Update 51 packages

[carpentries-bot]

🤖 This is an automated build

This will update 51 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- class  [required by clValid]
- nlme   [required by mgcv]
- class   [7.3-23 -> *]
- nlme    [3.1-168 -> *]
- R       [4.5.1 -> 4.5.2]

# CRAN -----------------------------------------------------------------------
- BiocManager     [repo: RSPM -> CRAN; ver: 1.30.26 -> 1.30.27]
- cluster         [repo: RSPM -> CRAN; ver: 2.1.8.1 -> 2.1.8.2]
- class           [* -> 7.3-23]

# RSPM -----------------------------------------------------------------------
- base64enc       [0.1-3 -> 0.1-6]
- BH              [1.87.0-1 -> 1.90.0-1]
- broom           [1.0.9 -> 1.0.12]
- bslib           [repo: CRAN -> RSPM; ver: 0.9.0 -> 0.10.0]
- Cairo           [1.6-5 -> 1.7-0]
- cpp11           [repo: CRAN -> RSPM; ver: 0.5.2 -> 0.5.3]
- digest          [repo: CRAN -> RSPM; ver: 0.6.37 -> 0.6.39]
- dplyr           [1.1.4 -> 1.2.0]
- futile.logger   [1.4.3 -> 1.4.9]
- ggbeeswarm      [0.7.2 -> 0.7.3]
- ggplot2         [3.5.2 -> 4.0.2]
- ggrepel         [0.9.6 -> 0.9.7]
- htmltools       [repo: CRAN -> RSPM; ver: 0.5.8.1 -> 0.5.9]
- httr            [repo: CRAN -> RSPM; ver: 1.4.7 -> 1.4.8]
- igraph          [2.1.4 -> 2.2.2]
- irlba           [2.3.5.1 -> 2.3.7]
- isoband         [0.2.7 -> 0.3.0]
- knitr           [1.50 -> 1.51]
- lattice         [0.22-7 -> 0.22-9]
- lifecycle       [repo: CRAN -> RSPM; ver: 1.0.4 -> 1.0.5]
- magrittr        [2.0.3 -> 2.0.4]
- Matrix          [repo: CRAN -> RSPM; ver: 1.7-3 -> 1.7-4]
- mgcv            [1.9-1 -> *]
- openssl         [2.3.3 -> 2.3.5]
- pillar          [1.11.0 -> 1.11.1]
- purrr           [1.1.0 -> 1.2.1]
- ragg            [1.4.0 -> 1.5.0]
- rappdirs        [repo: CRAN -> RSPM; ver: 0.3.3 -> 0.3.4]
- Rcpp            [1.1.0 -> 1.1.1]
- RcppAnnoy       [0.0.22 -> 0.0.23]
- renv            [1.1.5 -> 1.1.7]
- reshape2        [1.4.4 -> 1.4.5]
- rlang           [1.1.6 -> 1.1.7]
- rmarkdown       [repo: CRAN -> RSPM; ver: 2.29 -> 2.30]
- statmod         [1.5.0 -> 1.5.1]
- stringr         [1.5.1 -> 1.6.0]
- survival        [3.8-3 -> 3.8-6]
- systemfonts     [1.2.3 -> 1.3.1]
- textshaping     [repo: CRAN -> RSPM; ver: 1.0.2 -> 1.0.4]
- tibble          [3.3.0 -> 3.3.1]
- tidyr           [1.3.1 -> 1.3.2]
- tinytex         [0.57 -> 0.58]
- uwot            [0.2.3 -> 0.2.4]
- vctrs           [repo: CRAN -> RSPM; ver: 0.6.5 -> 0.7.1]
- viridisLite     [0.4.2 -> 0.4.3]
- xfun            [0.53 -> 0.56]
- yaml            [2.3.10 -> 2.3.12]
- S7              [* -> 0.2.1]

⏱️ 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 2026-03-03

[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/carpentries-incubator/high-dimensional-stats-r/compare/md-outputs..md-outputs-PR-192

The following changes were observed in the rendered markdown documents:

 01-introduction-to-high-dimensional-data.md        |  56 +++-
 02-high-dimensional-regression.md                  |  20 +-
 03-regression-regularisation.md                    |  33 +--
 07-hierarchical.md                                 | 299 ++++++++++++---------
 ...nsional-regression-rendered-heatmap-1.png (new) | Bin 0 -> 61935 bytes
 ...egularisation-rendered-elastic-plot-1.png (new) | Bin 0 -> 14588 bytes
 fig/07-hierarchical-rendered-cutree-1.png (new)    | Bin 0 -> 15367 bytes
 fig/07-hierarchical-rendered-h-k-ex-plot-1.png     | Bin 15875 -> 73885 bytes
 ...7-hierarchical-rendered-hclust-fig3-1.png (new) | Bin 0 -> 18840 bytes
 ...7-hierarchical-rendered-hclust-fig4-1.png (new) | Bin 0 -> 17432 bytes
 ...hierarchical-rendered-heatmap-clust-1.png (new) | Bin 0 -> 46930 bytes
 ...archical-rendered-heatmap-cor-cor-example-1.png | Bin 15791 -> 16349 bytes
 ...al-rendered-heatmap-cor-cor-example-2.png (new) | Bin 0 -> 15791 bytes
 ...chical-rendered-heatmap-cor-example-1.png (new) | Bin 0 -> 16411 bytes
 ...erarchical-rendered-heatmap-noclust-1.png (new) | Bin 0 -> 44655 bytes
 fig/07-hierarchical-rendered-plot-clust-dunn-1.png | Bin 15875 -> 73667 bytes
 ...7-hierarchical-rendered-plot-clust-method-1.png | Bin 16564 -> 80387 bytes
 ...hierarchical-rendered-plot-clusters-1.png (new) | Bin 0 -> 15523 bytes
 ...rarchical-rendered-plot-coloured-branches-1.png | Bin 8681 -> 22277 bytes
 md5sum.txt                                         |   8 +-
 20 files changed, 230 insertions(+), 186 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 2026-03-03 13:41:56 +0000

[alanocallaghan]

Outputs are fine but I want to suppress some of these messages/warnings before merging :)

[alanocallaghan]

Two PRs submitted to PCAtools, will wait a few weeks for response

[alanocallaghan]

PCAtools still broken

[alanocallaghan]

Found some errors in there as well... oops!