Check that installed packages are consistent (neither out-of-date nor too new) with the version of R and Bioconductor in use.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 biocValid
print(x, ...)
A character() vector of package names for checking, or
a matrix as returned by installed.packages
.
A character() vector of library location(s) of
packages to be validated; see installed.packages()
.
character(1) Check validity of all, "base", or
"recommended" packages; see installed.packages()
.
character(1) The type of available package (e.g.,
binary, source) to check validity against; see
available.packages()
.
character(1) Filter available packages to check
validity against; see available.packages()
.
Additional arguments, passed to
BiocManager::install()
when fix=TRUE
.
character(1)
. See ?install
.
A `biocValid` object returned by `BiocManager::valid()`.
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installed locations that are too new or out-of-date for the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.
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Packages are reported as 'out-of-date' if a more recent version is available at the repositories specified by `BiocManager::repositories()`.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.
BiocManager::install()
to update installed
packages.
# NOT RUN {
BiocManager::valid()
# }
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