prep for rspm release 0.9.6, [skip vbump]

[shajoezhu]

close #1310

[github-actions]

Unit Tests Summary

    1 files     84 suites   1m 11s ⏱️
  855 tests   843 ✅  12 💤 0 ❌
1 836 runs  1 154 ✅ 682 💤 0 ❌

Results for commit cb513d9.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
analyze_vars_in_cols	💔	$2.43$	$+3.15$	$+17$	$-7$	$0$	$0$
count_occurrences	💔	$0.74$	$+1.61$	$+10$	$-8$	$0$	$0$
summarize_coxreg	💔	$3.08$	$+2.43$	$+13$	$-13$	$0$	$0$
summarize_num_patients	💔	$1.06$	$+1.14$	$+18$	$-16$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
analyze_vars_in_cols	💔	$0.48$	$+1.45$	summarize_works_with_nested_analyze
summarize_coxreg	💔	$0.44$	$+1.07$	summarize_coxreg_adds_the_multivariate_Cox_regression_layer_to_rtables

Results for commit b65c62a

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      65       0  100.00%
R/abnormal_by_marked.R                        55       5  90.91%   92-96
R/abnormal_by_worst_grade_worsen.R           116       3  97.41%   262-264
R/abnormal_by_worst_grade.R                   60       0  100.00%
R/abnormal.R                                  43       0  100.00%
R/analyze_variables.R                        166       2  98.80%   492, 632
R/analyze_vars_in_cols.R                     176      13  92.61%   178, 221, 235-236, 244-252
R/bland_altman.R                              92       1  98.91%   43
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                         84       2  97.62%   255, 314
R/control_incidence_rate.R                    10       0  100.00%
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                          50       1  98.00%   73
R/count_missed_doses.R                        34       0  100.00%
R/count_occurrences_by_grade.R               113       1  99.12%   166
R/count_occurrences.R                        115       1  99.13%   115
R/count_patients_events_in_cols.R             67       1  98.51%   59
R/count_patients_with_event.R                 47       0  100.00%
R/count_patients_with_flags.R                 58       0  100.00%
R/count_values.R                              27       0  100.00%
R/cox_regression_inter.R                     154       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    167       7  95.81%   191-195, 238, 253, 261, 267-268
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            113       0  100.00%
R/desctools_binom_diff.R                     621      64  89.69%   53, 88-89, 125-126, 129, 199, 223-232, 264, 266, 286, 290, 294, 298, 353, 356, 359, 362, 422, 430, 439, 444-447, 454, 457, 466, 469, 516-517, 519-520, 522-523, 525-526, 593, 604-616, 620, 663, 676, 680
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  50       1  98.00%   64
R/estimate_proportion.R                      205      11  94.63%   82-89, 93, 98, 319, 485
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     183       2  98.91%   143, 278
R/g_forest.R                                 585      59  89.91%   241, 253-256, 261-262, 278, 288-291, 336-339, 346, 415, 502, 515, 519-520, 525-526, 539, 555, 602, 633, 708, 717, 723, 742, 797-817, 820, 831, 850, 905, 908, 1043-1048
R/g_ipp.R                                    133       0  100.00%
R/g_km.R                                     350      57  83.71%   286-289, 308-310, 364-367, 401, 429, 433-476, 483-487
R/g_lineplot.R                               243      22  90.95%   196, 370-377, 416-426, 518, 526
R/g_step.R                                    68       1  98.53%   109
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        73       0  100.00%
R/h_biomarkers_subgroups.R                    46       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_incidence_rate.R                          45       0  100.00%
R/h_km.R                                     508      41  91.93%   137, 189-194, 287, 378, 380-381, 392-394, 413, 420-421, 423-425, 433-435, 460, 465-468, 651-654, 1108-1119
R/h_logistic_regression.R                    468       3  99.36%   203-204, 273
R/h_map_for_count_abnormal.R                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           90      12  86.67%   50-55, 107-112
R/h_response_subgroups.R                     178      18  89.89%   257-270, 329-334
R/h_stack_by_baskets.R                        64       1  98.44%   89
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           88       6  93.18%   111-116
R/h_survival_duration_subgroups.R            207      18  91.30%   259-271, 336-341
R/imputation_rule.R                           17       0  100.00%
R/incidence_rate.R                            86       7  91.86%   66-71, 151
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               109       0  100.00%
R/prop_diff_test.R                            91       0  100.00%
R/prop_diff.R                                265      15  94.34%   69-72, 104, 289-296, 439, 604
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R             69       6  91.30%   196-201
R/response_subgroups.R                       213       8  96.24%   100-105, 260-261
R/riskdiff.R                                  65       5  92.31%   102-105, 114
R/rtables_access.R                            38       0  100.00%
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      59       0  100.00%
R/summarize_ancova.R                         106       2  98.11%   182, 187
R/summarize_change.R                          30       0  100.00%
R/summarize_colvars.R                         10       0  100.00%
R/summarize_coxreg.R                         172       0  100.00%
R/summarize_glm_count.R                      209       3  98.56%   192-193, 489
R/summarize_num_patients.R                    94       4  95.74%   116-118, 265
R/summarize_patients_exposure_in_cols.R       96       1  98.96%   55
R/survival_biomarkers_subgroups.R             78       6  92.31%   117-122
R/survival_coxph_pairwise.R                   79      11  86.08%   50-51, 63-71
R/survival_duration_subgroups.R              211       6  97.16%   124-129
R/survival_time.R                             79       0  100.00%
R/survival_timepoint.R                       113       7  93.81%   124-130
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       124       0  100.00%
R/utils_factor.R                             109       2  98.17%   84, 302
R/utils_ggplot.R                             110       0  100.00%
R/utils_grid.R                               126       5  96.03%   164, 279-286
R/utils_rtables.R                            100       4  96.00%   39, 46, 403-404
R/utils_split_funs.R                          52       2  96.15%   82, 94
R/utils.R                                    141       7  95.04%   118, 121, 124, 128, 137-138, 332
TOTAL                                      10514     459  95.63%

