Update 45 packages

[sstevens2]

🤖 This is an automated build

This will update 45 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- MASS  [required by ggplot2]
- nlme  [required by mgcv]
- backports       [1.4.1 -> *]
- blob            [1.2.4 -> *]
- broom           [1.0.5 -> *]
- conflicted      [1.2.0 -> *]
- curl            [5.0.2 -> *]
- data.table      [1.14.8 -> *]
- DBI             [1.1.3 -> *]
- dbplyr          [2.3.3 -> *]
- dtplyr          [1.3.1 -> *]
- forcats         [1.0.0 -> *]
- gargle          [1.5.2 -> *]
- googledrive     [2.1.1 -> *]
- googlesheets4   [1.1.1 -> *]
- haven           [2.5.3 -> *]
- httr            [1.4.7 -> *]
- ids             [1.0.1 -> *]
- lubridate       [1.9.2 -> *]
- MASS            [7.3-60 -> *]
- modelr          [0.1.11 -> *]
- nlme            [3.1-163 -> *]
- openssl         [2.1.0 -> *]
- processx        [3.8.2 -> *]
- ps              [1.7.5 -> *]
- ragg            [1.2.5 -> *]
- rematch2        [2.1.2 -> *]
- reprex          [2.0.2 -> *]
- rstudioapi      [0.15.0 -> *]
- rvest           [1.0.3 -> *]
- selectr         [0.4-2 -> *]
- sys             [3.4.2 -> *]
- tidyverse       [2.0.0 -> *]
- timechange      [0.2.0 -> *]
- xml2            [1.3.5 -> *]
- askpass         [1.2.0 -> *]
- callr           [3.7.3 -> *]
- systemfonts     [1.0.4 -> *]
- textshaping     [0.3.6 -> *]
- uuid            [1.1-1 -> *]
- R               [4.3.1 -> 4.4.0]

# CRAN -----------------------------------------------------------------------
- bslib         [0.5.1 -> 0.7.0]
- cachem        [1.0.8 -> 1.1.0]
- cli           [3.6.1 -> 3.6.2]
- cpp11         [0.4.6 -> 0.4.7]
- digest        [0.6.33 -> 0.6.35]
- 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]
- farver        [2.1.1 -> 2.1.2]
- fastmap       [1.1.1 -> 1.2.0]
- fs            [1.6.3 -> 1.6.4]
- ggplot2       [repo: RSPM -> CRAN; ver: 3.4.3 -> 3.5.1]
- glue          [repo: RSPM -> CRAN; ver: 1.6.2 -> 1.7.0]
- gtable        [0.3.4 -> 0.3.5]
- highr         [repo: RSPM -> CRAN; ver: 0.10 -> 0.11]
- htmltools     [0.5.6 -> 0.5.8.1]
- jsonlite      [1.8.7 -> 1.8.8]
- knitr         [1.43 -> 1.46]
- lattice       [0.21-8 -> 0.22-6]
- lifecycle     [repo: RSPM -> CRAN; ver: 1.0.3 -> 1.0.4]
- Matrix        [1.6-1 -> 1.7-0]
- mgcv          [1.9-0 -> 1.9-1]
- munsell       [0.5.0 -> 0.5.1]
- prettyunits   [1.1.1 -> 1.2.0]
- progress      [1.2.2 -> 1.2.3]
- readr         [2.1.4 -> 2.1.5]
- renv          [1.0.2 -> 1.0.7]
- rlang         [1.1.1 -> 1.1.3]
- rmarkdown     [2.24 -> 2.27]
- sass          [0.4.7 -> 0.4.9]
- scales        [1.2.1 -> 1.3.0]
- stringr       [repo: RSPM -> CRAN; ver: 1.5.0 -> 1.5.1]
- tidyr         [1.3.0 -> 1.3.1]
- tidyselect    [repo: RSPM -> CRAN; ver: 1.2.0 -> 1.2.1]
- tinytex       [0.46 -> 0.51]
- 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 -> 3.0.0]
- xfun          [0.40 -> 0.44]
- yaml          [2.3.7 -> 2.3.8]
- MASS          [* -> 7.3-60.2]
- nlme          [* -> 3.1-164]

# RSPM -----------------------------------------------------------------------
- ellipsis      [0.3.2 -> *]

# carpentries ----------------------------------------------------------------
- stringi       [repo: RSPM -> carpentries; ver: 1.7.12 -> 1.8.4]

⏱️ 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 2024-05-28

[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/UW-Madison-DataScience/phmsci756-genomics-r-intro/compare/md-outputs..md-outputs-PR-4

The following changes were observed in the rendered markdown documents:

 00-introduction.md                                 |  30 +-
 01-r-basics.md                                     |  46 +-
 05-dplyr.md                                        | 148 ++--
 06-data-visualization.md                           |  75 +-
 07-r-help.md                                       |   6 +-
 08-vectors-extra.md                                | 126 +--
 09-basics-factors-dataframes.md                    | 202 +++--
 10-bioconductor-vcfr.md                            |   6 +-
 config.yaml (gone)                                 |  89 --
 depth.pdf                                          | Bin 45066 -> 45059 bytes
 ...ta-visualization-rendered-add-axis-labels-1.png | Bin 54735 -> 54734 bytes
 ...ata-visualization-rendered-add-main-title-1.png | Bin 56188 -> 56184 bytes
 ...lization-rendered-add-main-title-asobject-1.png | Bin 56188 -> 56184 bytes
 fig/06-data-visualization-rendered-barplot-1.png   | Bin 6215 -> 6219 bytes
 ...visualization-rendered-change-font-family-1.png | Bin 55515 -> 55514 bytes
 ...-visualization-rendered-color-by-sample-1-1.png | Bin 52809 -> 52806 bytes
 ...-visualization-rendered-color-by-sample-2-1.png | Bin 40793 -> 40792 bytes
 fig/06-data-visualization-rendered-density-1.png   | Bin 9353 -> 9389 bytes
 ...-visualization-rendered-density-challenge-1.png | Bin 22858 -> 22663 bytes
 ...6-data-visualization-rendered-first-facet-1.png | Bin 21523 -> 21530 bytes
 ...-visualization-rendered-scatter-challenge-1.png | Bin 18293 -> 18292 bytes
 ...isualization-rendered-scatter-challenge-2-1.png | Bin 56612 -> 56608 bytes
 ...-data-visualization-rendered-second-facet-1.png | Bin 26328 -> 26338 bytes
 md5sum.txt                                         |  38 +-
 renv.lock (gone)                                   | 979 ---------------------
 25 files changed, 338 insertions(+), 1407 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 2024-05-28 20:46:02 +0000