Biocthis GHA recently fails for macOS
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@jeroengilis-21551
Last seen 1 day ago

About two months ago I set up Github actions for a package using biocthis. Back then, all checks (R CMD / biocChecks) were successful.

Now, however, the install macOS system dependencies fails. This has been reported recently, e.g., https://github.com/actions/virtual-environments/issues/1864 and https://github.com/actions/virtual-environments/issues/1811. The issue should be resolved by adapting .github/workflows/check-bioc.yml.

Question: Is this a known issue and will it be resolved soon?

PS: let me know if it would be better for me to raise an issue on the biocthis git, I was unsure which channel is desired in this case.

biocthis • 61 views
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@lcolladotor
Last seen 3 days ago
United States

Hi jeroen.gilis,

From https://github.com/r-lib/actions/issues/230, it looks like this issue has been resolved (thanks in part to https://github.com/r-lib/actions/pull/229). I don't anticipate there being an issue with:

## Enable installing XML from source if needed
brew install libxml2
echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV

## Required to install magick as noted at
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
brew install imagemagick@6

## For textshaping, required by ragg, and required by pkgdown
brew install harfbuzz fribidi

## For installing usethis's dependency gert
brew install libgit2

If they are, several of these lines might not be needed by your use case.

Best, Leo

PS For some reason, your message went to my spam. Anyways, biocthis has several non-R dependencies, so some issues are resolved upstream of it.

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