Update 50 packages

[carpentries-bot]

🤖 This is an automated build

This will update 50 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- codetools   [required by foreach, globals]
- KernSmooth  [required by gplots, prodlim]
- lattice     [required by caret]
- Matrix      [required by recipes]
- nlme        [required by caret]
- nnet        [required by Hmisc, ipred]
- rpart       [required by Hmisc, ipred]
- survival    [required by genefilter, ipred, lava, and 1 other]
- hgu95acdf        [* -> 2.18.0]
- affy             [* -> 1.88.0]
- affyio           [* -> 1.80.0]
- annotate         [* -> 1.88.0]
- AnnotationDbi    [* -> 1.72.0]
- Biobase          [* -> 2.70.0]
- BiocGenerics     [* -> 0.56.0]
- BiocVersion      [* -> 3.22.0]
- Biostrings       [* -> 2.78.0]
- genefilter       [* -> 1.92.0]
- IRanges          [* -> 2.44.0]
- KEGGREST         [* -> 1.50.0]
- MatrixGenerics   [* -> 1.22.0]
- preprocessCore   [* -> 1.72.0]
- S4Vectors        [* -> 0.48.0]
- Seqinfo          [* -> 1.0.0]
- SpikeIn          [* -> 1.52.0]
- XVector          [* -> 0.50.0]
- codetools        [0.2-19 -> *]
- KernSmooth       [2.23-26 -> *]
- lattice          [0.22-5 -> *]
- Matrix           [1.7-4 -> *]
- nlme             [3.1-168 -> *]
- nnet             [7.3-20 -> *]
- rpart            [4.1.24 -> *]
- survival         [3.8-6 -> *]
- askpass          [* -> 1.2.1]
- bit              [* -> 4.6.0]
- bit64            [* -> 4.6.0-1]
- blob             [* -> 1.3.0]
- crayon           [* -> 1.5.3]
- curl             [* -> 7.0.0]
- DBI              [* -> 1.3.0]
- httr             [* -> 1.4.8]
- matrixStats      [* -> 1.5.0]
- openssl          [* -> 2.3.5]
- png              [* -> 0.1-8]
- RSQLite          [* -> 2.4.6]
- sys              [* -> 3.4.3]
- XML              [* -> 3.99-0.22]
- xtable           [* -> 1.8-8]

# CRAN -----------------------------------------------------------------------
- checkmate      [2.3.3 -> 2.3.4]
- cluster        [repo: RSPM -> CRAN; ver: 2.1.8.1 -> 2.1.8.2]
- dplyr          [1.1.4 -> 1.2.0]
- foreign        [repo: RSPM -> CRAN; ver: 0.8-90 -> 0.8-91]
- future.apply   [1.20.1 -> 1.20.2]
- ggplot2        [4.0.1 -> 4.0.2]
- lubridate      [1.9.4 -> 1.9.5]
- UsingR         [repo: RSPM -> CRAN; ver: 2.0-7 -> 2.0-8]
- viridisLite    [0.4.2 -> 0.4.3]
- codetools      [* -> 0.2-19]
- KernSmooth     [* -> 2.23-26]
- lattice        [* -> 0.22-5]
- Matrix         [* -> 1.7-4]
- nlme           [* -> 3.1-168]
- nnet           [* -> 7.3-20]
- rpart          [* -> 4.1.24]
- survival       [* -> 3.8-6]

⏱️ 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]

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Results of any additional workflows will appear here when they are done.