Update 23 packages

[carpentries-bot]

🤖 This is an automated build

This will update 23 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- codetools  [required by BiocParallel]
- codetools   [0.2-19 -> *]

# Bioconductor ---------------------------------------------------------------
- BiocStyle       [2.28.0 -> 2.28.1]
- GenomeInfoDb    [1.36.2 -> 1.36.4]
- GenomicRanges   [1.52.0 -> 1.52.1]
- S4Vectors       [0.38.1 -> 0.38.2]

# CRAN -----------------------------------------------------------------------
- bookdown        [0.35 -> 0.36]
- curl            [5.0.2 -> 5.1.0]
- evaluate        [0.21 -> 0.23]
- htmltools       [0.5.6 -> 0.5.7]
- knitr           [1.43 -> 1.45]
- lattice         [0.21-8 -> 0.22-5]
- lubridate       [1.9.2 -> 1.9.3]
- Matrix          [1.6-1 -> 1.6-1.1]
- openssl         [2.1.0 -> 2.1.1]
- plyr            [1.8.8 -> 1.8.9]
- RCurl           [1.98-1.12 -> 1.98-1.13]
- renv            [1.0.2 -> 1.0.3]
- rlang           [1.1.1 -> 1.1.2]
- rmarkdown       [2.24 -> 2.25]
- tinytex         [0.46 -> 0.48]
- vctrs           [0.6.3 -> 0.6.4]
- xfun            [0.40 -> 0.41]
- XML             [3.99-0.14 -> 3.99-0.15]
- codetools       [* -> 0.2-19]

⏱️ 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 2023-11-07

[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/carpentries-incubator/bioc-project/compare/md-outputs..md-outputs-PR-76

The following changes were observed in the rendered markdown documents:

 03-installing-bioconductor.md |   50 +-
 config.yaml (gone)            |   85 ---
 md5sum.txt                    |   34 +-
 renv.lock (gone)              | 1165 -----------------------------------------
 4 files changed, 65 insertions(+), 1269 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 2023-11-07 01:43:24 +0000

[zkamvar]

Just a note: this is the first time I've ever seen the "package too new" message from BioConductor. It seems that nothing else in the lesson has changed, so it should be fine.

[kevinrue]

I usually have that message when I install a package from GitHub, which can give me a version more recent than the one currently available from Bioconductor.
It might also be possible when the versions available as source/binary are different.
I usually don't worry about that if the installed package works as expected :)