worsen_by_baseline.R:12:1', 'test-abnormal_lab_worsen_by_baseline.R:67:1', 'test-abnormal_lab_worsen_by_baseline.R:85:1', 'test-abnormal_lab_worsen_by_baseline.R:105:1', 'test-abnormal_lab_worsen_by_baseline.R:125:1', 'test-abnormal_lab_worsen_by_baseline.R:145:1', 'test-abnormal_lab_worsen_by_baseline.R:165:1', 'test-abnormal_lab_worsen_by_baseline.R:187:1', 'test-analyze_variables.R:1:1', 'test-analyze_variables.R:10:1', 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'test-summarize_colvars.R:17:1', 'test-summarize_colvars.R:31:1', 'test-summarize_colvars.R:46:1', 'test-summarize_coxreg.R:28:1', 'test-summarize_coxreg.R:39:1', 'test-summarize_coxreg.R:51:1', 'test-summarize_coxreg.R:65:1', 'test-summarize_coxreg.R:81:1', 'test-summarize_coxreg.R:122:1', 'test-summarize_coxreg.R:134:1', 'test-summarize_coxreg.R:148:1', 'test-summarize_coxreg.R:163:1', 'test-summarize_coxreg.R:176:1', 'test-summarize_coxreg.R:188:1', 'test-summarize_coxreg.R:202:1', 'test-summarize_coxreg.R:232:1', 'test-summarize_glm_count.R:1:1', 'test-summarize_glm_count.R:21:1', 'test-summarize_glm_count.R:56:1', 'test-summarize_glm_count.R:76:1', 'test-summarize_glm_count.R:93:1', 'test-summarize_glm_count.R:113:1', 'test-summarize_glm_count.R:147:1', 'test-summarize_glm_count.R:167:1', 'test-summarize_glm_count.R:201:1', 'test-summarize_glm_count.R:222:1', 'test-summarize_glm_count.R:257:1', 'test-summarize_glm_count.R:305:1', 'test-summarize_glm_count.R:327:1', 'test-summarize_glm_count.R:349:1', 'test-summarize_glm_count.R:373:1', 'test-summarize_glm_count.R:411:1', 'test-summarize_glm_count.R:442:1', 'test-summarize_num_patients.R:1:1', 'test-summarize_num_patients.R:9:1', 'test-summarize_num_patients.R:17:1', 'test-summarize_num_patients.R:25:1', 'test-summarize_num_patients.R:36:1', 'test-summarize_num_patients.R:84:1', 'test-summarize_num_patients.R:93:1', 'test-summarize_num_patients.R:102:1', 'test-summarize_num_patients.R:111:1', 'test-summarize_num_patients.R:122:1', 'test-summarize_num_patients.R:133:1', 'test-summarize_num_patients.R:144:1', 'test-summarize_num_patients.R:192:1', 'test-summarize_num_patients.R:212:1', 'test-summarize_num_patients.R:229:1', 'test-summarize_num_patients.R:276:1', 'test-summarize_num_patients.R:305:1', 'test-summarize_patients_exposure_in_cols.R:17:1', 'test-summarize_patients_exposure_in_cols.R:26:1', 'test-summarize_patients_exposure_in_cols.R:39:1', 'test-summarize_patients_exposure_in_cols.R:53:1', 'test-summarize_patients_exposure_in_cols.R:76:1', 'test-summarize_patients_exposure_in_cols.R:100:1', 'test-summarize_patients_exposure_in_cols.R:113:1', 'test-summarize_patients_exposure_in_cols.R:130:1', 'test-summarize_patients_exposure_in_cols.R:149:1', 'test-survival_biomarkers_subgroups.R:22:1', 'test-survival_biomarkers_subgroups.R:39:1', 'test-survival_biomarkers_subgroups.R:70:1', 'test-survival_biomarkers_subgroups.R:91:1', 'test-survival_biomarkers_subgroups.R:108:1', 'test-survival_biomarkers_subgroups.R:132:1', 'test-survival_biomarkers_subgroups.R:156:1', 'test-survival_coxph_pairwise.R:1:1', 'test-survival_coxph_pairwise.R:20:1', 'test-survival_coxph_pairwise.R:39:1', 'test-survival_coxph_pairwise.R:58:1', 'test-survival_coxph_pairwise.R:77:1', 'test-survival_coxph_pairwise.R:134:1', 'test-survival_coxph_pairwise.R:156:1', 'test-survival_coxph_pairwise.R:179:1', 'test-survival_coxph_pairwise.R:201:1', 'test-survival_coxph_pairwise.R:264:1', 'test-survival_duration_subgroups.R:24:1', 'test-survival_duration_subgroups.R:36:1', 