Adds min package version #1012

averissimo · 2023-07-26T06:49:42Z

WIP :: parent issue: insightsengineering/nestdevs-tasks#7

Supersede:

specify minimal version of dependencies #957

🔴 Checklist for PR Reviewer

(~~max strategy fails due to tidyverse/ggplot2#5436~~ corrected upstream)

Tag yourself next to this repo on Specify minimal version dependencies + add action nestdevs-tasks#7
Package versions are the same or higher than main
Package list is the same
- Only exception is rmarkdown (may have been removed on Suggests)
All packages in Imports, Depends & Suggests are in new section Config/Needs/verdepcheck
Added entry to NEWS.md
Last scheduled.yaml action was run succesfully (all 4 strategies)
- important: it's not the last commit, it's the one that runs 4 Scheduled 🕰️ / Dependency actions
scheduled.yaml SHOULD NOT have any push on any branches

🔴 What's needed before merging?

This PR depends on some upstream changes that need to be finalized/merged before being ready to review.

Change in code

verdepcheck.yml action (see comments)
- Remove on: push section
- Change branch to main

PRS

verdepcheck
- Training verdepcheck#24
- Fixes and improvements for strategies verdepcheck#26
verdepcheck-action
- Supports new strategies min_isolated and min_cohort r-verdepcheck-action#16

Changes description

Adds minimum version for packages DESCRIPTION
Adds Config/Need/verdepcheck section in DESCRIPTION
Updates verdepcheck action

DESCRIPTION

github-actions · 2023-09-26T11:35:58Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      67       2  97.01%   76-77
R/abnormal_by_marked.R                        54       5  90.74%   115-119
R/abnormal_by_worst_grade_worsen.R           115       3  97.39%   233-235
R/abnormal_by_worst_grade.R                   39       0  100.00%
R/abnormal.R                                  42       0  100.00%
R/analyze_variables.R                        199       9  95.48%   476-477, 493, 696-697, 702-703, 721-722
R/analyze_vars_in_cols.R                     176      34  80.68%   167-168, 205-210, 225, 239-240, 248-256, 262-268, 347-353
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        124      17  86.29%   127-131, 243, 321-330, 384-385, 391
R/control_incidence_rate.R                    20       8  60.00%   32-35, 38-41
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                          49       1  97.96%   63
R/count_missed_doses.R                        33       0  100.00%
R/count_occurrences_by_grade.R               105       4  96.19%   156-158, 161
R/count_occurrences.R                         74       1  98.65%   92
R/count_patients_events_in_cols.R             68       1  98.53%   62
R/count_patients_with_event.R                 46       0  100.00%
R/count_patients_with_flags.R                 57       4  92.98%   71-72, 77-78
R/count_values.R                              26       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, 239, 254, 262, 268-269
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            168      40  76.19%   232-263, 323-325, 331, 352-389
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                  49       1  97.96%   60
R/estimate_proportion.R                      201      12  94.03%   75-82, 86, 91, 298, 465, 570
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     174       3  98.28%   145, 155, 280
R/g_forest.R                                 438      21  95.21%   199, 319, 336-337, 342-343, 356, 372, 419, 450, 526, 535, 616-620, 630, 705, 708, 832
R/g_lineplot.R                               200      30  85.00%   162, 175, 204, 230-233, 309-316, 334-335, 341-351, 443, 449, 451
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                    42       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_logistic_regression.R                    468       3  99.36%   206-207, 276
R/h_map_for_count_abnormal.R                  57       2  96.49%   77-78
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           75       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   257-270
R/h_stack_by_baskets.R                        67       3  95.52%   68-69, 95
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           79       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/imputation_rule.R                           17       2  88.24%   54-55
R/incidence_rate.R                            95       7  92.63%   53-60
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        683      65  90.48%   230-233, 273-308, 317-321, 530, 717-719, 727-729, 761-762, 935-938, 1161, 1478-1489
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               108       0  100.00%
R/prop_diff_test.R                            90       0  100.00%
R/prop_diff.R                                262      16  93.89%   72-75, 107, 271-278, 417, 477, 582
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             60       0  100.00%
R/response_subgroups.R                       165       4  97.58%   268, 312-314
R/riskdiff.R                                  48       7  85.42%   85-88, 95, 105-106
R/rtables_access.R                            38       4  89.47%   159-162
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      59       3  94.92%   73-74, 129
R/summarize_ancova.R                          97       1  98.97%   180
R/summarize_change.R                          29       0  100.00%
R/summarize_colvars.R                         12       2  83.33%   72-73
R/summarize_coxreg.R                         174       6  96.55%   196-197, 204, 340-341, 434
R/summarize_glm_count.R                      166      29  82.53%   158, 162-213, 261-262
R/summarize_num_patients.R                   101       9  91.09%   105-107, 156-157, 240-245
R/summarize_patients_exposure_in_cols.R       98       1  98.98%   56
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   75       9  88.00%   59-67
R/survival_duration_subgroups.R              174       0  100.00%
R/survival_time.R                             49       0  100.00%
R/survival_timepoint.R                       120       7  94.17%   126-132
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R        95       3  96.84%   408-411
R/utils_factor.R                             109       2  98.17%   84, 302
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                             90       7  92.22%   24, 31-35, 376-377
R/utils.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9613     514  94.65%

Diff against main

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

Results for commit: 93cae1d

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-09-26T11:38:14Z

Unit Tests Summary

      1 files     80 suites 1m 18s ⏱️
  781 tests   761 ✔️   20 💤 0 ❌
1 658 runs 1 030 ✔️ 628 💤 0 ❌

Results for commit 93cae1d.

♻️ This comment has been updated with latest results.

averissimo · 2023-09-26T13:52:30Z

Blocked until discussion about rmarkdown is resolved insightsengineering/teal.logger#49 (comment)

pawelru · 2023-10-20T08:56:06Z

DESCRIPTION

-    lattice,
-    lubridate,
+    knitr (>= 1.42),
+    rmarkdown (>= 2.19),


pls move it down to keep alphabetical order

DESCRIPTION

Co-authored-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>

pawelru

hey @shajoezhu, this guy is good to go. tern is right after release. Shall we move on and merge?

shajoezhu · 2023-10-20T16:51:13Z

Fantastic! Please pull the trigger! @pawelru

averissimo mentioned this pull request Jul 26, 2023

Specify minimal version dependencies + add action insightsengineering/nestdevs-tasks#7

Closed

55 tasks

averissimo changed the title ~~Verdepcheck action~~ Adds min package version Jul 26, 2023

pawelru reviewed Aug 7, 2023

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averissimo force-pushed the verdepcheck_action branch from c8913f9 to 305eb2a Compare September 1, 2023 13:57

averissimo force-pushed the verdepcheck_action branch from ee894e6 to 03fd634 Compare September 20, 2023 12:38

averissimo mentioned this pull request Sep 25, 2023

Adds min package version insightsengineering/teal.logger#49

Merged

11 tasks

averissimo force-pushed the verdepcheck_action branch from 03fd634 to fb2de65 Compare September 25, 2023 21:59

averissimo marked this pull request as ready for review September 26, 2023 11:28

averissimo added the core label Sep 26, 2023

averissimo added the blocked label Sep 26, 2023

averissimo force-pushed the verdepcheck_action branch 2 times, most recently from dce14b7 to 7cb096f Compare October 18, 2023 12:15

pawelru reviewed Oct 20, 2023

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DESCRIPTION Outdated

lattice,

lubridate,

knitr (>= 1.42),

rmarkdown (>= 2.19),

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pawelru Oct 20, 2023

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pls move it down to keep alphabetical order

pawelru reviewed Oct 20, 2023

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averissimo added 13 commits October 20, 2023 13:54

docs: adds minimum version to dependencies

189f4cc

ci: adds temporary action on push

b26ecde

docs: add minimal version of deps

228dcd1

docs: update versions

549d98f

docs: remove rmarkdown in favor or recent knitr

951c23e

docs: typo on NEWS.md

10f1edc

docs: updates news

c258274

docs: bumps minimum broom version

8c9672b

docs: revert broom and bump emmeans

660fa28

docs: bump testthat to include expect_contains

e5eb050

docs: bumps vdiffr as 1.0.6 had compilation issues

75b69dc

specify version for rmarkdown

5388ac7

correct news after rebase

d0add23

averissimo and others added 2 commits October 20, 2023 13:54

Update DESCRIPTION

c01069c

Co-authored-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com> Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>

rebase after release

93cae1d

averissimo force-pushed the verdepcheck_action branch from 29070f8 to 93cae1d Compare October 20, 2023 11:55

pawelru approved these changes Oct 20, 2023

View reviewed changes

shajoezhu merged commit ae1a386 into main Oct 23, 2023
29 of 30 checks passed

shajoezhu deleted the verdepcheck_action branch October 23, 2023 01:59

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Adds min package version #1012

Adds min package version #1012

averissimo commented Jul 26, 2023 •

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averissimo commented Sep 26, 2023

pawelru Oct 20, 2023

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shajoezhu commented Oct 20, 2023

Adds min package version #1012

Adds min package version #1012

Conversation

averissimo commented Jul 26, 2023 • edited Loading

🔴 Checklist for PR Reviewer

🔴 What's needed before merging?

Change in code

PRS

Changes description

github-actions bot commented Sep 26, 2023 • edited Loading

Code Coverage Summary

Diff against main

github-actions bot commented Sep 26, 2023 • edited Loading

Unit Tests Summary

averissimo commented Sep 26, 2023

pawelru Oct 20, 2023

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shajoezhu commented Oct 20, 2023

averissimo commented Jul 26, 2023 •

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