update 50 packages

[zkamvar]

I've run the package update manually because the automated workflow was having trouble after the release of {renv} 1.0.0.

This brings in updates to 50 packages. Please wait for the output to run and then check for any new errors, warnings or surprising output changes.

I ran the following commands to update the cache with {renv} 1.0.2

sandpaper::manage_deps()
sandpaper::update_cache()

- 50 packages have updates available.

# BioCsoft -------------------------------------------------------------------
- affy              [1.78.0 -> 1.78.2]
- clusterProfiler   [4.8.1 -> 4.8.3]
- DelayedArray      [0.26.6 -> 0.26.7]
- enrichplot        [1.20.0 -> 1.20.1]
- GenomeInfoDb      [1.36.1 -> 1.36.2]
- ggtree            [3.8.0 -> 3.8.2]
- GOSemSim          [2.26.0 -> 2.26.1]
- MatrixGenerics    [1.12.2 -> 1.12.3]
- S4Arrays          [1.0.4 -> 1.0.6]
- treeio            [1.24.1 -> 1.24.3]

# CRAN -----------------------------------------------------------------------
- aplot             [0.1.10 -> 0.2.0]
- askpass           [1.1 -> 1.2.0]
- BiocManager       [1.30.21 -> 1.30.22]
- boot              [1.3-28 -> 1.3-28.1]
- bslib             [repo: RSPM -> CRAN; ver: 0.5.0 -> 0.5.1]
- cpp11             [repo: RSPM -> CRAN; ver: 0.4.4 -> 0.4.6]
- curl              [repo: RSPM -> CRAN; ver: 5.0.1 -> 5.0.2]
- dplyr             [1.1.2 -> 1.1.3]
- DT                [0.28 -> 0.29]
- fastmatch         [1.1-3 -> 1.1-4]
- fontawesome       [0.5.1 -> 0.5.2]
- foreign           [0.8-82 -> 0.8-84]
- fs                [1.6.2 -> 1.6.3]
- ggfun             [0.1.1 -> 0.1.2]
- ggplot2           [3.4.2 -> 3.4.3]
- ggplotify         [0.1.1 -> 0.1.2]
- gtable            [0.3.3 -> 0.3.4]
- htmltools         [repo: RSPM -> CRAN; ver: 0.5.5 -> 0.5.6]
- httr              [1.4.6 -> 1.4.7]
- igraph            [1.5.0 -> 1.5.1]
- labeling          [0.4.2 -> 0.4.3]
- Matrix            [1.5-4.1 -> 1.6-1]
- mgcv              [1.8-42 -> 1.9-0]
- mvtnorm           [1.2-2 -> 1.2-3]
- nlme              [3.1-162 -> 3.1-163]
- openssl           [2.0.6 -> 2.1.0]
- patchwork         [1.1.2 -> 1.1.3]
- promises          [repo: RSPM -> CRAN; ver: 1.2.0.1 -> 1.2.1]
- purrr             [repo: RSPM -> CRAN; ver: 1.0.1 -> 1.0.2]
- RcppArmadillo     [0.12.4.1.0 -> 0.12.6.3.0]
- renv              [0.17.3 -> 1.0.2]
- rmarkdown         [repo: RSPM -> CRAN; ver: 2.23 -> 2.24]
- sass              [0.4.6 -> 0.4.7]
- shiny             [1.7.4.1 -> 1.7.5]
- survival          [3.5-5 -> 3.5-7]
- tidytree          [0.4.2 -> 0.4.5]
- tinytex           [0.45 -> 0.46]
- viridis           [0.6.3 -> 0.6.4]
- xfun              [0.39 -> 0.40]
- yulab.utils       [0.0.6 -> 0.0.9]

[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/carpentries-incubator/bioc-rnaseq/compare/md-outputs..md-outputs-PR-79

The following changes were observed in the rendered markdown documents:

 03-import-annotate.md                              |   17 +-
 04-exploratory-qc.md                               |   34 +-
 07-gene-set-analysis.md                            |    8 +-
 config.yaml (gone)                                 |   86 -
 ...tial-expression-rendered-unnamed-chunk-19-1.png |  Bin 22609 -> 22606 bytes
 ...a-design-rendered-unnamed-chunk-13-2.png (gone) |  Bin 19957 -> 0 bytes
 ...a-design-rendered-unnamed-chunk-18-2.png (gone) |  Bin 19957 -> 0 bytes
 ...a-design-rendered-unnamed-chunk-23-2.png (gone) |  Bin 19957 -> 0 bytes
 ...a-design-rendered-unnamed-chunk-26-2.png (gone) |  Bin 19957 -> 0 bytes
 ...ne-set-analysis-rendered-unnamed-chunk-15-1.png |  Bin 191067 -> 191001 bytes
 md5sum.txt                                         |   36 +-
 renv.lock (gone)                                   | 2762 --------------------
 12 files changed, 48 insertions(+), 2895 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 2023-09-05 16:15:36 +0000

[csoneson]

Thanks @zkamvar! Just wanted to be sure - should the config.yaml and renv.lock files disappear (the figures may be ok, perhaps I should actually render them in another way)? I see the same happened in the other bioc lessons.

[zkamvar]

Just wanted to be sure - should the config.yaml and renv.lock files disappear (the figures may be ok, perhaps I should actually render them in another way)? I see the same happened in the other bioc lessons.

This is a weird thing that happens only in the pull request previews and I'm not sure why, but these actions are ultimately harmless as they always end up appearing in the correct places in the end.

[csoneson]

Ok, thanks!

[zkamvar]

I think for the images, it's a bit confusing as to why they would disappear like that and I'm running the lesson locally now to see if that's a real problem or if that's an artefact of the PR process. One thing I would recommend is to use a package like {namer} to name the chunks: https://jumpingrivers.github.io/namer/ and then continue to name them as you go along.

[zkamvar]

It looks like they appear locally, so it's likely a bug in the PR preview mechanism.

[csoneson]

👍🏻 And yes, totally agree about the naming, this was an oversight from my side - I'll update the chunks.