--- re-building 'EWCE.Rmd' using rmarkdown

processing vignette 'extended.Rmd' failed with diagnostics:

Vignette re-building failed.

Build process failed

Process completed with exit code 1.

No such keg: /opt/homebrew/Cellar/r

[Workflow Telemetry] Unable to finish stat collector

[Workflow Telemetry] Error

Error: connect ECONNREFUSED 127.0.0.1:7777

[Workflow Telemetry] Unable to report stat collector result

[Workflow Telemetry] Error

Error: connect ECONNREFUSED 127.0.0.1:7777

dependency 'BiocStyle' is not available

No files were found with the provided path: check. No artifacts will be uploaded.

The following actions uses Node.js version which is deprecated and will be forced to run on node20: runforesight/workflow-telemetry-action@v1, actions/cache@v3, actions/upload-artifact@v3. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

pkg-config 0.29.2_3 is already installed and up-to-date. To reinstall 0.29.2_3, run: brew reinstall pkg-config

HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK is set: not checking for outdated dependents or dependents with broken linkage!

harfbuzz 8.5.0 is already installed and up-to-date. To reinstall 8.5.0, run: brew reinstall harfbuzz

macOS's Gatekeeper has been disabled for this Cask

dependency ‘BiocStyle’ is not available

sctSpecies_origin not provided. Setting to 'mouse' by default.

sctSpecies_origin not provided. Setting to 'mouse' by default.

genelistSpecies not provided. Setting to 'human' by default.

sctSpecies_origin not provided. Setting to 'mouse' by default.

sctSpecies_origin not provided. Setting to 'mouse' by default.

Input 'repository' has been deprecated with message: v2 is now available through docker/build-push-action@v2