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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 BasicsR package installation basics are outlined in Chapter 6 of
the R Installation and Administration Guide. There are two ways to install packages from
the command line: from
the R command line and from
the shell command line. For this first example on Oracle Linux using Oracle R Distribution, we’ll install
the arules package as root so that packages will be installed in
the default R system-wide location where all users can access it, /usr/lib64/R/library.Within R, using
the install.packages function always attempts to install
the latest version of
the requested package available on CRAN:R> install.packages("arules")If
the arules package depends upon other packages that are not already installed locally,
the R installer automatically downloads and installs those required packages. This is a huge benefit that frees users from
the task of identifying and resolving those dependencies.You can also install R from
the shell command line. This is useful for some packages when an internet connection is not available or for installing packages not uploaded to CRAN. To install packages this way, first locate
the package on CRAN and then download
the package source to your local
machine. For example:$ wget http://cran.r-project.org/src/contrib/arules_1.1-2.tar.gz
Then, install
the package using
the command R CMD INSTALL:$ R CMD INSTALL arules_1.1-2.tar.gzA 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. If you don’t run R as root, you won’t have permission to write packages into
the default system-wide location and you will be prompted to create a personal library accessible by your userid. You can accept
the personal library path chosen by R, or specify
the library location by passing parameters to
the install.packages function. For example, to create an R package repository in your home directory:
R> install.packages("arules", lib="/home/username/Rpackages")or$ R CMD INSTALL arules_1.1-2.tar.gz --library=/home/username/RpackagesRefer 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 RepositoryEach time you install an R package from
the R command line, you are asked which CRAN mirror, or server, R should use. To set
the repository and avoid having to specify this during every package installation, create
the R startup command file .Rprofile in your home directory and add
the following R code to it:cat("Setting Seattle repository")r = getOption("repos") r["CRAN"] = "http://cran.fhcrc.org/"options(repos = r)rm(r)
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 EnterpriseEmbedded R execution with Oracle R Enterprise allows
the use of CRAN or other third-party R packages in user-defined R functions executed on
the Oracle Database server.
The steps for installing and configuring packages for use with Oracle R Enterprise are
the same as for open source R.
The database-side R engine just needs to know where to find
the R packages.
The Oracle R Enterprise installation is performed by user oracle, which typically does not have write permission to
the default site-wide library, /usr/lib64/R/library. On Linux and UNIX platforms,
the Oracle R Enterprise Server installation provides
the ORE script, which is executed from
the operating system shell to install R packages and to start R.
The ORE script is a wrapper for
the default R script, a shell wrapper for
the R executable. It can be used to start R, run batch scripts, and build or install R packages. Unlike
the default R script,
the ORE script installs packages to a location writable by user oracle and accessible by all ORE users - $ORACLE_HOME/R/library.To install a package on
the database server so that it can be used by any R user and for use in embedded R execution, an Oracle DBA would typically download the package source from CRAN using wget. If
the package depends on any packages that are not in
the R distribution in use, download
the sources for those packages, also.
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. $ wget http://cran.r-project.org/src/contrib/arules_1.1-2.tar.gz$ ORE CMD INSTALL arules_1.1-2.tar.gzBehind
the scenes,
the ORE script performs
the equivalent of setting R_LIBS_USER to
the value of $ORACLE_HOME/R/library, and all R packages installed with
the ORE script are installed to this location. For installing a package on multiple database servers, such as those in an Oracle Real Application Clusters (Oracle RAC) or a multinode Oracle Exadata Database
Machine environment, use
the ORE script in conjunction with
the Exadata Distributed Command Line Interface (DCLI) utility.$ dcli -g nodes -l oracle ORE CMD INSTALL arules_1.1-1.tar.gz
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 ViewsCRAN also maintains a set of Task Views that identify packages associated with a particular task or methodology. Task Views are helpful in guiding users through
the huge set of available R packages. They are actively maintained by volunteers who include detailed annotations for routines and packages. If you find one of
the task views is a perfect match, you can install every package in that view using
the ctv package - an R package for automating package installation.
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 To use a package, start up R and load packages one at a time with
the library command.Load
the arules package in your R session.
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
packageR> ?aproposOver 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> myLocalPackagesTo 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 ProblemsInstalling Older Versions of R packagesIf you immediately upgrade to
the latest version of R, you will have no problem installing
the most recent versions of R packages. However, if your version of R is older, some of
the more recent package releases will not work and install.packages will generate a message such as:
Warning message: In install.packages("arules")
: package ‘arules’ is not availableThis 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 --versionOracle 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.gzFor use with ORE:$ ORE CMD INSTALL arules_1.1-1.tar.gzThe "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 pathOn 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.$ ORER> 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 $ORACLE_HOME/R/library. This path should be writable by
the user oracle, or
the userid for
the DBA tasked with installing R packages.Binary package compiled with different version of RBy default, R will install pre-compiled versions of packages if they are found. If
the version of R under which
the package was compiled does not match your installed version of R you will get an error message:Warning message: package ‘xxx’ was built under R version 3.0.0The solution is to download
the package source and build it for your version of R.$ wget http://cran.r-project.org/src/contrib/Archive/arules/arules_1.1-1.tar.gz$ R CMD INSTALL arules_1.1-1.tar.gzFor use with ORE:$ ORE CMD INSTALL arules_1.1-1.tar.gzUnable to execute files in /tmp directoryBy 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>/tmpThis 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 packageCreating 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.
