update 50 packages #79

zkamvar · 2023-09-05T16:02:54Z

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 · 2023-09-05T16:03:11Z

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-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.

⏱️ Updated at 2023-09-05 16:15:36 +0000

csoneson · 2023-09-05T16:55:51Z

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 · 2023-09-05T17:13:51Z

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 · 2023-09-05T17:19:02Z

Ok, thanks!

zkamvar · 2023-09-05T17:25:17Z

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 · 2023-09-05T17:27:48Z

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

csoneson · 2023-09-05T17:28:34Z

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

Auto-generated via {sandpaper} Source : 047cf62 Branch : main Author : Charlotte Soneson <[email protected]> Time : 2023-09-05 17:19:07 +0000 Message : Merge pull request #79 from carpentries-incubator/znk/update/packages update 50 packages

Auto-generated via {sandpaper} Source : 3c789c8 Branch : md-outputs Author : GitHub Actions <[email protected]> Time : 2023-09-05 17:31:41 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 047cf62 Branch : main Author : Charlotte Soneson <[email protected]> Time : 2023-09-05 17:19:07 +0000 Message : Merge pull request #79 from carpentries-incubator/znk/update/packages update 50 packages

update 50 packages

a97fde2

github-actions bot pushed a commit that referenced this pull request Sep 5, 2023

differences for PR #79

182bf2d

csoneson merged commit 047cf62 into main Sep 5, 2023
3 checks passed

zkamvar deleted the znk/update/packages branch September 5, 2023 17:28

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update 50 packages #79

update 50 packages #79

zkamvar commented Sep 5, 2023

github-actions bot commented Sep 5, 2023 •

edited

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csoneson commented Sep 5, 2023

zkamvar commented Sep 5, 2023

csoneson commented Sep 5, 2023

zkamvar commented Sep 5, 2023

zkamvar commented Sep 5, 2023

csoneson commented Sep 5, 2023

update 50 packages #79

update 50 packages #79

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zkamvar commented Sep 5, 2023

github-actions bot commented Sep 5, 2023 • edited Loading

Thank you!

Rendered Changes

csoneson commented Sep 5, 2023

zkamvar commented Sep 5, 2023

csoneson commented Sep 5, 2023

zkamvar commented Sep 5, 2023

zkamvar commented Sep 5, 2023

csoneson commented Sep 5, 2023

github-actions bot commented Sep 5, 2023 •

edited

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