| name | bioconductor-biocviews |
| description | 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.
- 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
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