218: fix bioc devel problems

[danielinteractive]

part of #218

[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: ad0fd06

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   23 suites   1m 4s ⏱️
273 tests 256 ✅ 17 💤 0 ❌
849 runs  827 ✅ 22 💤 0 ❌

Results for commit ad0fd06.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
differential	💚	$29.69$	$-1.25$	$0$	$0$	$0$	$0$

Results for commit c3cb59d

♻️ This comment has been updated with latest results.

[BFalquet]

That looks like some pretty subtle changes. I see in the tests that the roxygene version is not matching perfectly and there seem to be a small issue in a vignette. Once these little technicalities are solved, it should be good to go.

[danielinteractive]

Thanks @BFalquet , hm strange, somehow the summarized_experiment object is not found anymore?