Fix CI pipelines

[m7pr]

Part of insightsengineering/nestdevs-tasks#98

[m7pr]

Started a job in here https://github.com/insightsengineering/teal/actions/runs/12784552889

[m7pr]

Started a new job after recent changes https://github.com/insightsengineering/teal/actions/runs/12784947499

[m7pr]

one more run https://github.com/insightsengineering/teal/actions/runs/12785524755

[m7pr]

@pawelru an interesting case for you.
teal depends on MultiAssayExperiment in Suggests, but during min_isolated build
https://github.com/insightsengineering/teal/actions/runs/12784947499/job/35639440420#step:9:710 you can see that it tries to load very old version of SummarizedExperiment which is a dependency of MultiAssayExperiment. This old version depends on old MatrixGenerics that depends on matrixStats that can not be installed.

However, newest version of SummarizedExperiment depends on newer MatrixGenerics that doesn't have installation issues and all the build is satisfied https://github.com/insightsengineering/teal/actions/runs/12785524755 but I needed to add SummarizedExperiment experiment to package Suggests just to satisfy the build, even though this package is not directly needed for teal.

Do you have any advice on how we should proceed? Let the min_isolated fail, allow SummarizedExperiment to be added to Suggests, or to some Enhances or Linking to fields?

[pawelru]

Please have a look at the extra-deps workflow parameter. It was designed to handle such cases and allow to provide specification of indirect dependencies not to pollute DESCIRPTION file as you mentioned

[m7pr]

Amazing, thanks for the hint :)!

[m7pr]

Running once more https://github.com/insightsengineering/teal/actions/runs/12789723140

[llrs-roche]

The extra-deps fixed the min_isolate check: before vs after.
The other dependencies fixed the rest.

[github-actions]

Unit Tests Summary

  1 files   27 suites   10m 22s ⏱️
276 tests 272 ✅ 4 💤 0 ❌
537 runs  533 ✅ 4 💤 0 ❌

Results for commit 7702273.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
module_teal	💚	$150.20$	$-2.21$	$0$	$0$	$0$	$0$

Results for commit fe3755b

♻️ This comment has been updated with latest results.