Update 8 packages

[epiverse-trace-bot]

🤖 This is an automated build

This will update 8 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- MASS      [required by fitdistrplus, ggplot2]
- Matrix    [required by igraph]
- mgcv      [required by ggplot2]
- survival  [required by fitdistrplus]
- MASS       [7.3-65 -> *]
- Matrix     [1.7-3 -> *]
- mgcv       [1.9-1 -> *]
- nlme       [3.1-168 -> *]
- survival   [3.8-3 -> *]
- lattice    [0.22-7 -> *]

# CRAN -----------------------------------------------------------------------
- incidence2   [2.6.2 -> 2.6.3]
- V8           [6.0.3 -> 6.0.4]
- MASS         [* -> 7.3-65]
- Matrix       [* -> 1.7-3]
- mgcv         [* -> 1.9-1]
- nlme         [* -> 3.1-168]
- survival     [* -> 3.8-3]

# RSPM -----------------------------------------------------------------------
- lattice      [* -> 0.22-7]

⏱️ In a few minutes, a comment will appear that will show you how the output has changed based on these updates.

If you want to inspect these changes locally, you can use the following code to check out a new branch:

git fetch origin update/packages
git checkout update/packages

• Auto-generated by create-pull-request on 2025-06-05

[github-actions]

🆗 Pre-flight checks passed 😃

This pull request has been checked and contains no modified workflow files or spoofing.

It should be safe to Approve and Run the workflows that need maintainer approval.

[Bisaloo]

@avallecam, I don't have a solution for the RcppParallel issue.

Even if we could, keeping the version pinned is probably not a viable option in the long-run so what we want is to understand why the install is failing and fix it. But I haven't been successful here.

My last hope is that wider changes in the Carpentries infrastructure (carpentries/sandpaper#650) may be able to address this at some point but I'm not completely sure when the switch will happen.

[froggleston]

Hey @Bisaloo - you could test out the new workflows here too and I'm happy to support if possible!

[Bisaloo]

Thanks for the offer @froggleston! It sounds great but I'm still slightly hesitant as I'm leaving this project at the end of the week and I don't want to leave the burden of learning a new workflow to the team, especially as the availability for maintenance is going to decrease even more soon.

I have made the switch in my fork: Bisaloo#1 but I'll keep thinking about this more before I potentially flick the switch here 🤔

[Bisaloo]

After taking more time for thinking this through and chatting with the team, we still stick with the current workflow for now. Thanks a lot for the support offer anyways @froggleston.

I do think this conversation was still helpful because it gives you one extra data point for your work on carpentries/sandpaper#650:

• I could confirm that it fixes the RcppParallel installation issues we see here
• I could confirm the workflow works fine once set up. The set up process was a bit confusing IMO because the cache was not yet created so automatically triggered workflows were failing and I wasn't completely sure in which order I should manually trigger which workflows to get to a working state.

[froggleston]

I do think this conversation was still helpful because it gives you one extra data point for your work on carpentries/sandpaper#650:

• I could confirm that it fixes the RcppParallel installation issues we see here

Great! I'm hopeful that people will experience fewer issues when using the dockerised workflows.

• The set up process was a bit confusing IMO because the cache was not yet created so automatically triggered workflows were failing and I wasn't completely sure in which order I should manually trigger which workflows to get to a working state.

This is correct, as non-Rmarkdown lessons should build straightaway, but the R lessons will need the check and apply workflows run. I do document this in the output of the workflow when it fails due to the cache not being available:

Please do let me know if there are other improvements I can make that will make the process easier!