Adds min package version (#1012)

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]>

Author: averissimo

.github/workflows/scheduled.yaml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        test-strategy: ["min", "release", "max"]
+        test-strategy: ["min_cohort", "min_isolated", "release", "max"]
     uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main
     name: Dependency Test - ${{ matrix.test-strategy }} 🔢
     secrets:

DESCRIPTION

@@ -23,44 +23,71 @@ Depends:
     R (>= 3.6),
     rtables (>= 0.6.5)
 Imports:
-    broom,
-    car,
-    checkmate,
-    cowplot,
-    dplyr,
-    emmeans (>= 1.4.5),
+    broom (>= 0.5.4),
+    car (>= 3.0-13),
+    checkmate (>= 2.1.0),
+    cowplot (>= 0.7.0),
+    dplyr (>= 1.0.0),
+    emmeans (>= 1.8.0),
     forcats (>= 1.0.0),
     formatters (>= 0.5.4),
     ggplot2 (>= 3.4.0),
     grid,
-    gridExtra,
-    gtable,
+    gridExtra (>= 2.0.0),
+    gtable (>= 0.3.0),
     labeling,
-    lifecycle,
-    magrittr,
+    lifecycle (>= 0.2.0),
+    magrittr (>= 1.5),
     methods,
-    Rdpack,
-    rlang,
-    scales,
+    Rdpack (>= 2.4),
+    rlang (>= 1.1.0),
+    scales (>= 1.2.0),
     stats,
     survival (>= 3.2-13),
-    tibble,
-    tidyr,
+    tibble (>= 2.0.0),
+    tidyr (>= 0.8.3),
     utils
 Suggests:
-    knitr,
-    lattice,
-    lubridate,
+    knitr (>= 1.42),
+    lattice (>= 0.18-4),
+    lubridate (>= 1.7.9),
     nestcolor (>= 0.1.1),
-    rmarkdown,
-    stringr,
-    testthat (>= 3.0),
-    vdiffr (>= 1.0.0)
+    rmarkdown (>= 2.19),
+    stringr (>= 1.4.1),
+    testthat (>= 3.1.9),
+    vdiffr (>= 1.0.7)
 VignetteBuilder:
     knitr
 RdMacros:
     lifecycle,
     Rdpack
+Config/Needs/verdepcheck:
+    insightsengineering/rtables,
+    tidymodels/broom,
+    cran/car,
+    mllg/checkmate,
+    wilkelab/cowplot,
+    tidyverse/dplyr,
+    rvlenth/emmeans,
+    tidyverse/forcats,
+    insightsengineering/formatters,
+    tidyverse/ggplot2,
+    r-lib/gtable,
+    r-lib/lifecycle,
+    tidyverse/magrittr,
+    GeoBosh/Rdpack,
+    r-lib/rlang,
+    r-lib/scales,
+    tidyverse/tibble,
+    tidyverse/tidyr,
+    yihui/knitr,
+    deepayan/lattice,
+    tidyverse/lubridate,
+    insightsengineering/nestcolor,
+    rstudio/rmarkdown,
+    tidyverse/stringr,
+    r-lib/testthat,
+    r-lib/vdiffr
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Encoding: UTF-8

NEWS.md

@@ -1,5 +1,8 @@
 # tern 0.9.2.9000
 
+### Miscellaneous
+* Specified minimal version of package dependencies.
+
 # tern 0.9.2
 
 ### New Features
@@ -65,7 +68,7 @@
 ### Enhancements
 * Added `ylim` argument to `g_km` to allow the user to set custom limits for the y-axis.
 * Added assertion to `g_km` which checks whether there is one arm present in the data when `annot_coxph` is true.
-* Added `flag_labels` argument to `s_count_patients_with_flags` to enable more label handling options in `count_patients_by_flags`. 
+* Added `flag_labels` argument to `s_count_patients_with_flags` to enable more label handling options in `count_patients_by_flags`.
 * Added the `nested` argument to `analyze` wrapper functions `count_abnormal`, `count_abnormal_by_baseline`, `count_abnormal_by_marked`, `count_abnormal_by_worst_grade`, `count_abnormal_lab_worsen_by_baseline`, `count_cumulative`, `count_missed_doses`, `count_occurrences`, `count_occurrences_by_grade`, `count_patients_with_event`, `count_patients_with_flags`, `count_values`, `estimate_multinomial_response`, `estimate_proportion`, `estimate_incidence_rate`, `estimate_odds_ratio`, `estimate_proportion_diff`, `test_proportion_diff`, `summarize_ancova`, `summarize_change`, `summarize_glm_count`, `analyze_num_patients`, `coxph_pairwise`, `surv_time`, and `surv_timepoint`.
 
