Update 46 packages

[carpentries-bot]

:robot: This is an automated build

This will update 46 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- MASS  [required by ggplot2]
- mgcv  [required by ggplot2]
- lattice   [0.21-8 -> *]
- MASS      [7.3-60 -> *]
- Matrix    [1.6-1 -> *]
- mgcv      [1.9-0 -> *]
- nlme      [3.1-163 -> *]
- R         [4.3.1 -> 4.3.2]

# CRAN -----------------------------------------------------------------------
- bslib         [0.5.1 -> 0.6.1]
- cli           [3.6.1 -> 3.6.2]
- cpp11         [0.4.6 -> 0.4.7]
- data.table    [1.14.8 -> 1.14.10]
- DBI           [1.1.3 -> 1.2.0]
- dbplyr        [2.3.3 -> 2.4.0]
- dplyr         [repo: RSPM -> CRAN; ver: 1.1.3 -> 1.1.4]
- evaluate      [0.21 -> 0.23]
- fansi         [repo: RSPM -> CRAN; ver: 1.0.4 -> 1.0.6]
- ggplot2       [repo: RSPM -> CRAN; ver: 3.4.3 -> 3.4.4]
- haven         [repo: RSPM -> CRAN; ver: 2.5.3 -> 2.5.4]
- htmltools     [0.5.6 -> 0.5.7]
- hunspell      [3.0.2 -> 3.0.3]
- jsonlite      [repo: RSPM -> CRAN; ver: 1.8.7 -> 1.8.8]
- knitr         [1.43 -> 1.45]
- lifecycle     [repo: RSPM -> CRAN; ver: 1.0.3 -> 1.0.4]
- lubridate     [1.9.2 -> 1.9.3]
- openssl       [2.1.0 -> 2.1.1]
- prettyunits   [1.1.1 -> 1.2.0]
- processx      [repo: RSPM -> CRAN; ver: 3.8.2 -> 3.8.3]
- progress      [1.2.2 -> 1.2.3]
- renv          [1.0.2 -> 1.0.3]
- rlang         [1.1.1 -> 1.1.2]
- rmarkdown     [2.24 -> 2.25]
- RSQLite       [2.3.1 -> 2.3.4]
- sass          [0.4.7 -> 0.4.8]
- scales        [1.2.1 -> 1.3.0]
- stringr       [repo: RSPM -> CRAN; ver: 1.5.0 -> 1.5.1]
- tinytex       [0.46 -> 0.49]
- utf8          [repo: RSPM -> CRAN; ver: 1.2.3 -> 1.2.4]
- vctrs         [0.6.3 -> 0.6.5]
- vroom         [1.6.3 -> 1.6.5]
- withr         [repo: RSPM -> CRAN; ver: 2.5.0 -> 2.5.2]
- xfun          [0.40 -> 0.41]
- yaml          [2.3.7 -> 2.3.8]
- lattice       [* -> 0.22-5]
- MASS          [* -> 7.3-60]
- Matrix        [* -> 1.6-4]
- mgcv          [* -> 1.9-1]
- nlme          [* -> 3.1-164]

# https://carpentries.r-universe.dev -----------------------------------------
- curl          [repo: CRAN -> https://carpentries.r-universe.dev; ver: 5.0.2 -> 5.2.0]
- ragg          [repo: CRAN -> https://carpentries.r-universe.dev; ver: 1.2.5 -> 1.2.7]
- stringi       [repo: RSPM -> https://carpentries.r-universe.dev; ver: 1.7.12 -> 1.8.3]
- systemfonts   [repo: RSPM -> https://carpentries.r-universe.dev; ver: 1.0.4 -> 1.0.5]
- textshaping   [repo: RSPM -> https://carpentries.r-universe.dev; ver: 0.3.6 -> 0.3.7]
- xml2          [repo: CRAN -> https://carpentries.r-universe.dev; ver: 1.3.5 -> 1.3.6]

:stopwatch: 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 2024-01-02

[github-actions[bot]]

Thank you!

Thank you for your pull request :smiley:

:robot: 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:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
• :bangbang: new errors

Rendered Changes

:mag: Inspect the changes: https://github.com/datacarpentry/R-ecology-lesson/compare/md-outputs..md-outputs-PR-878

The following changes were observed in the rendered markdown documents:

 00-before-we-start.md                              |   26 +-
 05-r-and-databases.md                              |   14 +-
 config.yaml (gone)                                 |   86 --
 ...tion-ggplot2-rendered-boxplot-with-points-1.png |  Bin 79734 -> 79838 bytes
 ...ization-ggplot2-rendered-unnamed-chunk-10-1.png |  Bin 97757 -> 97450 bytes
 ...ization-ggplot2-rendered-unnamed-chunk-11-1.png |  Bin 64738 -> 64225 bytes
 ...lization-ggplot2-rendered-unnamed-chunk-9-1.png |  Bin 82105 -> 82671 bytes
 md5sum.txt                                         |   34 +-
 renv.lock (gone)                                   | 1581 --------------------
 9 files changed, 37 insertions(+), 1704 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.

:stopwatch: Updated at 2024-01-02 00:24:15 +0000

[zkamvar]

Note: I manually triggered this yesterday. It normally gets triggered the first Tuesday of every month.

[jamesmbaazam]

Thanks @zkamvar. All the checks have passed. Can I merge?

[zkamvar]

@jamesmbaazam, The checks pass and it's important to double check the link from https://github.com/datacarpentry/R-ecology-lesson/pull/878#issuecomment-1775977163 to make sure that the only changes in the content are expected.

When I look at the link from the above comment (https://github.com/datacarpentry/R-ecology-lesson/compare/md-outputs..md-outputs-PR-878), I see no significant changes, which means that it's okay to merge.

[zkamvar]

Just a reminder that this is safe to merge.