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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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Gene set enrichment analysis episode #53

Closed jokergoo closed 1 year ago

jokergoo commented 1 year ago

I have finished the first version of gene set enrichment analysis episode. You can get a preview here: https://jokergoo.github.io/bioc-rnaseq/06-gene-set-analysis.html

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-53

The following changes were observed in the rendered markdown documents:

 06-gene-set-analysis.md                            | 2360 ++++++++++++++++----
 data/GSE96870_se.rds                               |  Bin 2411114 -> 2411113 bytes
 ...-analysis-rendered-unnamed-chunk-12-1.png (new) |  Bin 0 -> 191109 bytes
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 ...t-analysis-rendered-unnamed-chunk-5-1.png (new) |  Bin 0 -> 28328 bytes
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 ...-analysis-rendered-unnamed-chunk-56-1.png (new) |  Bin 0 -> 141458 bytes
 fig/geneset.svg (new)                              |    4 +
 fig/msigdb.png (new)                               |  Bin 0 -> 358524 bytes
 fig/simplifyEnrichment.png (new)                   |  Bin 0 -> 788431 bytes
 md5sum.txt                                         |    2 +-
 15 files changed, 1929 insertions(+), 437 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 2023-07-18 18:25:01 +0000

jdrnevich commented 1 year ago

@jokergoo thanks so much for all of this! Unfortunately, one of the checks is failing as RcppParallel failed to install (line 1338 of https://github.com/carpentries-incubator/bioc-rnaseq/actions/runs/5573576144/jobs/10190480687?pr=53). Any idea of what could be causing this and/or what package is requiring it? I don't see you explicitly loading this package and most users on Windows systems can't make use of RcppParallel anyway.

jokergoo commented 1 year ago

I also noticed that error but I have no idea where it comes from.

According to the error message, it seems it is a problem of the building system not our code?

Also I don't know where RcppParallel is required in the course code. I will try to have a deeper look.

Error: Error: package or namespace load failed for ‘RcppParallel’: .onLoad failed in loadNamespace() for 'RcppParallel', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/home/runner/work/bioc-rnaseq/bioc-rnaseq/renv/profiles/lesson-requirements/renv/library/R-4.3/x86_64-pc-linux-gnu/.renv/1/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so': /home/runner/work/bioc-rnaseq/bioc-rnaseq/renv/profiles/lesson-requirements/renv/library/R-4.3/x86_64-pc-linux-gnu/.renv/1/00LOCK-RcppParallel/00new/RcppParallel/libs/RcppParallel.so: undefined symbol: _ZN3tbb10interface58internal9task_base7destroyERNS_4taskE

jdrnevich commented 1 year ago

@jokergoo I saw you just pushed another commit. I'm running the checks now, so hopefully that will fix the problem. Are you able to join us tomorrow 3 pm CEST for the meeting?

jokergoo commented 1 year ago

All checks passed!

Yes I will join the meeting tomorrow.

jdrnevich commented 1 year ago

Great to have something! Looking over it, it might be longer and more detailed than we have time for. We also need to add whatever packages are needed to the summary & set up section, if that hasn't been done. See you tomorrow!