update staged.dependencies

[BFalquet]

add nestcolor as upstream dependencies

thank you for the review

[github-actions]

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  ---------
R/aet01.R                            312     312  0.00%    39-584
R/aet02.R                            197     197  0.00%    29-479
R/aet03.R                             66      66  0.00%    37-153
R/aet04.R                             86      86  0.00%    48-181
R/assertions.R                        42      42  0.00%    21-104
R/checks.R                            14      14  0.00%    15-48
R/chevron_tlg-S4class.R               19      19  0.00%    37-90
R/chevron_tlg-S4methods.R             14      14  0.00%    15-117
R/cmt01a.R                           156     156  0.00%    46-433
R/cmt02_pt.R                          37      37  0.00%    34-108
R/dmt01.R                             29      29  0.00%    44-125
R/dst01.R                            231     231  0.00%    5-619
R/dtht01.R                            77      77  0.00%    42-190
R/egt01.R                             44      44  0.00%    44-134
R/egt02.R                             56      56  0.00%    38-222
R/ext01.R                             69      69  0.00%    38-254
R/gen_args.R                           1       1  0.00%    19
R/lbt01.R                             39      39  0.00%    41-123
R/mht01.R                             57      57  0.00%    38-138
R/sample_study_object.R               14      14  0.00%    14-35
R/standard_data_preprocessing.R      240     240  0.00%    52-531
R/utils.R                            125     125  0.00%    11-274
R/vst01.R                             45      45  0.00%    44-136
R/vst02.R                             92      92  0.00%    39-259
TOTAL                               2062    2062  0.00%

Results for commit: 1f3932bc7a1f5536e47f28032a1b150214457777

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[edelarua]

Hi @BFalquet, please add nestcolor under Suggests in the DESCRIPTION file.

[edelarua]

Looks good to me!

[pawelru]

Addition of the nestcolor looks fine but I have two comments

• You have added a lot of library(dplyr) (next to another already existing library(dm)) - is that needed? If examples run only functions from a package (and assuming that package prefixes / imports into the NAMESPACE everything it need) then that seems to be obsolete. It's needed only if you actually uses dplyr/dm functions in examples but that's not the case. For simplicity (as well as performance) I would suggest to remove it.
• So the soft-dependency is correctly added but is it used? Do we have an example with plots (not tables)? If yes, then let's use it in there. Otherwise I would expect that some static code analysis should complain that dependent package is not being used at all. We probably need it in the long term but I am not sure if now but let's leave that.

[BFalquet]

We will use it in mng01 which is (hopefully) about to be merged. For the library call, all the examples should be reformatted because they look terrible in the documentation. I ll open an issue for that.

[pawelru]

I ll open an issue for that

Already there -> #223

So here I would suggest to revert library calls not to make it even more difficult.