Update 22 packages

[carpentries-bot]

🤖 This is an automated build

This will update 22 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- class     [required by clValid]
- Matrix    [required by beachmat, BiocSingular, bluster, and 17 others]
- mgcv      [required by ggplot2]
- survival  [required by glmnet]
- class      [7.3-23 -> *]
- mgcv       [1.9-1 -> *]
- nlme       [3.1-167 -> *]
- survival   [3.8-3 -> *]
- Matrix     [1.7-3 -> *]
- R          [4.4.3 -> 4.5.0]

# Bioconductor ---------------------------------------------------------------
- BiocParallel   [repo: Bioconductor 3.20 -> *; ver: 1.40.0 -> 1.40.2]

# CRAN -----------------------------------------------------------------------
- class          [* -> 7.3-23]
- Matrix         [* -> 1.7-3]
- mgcv           [* -> 1.9-1]
- survival       [* -> 3.8-3]

# RSPM -----------------------------------------------------------------------
- cli            [3.6.4 -> 3.6.5]
- colorspace     [2.1-1 -> *]
- fs             [repo: CRAN -> RSPM; ver: 1.6.5 -> 1.6.6]
- ggplot2        [3.5.1 -> 3.5.2]
- lattice        [0.22-6 -> 0.22-7]
- munsell        [0.5.1 -> *]
- pillar         [1.10.1 -> 1.10.2]
- ragg           [1.3.3 -> 1.4.0]
- rlang          [repo: CRAN -> RSPM; ver: 1.1.5 -> 1.1.6]
- sass           [repo: CRAN -> RSPM; ver: 0.4.9 -> 0.4.10]
- scales         [1.3.0 -> 1.4.0]
- systemfonts    [1.2.1 -> 1.2.3]
- textshaping    [1.0.0 -> 1.0.1]
- tinytex        [0.56 -> 0.57]
- utf8           [1.2.4 -> 1.2.5]
- xfun           [0.51 -> 0.52]
- nlme           [* -> 3.1-168]

⏱️ 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 2025-05-06

[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-189

The following changes were observed in the rendered markdown documents:

 02-high-dimensional-regression.md                  |  62 ++++++++++-----------
 03-regression-regularisation.md                    |  16 +++---
 07-hierarchical.md                                 |   6 +-
 ...gression-regularisation-rendered-binomial-1.png | Bin 26891 -> 26638 bytes
 ...sion-regularisation-rendered-chooselambda-1.png | Bin 43815 -> 42239 bytes
 ...egression-regularisation-rendered-elastic-1.png | Bin 66277 -> 69006 bytes
 ...ession-regularisation-rendered-elastic-cv-1.png | Bin 25206 -> 25567 bytes
 ...gression-regularisation-rendered-lasso-cv-1.png | Bin 23898 -> 23583 bytes
 ...ession-regularisation-rendered-plot-ridge-1.png | Bin 42860 -> 42578 bytes
 ...egression-regularisation-rendered-plotlas-1.png | Bin 91862 -> 53174 bytes
 ...omponent-analysis-rendered-pca-biplot-ex2-1.png | Bin 48857 -> 48523 bytes
 ...-component-analysis-rendered-stats-biplot-1.png | Bin 42019 -> 42580 bytes
 ...-factor-analysis-rendered-unnamed-chunk-1-1.png | Bin 3875 -> 3220 bytes
 ...rarchical-rendered-plot-coloured-branches-1.png | Bin 6840 -> 6621 bytes
 md5sum.txt                                         |  34 +++++------
 15 files changed, 61 insertions(+), 57 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 2025-09-02 08:37:33 +0000

[alanocallaghan]

lgtm