R-CMD-check-bioc

Added note output object compatibility #125

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5 errors and 32 warnings

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

there is no package called ‘xlsx’

invalid font type

unable to start data viewer

conditions written in contrasts should be in the condition-indicating column! This is not the case, which can lead to errors downstream.

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v3, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:

harfbuzz 8.4.0 is already installed and up-to-date. To reinstall 8.4.0, run: brew reinstall harfbuzz

macOS's Gatekeeper has been disabled for this Cask

cairo 1.18.0 is already installed and up-to-date. To reinstall 1.18.0, run: brew reinstall cairo

unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3:

unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-arm64/contrib/4.3:

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!

'::' or ':::' import not declared from: ‘scuttle’

Codoc mismatches from documentation object 'get_frac_exprs_sampleAgnostic':

Undocumented arguments in documentation object 'process_abundance_expression_info'

Files in the 'vignettes' directory but no files in 'inst/doc':

Directory 'inst/doc' does not exist.

unable to open display

'::' or ':::' import not declared from: ‘scuttle’

Codoc mismatches from documentation object 'get_frac_exprs_sampleAgnostic':

Undocumented arguments in documentation object 'process_abundance_expression_info'

Files in the 'vignettes' directory but no files in 'inst/doc':

This job succeeded