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cat("::group::Register Repositories\n") fails #605

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chrbknudsen opened this issue Oct 1, 2024 · 6 comments
Closed

cat("::group::Register Repositories\n") fails #605

chrbknudsen opened this issue Oct 1, 2024 · 6 comments

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@chrbknudsen
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The build full site workflow fails right after
cat("::group::Install remotes\n")
With the message:
Error: Rscript: command not found

Setting install-r: to true in sandpaper-main.yaml resolves the issue.

@froggleston
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@chrbknudsen can you point us to your repository and workflow where this fails?

@froggleston
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froggleston commented Oct 1, 2024

I found an example in one of your repositories. This is most likely because you are using ubuntu 24.04. Could you roll back to 22.04 (jammy) and try again? 24.04 is known to be very buggy at the moment so we would recommend sticking to 22.04 for a few more months at least to allow issues to be resolved in the main OS.

From this information about 24.04 runners, a lot of software isn't available due to "maintenance reasons".

@chrbknudsen
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Thank you! That appears to solve the problem.
Let me add that the workflow came directly from the sandpaper workflows - it would appear that the problem might not be specific to my repo.

@froggleston
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That's correct @chrbknudsen - this would affect all future lesson builds so we've raised a PR to revert to 22.04 in the sandpaper workflows. Thank you for raising this issue!

@btmoyers
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btmoyers commented Jan 8, 2025

I am having the same issue with building a modified lesson (https://github.com/btmoyers/bash-genomics) which worked in August 2024. Any suggestions for modifications I can make on my own end?

@btmoyers
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btmoyers commented Jan 8, 2025

Nevermind! I followed through to your workaround and just copied it over. Thanks!

neutvd added a commit to SS-NES/SS-NES-lesson that referenced this issue Jan 21, 2025
Need to pin the Ubuntu version as 24.04 doesn't have Rscript.
See carpentries/sandpaper#605
and carpentries/sandpaper#606
lauracmurphy added a commit to IGC-Advanced-Imaging-Resource/image-analysis-python-napari that referenced this issue Jan 28, 2025
Change install-r to true to see if fixes build issue as per carpentries/sandpaper#605
johnbradley added a commit to Imageomics/snakemake-workshop that referenced this issue Feb 18, 2025
Removes automated build since the workshop is no longer rapidly changing and pins to a functional ubuntu version.
carpentries/sandpaper#605

Fixes #13
johnbradley added a commit to Imageomics/snakemake-workshop that referenced this issue Feb 18, 2025
Pins to a version of ubuntu that is compatible with the sandpaper
package used to render the lesson. Removes cron setting from
GitHub actions since the lesson is no longer rapidly changing.
carpentries/sandpaper#605

Fixes #13
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3 participants