Check that installed packages are consistent (neither out-of-date nor
too new) with the version of R and Bioconductor in use, using
biocLite
for validation.
biocValid(pkgs = installed.packages(lib.loc, priority = priority), lib.loc = NULL, priority = "NA", type = getOption("pkgType"), filters = NULL, silent = FALSE, ..., fix=FALSE)
installed.packages
.installed.packages
.installed.packages
.available.packages
.available.packages
.silent=FALSE
,
default) and abort execution, or return a logical(1)
(silent=TRUE
) indicating the overall validity of installed
packages.biocLite
when fix=TRUE
.TRUE
, invoke biocLite
to reinstall
(update or downgrade, as appropriate) invalid packages.logical(1)
indicating overall validity of installed packages.
Packages are reported as out-of-date if a more recent version
is available at the repositories specified by
biocinstallRepos()
. Usually, biocLite()
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
biocinstallRepos()
repositories. It is possible to down-grade
by re-installing a too new package PkgA with
biocLite("PkgA")
. It is important for the user to understand
how their installation became too new, and to avoid this in the
future.
biocLite
to update installed packages.