biocLite {BiocInstaller} | R Documentation |
biocLite
installs or updates Bioconductor and CRAN packages in
a Bioconductor release. Upgrading to a new Bioconductor release
requires additional steps; see https://bioconductor.org/install.
biocLite(pkgs=c("Biobase", "IRanges", "AnnotationDbi"), suppressUpdates=FALSE, suppressAutoUpdate=FALSE, siteRepos=character(), ask=TRUE, ...)
pkgs |
|
suppressUpdates |
|
suppressAutoUpdate |
|
siteRepos |
|
ask |
|
... |
Additional arguments. When installing CRAN or Bioconductor packages, typical arguments
include: When installing github packages, |
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 install_github()
function from the
devtools
package. For this reason it usually makes sense, when
complicated installation options are needed, to invoke
biocLite()
separately for Bioconductor / CRAN packages and for
github packages.
biocLite()
returns the pkgs
argument, invisibly.
biocinstallRepos
returns the Bioconductor and CRAN
repositories used by biocLite
.
install.packages
installs the packages themselves.
update.packages
updates all installed packages.
chooseBioCmirror
lets you choose from a list of all
public Bioconductor mirror URLs.
chooseCRANmirror
lets you choose from a list of all
public CRAN mirror URLs.
monograph_group
, RBioinf_group
and
biocases_group
return package names associated
with Bioconductor publications.
all_group
returns the names of all Bioconductor
software packages.
## Not run: ## Change default Bioconductor and CRAN mirrors chooseBioCmirror() chooseCRANmirror() ## If you don't have the BiocInstaller package installed, you can ## quickly install and load it as follows: source("https://bioconductor.org/biocLite.R") # 'http' if 'https' unavailable ## The most recent version of the BiocInstaller package is now loaded. ## No need to load it with library(). # installs default packages (if not already installed) and updates # previously installed packages biocLite() ## Now install a CRAN package: biocLite("survival") ## install a Bioconductor package, but don't update all installed ## packages as well: biocLite("GenomicRanges", suppressUpdates=TRUE) ## Install default packages, but do not update any package whose name ## starts with "org." or "BSgenome." biocLite(suppressUpdates=c("^org\.", "^BSgenome\.")) ## install a package from source: biocLite("IRanges", type="source") ## install all Bioconductor software packages biocLite(all_group()) ## End(Not run) ## Show the Bioconductor and CRAN repositories that will be used to ## install/update packages. biocinstallRepos()