'test-survival_duration_subgroups.R:59:1', 'test-survival_duration_subgroups.R:71:1', 'test-survival_duration_subgroups.R:91:1', 'test-survival_duration_subgroups.R:106:1', 'test-survival_duration_subgroups.R:121:1', 'test-survival_duration_subgroups.R:138:1', 'test-survival_duration_subgroups.R:157:1', 'test-survival_duration_subgroups.R:200:1', 'test-survival_duration_subgroups.R:214:1', 'test-survival_duration_subgroups.R:233:1', 'test-survival_duration_subgroups.R:253:1', 'test-survival_duration_subgroups.R:271:1', 'test-survival_time.R:1:1', 'test-survival_time.R:19:1', 'test-survival_time.R:40:1', 'test-survival_time.R:61:1', 'test-survival_time.R:88:1', 'test-survival_time.R:111:1', 'test-survival_time.R:135:1', 'test-survival_timepoint.R:1:1', 'test-survival_timepoint.R:20:1', 'test-survival_timepoint.R:42:1', 'test-survival_timepoint.R:64:1', 'test-survival_timepoint.R:89:1', 'test-survival_timepoint.R:115:1', 'test-survival_timepoint.R:140:1', 'test-survival_timepoint.R:165:1', 'test-survival_timepoint.R:191:1', 'test-survival_timepoint.R:218:1', 'test-test_proportion_diff.R:1:1', 'test-test_proportion_diff.R:23:1', 'test-test_proportion_diff.R:58:1', 'test-test_proportion_diff.R:93:1', 'test-test_proportion_diff.R:118:1', 'test-test_proportion_diff.R:140:1', 'test-test_proportion_diff.R:166:1', 'test-test_proportion_diff.R:191:1', 'test-test_proportion_diff.R:260:1', 'test-test_proportion_diff.R:305:1', 'test-test_proportion_diff.R:329:1', 'test-test_proportion_diff.R:425:1', 'test-test_proportion_diff.R:445:1', 'test-test_proportion_diff.R:467:1', 'test-test_proportion_diff.R:485:1', 'test-test_proportion_diff.R:503:1', 'test-test_proportion_diff.R:523:1', 'test-test_proportion_diff.R:545:1', 'test-test_proportion_diff.R:567:1', 'test-utils.R:1:1', 'test-utils.R:13:1', 'test-utils.R:25:1', 'test-utils.R:33:1', 'test-utils.R:52:1', 'test-utils.R:60:1', 'test-utils.R:68:1', 'test-utils.R:89:1', 'test-utils.R:99:1', 'test-utils.R:108:1', 'test-utils.R:116:1', 'test-utils.R:162:1', 'test-utils.R:174:1', 'test-utils.R:183:1', 'test-utils.R:192:1', 'test-utils.R:204:1', 'test-utils.R:215:1', 'test-utils.R:224:1', 'test-utils.R:236:1', 'test-utils.R:248:1', 'test-utils.R:259:1', 'test-utils.R:268:1', 'test-utils.R:280:1', 'test-utils.R:292:1', 'test-utils.R:303:1', 'test-utils.R:312:1', 'test-utils.R:324:1', 'test-utils.R:336:1', 'test-utils.R:347:1', 'test-utils.R:356:1', 'test-utils.R:368:1', 'test-utils.R:380:1', 'test-utils.R:391:1', 'test-utils.R:400:1', 'test-utils.R:412:1', 'test-utils.R:424:1', 'test-utils.R:438:1', 'test-utils.R:447:1', 'test-utils.R:459:1', 'test-utils.R:471:1', 'test-utils.R:494:1', 'test-utils.R:506:1', 'test-utils.R:518:1', 'test-utils.R:532:1', 'test-utils.R:541:1', 'test-utils.R:553:1', 'test-utils.R:565:1', 'test-utils.R:576:1', 'test-utils.R:585:1', 'test-utils.R:597:1', 'test-utils.R:609:1', 'test-utils.R:623:1', 'test-utils.R:632:1', 'test-utils.R:644:1', 'test-utils.R:656:1', 'test-utils.R:670:1', 'test-utils.R:679:1', 'test-utils.R:691:1', 'test-utils.R:703:1', 'test-utils_default_stats_formats_labels.R:1:1', 'test-utils_default_stats_formats_labels.R:110:1', 'test-utils_default_stats_formats_labels.R:204:1', 'test-utils_default_stats_formats_labels.R:222:1', 'test-utils_default_stats_formats_labels.R:236:1', 'test-utils_default_stats_formats_labels.R:246:1', 'test-utils_factor.R:17:1', 'test-utils_factor.R:28:1', 'test-utils_factor.R:47:1', 'test-utils_factor.R:56:1', 'test-utils_factor.R:69:1', 'test-utils_factor.R:82:1', 