Update Bioconductor and CRAN Packages

Description Usage Arguments Details Value See Also Examples

View source: R/biocLite.R

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`	`character()` of package names to install or update. A missing value and `suppressUpdates=FALSE` updates installed packages, perhaps also installing `Biobase`, `IRanges`, and `AnnotationDbi` if they are not already installed. Package names containing a ‘/’ are treated as github repositories and installed using the `install_github()` function of the `devtools` package.
`suppressUpdates`	`logical(1)` indicating whether to suppress automatic updating of all installed packages, or `character()` of regular expressions specifying which packages to NOT automatically update.
`suppressAutoUpdate`	`logical(1)` indicating whether the `BiocInstaller` package updates itself.
`siteRepos`	`character()` representing an additional repository in which to look for packages to install. This repository will be prepended to the default repositories (which you can see with `biocinstallRepos`).
`ask`	`logical(1)` indicating whether to prompt user before installed packages are updated, or the character string 'graphics', which brings up a widget for choosing which packages to update. If TRUE, user can choose whether to update all outdated packages without further prompting, to pick and choose packages to update, or to cancel updating (in a non-interactive session, no packages will be updated). Otherwise, the value is passed to `update.packages`.
`...`	Additional arguments. `lib.loc` is passed to `old.packages` (used to determine the library location of installed packages to be updated). `lib` is passed to `install.packages` (used to determine the library location where `pkgs` are to be installed).

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()