Fix missing attached packages

[llrs-roche]

Pull Request

Fixes #786

This PR load the packages needed before the code is evaluated inside the qenv.
This makes the modules' code more reproducible and solve these errors:

We (@m7pr + me) decided to still add the prefixes on functions to avoid namespace conflicts.

[m7pr]

This change fixes #786 + adds direct library calls, so that Show R Code panel actually includes them.
So the code from Show R Code was not reproducible before.

We decided to pay attention to prefixes, to avoid name conflicts. Hovewer we decided not to prefix operators + and %>% - those need direct library(package) call. magrittr is not used as we import pipe from dplyr.

[llrs-roche]

I think it is ready for review, I'll fix the SuperLinter issues with the review comments.

[github-actions]

Code Coverage Summary

Filename                      Stmts    Miss  Cover    Missing
--------------------------  -------  ------  -------  ---------------------------------------
R/tm_a_pca.R                    888     888  0.00%    136-1157
R/tm_a_regression.R             777     777  0.00%    175-1057
R/tm_data_table.R               211     211  0.00%    100-359
R/tm_file_viewer.R              173     173  0.00%    47-255
R/tm_front_page.R               144     133  7.64%    77-247
R/tm_g_association.R            346     346  0.00%    156-577
R/tm_g_bivariate.R              690     426  38.26%   328-815, 856, 967, 984, 1002, 1013-1035
R/tm_g_distribution.R          1123    1123  0.00%    153-1423
R/tm_g_response.R               369     369  0.00%    174-622
R/tm_g_scatterplot.R            731     731  0.00%    257-1092
R/tm_g_scatterplotmatrix.R      296     277  6.42%    195-528, 589, 603
R/tm_missing_data.R            1133    1133  0.00%    121-1431
R/tm_outliers.R                1044    1044  0.00%    160-1355
R/tm_t_crosstable.R             261     261  0.00%    160-469
R/tm_variable_browser.R         832     827  0.60%    89-1078, 1116-1299
R/utils.R                       151     135  10.60%   89-274, 304-340, 352-361, 366, 380-399
R/zzz.R                           2       2  0.00%    2-3
TOTAL                          9171    8856  3.43%

Diff against main

Filename                      Stmts    Miss  Cover
--------------------------  -------  ------  --------
R/tm_a_pca.R                     +3      +3  +100.00%
R/tm_a_regression.R              +4      +4  +100.00%
R/tm_data_table.R                +4      +4  +100.00%
R/tm_g_association.R             +5      +5  +100.00%
R/tm_g_bivariate.R               +4      +4  -0.22%
R/tm_g_distribution.R           +11     +11  +100.00%
R/tm_g_response.R                +4      +4  +100.00%
R/tm_g_scatterplot.R             +1      +1  +100.00%
R/tm_g_scatterplotmatrix.R       +1      +1  -0.02%
R/tm_missing_data.R              +7      +7  +100.00%
R/tm_outliers.R                  +9      +9  +100.00%
R/tm_t_crosstable.R              +1      +1  +100.00%
TOTAL                           +54     +54  -0.02%

Results for commit: 3037961

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   22 suites   13m 43s ⏱️
144 tests 144 ✅ 0 💤 0 ❌
475 runs  475 ✅ 0 💤 0 ❌

Results for commit 3037961.

♻️ 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	💔	$117.36$	$+4.90$	$0$	$0$	$0$	$0$
shinytest2-tm_a_regression	💔	$53.60$	$+2.58$	$0$	$0$	$0$	$0$
shinytest2-tm_file_viewer	💔	$29.20$	$+1.06$	$0$	$0$	$0$	$0$
shinytest2-tm_front_page	💔	$20.72$	$+1.13$	$0$	$0$	$0$	$0$
shinytest2-tm_g_association	💔	$31.37$	$+2.18$	$0$	$0$	$0$	$0$
shinytest2-tm_g_bivariate	💔	$75.17$	$+1.93$	$0$	$0$	$0$	$0$
shinytest2-tm_g_distribution	💔	$58.06$	$+2.10$	$0$	$0$	$0$	$0$
shinytest2-tm_g_response	💔	$29.68$	$+1.59$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplot	💔	$73.91$	$+2.92$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplotmatrix	💔	$28.00$	$+1.64$	$0$	$0$	$0$	$0$
shinytest2-tm_misssing_data	💔	$47.49$	$+1.97$	$0$	$0$	$0$	$0$
shinytest2-tm_outliers	💔	$111.22$	$+6.96$	$0$	$0$	$0$	$0$
shinytest2-tm_t_crosstable	💔	$31.34$	$+1.80$	$0$	$0$	$0$	$0$
shinytest2-tm_variable_browser	💔	$56.53$	$+2.31$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
shinytest2-tm_g_bivariate	💔	$25.88$	$+1.18$	e2e_tm_g_bivariate_Setting_encoding_inputs_produces_outputs_without_validation_errors.
shinytest2-tm_g_scatterplot	💔	$42.71$	$+1.22$	e2e_tm_g_scatterplot_The_encoding_inputs_produce_output_without_validation_errors.
shinytest2-tm_outliers	💔	$9.98$	$+1.07$	e2e_tm_outliers_Data_extract_spec_elements_are_initialized_with_the_default_values_specified_by_outlier_var_and_categorical_var_argument.
shinytest2-tm_outliers	💔	$25.33$	$+1.24$	e2e_tm_outliers_Outlier_definition_text_and_range_are_displayed_properly_depending_on_method.

Results for commit 934bf2a

♻️ This comment has been updated with latest results.

[m7pr]

hey @llrs-roche , really great job with the modules on tmg! I will review each module separately! it might take some time : )

In the meantime, can you have a look at the SuperLinter fail?

[llrs-roche]

Addressing the remaining comments.
I also found some other calls missing a prefix.