Update 109 packages #1

cjfields · 2024-12-12T20:11:51Z

🤖 This is an automated build

This will update 109 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- SummarizedExperiment
- tidySummarizedExperiment
- lattice  [required by hexbin]
- MASS     [required by ggplot2]
- mgcv     [required by ggplot2]
- askpass         [* -> 1.2.1]
- backports       [* -> 1.5.0]
- base64enc       [* -> 0.1-3]
- bit             [* -> 4.5.0.1]
- bit64           [* -> 4.5.2]
- blob            [* -> 1.2.4]
- broom           [* -> 1.0.7]
- bslib           [* -> 0.8.0]
- cachem          [* -> 1.1.0]
- callr           [* -> 3.7.6]
- cellranger      [* -> 1.1.0]
- cli             [* -> 3.6.3]
- clipr           [* -> 0.8.0]
- colorspace      [* -> 2.1-1]
- conflicted      [* -> 1.2.0]
- cpp11           [* -> 0.5.1]
- crayon          [* -> 1.5.3]
- curl            [* -> 6.0.1]
- data.table      [* -> 1.16.4]
- DBI             [* -> 1.2.3]
- dbplyr          [* -> 2.5.0]
- digest          [* -> 0.6.37]
- dplyr           [* -> 1.1.4]
- dtplyr          [* -> 1.3.1]
- evaluate        [* -> 1.0.1]
- fansi           [* -> 1.0.6]
- farver          [* -> 2.1.2]
- fastmap         [* -> 1.2.0]
- fontawesome     [* -> 0.5.3]
- forcats         [* -> 1.0.0]
- fs              [* -> 1.6.5]
- gargle          [* -> 1.5.2]
- generics        [* -> 0.1.3]
- ggplot2         [* -> 3.5.1]
- glue            [* -> 1.8.0]
- googledrive     [* -> 2.1.1]
- googlesheets4   [* -> 1.1.1]
- gridExtra       [* -> 2.3]
- gtable          [* -> 0.3.6]
- haven           [* -> 2.5.4]
- hexbin          [* -> 1.28.5]
- highr           [* -> 0.11]
- hms             [* -> 1.1.3]
- htmltools       [* -> 0.5.8.1]
- httr            [* -> 1.4.7]
- ids             [* -> 1.0.1]
- isoband         [* -> 0.2.7]
- jquerylib       [* -> 0.1.4]
- jsonlite        [* -> 1.8.9]
- knitr           [* -> 1.49]
- labeling        [* -> 0.4.3]
- lifecycle       [* -> 1.0.4]
- lubridate       [* -> 1.9.4]
- magrittr        [* -> 2.0.3]
- memoise         [* -> 2.0.1]
- mime            [* -> 0.12]
- modelr          [* -> 0.1.11]
- munsell         [* -> 0.5.1]
- openssl         [* -> 2.2.2]
- patchwork       [* -> 1.3.0]
- pillar          [* -> 1.9.0]
- pkgconfig       [* -> 2.0.3]
- prettyunits     [* -> 1.2.0]
- processx        [* -> 3.8.4]
- progress        [* -> 1.2.3]
- ps              [* -> 1.8.1]
- purrr           [* -> 1.0.2]
- R6              [* -> 2.5.1]
- ragg            [* -> 1.3.3]
- rappdirs        [* -> 0.3.3]
- RColorBrewer    [* -> 1.1-3]
- readr           [* -> 2.1.5]
- readxl          [* -> 1.4.3]
- rematch         [* -> 2.0.0]
- rematch2        [* -> 2.1.2]
- reprex          [* -> 2.1.1]
- rlang           [* -> 1.1.4]
- rmarkdown       [* -> 2.29]
- rstudioapi      [* -> 0.17.1]
- rvest           [* -> 1.0.4]
- sass            [* -> 0.4.9]
- scales          [* -> 1.3.0]
- selectr         [* -> 0.4-2]
- stringi         [* -> 1.8.4]
- stringr         [* -> 1.5.1]
- sys             [* -> 3.4.3]
- systemfonts     [* -> 1.1.0]
- textshaping     [* -> 0.4.1]
- tibble          [* -> 3.2.1]
- tidyr           [* -> 1.3.1]
- tidyselect      [* -> 1.2.1]
- tidyverse       [* -> 2.0.0]
- timechange      [* -> 0.3.0]
- tinytex         [* -> 0.54]
- tzdb            [* -> 0.4.0]
- utf8            [* -> 1.2.4]
- uuid            [* -> 1.2-1]
- vctrs           [* -> 0.6.5]
- viridisLite     [* -> 0.4.2]
- vroom           [* -> 1.6.5]
- withr           [* -> 3.0.2]
- xfun            [* -> 0.49]
- xml2            [* -> 1.3.6]
- yaml            [* -> 2.3.10]
- R               [4.4.1 -> 4.4.2]

# CRAN -----------------------------------------------------------------------
- lattice   [* -> 0.22-6]
- MASS      [* -> 7.3-61]
- Matrix    [* -> 1.7-1]
- mgcv      [* -> 1.9-1]
- nlme      [* -> 3.1-166]

⏱️ 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 2024-12-12

github-actions · 2024-12-12T20:12:04Z

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/HPCBio/hpcbio-swc-bioc-intro/compare/md-outputs..md-outputs-PR-1

The following changes were observed in the rendered markdown documents:

 20-r-rstudio.md                                    |   38 +-
 23-starting-with-r.md                              |  362 ++--
 25-starting-with-data.md                           |  148 +-
 30-dplyr.md                                        |  296 +--
 40-visualization.md                                |  164 +-
 60-next-steps.md                                   |  148 +-
 config.yaml (gone)                                 |   85 -
 ...starting-with-r-rendered-unnamed-chunk-61-1.png |  Bin 13142 -> 13155 bytes
 ...visualization-rendered-boxplot-color-time-1.png |  Bin 301654 -> 301632 bytes
 ...visualization-rendered-boxplot-color-time-2.png |  Bin 259692 -> 259489 bytes
 ...isualization-rendered-boxplot-with-points-1.png |  Bin 335420 -> 336237 bytes
 ...sualization-rendered-boxplot-with-points2-1.png |  Bin 345173 -> 344366 bytes
 ...ualization-rendered-boxplot-xaxis-rotated-1.png |  Bin 307189 -> 306867 bytes
 ...alization-rendered-color-by-gene_biotype3-1.png |  Bin 52509 -> 52512 bytes
 fig/40-visualization-rendered-plotmethod-1.png     |  Bin 11325 -> 11653 bytes
 ...0-visualization-rendered-unnamed-chunk-12-1.png |  Bin 63448 -> 63644 bytes
 ...0-visualization-rendered-unnamed-chunk-13-1.png |  Bin 62541 -> 62408 bytes
 fig/60-next-steps-rendered-tidySE-plot-1.png       |  Bin 50957 -> 50895 bytes
 md5sum.txt                                         |   34 +-
 renv.lock (gone)                                   | 1980 --------------------
 20 files changed, 595 insertions(+), 2660 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 2024-12-12 20:22:55 +0000