Install or update Bioconductor, CRAN, or GitHub packages

This package provides tools for managing Bioconductor and other packages in a manner consistent with Bioconductor's package versioning and release system.

Details

Main functions are as follows; additional help is available for each function, e.g., ?BiocManager::version.

• BiocManager::install(): Install or update packages from Bioconductor, CRAN, and GitHub.

• BiocManager::version(): Report the version of Bioconductor in use.

• BiocManager::available(): Return a character() vector of package names available (at BiocManager::repositories()) for installation.

• BiocManager::valid(): Determine whether installed packages are from the same version of Bioconductor.

• BiocManager::repositories(): Bioconductor and other repository URLs to discover packages for installation.

The version of Bioconductor in use is determined by the installed version of a second package, BiocVersion. BiocVersion is installed automatically during first use of BiocManager::install(). If BiocVersion has not yet been installed, the version is determined by code in base R.

Options influencing package behavior (see ?options, ?getOption) include:

• "repos", "BiocManager.check_repositories": URLs of additional repositories for use by BiocManger::install(). See ?repositories.

• "pkgType": The default type of packages to be downloaded and installed; see ?install.packages.

• "timeout": The maximum time allowed for download of a single package, in seconds. BiocManager increases this to 300 seconds to accommodate download of large BSgenome and other packages.

System environment variables influencing package behavior include:

• BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS advanced configuration to avoid Bioconductor version checks. See ?install.

• BIOCONDUCTOR_CONFIG_FILE for offline use of BiocManager versioning functionality. See ?install.

• BIOCONDUCTOR_USE_CONTAINER_REPOSITORY opt out of binary package installations. See ?containerRepository.

• BIOCMANAGER_CHECK_REPOSITORIES silence messages regarding non-standard CRAN or Bioconductor repositories. See ?repositories.

• BIOCMANAGER_SITE_REPOSITORY configure a more permanent site_repository input to repositories(). See ?repositories.

• R_BIOC_VERSION use a specific, possibly unsupported, version of Bioconductor. install(), version(), available(), valid(), and repositories() all use the version without checking that it is consistent with the version of R in use.

See also

Useful links:

• https://bioconductor.github.io/BiocManager/

• Report bugs at https://github.com/Bioconductor/BiocManager/issues

Author

Maintainer: Marcel Ramos marcel.ramos@roswellpark.org (ORCID)

Authors:

• Martin Morgan martin.morgan@roswellpark.org (ORCID)

Examples

R.version.string
#> [1] "R version 4.4.1 (2024-06-14)"
packageVersion("BiocManager")
#> [1] ‘1.30.25’
if (requireNamespace("BiocVersion", quietly = TRUE))
    packageVersion("BiocVersion")
#> [1] ‘3.19.1’
BiocManager::version()
#> [1] ‘3.19’