Installation of Bioconductor and CRAN packages use R's standard
functions for library management -- install.packages()
,
available.packages()
, update.packages()
. Installation of GitHub
packages uses the remotes::install_github()
.
When installing CRAN or Bioconductor packages, typical arguments
include: lib.loc
, passed to old.packages()
and used to
determine the library location of installed packages to be updated;
and lib
, passed to install.packages()
to determine the
library location where pkgs
are to be installed.
When installing GitHub packages, ...
is passed to the
remotes package functions install_github()
and remotes:::install()
. A typical use is to build vignettes, via
dependencies=TRUE, build_vignettes=TRUE
.
BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS
is an environment
variable or global options()
which, when set to FALSE
, avoids
the R and Bioconductor version checks that are done by querying
an online configuration file. Setting
BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS
to FALSE
can speed
package loading when internet access is slow or non-existent, but
may result in out-of-date information about the current release and
development versions of Bioconductor.