Diff against main

Filename              Stmts    Miss  Cover
------------------  -------  ------  -------
R/incidence_rate.R       +2      +2  -2.19%
TOTAL                    +2      +2  -0.02%

Results for commit: cb513d9

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[Melkiades]

Lgtm! Thanks Joe

[shajoezhu]

• using log directory 'd:/RCompile/CRANguest/R-devel/tern.Rcheck'
• using R Under development (unstable) (2024-09-21 r87186 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by
  gcc.exe (GCC) 13.2.0
  GNU Fortran (GCC) 13.2.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• checking for file 'tern/DESCRIPTION' ... OK
• this is package 'tern' version '0.9.6'
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [19s] NOTE
  Maintainer: 'Joe Zhu joe.zhu@roche.com'

Found the following (possibly) invalid URLs:
URL: https://insightsengineering.github.io/rtables/latest-tag/articles/introduction.html
From: inst/doc/tables.html
inst/doc/tern.html
Status: 404
Message: Not Found

• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'tern' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [50s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE
  Found the following Rd file(s) with Rd \link{} targets missing package
  anchors:
  control_riskdiff.Rd: list_valid_format_labels
  summarize_colvars.Rd: split_cols_by, split_cols_by_multivar
  Please provide package anchors for all Rd \link{} targets not in the
  package itself and the base packages.
• 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 ... [97s] OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [119s] OK
  Running 'testthat.R' [119s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [16s] OK
• checking PDF version of manual ... [39s] OK
• checking HTML version of manual ... [39s] OK
• DONE
  Status: 2 NOTEs

[shajoezhu]

✔ | 6 | aet05_all [3.5s]
✔ | 6 | aet05 [3.3s]