Check as-cran + default landing page

[arkadiuszbeer]

Solves these two issues:
https://github.com/insightsengineering/idr-tasks/issues/477
https://github.com/insightsengineering/idr-tasks/issues/478

[github-actions]

Unit Tests Summary

       1 files    77 suites   1m 31s ⏱️
   719 tests 719 ✔️     0 💤 0 ❌
1 532 runs  966 ✔️ 566 💤 0 ❌

Results for commit 98cbccd.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
abnormal_by_marked	💔	$41.04$	$+5.44$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
abnormal_by_marked	💔	$7.53$	$+1.07$	count_abnormal_by_marked_works_as_expected
abnormal_by_marked	💔	$7.21$	$+1.08$	s_count_abnormal_by_marked_returns_an_error_when_abn_dir_contains_two_direction_values
abnormal_by_marked	💔	$26.31$	$+3.29$	s_count_abnormal_by_marked_works_as_expected

Results for commit c6daa55

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      63       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   124-128
R/abnormal_by_worst_grade_worsen.R           113       3  97.35%   234-236
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/analyze_vars_in_cols.R                      37       1  97.30%   114
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        138       3  97.83%   133, 243, 260
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                          47       1  97.87%   60
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       6  92.86%   152-154, 157, 172-173
R/count_occurrences.R                         61       1  98.36%   89
R/count_patients_events_in_cols.R             67       1  98.51%   72
R/count_patients_with_event.R                 72       0  100.00%
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     142       6  95.77%   92, 172-176
R/cox_regression.R                           208      11  94.71%   367-375, 394-396
R/coxph.R                                    168       7  95.83%   224-228, 272, 287, 295, 301-302
R/d_pkparam.R                                405       0  100.00%
R/decorate_grob.R                            167       6  96.41%   269-275, 382, 414, 424, 431
R/desctools_binom_diff.R                     668      68  89.82%   65, 100-101, 141-142, 145, 224, 250-261, 300, 302, 322, 326, 330, 334, 386, 389, 392, 395, 456, 464, 476-477, 483-486, 494, 497, 506, 509, 557-558, 560-561, 563-564, 566-567, 640, 652-665, 670, 717, 730, 734
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   56
R/estimate_proportion.R                      198      11  94.44%   74-81, 85, 90, 458, 565
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/footnotes.R                                 11       0  100.00%
R/formats.R                                  115       3  97.39%   101, 138, 148
R/g_forest.R                                 437      23  94.74%   199, 250-251, 318, 335-336, 341-342, 355, 371, 418, 449, 525, 534, 615-619, 629, 697, 700, 824
R/g_lineplot.R                               199      29  85.43%   175, 188, 216, 242-245, 322-329, 347-348, 354-364, 462, 470
R/g_step.R                                    68       1  98.53%   107
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        74       0  100.00%
R/h_biomarkers_subgroups.R                    38       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_logistic_regression.R                    468       3  99.36%   197-198, 265
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           74       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   244-257
R/h_stack_by_baskets.R                        65       1  98.46%   94
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           78       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   250-262
R/incidence_rate.R                            93       7  92.47%   68-75
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        532      29  94.55%   256-260, 455, 622-624, 632-634, 660, 667-668, 839, 1020, 1258-1269
R/logistic_regression.R                      101       0  100.00%
R/missing_data.R                              21       3  85.71%   30, 61, 71
R/odds_ratio.R                               106       0  100.00%
R/prop_diff_test.R                            87       0  100.00%
R/prop_diff.R                                255      12  95.29%   95, 250-257, 398, 461, 572
R/prune_occurrences.R                         57      10  82.46%   130-134, 174-178
R/response_biomarkers_subgroups.R             59       0  100.00%
R/response_subgroups.R                       164       4  97.56%   263, 305-307
R/rtables_access.R                            36       2  94.44%   143-144
R/score_occurrences.R                         20       1  95.00%   114
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       3  93.62%   76-77, 132
R/summarize_ancova.R                          95       1  98.95%   187
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_glm_count.R                      164       4  97.56%   181, 186, 249, 318
R/summarize_num_patients.R                    67       5  92.54%   95-97, 189-190
R/summarize_patients_exposure_in_cols.R       46       0  100.00%
R/summarize_variables.R                      212       2  99.06%   264, 467
R/survival_biomarkers_subgroups.R             59       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   66-74
R/survival_duration_subgroups.R              171       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       114       7  93.86%   145-151
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              87       1  98.85%   93
R/utils_grid.R                               111       5  95.50%   148, 257-263
R/utils_rtables.R                             84       7  91.67%   25, 32-36, 344-345
R/utils.R                                    137      10  92.70%   100, 102, 106, 126, 129, 132, 136, 145-146, 332
TOTAL                                       8767     338  96.14%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 3a2fdfb

