repositories() reports the URLs from which to
install Bioconductor and CRAN packages. It is used by
BiocManager::install() and other functions.
containerRepository() reports the location of the repository
of binary packages for fast installation within containerized versions
of Bioconductor, if available.
repositories( site_repository = character(), version = BiocManager::version(), ..., type = "both" ) containerRepository(version = BiocManager::version(), type = "binary")
Additional parameters passed to lower level functions, not used.
repositories() returns the appropriate software package
repositories for your version of Bioconductor.
Bioconductor has a 'release' and a 'devel' semi-annual release cycle. Packages within a release have been tested against each other and the current version of packages on CRAN. Bioconductor best practice is to use packages from the same release, and from the appropriate CRAN repository.
To install binary packages on containerized versions of Bioconductor,
a default binary package location URL is set as a package constant,
BiocManager:::BINARY_BASE_URL. Binary package installations
are enabled by default for Bioconductor Docker containers. Anyone
wishing to opt out of the binary package installation can set either the
variable or the option, BIOCONDUCTOR_USE_CONTAINER_REPOSITORY, to
FALSE. Note that the availability of Bioconductor package binaries is
experimental and binary installations are intended to be used with
bioconductor/bioconductor_docker images where such installations
correspond to specific versions of Linux / Ubuntu.
If alternative default repositories are known to provide appropriate
versions of CRAN or Bioconductor packages, the message may be silenced
by setting either the option or the variable to
options(BiocManager.check_repositories = FALSE) or
BIOCMANAGER_CHECK_REPOSITORIES=FALSE. Alternative default
repositories are not guaranteed to work without issues related to
incompatible package installations and are used at the user's own risk.
The intended use of
site_repository = is to enable installation of
packages not available in the default repositories, e.g., packages
internal to an organization and not yet publicly available. A
secondary use might provide alternative versions (e.g., compiled
binaries) of packages available in the default repositories. Note
that R's standard rules of package selection apply, so the most
recent version of candidate packages is selected independent of the
location of the repository in the vector returned by
To set a more permenanent
site_repository, one can use either the
BIOCMANAGER_SITE_REPOSITORY environment variable or the
options(BiocManager.site_repository = ...) option.
For greater flexiblity in installing packages while still adhering
as much as possible to Bioconductor best practices, use
repositories() as a basis for constructing the
repos = argument
install.packages() and related functions.
The unexported URL to the base repository is available with
BIOCONDUCTOR_USE_CONTAINER_REPOSITORY is an environment
variable or global
options() which, when set to
the fast installation of binary packages within containerized
versions of Bioconductor.
character() of repositories.
containerRepository(): character(1) location of binary repository,
if available, or character(0) if not.
BiocManager::install() Installs or updates Bioconductor,
CRAN, and GitHub packages.
chooseBioCmirror() choose an alternative Bioconductor
mirror; not usually necessary.
chooseCRANmirror() choose an alternative CRAN mirror; not
setRepositories() Select additional repositories for
BiocManager::repositories() ## Not run: BiocManager::repositories(version="3.8") ## End(Not run) containerRepository() # character(0) if not within a Bioconductor container
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