Ensures required packages are in Imports section

[averissimo]

Pull Request

Fixes #518

Note on removals:

• Remove broom as the broom:glances method can be replaced with generics::glances
  • According to my tests (methods are being deprecated as well)

Changes description

• Removed conditional use of packages
• Removes {broom} dependency
• Uses rlang conditionally
• Uses Suggested packages conditional on tests

[github-actions]

Code Coverage Summary

Filename                      Stmts    Miss  Cover    Missing
--------------------------  -------  ------  -------  -------------------------------------------------
R/tm_a_pca.R                    884     884  0.00%    138-1155
R/tm_a_regression.R             772     772  0.00%    162-1036
R/tm_data_table.R               215     215  0.00%    110-380
R/tm_file_viewer.R              173     173  0.00%    47-255
R/tm_front_page.R               133     122  8.27%    73-231
R/tm_g_association.R            340     340  0.00%    143-556
R/tm_g_bivariate.R              685     421  38.54%   315-794, 835, 946, 963, 981, 992-1014
R/tm_g_distribution.R          1103    1103  0.00%    155-1401
R/tm_g_response.R               364     364  0.00%    161-601
R/tm_g_scatterplot.R            729     729  0.00%    244-1075
R/tm_g_scatterplotmatrix.R      294     275  6.46%    182-511, 572, 586
R/tm_missing_data.R            1115    1115  0.00%    122-1410
R/tm_outliers.R                1031    1031  0.00%    162-1342
R/tm_t_crosstable.R             259     259  0.00%    148-454
R/tm_variable_browser.R         824     819  0.61%    89-1070, 1108-1291
R/utils.R                       156     125  19.87%   81-266, 296-327, 348, 351, 356, 371-392, 403, 408
R/zzz.R                           2       2  0.00%    2-3
TOTAL                          9079    8749  3.63%

Diff against main

Filename                      Stmts    Miss  Cover
--------------------------  -------  ------  --------
R/tm_g_distribution.R            -7      -7  +100.00%
R/tm_g_scatterplot.R             -7      -7  +100.00%
R/tm_g_scatterplotmatrix.R       -2      -2  +0.04%
R/tm_missing_data.R              +4      +4  +100.00%
R/tm_t_crosstable.R              -2      -2  +100.00%
R/tm_variable_browser.R          -6      -6  +0.00%
TOTAL                           -20     -20  +0.01%

Results for commit: ad8ba68

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   22 suites   13m 16s ⏱️
145 tests 107 ✅ 38 💤 0 ❌
476 runs  438 ✅ 38 💤 0 ❌

Results for commit 7526473.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_pca	💔	$118.46$	$+4.10$	$0$	$0$	$0$	$0$
shinytest2-tm_g_bivariate	💔	$74.18$	$+1.08$	$0$	$0$	$0$	$0$
shinytest2-tm_g_distribution	💚	$60.35$	$-1.29$	$0$	$0$	$0$	$0$

Results for commit 2e4666c

♻️ This comment has been updated with latest results.

[m7pr]

@averissimo is this still relevant?
Should we add to this sprint and get someone to review?

[averissimo]

@m7pr it is, although it needs a new pass to make sure that nothing new has created a conflict here

I'm moving it to draft

[pawelru]

I see changes in dependencies and I immediately think about verdepcheck. Can you please confirm that it is passing on this? If not - let's work on the deps versions.

This might need to wait for https://github.com/insightsengineering/teal.modules.general/pull/774/files#r1890465398

[m7pr]

Yes, once min_cohort is satisfied I will try to put minimal versions of packages in the DESCRIPTION file

[llrs-roche]

I left a couple of comments, as I haven't checked the code locally yet

[llrs-roche]

I thought this could affect the release, and the scheduled CI, so decided to pick it. I updated the PR and fixed a note about lifecycle.

Namespace in Imports field not imported from: 'lifecycle'
    All declared Imports should be used.

Feel free to review it @m7pr and decide how to proceed.

[m7pr]

Thanks @llrs-roche
Would you be able to start a Scheduled job on this PR?

[m7pr]

Started the job in here https://github.com/insightsengineering/teal.modules.general/actions/runs/12787826187

[m7pr]

needed to vbump teal.reporter, restarting the job

[m7pr]

https://github.com/insightsengineering/teal.modules.general/actions/runs/12789415938

[m7pr]

Scheduled job is still failing because of the inability to install teal.slice.
Updated teal version to overcome this.
Restarted job in here https://github.com/insightsengineering/teal.modules.general/actions/runs/12806234604

[m7pr]

Needed to extend extra-deps parameter of the job configuration (Scheduled yaml in .github/workflows folder) so that min version of teal.slice is installed, but the DESCRIPTION file is not polluted as this package is not really a direct dependency of tmg

New job https://github.com/insightsengineering/teal.modules.general/actions/runs/12807745141

[m7pr]

Also specified version of SummarizedExperiment in extra-deps for teal.slice. So a 3rd level dependency.
Restarting the build https://github.com/insightsengineering/teal.modules.general/actions/runs/12807968854

[m7pr]

Also added MultiAssayExperiment to extra-deps, to get teal.slice to install.
New job https://github.com/insightsengineering/teal.modules.general/actions/runs/12808942137