build-dbs: Helper functions to generate HTML pages for reference manuals

In Bioconductor/biocViews: Categorized views of R package repositories

Helper functions to generate HTML pages for reference manuals

Description

Helper functions to generate HTML pages for reference manuals

Usage

build_db_from_source(package_dir, reposRoot)

build_meta_aliases_db(web_dir, aliases_db_file, force = FALSE)

build_meta_rdxrefs_db(web_dir, rdxrefs_db_file, force = FALSE)

Arguments

package_dir	'character(1)' The local path to a package for which to build the aliases and cross-ref databases ('rds' files).
reposRoot	'character(1)' The path to the base hosting directory for the package repository. This is typically a location on the BBS server.
web_dir	'character(1)' The 'web/packages' local directory that is also hosted on the website e.g., for CRAN https://cran.r-project.org/web/packages/
aliases_db_file	'character(1)' The file path to 'aliases.rds' file generated by the 'build_db_from_source' function.
force	'logical(1)' If 'FALSE', the function will only update the database entries for which the aliases/rdxrefs file is more recent than the database file. If 'TRUE', the function will read all aliases/rdxrefs files.
rdxrefs_db_file	'character(1)' The file path to 'rdxrefs.rds' file generated by the 'build_db_from_source' function.

Details

These functions are used to generate the 'aliases.rds' and 'rdxrefs.rds' files for each package. These files are used to generate a metadata database 'Rds' file via the 'build_meta_aliases_db' and 'build_meta_rdxrefs_db' functions for all packages. The 'aliases.rds' file is a list of aliases within each '.Rd' page in the package. The 'rdxrefs.rds' file is a matrix of cross-references between an external topic and the originating '.Rd' page. The individual package databases are then combined into a single database file for the entire repository. Each package's database is stored in the 'web/packages' directory in 'reposRoot'. The collective metadata database files are stored in the 'src/contrib/Meta' directory in 'reposRoot'.

The alias and cross-reference files are generated from the package source directory but may also be generated from a built package tarball (functionality not included). The code is meant to run on the BBS, typically after a package has been built or updated.

The 'build_html_mans' function is used to generate the HTML manuals for each package. These pages will be hosted on the BBS server and linked in the package landing page.

Examples

if (interactive()) {
    library(BiocPkgTools)
    bioc_sub <- pkgBiocDeps(
        "SummarizedExperiment", pkgType = "software",
        recursive = TRUE, only.bioc = TRUE
    )
    bioc_sub <- unlist(bioc_sub, use.names = FALSE)

    ## generate from Bioc package source dirs
    packages <- file.path(normalizePath("~/bioc"), bioc_sub)
    reposRoot <- "~/minibioc/packages/3.20/bioc"

    for (package in packages) {
       build_db_from_source(package, reposRoot)
    }
}
if (interactive()) {
    reposRoot <- "~/minibioc/packages/3.20/bioc/"
    web_dir <- file.path(reposRoot, "web", "packages")

    meta_folder <- file.path(contrib.url(reposRoot), "Meta")
    if (!dir.exists(meta_folder)) dir.create(meta_folder, recursive = TRUE)
    aliases_db_file <- file.path(meta_folder, "aliases.rds")

    meta_aliases_db <- build_meta_aliases_db(web_dir, aliases_db_file)

    saveRDS(meta_aliases_db, aliases_db_file, version = 2)
}
if (interactive()) {
    reposRoot <- "~/minibioc/packages/3.20/bioc/"
    web_dir <- file.path(reposRoot, "web", "packages")

    meta_folder <- file.path(contrib.url(reposRoot), "Meta")
    if (!dir.exists(meta_folder)) dir.create(meta_folder, recursive = TRUE)
    rdxrefs_db_file <- file.path(meta_folder, "rdxrefs.rds")

    meta_rdxrefs_db <- build_meta_rdxrefs_db(web_dir, rdxrefs_db_file)

    saveRDS(meta_rdxrefs_db, rdxrefs_db_file, version = 2)
}

Bioconductor/biocViews documentation built on June 14, 2025, 5:51 p.m.