Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '
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Use bioconductor-biocviews to Using [CRAN-style repository directory] and [BiocViews vocabulary DOT file], generate repository control files and HTML BiocViews in [output directory]; prerequisite: use R 4.6+ with biocViews 1.80.0 and its documented imports installed.
Required inputs
[CRAN-style repository directory]
[BiocViews vocabulary DOT file]
[output directory]
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SKILL.md
name: bioconductor-biocviewsdescription: Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'when_to_use: "Use when: Generating repository HTML and control files (PACKAGES, VIEWS) for a CRAN-style layout using genReposControlFiles and writeRepositoryHtml.; Extracting package vignettes from source packages to a local directory using extractVignettes.; Querying a repository to generate a list of BiocViews objects for specific top-level terms (e.g., \"Software\") using getBiocSubViews.; Querying available vocabulary . Not for: For general package development tasks like linting or unit testing; use BiocCheck or devtools instead because biocViews focuses on repository HTML and vocabulary generation.; For searching Bioconductor packages interactively in a user-friendly GUI; u"user-invocable: false
biocViews
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
Generating repository HTML and control files (PACKAGES, VIEWS) for a CRAN-style layout using genReposControlFiles and writeRepositoryHtml.
Extracting package vignettes from source packages to a local directory using extractVignettes.
Querying a repository to generate a list of BiocViews objects for specific top-level terms (e.g., "Software") using getBiocSubViews.
Querying available vocabulary subterms from a graphNEL object using getSubTerms.
When NOT to Use
For general package development tasks like linting or unit testing; use BiocCheck or devtools instead because biocViews focuses on repository HTML and vocabulary generation.
For searching Bioconductor packages interactively in a user-friendly GUI; use the Bioconductor website search or BiocPkgTools instead because biocViews generates static HTML views.
Data Requirements
A CRAN-style repository directory containing source packages (src/contrib) and binary packages (bin/windows/contrib, bin/macosx/contrib).
A vocabulary of terms defined in a dot format file (e.g., biocViewsVocab.dot) which is converted to a graphNEL object.
Key Parameters
reposRoot: The top-level directory path for the repository.
contribPaths: A named character vector specifying paths to source and binary packages.
reposUrl: The URL or file path of the repository to query.
topTerm: The top-level vocabulary node to query (e.g., "Software").
term: The base term for which all subterms should be returned in getSubTerms.
dir: Output directory path for generated HTML views in writeBiocViews.
Best Practices
Establish a standard CRAN-style layout with src/contrib and bin directories before running genReposControlFiles.
Extract vignettes using extractVignettes before generating the repository HTML.
Use getBiocSubViews with a valid graphNEL vocabulary object (like biocViewsVocab) to categorize packages.
Generate the final HTML views using writeBiocViews pointing to a dedicated output directory.
Common Pitfalls
Missing repository structure: Running genReposControlFiles without the correct contribPaths names. Fix: Ensure the contribPaths vector has exact names like "source", "win.binary", and "mac.binary".
Vocabulary terms with spaces: Adding terms to the dot file with spaces, which breaks the graph. Fix: Ensure terms use underscores instead of spaces.
Missing tools for vocabulary update: Failing to convert the dot file to GXL. Fix: Ensure dot2gxl from graphviz is installed and on your PATH.
Alternatives
BiocPkgTools: For advanced, user-facing exploration and network analysis of Bioconductor packages and their metadata.
BiocCheck: For verifying package compliance with Bioconductor standards, including biocViews validation.
pkgdown: For generating documentation websites for individual R packages rather than entire repositories.
Citations
Gentleman, R. et al. (2024). biocViews: Categorized views of R package repositories. R package version 1.74.0.
This skill is the knowledge layer — when, why, and how to use biocviews. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.