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carpentries-incubator / bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
https://carpentries-incubator.github.io/bioc-rnaseq
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build locally with new env/deps #40

Closed lgatto closed 1 year ago

github-actions[bot] commented 1 year ago

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:

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/bioc-rnaseq/compare/md-outputs..md-outputs-PR-40

The following changes were observed in the rendered markdown documents:

 01-introduction.md                                 |   2 +-
 02-intro-to-rnaseq.md                              |   2 +-
 05-import-annotate.md                              |  43 ++--
 06-exploratory-qc.md                               |  68 +++--
 08-gene-set-analysis.md                            | 277 +++++++++++----------
 data/GSE96870_se.rds                               | Bin 2411111 -> 2411114 bytes
 ...ntial-expression-rendered-unnamed-chunk-8-1.png | Bin 20389 -> 20412 bytes
 index.md                                           |   6 +-
 md5sum.txt                                         |  38 +--
 9 files changed, 224 insertions(+), 212 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 2023-05-12 15:51:09 +0000

lgatto commented 1 year ago

@jdrnevich - as discussed earlier, here's a PR (based on this) that will hopefully sort out the current issues.

lgatto commented 1 year ago

@jdrnevich - this builds fine :-)

I think you should be able to merge this PR, and then to other ones should work.

Once this is done, I will also update the config to add handouts, so let me know.