 ## Miscellaneous
@@ -139,19 +142,19 @@
 ### Enhancements
 * Added `summarize_glm_count` function to analyze count data using a linear model.
 * Added legend to `g_step`.
-* Added formatting functions `format_fraction_fixed_dp` and 
+* Added formatting functions `format_fraction_fixed_dp` and
   `format_count_fraction_fixed_dp` with fixed single decimal place in percentages.
 * Added `na_level` and `labelstr` arguments to `summarize_vars_in_cols`.
 * Added `analyze_num_patients` to include summary at the beginning that does not
   repeat when paginating.
 * Added `h_row_first_values` function as a more general helper function to retrieve
   first values from specific rows.
 * Added option to remove `"(n)"` suffix from `unique_count` labels for `s_num_patients`.
-* Added options to `g_km` to annotate with statistics (`annot_stats`) and add corresponding 
+* Added options to `g_km` to annotate with statistics (`annot_stats`) and add corresponding
   vertical lines (`annot_stats_lines`).
 
 ### Bug Fixes
-* Fixed bug causing incorrect ordering of numeric grade levels when missing 
+* Fixed bug causing incorrect ordering of numeric grade levels when missing
   grades are present in `s_count_occurrences_by_grade`.
 * Refactored `summarize_vars_in_cols` to work with pagination machinery.
 * Fixed bug to allow passing of `conf_level` argument to `emmeans::contrast()` in `s_ancova`.
@@ -166,11 +169,11 @@
 * Added more tests to increase code coverage.
 * Created separate documentation files for functions in different sections of `pkgdown` reference.
 * Created separate `.R` files for logistic regression and cox regression helper functions.
-* Fixed table tests using `analyze_num_patients` to generate an initial summary so there is no 
+* Fixed table tests using `analyze_num_patients` to generate an initial summary so there is no
   repetition when paginating.
 * Updated tests to use `testthat` 3rd edition and replaced applicable tests with snapshot testing.
 * Updated `summarize_ancova` examples to use `iris` dataset instead of `scda` data.
-* Created vignette which saves cached synthetic `CDISC` dataset files to the `data/` folder and 
+* Created vignette which saves cached synthetic `CDISC` dataset files to the `data/` folder and
   generated cached synthetic datasets.
 * Updated all examples/tests to use datasets from the `data/` folder instead of `scda` datasets.
 * Removed all template tests from `tern`. These tests are in internal repo `scda.test`.
@@ -189,40 +192,40 @@
 ### New Features
 * Added stratified `Newcombe` and stratified Wilson statistics to `estimate_proportion` and
   `estimate_proportion_diff` with relative tests.
-* Added `stat_mean_pval`, a new summary statistic to calculate the p-value of 
+* Added `stat_mean_pval`, a new summary statistic to calculate the p-value of
   the mean.
-* Added statistic `mean_se` (mean with standard error) for `summarize_variables` 
+* Added statistic `mean_se` (mean with standard error) for `summarize_variables`
   and related functions.
 * Introduced again `Rdpack` for references.
 
-### Enhancements 
-* Redesign of data handling in tests by removing repetitive data loads and 
+### Enhancements
+* Redesign of data handling in tests by removing repetitive data loads and
   library calls.
 * Added `DescTools::BinomDiffCI` function within `tern`.
-* Added new parameter to `summarize_logistic` to specify which pivoted value 
+* Added new parameter to `summarize_logistic` to specify which pivoted value
   to use during analysis.
-* Updated `s_coxph_pairwise` to generate log-rank p-value using original 
+* Updated `s_coxph_pairwise` to generate log-rank p-value using original
   log-rank test instead of Cox Proportional-Hazards Model.
-* Implemented `nestcolor` in all examples by adapting `g_km`, `g_ipp`, 
+* Implemented `nestcolor` in all examples by adapting `g_km`, `g_ipp`,
   `g_waterfall`, `g_step`, `g_lineplot`, and `g_forest`.
-* Added parameters `interaction_y` and `interaction_item` in `ANCOVA` to make the 
+* Added parameters `interaction_y` and `interaction_item` in `ANCOVA` to make the
   interaction calculations available.
 * Added new parameter `footnotes` to add footnotes to `g_km`.
 
