Installing R Packages

• When you download R from the Comprehensive R Archive Network (CRAN), you get that ``base" R system

• The base R system comes with basic functionality; implements the R language

• One reason R is so useful is the large collection of packages that extend the basic functionality of R

• R packages are developed and published by the larger R community

• The primary location for obtaining R packages is CRAN

• For biological applications, many packages are available from the Bioconductor Project

• You can obtain information about the available packages on CRAN with the available.packages() function

a <- available.packages()
head(rownames(a), 3)  ## Show the names of the first few packages

## [1] "A3"       "abc"      "abcdeFBA"

• There are approximately 5200 packages on CRAN covering a wide range of topics

• A list of some topics is available through the Task Views link, which groups together many R packages related to a given topic

• Packages can be installed with the install.packages() function in R

• To install a single package, pass the name of the lecture to the install.packages() function as the first argument

• The following the code installs the slidify package from CRAN

install.packages("slidify")

• This command downloads the slidify package from CRAN and installs it on your computer

• Any packages on which this package depends will also be downloaded and installed

• You can install multiple R packages at once with a single call to install.packages()

• Place the names of the R packages in a character vector

install.packages(c("slidify", "ggplot2", "devtools"))

• To get the basic installer and basic set of R packages (warning, will install multiple packages)

source("http://bioconductor.org/biocLite.R")
biocLite()

• Place the names of the R packages in a character vector

biocLite(c("GenomicFeatures", "AnnotationDbi"))

http://www.bioconductor.org/install/

• Installing a package does not make it immediately available to you in R; you must load the package

• The library() function is used to load packages into R

• The following code is used to load the ggplot2 package into R

library(ggplot2)

• Any packages that need to be loaded as dependencies will be loaded first, before the named package is loaded

• NOTE: Do not put the package name in quotes!

• Some packages produce messages when they are loaded (but some don't)

After loading a package, the functions exported by that package will be attached to the top of the search() list (after the workspace)

library(ggplot2)
search()

##  [1] ".GlobalEnv"         "package:kernlab"    "package:caret"     
##  [4] "package:lattice"    "package:ggplot2"    "package:makeslides"
##  [7] "package:knitr"      "package:slidify"    "tools:rstudio"     
## [10] "package:stats"      "package:graphics"   "package:grDevices" 
## [13] "package:utils"      "package:datasets"   "package:methods"   
## [16] "Autoloads"          "package:base"

• R packages provide a powerful mechanism for extending the functionality of R

• R packages can be obtained from CRAN or other repositories

• The install.packages() can be used to install packages at the R console

• The library() function loads packages that have been installed so that you may access the functionality in the package