Support more MAE and SE versions in CI Pipelines

[m7pr]

A follow-up after #634 that allows to use older MAE and SE versions

[m7pr]

https://github.com/insightsengineering/teal.slice/actions/runs/12909783684

[github-actions]

Unit Tests Summary

  1 files   29 suites   27s ⏱️
369 tests 369 ✅ 0 💤 0 ❌
821 runs  821 ✅ 0 💤 0 ❌

Results for commit a8510fa.

♻️ This comment has been updated with latest results.

[m7pr]

Hi, cc @llrs-roche, @gogonzo, and @donyunardi, as you previously expressed interest in the recent updates to fixing our pipelines.

Initially, I thought we needed to specify higher version requirements for MultiAssayExperiment and SummarizedExperiment (which are listed in Suggests) to ensure the Scheduled job scenarios could install all dependencies without issues. This was because one of the dependencies, matrixStats, was causing a crash. However, I later realized we only need to specify this third-level dependency (matrixStats) to be built from the latest Bioconductor release. This allows us to avoid version-locking MultiAssayExperiment and SummarizedExperiment, keeping them compatible with older versions of those packages as well.

Since this approach worked for teal.slice, I applied the same reduction of version requirements to teal and tmg. I’ll also make similar changes to tmc and other teal.modules.* packages.

Here are the relevant pull requests:

• teal PR #1460](Simplify CI Pipelines teal#1460)
• teal.modules.general PR #830(simplify builds dependencies of extra-deps teal.modules.general#830)

On a personal note, I find this to be an unnecessary complication since MultiAssayExperiment and SummarizedExperiment are only listed in Suggests.

[donyunardi]

On a personal note, I find this to be an unnecessary complication since MultiAssayExperiment and SummarizedExperiment are only listed in Suggests.

We need to start looking into this issue:

• Separate bioconductor dependencies from teal.slice #500

Let's do it this year.

[llrs-roche]

The change makes sense and a the checks remained with the same failure as main on this branch