Issues with installing Bioc package dependencies in GHA workflow about biocthis HOT 7 CLOSED

Noticing related issues on a related project,rworkflows
neurogenomics/rworkflows#58

From what I can tell, this doesn't seem to be specific to 3.18, but rather all Bioc versions @lmweber

from biocthis.

DropletUtils is truly not available on bioc 3.18 https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html

There's no source tar ball available (and no binaries either; though without a source tar ball there would never be binaries available).

from biocthis.

Thanks @lmweber @bschilder @LiNk-NY!

This should be resolved now in both release (1.10.1) and devel (1.11.1).

from biocthis.

Awesome thank you!

from biocthis.

Hmm it's still not finding some of the Bioc dependency packages -- e.g. see error in this workflow run when it can't find DropletUtils: https://github.com/drighelli/SpatialExperiment/actions/runs/4899765833/jobs/8749964157

I'm not sure why this is. Maybe GHA somehow can't connect to the Bioc package repositories correctly.

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Btw, unless it's a brand new package, I typically have GHA set to the latest bioc release branch. Then I let the Bioc build machines deal with the bioc devel branch.

Of course, if dependencies are changing a lot on the devel branch, I switch to the bioc devel branch. But that tends to be rare.

from biocthis.

Ah interesting, thanks for noticing that. The source / binaries for some other packages are not yet available in Bioc 3.18 either (I just clicked through a few to check).

Good idea -- I'll switch it over to Bioc release for the purposes of GitHub Actions testing, and rely on the Bioc builders for checking in Bioc devel. Thanks for the suggestion!

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