 ### Migration from `assertthat` to `checkmate`
-* Implemented `checkmate::assert_vector`, `checkmate::assert_set_equal`, and 
+* Implemented `checkmate::assert_vector`, `checkmate::assert_set_equal`, and
   `checkmate::assert_int` to check vector type, length, and values.
 * Replaced with standard assertions from `checkmate` the following functions:
-  `all_elements_in_ref`, `is_df_with_nlevels_factor`, `is_df_with_no_na_level`, 
-  `is_proportion_vector`, `is_quantiles_vector`, `is_character_or_factor`, 
-  `is_nonnegative_count`, `is_valid_character`, `assert_character_or_factor`, 
+  `all_elements_in_ref`, `is_df_with_nlevels_factor`, `is_df_with_no_na_level`,
+  `is_proportion_vector`, `is_quantiles_vector`, `is_character_or_factor`,
+  `is_nonnegative_count`, `is_valid_character`, `assert_character_or_factor`,
   `assert_equal_length` and `has_tabletree_colnames`.
-* Modified `is_proportion`, `is_equal_length`, `is_df_with_no_na_level`, 
-  `is_df_with_nlevels_factor`, `is_variables`, `is_df_with_variables`, 
+* Modified `is_proportion`, `is_equal_length`, `is_df_with_no_na_level`,
+  `is_df_with_nlevels_factor`, `is_variables`, `is_df_with_variables`,
   `is_df_with_factors`, `is_valid_factor` to use assertion logic.
 * Added more verbose warnings from `as_factor_keep_attributes`.
 * Made `assert_df_with_factors` and `assert_proportion_value` internal functions.
-* Renamed `assertthat.R` and `test-assertthat.R` to `utils_checkmate.R` and 
+* Renamed `assertthat.R` and `test-assertthat.R` to `utils_checkmate.R` and
   `test-utils_checkmate.R`.
 
 ### Documentation and NAMESPACE Polishing
@@ -252,7 +255,7 @@
    `estimate_multinomial_rsp`, `decorate_grob_set`, `extreme_format`, `fit_rsp_step`,
    `fit_survival_step`, `footnotes`, `footnotes-set`,
    `format_count_fraction`, `format_fraction_threshold`, `formatting_functions`,
-   `format_fraction`, `combination_function` (S4 method), `compare_variables` (S3 method), 
+   `format_fraction`, `combination_function` (S4 method), `compare_variables` (S3 method),
    `kaplan_meier`.
 * Internal keywords added, export removed, `_pkgdown.yml` updated, and `tern:::` added for
    tests/examples/vignettes where present for the following functions:
@@ -287,24 +290,24 @@
 * Fixed empty vector exception for `cut_quantile_bins`.
 * Fixed exception error when empty strings are present in pivoted columns (`rtables` split
   functions)
-* Fixed bug in `s_ancova` causing an error when the first level of the arm 
-  factor is not the control arm. 
+* Fixed bug in `s_ancova` causing an error when the first level of the arm
+  factor is not the control arm.
 * Fixed bug in `s_abnormal_by_worst_grade` when there is one `PARAM` level.
 * Fixed bug in `prop_diff_wald` when selecting all responders, updated tests accordingly.
 * Fixed bug in `h_ancova` that caused an error when deselecting all covariates.
 
 ### Miscellaneous
 * Added deprecated badge to `g_mmrm`.
-* Removed internal function calls in examples (`tern:::`) and added `dontrun` 
+* Removed internal function calls in examples (`tern:::`) and added `dontrun`
   to internal function examples.
 * Removed warnings and messages to console occurring in examples and tests.
-* Deprecated functions `color_palette` and `h_set_nest_theme` in favor of 
+* Deprecated functions `color_palette` and `h_set_nest_theme` in favor of
   `nestcolor::color_palette` and `nestcolor::theme_nest`, respectively.
-* Removed deprecated functions: `color_palette`, `color_palette_core`, 
+* Removed deprecated functions: `color_palette`, `color_palette_core`,
   `h_set_nest_theme`, `s_cox_univariate`.
-* Removed deprecated `mmrm` functions: `fit_mmrm`, `g_mmrm_diagnostic`, 
-  `g_mmrm_lsmeans`, `as.rtable.mmrm`, `h_mmrm_fixed`, `h_mmrm_cov`, 
-  `h_mmrm_diagnostic`, `tidy.mmrm`, `s_mmrm_lsmeans`, `s_mmrm_lsmeans_single`, 
+* Removed deprecated `mmrm` functions: `fit_mmrm`, `g_mmrm_diagnostic`,
+  `g_mmrm_lsmeans`, `as.rtable.mmrm`, `h_mmrm_fixed`, `h_mmrm_cov`,
+  `h_mmrm_diagnostic`, `tidy.mmrm`, `s_mmrm_lsmeans`, `s_mmrm_lsmeans_single`,
   `summarize_lsmeans`.
 * Renamed functions `arm` to `study_arm` and `extract` to `extract_by_name`.
 * Renamed `rtables.R` to `utils_rtables.R`.