options for strict tests; few enhancements

[pawelru]

• part of https://github.com/insightsengineering/coredev-tasks/issues/478
  • please read this for more info about the implementation: https://github.com/insightsengineering/coredev-tasks/issues/478#issuecomment-1909912778
• added skip if not installed for suggested package that I discovered locally

[github-actions]

Code Coverage Summary

Filename               Stmts    Miss  Cover    Missing
-------------------  -------  ------  -------  ----------
R/assert_data.R           63       0  100.00%
R/covariance_plot.R       52       5  90.38%   41, 84-87
R/fit_mmrm.R              44       0  100.00%
R/formula.R               45       0  100.00%
R/g_mmrm.R               313       7  97.76%   66-71, 302
R/labels.R                23       0  100.00%
R/lsmeans.R              205       0  100.00%
R/subgroups.R            265       0  100.00%
R/tabulate_mmrm.R         83       0  100.00%
R/utils.R                  4       0  100.00%
TOTAL                   1097      12  98.91%

Diff against main

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

Results for commit: f15242c

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   11 suites   18s ⏱️
110 tests  81 ✅ 29 💤 0 ❌
219 runs  178 ✅ 41 💤 0 ❌

Results for commit f15242c.

♻️ This comment has been updated with latest results.

[danielinteractive]

thanks @pawelru

[danielinteractive]

@pawelru hm quick question though.... when I just ran tern.mmrm tests locally, and I guess the new setup applies, I get this (and many more of the same):

Warning (test-table_mmrmt01.R:45:3): Fixed effects table is produced correctly
partial argument match of 'val' to 'vals'
Backtrace:
     ▆
  1. ├─tern::as.rtable(mmrm_results, type = "fixed", format = "xx.xx") at test-table_mmrmt01.R:45:3
  2. └─tern.mmrm:::as.rtable.tern_mmrm(...)
  3.   └─tern.mmrm::h_mmrm_fixed(x, ...) at tern.mmrm/R/tabulate_mmrm.R:58:3
  4.     ├─tern::as.rtable(fixed_table[, pvalue_column, drop = FALSE], format = "x.xxxx | (<0.0001)") at tern.mmrm/R/tabulate_mmrm.R:72:3
  5.     └─tern:::as.rtable.data.frame(...)
  6.       ├─base::do.call(...)
  7.       └─base::Map(...)
  8.         └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
  9.           └─tern (local) `<fn>`(row = dots[[1L]][[10L]], row_name = dots[[2L]][[10L]])
 10.             ├─base::do.call(rrow, c(as.list(unname(row)), row.name = row_name))
 11.             └─rtables (local) `<fn>`(0.851692307948709, row.name = "ARMCDTRT:AVISITVIS4")
 12.               └─rtables::DataRow(...)

Is this from the new options?

If yes I guess this is an issue in rtables ?... @shajoezhu fyi

[pawelru]

yes it is - there is a PR that aims to fix it insightsengineering/rtables#820

How did you get it? Is it a blocker for you?

[danielinteractive]

ah ok :D I thought this is ready already for merge... hm no worries

[pawelru]

This should have probably merged in sequence with rtables being first. Sorry about that.
In case it's a blocker - please just temporarily modify the condition to be always false so that the options won't be set.
Everything will be back clean again once we merge aforementioned PR.

[danielinteractive]

since we run checks here with --as-cran we don't use the settings on CI, so should be ok for now

[shajoezhu]

hi guys, sorry, we were busy on tmc release, so i put a hold on including those changes in all sme packages until tmc cran releases completion