Update 11 packages

[carpentries-bot]

🤖 This is an automated build

This will update 11 packages in your lesson with the following versions:

# NEW OR REMOVED PACKAGES -------------------------------
- lattice  [required by hexbin, Matrix]
- mgcv     [required by ggplot2]
- lattice   [0.22-5 -> *]
- mgcv      [1.9-1 -> *]
- nlme      [3.1-164 -> *]

# CRAN -----------------------------------------------------------------------
- callr        [repo: RSPM -> CRAN; ver: 3.7.3 -> 3.7.5]
- data.table   [1.15.0 -> 1.15.2]
- DBI          [1.2.1 -> 1.2.2]
- ggplot2      [3.4.4 -> 3.5.0]
- renv         [1.0.3 -> 1.0.5]
- rvest        [1.0.3 -> 1.0.4]
- xfun         [0.41 -> 0.42]
- lattice      [* -> 0.22-5]
- mgcv         [* -> 1.9-1]

# RSPM -----------------------------------------------------------------------
- nlme         [* -> 3.1-164]

# carpentries ----------------------------------------------------------------
- curl         [repo: RSPM -> carpentries; ver: 5.2.0 -> 5.2.1]

⏱️ 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 2024-03-05

[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-intro/compare/md-outputs..md-outputs-PR-124

The following changes were observed in the rendered markdown documents:

 20-r-rstudio.md                                    |    2 +-
 40-visualization.md                                |    5 +-
 config.yaml (gone)                                 |   85 -
 fig/40-visualization-rendered-adding-diag-1.png    |  Bin 52525 -> 52507 bytes
 ...visualization-rendered-boxplot-color-time-1.png |  Bin 301488 -> 302066 bytes
 ...visualization-rendered-boxplot-color-time-2.png |  Bin 258641 -> 259343 bytes
 ...isualization-rendered-boxplot-with-points-1.png |  Bin 336234 -> 336077 bytes
 ...sualization-rendered-boxplot-with-points2-1.png |  Bin 344980 -> 345382 bytes
 ...ualization-rendered-boxplot-xaxis-rotated-1.png |  Bin 306993 -> 306355 bytes
 ...alization-rendered-color-by-gene_biotype1-1.png |  Bin 48929 -> 48926 bytes
 ...alization-rendered-color-by-gene_biotype2-1.png |  Bin 48929 -> 48926 bytes
 ...alization-rendered-color-by-gene_biotype3-1.png |  Bin 52525 -> 52502 bytes
 ...ualization-rendered-facet-by-gene-and-sex-1.png |  Bin 51748 -> 51751 bytes
 ...-rendered-mean-exp-time-facet-sex-columns-1.png |  Bin 49462 -> 49460 bytes
 ...ion-rendered-mean-exp-time-facet-sex-rows-1.png |  Bin 43978 -> 44072 bytes
 ...ean_exp-time-with-right-labels-xfont-size-1.png |  Bin 54111 -> 54311 bytes
 ...ization-rendered-mean_exp-time-with-theme-1.png |  Bin 67979 -> 67974 bytes
 fig/40-visualization-rendered-plotmethod-1.png     |  Bin 11660 -> 11430 bytes
 ...lization-rendered-time-series-with-colors-1.png |  Bin 33618 -> 33573 bytes
 ...0-visualization-rendered-unnamed-chunk-12-1.png |  Bin 63435 -> 63448 bytes
 ...0-visualization-rendered-unnamed-chunk-13-1.png |  Bin 62546 -> 62541 bytes
 md5sum.txt                                         |   34 +-
 renv.lock (gone)                                   | 1981 --------------------
 23 files changed, 21 insertions(+), 2086 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 2024-03-05 00:39:16 +0000