Update 18 packages

[carpentries-bot]

🤖 This is an automated build

This will update 18 packages in your lesson with the following versions:

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

# CRAN -----------------------------------------------------------------------
- broom           [1.0.9 -> 1.0.10]
- dbplyr          [repo: RSPM -> CRAN; ver: 2.5.0 -> 2.5.1]
- dtplyr          [repo: RSPM -> CRAN; ver: 1.3.1 -> 1.3.2]
- forcats         [repo: RSPM -> CRAN; ver: 1.0.0 -> 1.0.1]
- gargle          [repo: RSPM -> CRAN; ver: 1.5.2 -> 1.6.0]
- ggplot2         [3.5.2 -> 4.0.0]
- googledrive     [repo: RSPM -> CRAN; ver: 2.1.1 -> 2.1.2]
- googlesheets4   [repo: RSPM -> CRAN; ver: 1.1.1 -> 1.1.2]
- magrittr        [repo: RSPM -> CRAN; ver: 2.0.3 -> 2.0.4]
- openssl         [2.3.3 -> 2.3.4]
- pillar          [1.11.0 -> 1.11.1]
- ragg            [1.4.0 -> 1.5.0]
- rmarkdown       [repo: RSPM -> CRAN; ver: 2.29 -> 2.30]
- stringr         [repo: RSPM -> CRAN; ver: 1.5.1 -> 1.5.2]
- systemfonts     [1.2.3 -> 1.3.1]
- textshaping     [1.0.2 -> 1.0.3]
- vroom           [repo: RSPM -> CRAN; ver: 1.6.5 -> 1.6.6]

# https://packagemanager.posit.co/cran/__linux__/jammy/latest ----------------
- S7              [* -> 0.2.0]

⏱️ 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 2025-10-07

[github-actions]

Thank you!

Thank you for your pull request 😃

🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

• 🎯 correct output
• 🖼️ correct figures
• ❓ new warnings
• ‼️ new errors

Rendered Changes

🔍 Inspect the changes: https://github.com/datacarpentry/R-ecology-lesson/compare/md-outputs..md-outputs-PR-942

The following changes were observed in the rendered markdown documents:

 config.yaml (gone)                                 |   86 -
 fig/visualizing-ggplot-rendered-facet-wrap-1.png   |  Bin 556197 -> 559955 bytes
 fig/visualizing-ggplot-rendered-scale-log-1.png    |  Bin 296058 -> 296674 bytes
 ...g-ggplot-rendered-violin-challenge-answer-1.png |  Bin 567548 -> 567552 bytes
 ...ggplot-rendered-violin-challenge-answer-2-1.png |  Bin 567495 -> 567490 bytes
 ...-data-rendered-date-plot-challenge-answer-1.png |  Bin 453296 -> 454737 bytes
 ...ata-rendered-time-series-challenge-answer-1.png |  Bin 212304 -> 212360 bytes
 md5sum.txt                                         |   26 +-
 renv.lock (gone)                                   | 4151 --------------------
 9 files changed, 13 insertions(+), 4250 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2025-10-07 16:08:55 +0000

[Bisaloo]

#943 didn't work because in more recent versions, ggplot2 ignores the global seed:

https://ggplot2.tidyverse.org/reference/position_jitter.html

We could take the seed into account by setting seed = NULL but it may add some overhead for learners and I don't think it's worth it.

What do you think @datacarpentry/r-ecology-lesson-maintainers?

[CarolynKoehn]

@Bisaloo I agree that having the learners use seed = NULL is an unnecessary cognitive burden. We could double up the code chunks, one to show the code and not run it, and the other to generate the plot but not show the code. Something like this:

```{r boxplot-jitter-code, warning=FALSE, eval=FALSE}
ggplot(data = complete_old, mapping = aes(x = plot_type, y = hindfoot_length)) +
geom_boxplot() +
geom_jitter(alpha = 0.2)
```

```{r boxplot-jitter-plot, warning=FALSE, echo=FALSE}
ggplot(data = complete_old, mapping = aes(x = plot_type, y = hindfoot_length)) +
geom_boxplot() +
geom_jitter(alpha = 0.2, seed=NULL)
```

[Bisaloo]

I've always found the echo = FALSE / eval = FALSE trick a bit annoying to maintain. At this point, I think it's becoming more inconvenient than the issue we're trying to resolve: the unnecessary diffs in the monthly package update.

Should we just accept the diffs and move forward?

[CarolynKoehn]

@Bisaloo, I'll defer to your judgement since you've been a maintainer for longer than I have, and I can see how doubling the code would be annoying to maintain. I think accepting the diffs is the best solution for now