Update Bioconductor and CRAN Packages

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/biocValid.R

Check that installed packages are consistent (neither out-of-date nor too new) with the version of R and Bioconductor in use, using biocLite for validation.

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biocValid(pkgs = installed.packages(lib.loc, priority = priority),
    lib.loc = NULL, priority = "NA", type = getOption("pkgType"),
    filters = NULL, silent = FALSE, ..., fix=FALSE)

`pkgs`	A character list of package names for checking, or a matrix as returned by `installed.packages`.
`lib.loc`	The library location(s) of packages to be validated; see `installed.packages`.
`priority`	check validity of all, “base”, or “recommended” packages; see `installed.packages`.
`type`	The type of available package (e.g., binary, source) to check validity against; see `available.packages`.
`filters`	Filter available packages to check validity against; see `available.packages`.
`silent`	Report how packages are invalid (`silent=FALSE`, default) and abort execution, or return a logical(1) (`silent=TRUE`) indicating the overall validity of installed packages.
`...`	Additional arguments, passed to `biocLite` when `fix=TRUE`.
`fix`	When `TRUE`, invoke `biocLite` to reinstall (update or downgrade, as appropriate) invalid packages.

This function compares the version of installed packages to the version of packages associated with the version of R and Bioconductor appropriate for the BiocInstaller package currently in use.

Packages are reported as ‘out-of-date’ if a more recent version is available at the repositories specified by biocinstallRepos(). Usually, biocLite() is sufficient to update packages to their most recent version.

Packages are reported as ‘too new’ if the installed version is more recent than the most recent available in the biocinstallRepos() repositories. It is possible to down-grade by re-installing a too new package “PkgA” with biocLite("PkgA"). It is important for the user to understand how their installation became too new, and to avoid this in the future.

logical(1) indicating overall validity of installed packages.

Martin Morgan mtmorgan@fhcrc.org

biocLite to update installed packages.