Tools for Bioconductor repositories

bioc_version() returns the Bioconductor version for the current or the specified R version.

Usage

bioc_version(r_ver = getRversion())

bioc_install_repos(r_ver = getRversion(), bioc_ver = bioc_version(r_ver))

Arguments

r_ver

R version to use. For bioc_install_repos() it is ignored if bioc_ver is specified.

bioc_ver

Bioconductor version to use. Defaults to the default one corresponding to r_ver.

Value

bioc_version() returns a Bioconductor version, a package_version

object.

bioc_install_repos() returns a named character vector of the URLs of the Bioconductor repositories, appropriate for the current or the specified R version.

Details

bioc_install_repos() deduces the URLs of the Bioconductor repositories.

Both functions observe the R_BIOC_VERSION environment variable, which can be set to force a Bioconductor version. If this is set, then the r_ver and bioc_ver arguments are ignored.

bioc_install_repos() observes the R_BIOC_MIRROR environment variable and also the BioC_mirror option, which can be set to the desired Bioconductor mirror. The option takes precedence if both are set. Its default value is https://bioconductor.org.

Examples

bioc_version()
#> [1] ‘3.17’
bioc_version("3.4")
#> [1] ‘3.6’
bioc_install_repos()
#>                                                 BioCsoft 
#>            "https://bioconductor.org/packages/3.17/bioc" 
#>                                                  BioCann 
#> "https://bioconductor.org/packages/3.17/data/annotation" 
#>                                                  BioCexp 
#> "https://bioconductor.org/packages/3.17/data/experiment" 
#>                                            BioCworkflows 
#>       "https://bioconductor.org/packages/3.17/workflows" 
#>                                                BioCbooks 
#>           "https://bioconductor.org/packages/3.17/books"