'test-utils_factor.R:89:1', 'test-utils_factor.R:110:1', 'test-utils_factor.R:133:1', 'test-utils_factor.R:143:1', 'test-utils_factor.R:154:1', 'test-utils_factor.R:162:1', 'test-utils_factor.R:170:1', 'test-utils_ggplot.R:1:1', 'test-utils_ggplot.R:34:1', 'test-utils_ggplot.R:90:1', 'test-utils_rtables.R:1:1', 'test-utils_rtables.R:39:1', 'test-utils_rtables.R:47:1', 'test-utils_rtables.R:55:1', 'test-utils_rtables.R:69:1', 'test-utils_rtables.R:83:1', 'test-utils_rtables.R:90:1', 'test-utils_rtables.R:97:1', 'test-utils_rtables.R:107:1', 'test-utils_rtables.R:122:1', 'test-utils_rtables.R:147:1', 'test-utils_rtables.R:162:1', 'test-utils_rtables.R:172:1', 'test-utils_rtables.R:192:1', 'test-utils_rtables.R:205:1', 'test-utils_rtables.R:224:1', 'test-utils_rtables.R:231:1', 'test-utils_rtables.R:238:1', 'test-utils_rtables.R:252:1', 'test-utils_split_fun.R:9:1', 'test-utils_split_fun.R:30:1', 'test-utils_split_fun.R:42:1', 'test-utils_split_fun.R:59:1', 'test-utils_split_fun.R:77:1', 'test-utils_split_fun.R:105:1' ── Failed tests ──────────────────────────────────────────────────────────────── Failure ('test-logistic_regression.R:23:3'): fit_logistic works with default paramters Expected `result1` to be identical to `expected1`. Differences: actual | expected [1] 4.14313472639153257404 - 4.14313472639153701493 [1] [2] -1.60943791243410116998 - -1.60943791243410383451 [2] [3] 16.42293379401698061315 - 16.42293379401603203860 [3] [4] 1.00790526135793800933 - 1.00790526135793934159 [4] [5] 1.10984054338721538358 - 1.10984054338721604971 [5] [6] 2458.76012225123849930242 - 2458.76012225050408233074 [6] [7] 4.11063905035036647462 - 4.11063905035036558644 [7] [8] -1.45015238632580745204 - -1.45015238632580900635 [8] [9] 0.00667935584500213737 - 0.00667935584500374720 [9] [10] 0.00003945655841248552 - 0.00003945655841248567 [10] ... ... ... and 2 more ... Failure ('test-logistic_regression.R:27:3'): fit_logistic works with default paramters Expected `result2` to be identical to `expected2`. Differences: `actual$Chisq`: 16.8973534022653666 2.1029940605643676 `expected$Chisq`: 16.8973534022653595 2.1029940605643715 `actual$Pr(>Chisq)`: 0.00003945655841248546 0.34941427363094307301 `expected$Pr(>Chisq)`: 0.00003945655841248559 0.34941427363094235137 Failure ('test-logistic_regression.R:31:3'): fit_logistic works with default paramters Expected `result3` to be identical to `expected3`. Differences: actual | expected [1] 1.0158730158730134 - 1.0158730158730158 [1] [2] -1.0158730158730136 - -1.0158730158730156 [2] [3] -1.0158730158730138 - -1.0158730158730154 [3] [4] -1.0158730158730136 - -1.0158730158730156 [4] [5] 1.2317460317460294 - 1.2317460317460311 [5] [6] 1.0158730158730138 - 1.0158730158730149 [6] [7] -1.0158730158730138 - -1.0158730158730154 [7] [8] 1.0158730158730138 - 1.0158730158730149 [8] [9] 6045501.3387729255482554 - 6045501.3387693138793111 [9] Failure ('test-logistic_regression.R:49:3'): fit_logistic works with covariates and interaction Expected `result1` to be identical to `expected1`. Differences: actual | expected [1] -1.341430970099093178 - -1.341430970099083630 [1] [2] -1.421604342788868491 - -1.421604342788867159 [2] [3] 17.536992014031721254 - 17.536992014088145453 [3] [4] 0.161642775722026594 - 0.161642775722026316 [4] [5] 17.825911177600463731 - 17.825911177184245560 [5] [6] 17.202548227956594218 - 17.202548220013873959 [6] [7] 1.018377569273993144 - 1.018377569773041280 [7] [8] -17.926334391418663472 - -17.926334391043805994 [8] [9] -18.105066978493642438 - -18.105066970550925731 [9] [10] -17.102940713284723984 - -17.102940705987148107 [10] ... ... ... and 30 more ... Failure ('test-logistic_regression.R:53:3'): fit_logistic works with covariates and interaction Expected `result2` to be identical to `expected2`. Differences: actual$Chisq | expected$Chisq [1] 0.2081491526896038 - 0.2081491526896005 [1] [2] 1.3718717877957138 - 1.3718717877957043 [2] [3] 2.8678464248651334 - 2.8678464248651174 [3] [4] 0.0000103670008907 - 0.0000103670009894 [4] [5] 0.0000079602555232 - 0.0000079602556304 [5] actual$Pr(>Chisq) | expected$Pr(>Chisq) [1] 0.64822196288278811 - 0.64822196288279077 [1] [2] 0.50361867530179993 - 0.50361867530180227 [2] [3] 0.09036571573813373 - 0.09036571573813448 [3] [4] 0.99999481651298905 - 0.99999481651293953 [4] [5] 0.99999999999207922 - 0.99999999999207934 [5] Failure ('test-logistic_regression.R:57:3'): fit_logistic works with covariates and interaction Expected `result3` to be identical to `expected3`. Differences: actual vs expected [, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [,10] - actual[1, ] 8.64494054 -0.37928337 -5.752307e-01 -0.263196437 -1.176739e+00 -2.981765e-01 6.514350e-01 7.990481e-01 2.723385e-02 -6.081502e-01 + expected[1, ] 8.64494054 -0.37928337 -5.752307e-01 -0.263196437 -1.176739e+00 -2.981765e-01 6.514350e-01 7.990481e-01 2.723382e-02 -6.081502e-01 actual[2, ] -0.37928337 1.47315338 1.082248e+00 -0.022927433 1.029849e+00 1.106382e+00 -1.449446e+00 -1.062751e+00 -1.503821e+00 -1.185334e+00 actual[3, ] -0.57523068 1.08224781 2.727056e+07 -0.016144524 1.033332e+00 1.087224e+00 -1.065554e+00 -2.727056e+07 -1.103844e+00 -2.727056e+07 actual[4, ] -0.26319644 -0.02292743 -1.614452e-02 0.009110804 4.677293e-03 -2.573503e-02 1.350664e-02 8.396864e-03 3.511398e-02 5.710842e-02 actual[5, ] -1.17673939 1.02984949 1.033332e+00 0.004677293 5.176236e+07 1.028407e+00 -5.176236e+07 -5.176236e+07 -1.023592e+00 -1.012301e+00 - actual[6, ] -0.29817653 1.10638240 1.087224e+00 -0.025735027 1.028407e+00 6.999040e+07 -1.079772e+00 -1.065339e+00 -6.999040e+07 -6.999040e+07 + expected[6, ] -0.29817651 1.10638241 1.087224e+00 -0.025735027 1.028407e+00 6.999040e+07 -1.079772e+00 -1.065339e+00 -6.999040e+07 -6.999040e+07 actual[7, ] 0.65143502 -1.44944584 -1.065554e+00 0.013506636 -5.176236e+07 -1.079772e+00 1.084750e+08 5.176236e+07 1.467512e+00 1.126282e+00 actual[8, ] 0.79904809 -1.06275074 -2.727056e+07 0.008396864 -5.176236e+07 -1.065339e+00 5.176236e+07 1.402499e+08 1.073983e+00 2.727056e+07 - actual[9, ] 0.02723385 -1.50382093 -1.103844e+00 0.035113975 -1.023592e+00 -6.999040e+07 1.467512e+00 1.073983e+00 6.999040e+07 6.999040e+07 + expected[9, ] 0.02723382 -1.50382094 -1.103844e+00 0.035113975 -1.023592e+00 -6.999040e+07 1.467512e+00 1.073983e+00 6.999040e+07 6.999040e+07 - actual[10, ] -0.60815015 -1.18533387 -2.727056e+07 0.057108418 -1.012301e+00 -6.999040e+07 1.126282e+00 2.727056e+07 6.999040e+07 1.622024e+08 + expected[10, ] -0.60815018 -1.18533387 -2.727056e+07 0.057108419 -1.012301e+00 -6.999040e+07 1.126282e+00 2.727056e+07 6.999040e+07 1.622024e+08 [ FAIL 6 | WARN 0 | SKIP 742 | PASS 1935 ] Error: ! Test failures. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [58s/151s] OK * checking PDF version of manual ... [17s/41s] OK * checking HTML version of manual ... [13s/31s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/localhost/ripley/R/packages/tests-MKL/tern.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 20:24.71, 527.19 + 24.13