update 26 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 26 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()

- 26 packages have updates available.

# BioCsoft -------------------------------------------------------------------
- DelayedArray     [0.26.6 -> 0.26.7]
- GenomeInfoDb     [1.36.1 -> 1.36.2]
- MatrixGenerics   [1.12.2 -> 1.12.3]
- rtracklayer      [1.60.0 -> 1.60.1]
- S4Arrays         [1.0.4 -> 1.0.6]

# CRAN -----------------------------------------------------------------------
- askpass          [1.1 -> 1.2.0]
- BiocManager      [1.30.21 -> 1.30.22]
- bookdown         [0.34 -> 0.35]
- 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]
- fontawesome      [0.5.1 -> 0.5.2]
- foreign          [0.8-82 -> 0.8-84]
- fs               [1.6.2 -> 1.6.3]
- htmltools        [repo: RSPM -> CRAN; ver: 0.5.5 -> 0.5.6]
- httr             [1.4.6 -> 1.4.7]
- Matrix           [1.5-4.1 -> 1.6-1]
- nlme             [3.1-162 -> 3.1-163]
- openssl          [2.0.6 -> 2.1.0]
- renv             [0.17.3 -> 1.0.2]
- rmarkdown        [repo: RSPM -> CRAN; ver: 2.23 -> 2.24]
- sass             [0.4.6 -> 0.4.7]
- survival         [3.5-5 -> 3.5-7]
- tinytex          [0.45 -> 0.46]
- xfun             [0.39 -> 0.40]

[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-project/compare/md-outputs..md-outputs-PR-73

The following changes were observed in the rendered markdown documents:

 03-installing-bioconductor.md |   54 +-
 config.yaml (gone)            |   85 ---
 md5sum.txt                    |   34 +-
 renv.lock (gone)              | 1152 -----------------------------------------
 4 files changed, 19 insertions(+), 1306 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 14:51:49 +0000

[kevinrue]

All checks look green. Not sure what else to check before merging.

I should probably compile it at least once locally and briefly inspect the resulting site. I can't think of anything else.

[zkamvar]

All checks look green. Not sure what else to check before merging.

I should probably compile it at least once locally and briefly inspect the resulting site. I can't think of anything else.

You shouldn't need to build on your local machine if you don't have the time. The pull request workflow is described in the Reviewing a Pull Request chapter in the Workbench documentation.

The key things to look at are the files that have changed, which is present in the diff between the md-outputs branch and the md-outputs-PR73 branch and shown in summary in the first comment (note: the renv.lock and config.yaml files disappearing is an ephemeral and cosmetic bug that I cannot pin down, but I assure you it is not a problem).

 03-installing-bioconductor.md |   54 +-
 config.yaml (gone)            |   85 ---
 md5sum.txt                    |   34 +-
 renv.lock (gone)              | 1152 -----------------------------------------
 4 files changed, 19 insertions(+), 1306 deletions(-)

One thing that I see is that the BiocManager::valid() now returns an output of [1] TRUE instead of a warning and sessionInfo()

[kevinrue]

Thanks.

One thing that I see is that the BiocManager::valid() now returns an output of [1] TRUE instead of a warning and sessionInfo()

Having a look at https://carpentries-incubator.github.io/bioc-project/03-installing-bioconductor.html I think your PR is good in that the automated code returns TRUE while the following note demonstrates an output that isn't TRUE.

In brief, it's a good thing that the evaluated code returns TRUE again.

[zkamvar]

Hopefully, we won't go more than a month without these updates.

As a maintainer, if you ever need to update the packages for this lesson, you can go to https://github.com/carpentries-incubator/bioc-project/actions/workflows/update-cache.yaml and trigger an update using the "Run Workflow" button on the right hand side.

If that does not work you should be able to use the commands above to update it manually on your local computer (and please raise an issue on https://github.com/carpentries/workbench/issues so the workbench maintainers can see if there is a solution to that problem)

This workflow runs on the first Tuesday of the month at 00:00 UTC (in reality, it runs every Tuesday, but only builds on the first Tuesday) and generates a pull request like https://github.com/carpentries-incubator/bioc-project/pull/72. It failed the last two months due to an update in {renv} that caused the bootstrapping mechanism to be invalidated.