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

processing vignette 'rna-velocity.Rmd' failed with diagnostics:

Vignette re-building failed.

Process completed with exit code 1.

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Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v1. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/

Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v1. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/

multiple methods tables found for 'union'

multiple methods tables found for 'intersect'

multiple methods tables found for 'setdiff'

multiple methods tables found for 'setequal'

multiple methods tables found for 'union'

multiple methods tables found for 'intersect'

multiple methods tables found for 'setdiff'

multiple methods tables found for 'intersect'

multiple methods tables found for 'union'

multiple methods tables found for 'intersect'

unable to access index for repository https://www.bioconductor.org/packages/3.21/workflows/bin/windows/contrib/4.5:

multiple methods tables found for 'union'

multiple methods tables found for 'intersect'

multiple methods tables found for 'setdiff'

multiple methods tables found for 'setequal'

multiple methods tables found for 'union'

multiple methods tables found for 'intersect'

multiple methods tables found for 'setdiff'

multiple methods tables found for 'intersect'

multiple methods tables found for 'union'

unable to access index for repository https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.5:

unable to access index for repository https://www.bioconductor.org/packages/3.21/workflows/bin/macosx/big-sur-x86_64/contrib/4.5:

unable to access index for repository https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.5:

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/cache@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, actions/cache@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/

unable to access index for repository https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.5:

unable to access index for repository https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.5:

harfbuzz 10.0.0 is already installed and up-to-date. To reinstall 10.0.0, run: brew reinstall harfbuzz

fribidi 1.0.15 is already installed and up-to-date. To reinstall 1.0.15, run: brew reinstall fribidi

unable to access index for repository https://www.bioconductor.org/packages/3.21/workflows/bin/macosx/big-sur-x86_64/contrib/4.5:

unable to access index for repository https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.5:

‘smin’ may be used uninitialized [-Wmaybe-uninitialized]

Unused dummy argument ‘itry’ at (1) [-Wunused-dummy-argument]

Unused variable ‘t4’ declared at (1) [-Wunused-variable]

Unused variable ‘t5’ declared at (1) [-Wunused-variable]

‘t2’ may be used uninitialized [-Wmaybe-uninitialized]

‘i2’ may be used uninitialized [-Wmaybe-uninitialized]

Unused dummy argument ‘a’ at (1) [-Wunused-dummy-argument]

Unused variable ‘i’ declared at (1) [-Wunused-variable]