Install or update Bioconductor, CRAN, or GitHub packagesSource:
This package provides tools for managing Bioconductor and other packages in a manner consistent with Bioconductor's package versioning and release system.
Main functions are as follows; additional help is available for
each function, e.g.,
BiocManager::install(): Install or update packages from Bioconductor, CRAN, and GitHub.
BiocManager::version(): Report the version of Bioconductor in use.
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
BiocVersion has not yet been installed, the version is determined
by code in base R.
"BiocManager.check_repositories": URLs of additional repositories for use by
"pkgType": The default type of packages to be downloaded and installed; see
"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_DIAGNOSISadvanced configuration to avoid Bioconductor version checks. See
BIOCONDUCTOR_CONFIG_FILEfor offline use of BiocManager versioning functionality. See
BIOCONDUCTOR_USE_CONTAINER_REPOSITORYopt out of binary package installations. See
BIOCMANAGER_CHECK_REPOSITORIESsilence messages regarding non-standard CRAN or Bioconductor repositories. See