valid | 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Check that installed packages are consistent (neither out-of-date nor too new) with the version of R and Bioconductor in use.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,
...,
checkBuilt = FALSE,
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
|
checkBuilt |
|
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Packages are reported as 'out-of-date' if a more recent version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installed locations that are too new or out-of-date for the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. 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.
Martin Morgan martin.morgan@roswellpark.org
BiocManager::install()
to update installed
packages.
if (interactive()) {
BiocManager::valid()
}
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