Bioconductor Biocviews

biocViews

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.80.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: Biobase, graph, RBGL, XML, RCurl, RUnit, BiocManager
• Install: BiocManager::install("biocViews")

When to Use

• 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.

References

• Homepage: bioconductor.org/packages/biocViews
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/biocViews/inst/doc/biocViews-HOWTO.pdf

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