Query Bioconductor version information — bioc

Various helper functions to deal with Bioconductor repositories. See https://www.bioconductor.org/ for more information on Bioconductor.

Usage

bioc_version(r_version = getRversion(), forget = FALSE)

bioc_version_map(forget = FALSE)

bioc_devel_version(forget = FALSE)

bioc_release_version(forget = FALSE)

bioc_repos(bioc_version = "auto", forget = FALSE)

Arguments

r_version: The R version number to match.
forget: Use TRUE to avoid caching the Bioconductor mapping.
bioc_version: Bioconductor version string or package_version object, or the string "auto" to use the one matching the current R version.

Value

bioc_version() returns a package_version object.

bioc_version_map() returns a data frame with columns:

bioc_version: package_version object, Bioconductor versions.
r_version: package_version object, the matching R versions.
bioc_status: factor, with levels: out-of-date, release, devel, future.

bioc_devel_version() returns a package_version object.

bioc_release_version() returns a package_version object.

bioc_repos() returns a named character vector.

Details

bioc_version() queries the matching Bioconductor version for an R version, defaulting to the current R version

bioc_version_map() returns the current mapping between R versions and Bioconductor versions.

bioc_devel_version() returns the version number of the current Bioconductor devel version.

bioc_release_version() returns the version number of the current Bioconductor release.

bioc_repos() returns the Bioconductor repository URLs.

See the BioC_mirror option and the R_BIOC_MIRROR and R_BIOC_VERSION environment variables in the pkgcache manual page. They can be used to customize the desired Bioconductor version.

Examples

bioc_version()
#> [1] ‘3.18’
bioc_version("4.0")
#> [1] ‘3.12’
bioc_version("4.1")
#> [1] ‘3.14’
bioc_version_map()
#> # A data frame: 40 × 3
#>    bioc_version r_version  bioc_status
#>    <pckg_vrs>   <pckg_vrs> <fct>      
#>  1 1.6          2.1        out-of-date
#>  2 1.7          2.2        out-of-date
#>  3 1.8          2.3        out-of-date
#>  4 1.9          2.4        out-of-date
#>  5 2.0          2.5        out-of-date
#>  6 2.1          2.6        out-of-date
#>  7 2.2          2.7        out-of-date
#>  8 2.3          2.8        out-of-date
#>  9 2.4          2.9        out-of-date
#> 10 2.5          2.10       out-of-date
#> # ℹ 30 more rows
bioc_devel_version()
#> [1] ‘3.19’
bioc_release_version()
#> [1] ‘3.18’
bioc_repos()
#>                                                 BioCsoft 
#>            "https://bioconductor.org/packages/3.18/bioc" 
#>                                                  BioCann 
#> "https://bioconductor.org/packages/3.18/data/annotation" 
#>                                                  BioCexp 
#> "https://bioconductor.org/packages/3.18/data/experiment" 
#>                                            BioCworkflows 
#>       "https://bioconductor.org/packages/3.18/workflows" 
#>                                                BioCbooks 
#>           "https://bioconductor.org/packages/3.18/books"