valid: Validate installed package versions against correct versions.

In BiocManager: Access the Bioconductor Project Package Repository

Validate installed package versions against correct versions.

Description

Check that installed packages are consistent (neither out-of-date nor too new) with the version of R and Bioconductor in use.

Usage

valid(
  pkgs = installed.packages(lib.loc, priority = priority),
  lib.loc = NULL,
  priority = "NA",
  type = getOption("pkgType"),
  filters = NULL,
  ...,
  checkBuilt = FALSE,
  site_repository = character()
)

## S3 method for class 'biocValid'
print(x, ...)

Arguments

pkgs	A character() vector of package names for checking, or a matrix as returned by installed.packages()'.
lib.loc	A character() vector of library location(s) of packages to be validated; see installed.packages().
priority	character(1) Check validity of all, "base", or "recommended" packages; see installed.packages().
type	character(1) The type of available package (e.g., binary, source) to check validity against; see available.packages().
filters	character(1) Filter available packages to check validity against; see available.packages().
...	Additional arguments, passed to BiocManager::install() when fix=TRUE.
checkBuilt	logical(1). If TRUE a package built under an earlier major.minor version of R (e.g., 3.4) is considered to be old.
site_repository	character(1). See ?install.
x	A 'biocValid' object returned by 'BiocManager::valid()'.

Details

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

Packages are reported as 'out-of-date' if a more recent version is available at the repositories specified by BiocManager::repositories().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.

Value

biocValid list object with elements too_new and out_of_date containing data.frames with packages and their installed locations that are too new or out-of-date for the current version of Bioconductor. When internet access is unavailable, an empty 'biocValid' list is returned. If all packages ('pkgs') are up to date, then TRUE is returned.

'print()' is invoked for its side effect.

Author(s)

Martin Morgan [e-mail]

See Also

BiocManager::install() to update installed packages.

Examples

if (interactive()) {
  BiocManager::valid()
}

BiocManager documentation built on Sept. 11, 2024, 8:07 p.m.