valid {BiocManager} | R Documentation |
Check that installed packages are consistent (neither out-of-date nor too new) with the version of R and Bioconductor in use.
valid(pkgs = installed.packages(lib.loc, priority = priority), lib.loc = NULL, priority = "NA", type = getOption("pkgType"), filters = NULL, ..., site_repository = character()) ## S3 method for class 'biocValid' print(x, ...)
pkgs |
A character() vector of package names for checking, or
a matrix as returned by |
lib.loc |
A character() vector of library location(s) of
packages to be validated; see |
priority |
character(1) Check validity of all, "base", or
"recommended" packages; see |
type |
character(1) The type of available package (e.g.,
binary, source) to check validity against; see
|
filters |
character(1) Filter available packages to check
validity against; see |
... |
Additional arguments, passed to
|
site_repository |
|
x |
A 'biocValid' object returned by 'BiocManager::valid()'. |
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Packages are reported as 'out-of-date' if a more recent version is available at the repositories specified by `BiocManager::repositories()`.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.
biocValid
list object with elements too_new
and
out_of_date
containing data.frame
s with packages and their
installed locations that are too new or out-of-date for the
current version of Bioconductor.
'print()' is invoked for its side effect.
Martin Morgan martin.morgan@roswellpark.org
BiocManager::install()
to update installed
packages.
BiocManager::valid()