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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/valid.R
\name{valid}
\alias{valid}
\alias{print.biocValid}
\title{Validate installed package versions against correct versions.}
\usage{
valid(pkgs = installed.packages(lib.loc, priority = priority),
lib.loc = NULL, priority = "NA", type = getOption("pkgType"),
filters = NULL, ..., checkBuilt = FALSE,
site_repository = character())
\method{print}{biocValid}(x, ...)
}
\arguments{
\item{pkgs}{A character() vector of package names for checking, or
a matrix as returned by \code{\link{installed.packages}}.}
\item{lib.loc}{A character() vector of library location(s) of
packages to be validated; see \code{\link{installed.packages}()}.}
\item{priority}{character(1) Check validity of all, "base", or
"recommended" packages; see \code{\link{installed.packages}()}.}
\item{type}{character(1) The type of available package (e.g.,
binary, source) to check validity against; see
\code{\link{available.packages}()}.}
\item{filters}{character(1) Filter available packages to check
validity against; see \code{\link{available.packages}()}.}
\item{\dots}{Additional arguments, passed to
\code{BiocManager::\link{install}()} when \code{fix=TRUE}.}
\item{checkBuilt}{\code{logical(1)}. If \code{TRUE} a package built under an
earlier major.minor version of R (e.g., 3.4) is considered to
be old.}
\item{site_repository}{\code{character(1)}. See \code{?install}.}
\item{x}{A `biocValid` object returned by `BiocManager::valid()`.}
}
\value{
\code{biocValid} list object with elements \code{too_new} and
\code{out_of_date} containing \code{data.frame}s with packages and their
installed locations that are too new or out-of-date for the
current version of \emph{Bioconductor}.
`print()` is invoked for its side effect.
}
\description{
Check that installed packages are consistent (neither out-of-date
nor too new) with the version of R and \emph{Bioconductor} in use.
}
\details{
This function compares the version of installed packages
to the version of packages associated with the version of \emph{R}
and \emph{Bioconductor} currently in use.\preformatted{Packages are reported as 'out-of-date' if a more recent version
is available at the repositories specified by
`BiocManager::repositories()`. Usually, `BiocManager::install()` 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
`BiocManager::repositories()`. It is possible to down-grade by
re-installing a too new package "PkgA" with
`BiocManger::install("PkgA")`. It is important for the user to
understand how their installation became too new, and to avoid
this in the future.
}
}
\examples{
BiocManager::valid()
}
\seealso{
\code{BiocManager::\link{install}()} to update installed
packages.
}
\author{
Martin Morgan \email{martin.morgan@roswellpark.org}
}
\keyword{environment}
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