BiocManager-package | R Documentation |
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::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.
Maintainer: Marcel Ramos marcel.ramos@roswellpark.org (ORCID)
Authors:
Martin Morgan martin.morgan@roswellpark.org (ORCID)
Useful links:
Report bugs at https://github.com/Bioconductor/BiocManager/issues
R.version.string
packageVersion("BiocManager")
if (requireNamespace("BiocVersion", quietly = TRUE))
packageVersion("BiocVersion")
BiocManager::version()
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