Programming languages give developers the opportunity to write reusable functions and to bundle those functions into logical deployable entities. In R, these are called packages. R has thousands of such packages provided by an almost equally large group of third-party contributors. To allow others to benefit from these packages, users can share packages on the CRAN system for use by the vast R development community worldwide.

R's package system along with the CRAN framework provides a process for authoring, documenting and distributing packages to millions of users. In this post, we'll illustrate the various ways in which such R packages can be installed for use with R and together with Oracle R Enterprise. In the following, the same instructions apply when using either open source R or Oracle R Distribution.

In this post, we cover the following package installation scenarios for:

R command line
Linux shell command line
Use with Oracle R Enterprise
Installation on Exadata or RAC
Installing all packages in a CRAN Task View
Troubleshooting common errors

1. R Package Installation Basics

Then, install the package using the command R CMD INSTALL:

$ R CMD INSTALL arules_1.1-2.tar.gz

A major difference between installing R packages using the R package installer at the R command line and shell command line is that package dependencies must be resolved manually at the shell command line. Package dependencies are listed in the Depends section of the package’s CRAN site. If dependencies are not identified and installed prior to the package’s installation, you will see an error similar to:

ERROR: dependency ‘xxx’ is not available for package ‘yyy’

As a best practice and to save time, always refer to the package’s CRAN site to understand the package dependencies prior to attempting an installation.

R> install.packages("arules", lib="/home/username/Rpackages")

or

$ R CMD INSTALL arules_1.1-2.tar.gz --library=/home/username/Rpackages

Refer to the install.packages help file in R or execute R CMD INSTALL --help at
the shell command line for a full list of command line options.

To set the library location and avoid having to specify this at every package install, simply create the R startup environment file .Renviron in your home area if it does not already exist, and add the following piece of code to it:

R_LIBS_USER = "/home/username/Rpackages"

2. Setting the Repository

This code snippet sets the R package repository to the Seattle CRAN mirror at the start of each R session.

3. Installing R Packages for use with Oracle R Enterprise

For a single Oracle Database instance, replace the R script with ORE to install the packages in the same location as the Oracle R Enterprise packages.

The DCLI -g flag designates a file containing a list of nodes to install on, and the -l flag specifies the user id to use when executing the commands. For more information on using DCLI with Oracle R Enterprise, see Chapter 5 in the Oracle R Enterprise Installation Guide.

If you are using an Oracle R Enterprise client, install the package the same as any R package, bearing in mind that you must install the same version of the package on both the client and server machines to avoid incompatibilities.

4. CRAN Task Views

To use the ctv package to install a task view, first, install and load the ctv package.

R> install.packages("ctv")
R> library(ctv)

Then query the names of the available task views and install the view you choose.

R> available.views()
R> install.views("TimeSeries")

5. Using and Managing R packages

R> library(arules)

Verify the version of arules installed.

R> packageVersion("arules")
[1] '1.1.2'

Verify the version of arules installed on the database server using embedded R execution.

R> ore.doEval(function() packageVersion("arules"))

View the help file for the apropos function in the arules
package

R> ?apropos

Over time, your package repository will contain more and more packages, especially if you are using the system-wide repository where others are adding additional packages. It’s good to know the entire set of R packages accessible in your environment. To list all available packages in your local R session, use the installed.packages command:

R> myLocalPackages <- row.names(installed.packages())
R> myLocalPackages

To access the list of available packages on the ORE database server from the ORE client, use the following embedded R syntax:

R> myServerPackages <-
ore.doEval(function() row.names(installed.packages())
R> myServerPackages

6. Troubleshooting Common Problems

Warning message:
In install.packages("arules")
: package ‘arules’ is not available

This is when you have to go to the Old sources link on the CRAN page for the arules
package and determine which version is compatible with your version of R.

Begin by determining what version of R you are using:

$ R --version
Oracle Distribution of R version 3.0.1 (--) -- "Good Sport"
Copyright (C) The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

Given that R-3.0.1 was released May 16, 2013, any version of the arules package released after this date may work. Scanning the arules archive, we might try installing version 0.1.1-1, released in January of 2014:

$ wget http://cran.r-project.org/src/contrib/Archive/arules/arules_1.1-1.tar.gz
$ R CMD INSTALL arules_1.1-1.tar.gz

For use with ORE:

$ ORE CMD INSTALL arules_1.1-1.tar.gz

The "package not available" error can also be thrown if the package you’re trying to install lives elsewhere, either another R package site, or it’s been removed from CRAN. A quick Google search usually leads to more information on the package’s location and status.

Oracle R Enterprise is not in the R library path

On Linux hosts, after installing the ORE server components, starting R, and attempting to load the ORE packages, you may receive the error:

R> library(ORE)
Error in library(ORE) : there is no package called ‘ORE’

If you know the ORE packages have been installed and you receive this error, this is the result of not starting R with the ORE script. To resolve this problem, exit R and restart using the ORE script. After restarting R and ">running the command to load the ORE packages, you should not receive any errors.

$ ORE
R> library(ORE)

On Windows servers, the solution is to make the location of the ORE packages visible to R by adding them to the R library paths. To accomplish this, exit R, then add the following lines to the .Rprofile file. On Windows, the .Rprofile file is located in R\etc directory C:\Program Files\R\R-<version>\etc. Add the following lines:

.libPaths("<path to $ORACLE_HOME>/R/library")

The above line will tell R to include the R directory in the Oracle home as part of its search path. When you start R, the path above will be included, and future R package installations will also be saved to $ORACLE_HOME/R/library. This path should be writable by the user oracle, or the userid for the DBA tasked with installing R packages.

Binary package compiled with different version of R

By default, R will install pre-compiled versions of packages if they are found. If the version of R under which the package was compiled does not match your installed version of R you will get an error message:

Warning message: package ‘xxx’ was built under R version 3.0.0

The solution is to download the package source and build it for your version of R.

$ wget http://cran.r-project.org/src/contrib/Archive/arules/arules_1.1-1.tar.gz
$ R CMD INSTALL arules_1.1-1.tar.gz

For use with ORE:

$ ORE CMD INSTALL arules_1.1-1.tar.gz

Unable to execute files in /tmp directory

By default, R uses the /tmp directory to install packages. On security conscious machines, the /tmp directory is often marked as "noexec" in the /etc/fstab file. This means that no file under /tmp can ever be executed, and users who attempt to install R package will receive an error:

ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual’

The solution is to set the TMP and TMPDIR environment variables to a location which R will use as the compilation directory. For example:

$ mkdir <some path>/tmp
$ export TMPDIR= <some path>/tmp
$ export TMP= <some path>/tmp

This error typically appears on Linux client machines and not database servers, as Oracle Database writes to the value of the TMP environment variable for several tasks, including holding temporary files during database installation.

7. Creating your own R package

Creating your own package and submitting to CRAN is for advanced users, but it is not difficult. The procedure to follow, along with details of R's package system, is detailed in the Writing R Extensions manual.