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[Melkiades]

Noice!!! 👍

[pawelru]

Let me jump into this PR as tern is the closest to CRAN submission.
My long term goal for this exercise is to find collection of env vars so that R CMD CHECK has zero notes and then we can fail our check-GHA on error, warning and notes. Currently there are some warning/notes that needs to be fixed so here in this PR I would like to achieve the state of leaving only fixable notes.

At the current state we have the following:

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Joe Zhu <[email protected]>’

Version contains large components (0.7.10.9042)

We can't avoid that until we release to CRAN. For some of the packages that would take some time. Therefore I propose to silent this note.
This consists of two parts - large version components as well as new maintainer. I looked into the source code of R and I have found that there might be a env var that could silent it - _R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_. However, I cannot find any(!) documentation about this so I might be wrong. For the latter part - there is a _R_CHECK_CRAN_INCOMING_ env var. It might happen that setting this one would also disable large version check so I would suggest to check this one first.

* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb

This note is acceptable thus I propose to silent it. There are two env vars for it: _R_CHECK_PKG_SIZES_ and _R_CHECK_PKG_SIZES_THRESHOLD_.

* checking Rd line widths ... NOTE
Rd file 'h_adsl_adlb_merge_using_worst_flag.Rd':
  \examples lines wider than 100 characters:
     adlb_out <- h_adsl_adlb_merge_using_worst_flag(tern_ex_adsl, tern_ex_adlb, worst_flag = c("WGRHIFL" = "Y"))

These lines will be truncated in the PDF manual.

This is fixable hence let's leave it.

[shajoezhu]

approve pr to unblock merging

[pawelru]

This comment is more for r.pkg.template than tern itself.

I tried to read log output to check if correctness. According to these lines I was looking for prints of env var used but I cannot find it here. In particular, I am looking for a line with _R_CHECK_CRAN_INCOMING_REMOTE_=false as specified in this PR. There are only prints of env vars set on workflow definition level,

[pawelru]

Let me jump into this PR as tern is the closest to CRAN submission. My long term goal for this exercise is to find collection of env vars so that R CMD CHECK has zero notes and then we can fail our check-GHA on error, warning and notes. Currently there are some warning/notes that needs to be fixed so here in this PR I would like to achieve the state of leaving only fixable notes.

At the current state we have the following:

* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Joe Zhu <[email protected]>’

Version contains large components (0.7.10.9042)

We can't avoid that until we release to CRAN. For some of the packages that would take some time. Therefore I propose to silent this note. This consists of two parts - large version components as well as new maintainer. I looked into the source code of R and I have found that there might be a env var that could silent it - _R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_. However, I cannot find any(!) documentation about this so I might be wrong. For the latter part - there is a _R_CHECK_CRAN_INCOMING_ env var. It might happen that setting this one would also disable large version check so I would suggest to check this one first.

* checking installed package size ... NOTE
  installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb

This note is acceptable thus I propose to silent it. There are two env vars for it: _R_CHECK_PKG_SIZES_ and _R_CHECK_PKG_SIZES_THRESHOLD_.

* checking Rd line widths ... NOTE
Rd file 'h_adsl_adlb_merge_using_worst_flag.Rd':
  \examples lines wider than 100 characters:
     adlb_out <- h_adsl_adlb_merge_using_worst_flag(tern_ex_adsl, tern_ex_adlb, worst_flag = c("WGRHIFL" = "Y"))

These lines will be truncated in the PDF manual.

This is fixable hence let's leave it.

I am sorry. I tend to confuse this issue scope with the one we have already discussed some time ago - https://github.com/insightsengineering/idr-tasks/issues/266. The blocklist mentioned there is the way how to implement fails on notes. Let's stick to the initial scope of the issue which is enabling --as-cran alongside with env var removing one check that resulted in warning. This has been correctly done. I will create a separate issue to populate note blocklist.