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
BiocManager::available(): Return a
character() vector of
package names available (at
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.
Options influencing package behavior (see
"BiocManager.snapshot": URLs of additional repositories for use
"pkgType": The default type of packages to be downloaded and
"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:
configuration to avoid Bioconductor version checks. See
Report bugs at https://github.com/Bioconductor/BiocManager/issues
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