Do not use testthat dependent features in the app

[vedhav]

teal.gallery e2e tests caught an error that originates here. If testthat package is not installed when running the app it throw an error in the app.

Warning: Error in makeExpectation: Package 'testthat' is required for checkmate's 'expect_*' extensions with backend 'testthat'
  195: stop
  194: makeExpectation [/tmp/RtmpCWBQUh/renv-package-new-52d51bba257/checkmate/R/makeExpectation.R#80]
  193: expect_proportion [/__w/teal.gallery/teal.gallery/RNA-seq/renv/staging/1/hermes#1]
  192: hermes::control_quality [/tmp/RtmpCWBQUh/renv-package-new-52d7cce5949/hermes/R/quality.R#39]
  191: <reactive> [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#300]
  171: control [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  170: <reactive> [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#309]
  150: object_flagged [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  149: <reactive> [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#325]
  129: object_final [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  128: <reactive> [/tmp/RtmpCWBQUh/renv-package-new-52d60c71064/teal.modules.hermes/R/tm_g_quality.R#346]
  108: plot_r [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/reactives.R#870]
  101: renderUI [/tmp/RtmpCWBQUh/renv-package-new-52d60693a47/teal.widgets/R/plot_with_settings.R#407]
  100: func [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/utils.R#1482]
   87: renderFunc [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/shinywrappers.R#263]
   86: output$teal-teal_modules-nav-quality_control-module-plot-plot_out_main [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/shinywrappers.R#133]
    1: shiny::runApp [/tmp/RtmpCWBQUh/renv-package-new-52d2e47a3fd/shiny/R/runapp.R#388]
    1) Navigates to all tabs without error

[github-actions]

Unit Tests Summary

  1 files   23 suites   1m 4s ⏱️
273 tests 267 ✅ 6 💤 0 ❌
786 runs  780 ✅ 6 💤 0 ❌

Results for commit afb6f89.

♻️ This comment has been updated with latest results.

[averissimo]

It seems that expect_ was used interchangebly with assert_, good catch on this PR

[github-actions]

Code Coverage Summary

Filename                   Stmts    Miss  Cover    Missing
-----------------------  -------  ------  -------  ------------------------
R/assertthat.R                19       1  94.74%   149
R/calc_cor.R                  25       0  100.00%
R/checkmate.R                  4       0  100.00%
R/connections.R              143     125  12.59%   27-161, 215-287, 356-381
R/differential.R             101       3  97.03%   190, 193, 196
R/dplyr_compatibility.R        3       1  66.67%   23
R/draw_barplot.R              34       0  100.00%
R/draw_boxplot.R              71       5  92.96%   81, 88-89, 106, 109
R/draw_heatmap.R              35       1  97.14%   71
R/draw_scatterplot.R          32       4  87.50%   73-74, 87, 93
R/GeneSpec-class.R            68       0  100.00%
R/graphs.R                   107       3  97.20%   107-109
R/HermesData-class.R          35       4  88.57%   134-137
R/HermesData-methods.R       194       0  100.00%
R/HermesData-validate.R       44       0  100.00%
R/join_cdisc.R                37       0  100.00%
R/normalization.R            100       2  98.00%   194, 223
R/pca_cor_samplevar.R         59       0  100.00%
R/pca.R                       28       0  100.00%
R/quality.R                   75       3  96.00%   109-112
R/top_genes.R                 51       0  100.00%
R/utils.R                     98       0  100.00%
TOTAL                       1363     152  88.85%

Diff against main

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

Results for commit: afb6f89

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[averissimo]

We should replace all expect_* to assert_* in the code. Otherwise, the same error might pop again in the future

[averissimo]

👍