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)
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: factor, with levels:out-of-date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] ‘3.20’
bioc_version("4.0")
#> [1] ‘3.12’
bioc_version("4.1")
#> [1] ‘3.14’
bioc_version_map()
#> # A data frame: 42 × 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 1 1.6 2.1 out-of-date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 2 1.7 2.2 out-of-date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 3 1.8 2.3 out-of-date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 4 1.9 2.4 out-of-date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 5 2.0 2.5 out-of-date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 6 2.1 2.6 out-of-date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 7 2.2 2.7 out-of-date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 8 2.3 2.8 out-of-date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 9 2.4 2.9 out-of-date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 10 2.5 2.10 out-of-date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 32 more rows
bioc_devel_version()
#> [1] ‘3.21’
bioc_release_version()
#> [1] ‘3.20’
bioc_repos()
#> BioCsoft
#> "https://bioconductor.org/packages/3.20/bioc"
#> BioCann
#> "https://bioconductor.org/packages/3.20/data/annotation"
#> BioCexp
#> "https://bioconductor.org/packages/3.20/data/experiment"
#> BioCworkflows
#> "https://bioconductor.org/packages/3.20/workflows"
#> BioCbooks
#> "https://bioconductor.org/packages/3.20/books"