Remove lookup-refs

[m7pr]

Part of https://github.com/insightsengineering/coredev-tasks/issues/609

From now on, we will provide development dependencies in

Remotes: repo/project@branch

format, so it's explicitly visible in the DESCRIPTION file and can be handled by pak::install, renv::install and remotes::install.

With development dependencies specified in CJ Pipelines configuration, this connection was hidden, and it was hard to install the package from the main branch (or any other branch) locally from user's machine.

[github-actions]

✅ All contributors have signed the CLA
_{Posted by the CLA Assistant Lite bot.}

[github-actions]

Unit Tests Summary

    1 files     84 suites   1m 14s ⏱️
  876 tests   867 ✅   9 💤 0 ❌
1 882 runs  1 185 ✅ 697 💤 0 ❌

Results for commit 032ca2c.

♻️ 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	💔	$2.35$	$+3.29$	$+17$	$-7$	$0$	$0$
count_occurrences	💔	$0.72$	$+1.62$	$+10$	$-8$	$0$	$0$
count_occurrences_by_grade	💔	$1.72$	$+1.05$	$+16$	$-17$	$0$	$0$
summarize_coxreg	💔	$3.11$	$+2.14$	$+13$	$-13$	$0$	$0$
summarize_num_patients	💔	$1.06$	$+1.28$	$+18$	$-16$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
analyze_vars_in_cols	💔	$0.46$	$+1.51$	summarize_works_with_nested_analyze

Results for commit a5c5d39

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      96       3  96.88%   235, 237-238
R/abnormal_by_marked.R                        83       8  90.36%   94-98, 274, 276-277
R/abnormal_by_worst_grade.R                   89       3  96.63%   208, 210-211
R/abnormal_lab_worsen_by_baseline.R          150      10  93.33%   194-197, 202, 204-205, 448-450
R/abnormal.R                                  73       2  97.26%   215, 217
R/analyze_variables.R                        277       5  98.19%   572-575, 764
R/analyze_vars_in_cols.R                     178      14  92.13%   178, 221, 235-236, 238, 246-254
R/bland_altman.R                              92       1  98.91%   46
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                         35       0  100.00%
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                          59       1  98.31%   74
R/count_missed_doses.R                        36       0  100.00%
R/count_occurrences_by_grade.R               153       2  98.69%   177, 272
R/count_occurrences.R                        115       1  99.13%   118
R/count_patients_events_in_cols.R             67       1  98.51%   60
R/count_patients_with_event.R                 61       1  98.36%   123
R/count_patients_with_flags.R                 84       1  98.81%   137
R/count_values.R                              67       2  97.01%   205, 208
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%   65
R/estimate_proportion.R                      205      11  94.63%   83-90, 94, 99, 320, 486
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%   141, 276
R/g_forest.R                                 585      60  89.74%   240, 252-255, 260-261, 275, 277, 287-290, 335-338, 345, 414, 501, 514, 518-519, 524-525, 538, 554, 601, 630, 705, 714, 720, 739, 794-814, 817, 828, 847, 902, 905, 1040-1045
R/g_ipp.R                                    133       0  100.00%
R/g_km.R                                     350      57  83.71%   285-288, 307-309, 363-366, 400, 428, 432-475, 482-486
R/g_lineplot.R                               260      22  91.54%   204, 378-385, 424-434, 543, 551
R/g_step.R                                    68       1  98.53%   108
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                                     509      41  91.94%   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%   67-72, 152
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               117       0  100.00%
R/prop_diff_test.R                            91       0  100.00%
R/prop_diff.R                                265      15  94.34%   70-73, 105, 290-297, 440, 605
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R             69       6  91.30%   196-201
R/response_subgroups.R                       214       8  96.26%   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%   183, 188
R/summarize_change.R                          76       1  98.68%   188
R/summarize_colvars.R                         10       0  100.00%
R/summarize_coxreg.R                         172       0  100.00%
R/summarize_glm_count.R                      238       8  96.64%   207-208, 401-405, 538
R/summarize_num_patients.R                    93       4  95.70%   117-119, 266
R/summarize_patients_exposure_in_cols.R       96       1  98.96%   56
R/survival_biomarkers_subgroups.R             78       6  92.31%   117-122
R/survival_coxph_pairwise.R                   84      12  85.71%   51-52, 64-73
R/survival_duration_subgroups.R              212       6  97.17%   124-129
R/survival_time.R                            111       0  100.00%
R/survival_timepoint.R                       124      10  91.94%   131-140
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       173       0  100.00%
R/utils_factor.R                              87       1  98.85%   84
R/utils_ggplot.R                             110       0  100.00%
R/utils_grid.R                               126       5  96.03%   164, 279-286
R/utils_rtables.R                            124       9  92.74%   39, 46, 403-404, 526-530
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                                      11062     499  95.49%

Diff against main

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

Results for commit: 032ca2c

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[m7pr]

I have read the CLA Document and I hereby sign the CLA

[m7pr]

recheck

[Melkiades]

Fine with me! Thanks

[llrs-roche]

nestcolor is required on a lower version than available on CRAN, no sure if it depends on a feature recently released or not. But there is no need for Remotes and lookup-refs can be safely removed now.