Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

specify minimal version of dependencies #957

Closed
wants to merge 15 commits into from
Closed

specify minimal version of dependencies #957

wants to merge 15 commits into from

Conversation

pawelru
Copy link
Contributor

@pawelru pawelru commented Jun 9, 2023

WIP

@github-actions
Copy link
Contributor

github-actions bot commented Jun 9, 2023

badge

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      62       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%   233-235
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/analyze_vars_in_cols.R                     113      23  79.65%   164, 188-193, 206, 219-225, 268-274, 305
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        139       5  96.40%   126-127, 137, 241, 259
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%   63
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       6  92.86%   156-158, 161, 176-177
R/count_occurrences.R                         61       1  98.36%   92
R/count_patients_events_in_cols.R             67       1  98.51%   74
R/count_patients_with_event.R                 33       0  100.00%
R/count_patients_with_flags.R                 39       0  100.00%
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     142       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    169       9  94.67%   19-20, 227-231, 275, 290, 298, 304-305
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            169      40  76.33%   232-263, 361-363, 370, 391-428
R/desctools_binom_diff.R                     663      66  90.05%   68, 103-104, 144-145, 148, 227, 253-262, 301, 303, 323, 327, 331, 335, 391, 394, 397, 400, 461, 469, 481-482, 488-491, 499, 502, 511, 514, 562-563, 565-566, 568-569, 571-572, 642, 654-667, 672, 719, 732, 736
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   60
R/estimate_proportion.R                      198      11  94.44%   75-82, 86, 91, 460, 565
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     115       3  97.39%   107, 145, 155
R/g_forest.R                                 437      23  94.74%   197, 248-249, 316, 333-334, 339-340, 353, 369, 416, 447, 523, 532, 613-617, 627, 697, 700, 824
R/g_lineplot.R                               199      29  85.43%   160, 173, 201, 227-230, 307-314, 332-333, 339-349, 441, 449
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        74       0  100.00%
R/h_biomarkers_subgroups.R                    40       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                  54       0  100.00%
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                        65       1  98.46%   91
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/incidence_rate.R                            93       7  92.47%   68-75
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        575      61  89.39%   248-283, 292-296, 494, 666-668, 676-678, 703, 710-711, 881, 1071, 1318-1329
R/logistic_regression.R                      101       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               106       0  100.00%
R/prop_diff_test.R                            88       0  100.00%
R/prop_diff.R                                260      16  93.85%   72-75, 107, 267-274, 413, 473, 578
R/prune_occurrences.R                         57      10  82.46%   140-144, 190-194
R/response_biomarkers_subgroups.R             60       0  100.00%
R/response_subgroups.R                       165       4  97.58%   279, 321-323
R/rtables_access.R                            38       4  89.47%   161-164
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       3  93.62%   73-74, 129
R/summarize_ancova.R                          95       1  98.95%   189
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_coxreg.R                         156       2  98.72%   194, 406
R/summarize_glm_count.R                      164       4  97.56%   188, 193, 254, 322
R/summarize_num_patients.R                    74       9  87.84%   103-105, 150-151, 217-222
R/summarize_patients_exposure_in_cols.R       97       1  98.97%   67
R/summarize_variables.R                      220       2  99.09%   266, 492
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   64-72
R/survival_duration_subgroups.R              172       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       116       7  93.97%   150-156
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              87       1  98.85%   91
R/utils_grid.R                               111       5  95.50%   152, 262-268
R/utils_rtables.R                             86       7  91.86%   24, 31-35, 346-347
R/utils.R                                    137      10  92.70%   105, 107, 111, 131, 134, 137, 141, 150-151, 334
TOTAL                                       9069     424  95.32%

Diff against main

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

Results for commit: 6b3ab19

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

@github-actions
Copy link
Contributor

github-actions bot commented Jun 9, 2023

Unit Tests Summary

       1 files    78 suites   57s ⏱️
   735 tests 735 ✔️     0 💤 0
1 560 runs  979 ✔️ 581 💤 0

Results for commit b951283.

♻️ This comment has been updated with latest results.

@pawelru
Copy link
Contributor Author

pawelru commented Jun 15, 2023

yay! min deps are fixed. max deps is to be resolved as most likely it would require changes in the codebase

@averissimo averissimo mentioned this pull request Jul 26, 2023
11 tasks
@pawelru pawelru closed this Aug 18, 2023
@pawelru pawelru deleted the min_deps branch August 18, 2023 09:22
shajoezhu pushed a commit that referenced this pull request Oct 23, 2023
WIP :: parent issue:
insightsengineering/nestdevs-tasks#7

Supersede:
* #957

### 🔴 Checklist for PR Reviewer

[![Scheduled
🕰️](https://github.com/insightsengineering/tern/actions/workflows/scheduled.yaml/badge.svg?branch=verdepcheck_action)](https://github.com/insightsengineering/tern/actions/workflows/scheduled.yaml)
_(~~max strategy fails due to
tidyverse/ggplot2#5436 corrected upstream)_

- [ ] Tag yourself next to this repo on
insightsengineering/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)
  - [x] Remove `on: push` section 
  - [x] Change branch to main

#### PRS

- [x] verdepcheck
  * insightsengineering/verdepcheck#24
  * insightsengineering/verdepcheck#26
- [x] verdepcheck-action
  * insightsengineering/r-verdepcheck-action#16

### Changes description

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

---------

Signed-off-by: André Veríssimo <[email protected]>
Co-authored-by: Pawel Rucki <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants