BiocManager-package {BiocManager} | R Documentation |
Install or update Bioconductor, CRAN, or GitHub packages
Description
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 acharacter()
vector of package names available (atBiocManager::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 byBiocManger::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 torepositories()
. See?repositories
.
Author(s)
Maintainer: Marcel Ramos marcel.ramos@roswellpark.org (ORCID)
Authors:
Martin Morgan martin.morgan@roswellpark.org (ORCID)
See Also
Useful links:
Report bugs at https://github.com/Bioconductor/BiocManager/issues
Examples
R.version.string
packageVersion("BiocManager")
if (requireNamespace("BiocVersion", quietly = TRUE))
packageVersion("BiocVersion")
BiocManager::version()