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grimbough / bioc-actions

GitHub Actions for developing and maintaining Bioconductor packages
MIT License
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`realpath` missing in macOS 12 and earlier #14

Closed csoneson closed 4 months ago

csoneson commented 4 months ago

👋🏻 I just ran into an issue with the setup-bioc action (after the recent modification to use get-r-version.sh instead of get-r-version.R) on the macos-latest GitHub Actions runner (running macOS 12), where the realpath command can not be found. From what I understand (e.g. here), it seems that this was indeed added in macOS 13 (which would explain why the biocActionsExamples passes this step). I could work around it by installing coreutils in macos-latest (or I guess I could have changed to macos-13), but I just wanted to bring it up as it may affect others.

grimbough commented 4 months ago

Annoying! Thanks for the report.

I made the change to using bash because GitHub seems to have removed R from the base macos-13 runner breaking the old version that ran Rscript. The I updated the test to use that runner and missed the new problem it introduced. Maybe there's something more portable than realpath?

I'll have a look and apply a fix ASAP.

grimbough commented 4 months ago

I think this is now fixed by adding a fallpack option if the built in tool doesn't exist, along with a separate issue that was causing the macos-13 pipelines to fail (https://github.com/r-lib/actions/issues/810)

csoneson commented 4 months ago

Awesome, thanks @grimbough!