NCmisc (version 1.1.6)

getRepositories: Detect all available R repositories.

Description

In addition to the default CRAN repository, there are other repositories such as R-Forge, Omegahat, and bioConductor (which is split in to software, annotation, experiments and extras). This function allows you to retrieve which are available. This function complements (and takes code from) utils::setRepositories(), which will just set, not return which are available, but see there for more information about how this works. Detecting the available repositories can be useful to precede a call to setRepositories, and allows you to utilise these repositories without calling setRepositories (which is hard to reverse). This function can be used to expand the search space of the function search.cran() to include bioconductor packages.

Usage

getRepositories(ind = NULL, table = FALSE)

Value

list of repositories with URLS, note that it is the URL that works best for use for passing a value for 'repos' to various functions.

Arguments

ind

index, same as for 'setRepositories', if NULL this function returns all available repositories, or if an index, returns a subset.

table

logical, if TRUE, return a table of information, else just return the URLs, which are the required input for the 'repos' argument for relevant functions, e.g, available.packages() or search.cran()

Author

Nicholas Cooper

Examples

repos <- "http://cran.ma.imperial.ac.uk/" # OR: repos <- getOption("repos")
getRepositories(table=TRUE) # shows all available
getRepositories(2:5,FALSE) # returns index for all bioconductor repositories (on my system at least)
search.cran("genoset",repos=getRepositories(1)) # does not find this bioconductor package on CRAN
search.cran("genoset",repos=getRepositories()) # should now, because all repositories are used