6.1.5 Installing a Third-Party Package for Use in Embedded R Execution

Embedded R execution allows the use of CRAN or other third-party packages in user-defined R functions executed on the Oracle Database server. To use a third-party package in embedded R execution, the package must be installed on the database server. If you are going to use the package from the R interface for embedded R execution, then the package must also be installed on the client, as well. To avoid incompatibilities, you must install the same version of the package on both the client and server machines.

An Oracle Database Administrator (DBA) can install a package on a database server so that it can be used by embedded R execution functions or by any R user. The DBA can install a package on a single database server or on multiple database servers.

A DBA would typically do the following:

  1. Download and install the package from CRAN. Downloading a package from CRAN requires an Internet connection.
  2. In an Oracle R Enterprise session running on the server, load the package. Verify that the package is installed correctly by using a function in the package.

To install a package on a single database server, do one of the following:

  • In an Oracle R Enterprise session running on the server, invoke the install.packages function, as shown in Example 6-1. The function downloads the package and installs dependencies automatically.

  • Download the package source from CRAN using wget. If the package depends on any packages that are not in the R distribution in use, then download those packages, also.

    From the operating system command line, use the ORE CMD INSTALL command to install the package or packages in the same location as the Oracle R Enterprise packages, which is $ORACLE_HOME/R/library. See Example 6-2.

To install a package, and any dependent packages, 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 Exadata Distributed Command Line Interface (DCLI) utility, as shown in Example 6-3. For detailed instructions on using DCLI to install packages, see Oracle R Enterprise Installation and Administration Guide.

To verify that the package is installed correctly, load the package and use a function in the package, as shown in Example 6-4.

Example 6-1 Installing a Package for a Single Database in an Oracle R Enterprise Session

This example invokes the install.packages function to download the C50 package from CRAN and to install it. The C50 package contains functions for creating C5.0 decision trees and rule-based models for pattern recognition.

The output this example, which is not shown, is almost identical to the output of the ORE CMD INSTALL command in Example 6-2.

install.packages("c50")

Example 6-2 Installing a Package for a Single Database from the Command Line

This example demonstrates downloading the C50 package from CRAN and installing it with ORE CMD INSTALL from a Linux command line.

wget http://cran.r-project.org/src/contrib/C50_0.1.0-19.tar.gz
ORE CMD INSTALL C50_0.1.0-19.tar.gz
Lising for Example 6-2 
$ wget http://cran.r-project.org/src/contrib/C50_0.1.0-19.tar.gz
# The output of wget is not shown.
$ ORE CMD INSTALL C50_0.1.0-19.tar.gz
* installing to library '/example/dbhome_1/R/library'
* installing *source* package 'C50' ...
** package 'C50' successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c attwinnow.c -o attwinnow.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c classify.c -o classify.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c confmat.c -o confmat.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c construct.c -o construct.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c contin.c -o contin.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c discr.c -o discr.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c formrules.c -o formrules.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c formtree.c -o formtree.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c getdata.c -o getdata.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c getnames.c -o getnames.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c global.c -o global.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c hash.c -o hash.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c hooks.c -o hooks.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c implicitatt.c -o implicitatt.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c info.c -o info.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c mcost.c -o mcost.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c modelfiles.c -o modelfiles.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c p-thresh.c -o p-thresh.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c prune.c -o prune.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c rc50.c -o rc50.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c redefine.c -o redefine.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c rsample.c -o rsample.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c rulebasedmodels.c -o rulebasedmodels.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c rules.c -o rules.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c ruletree.c -o ruletree.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c siftrules.c -o siftrules.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c sort.c -o sort.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c strbuf.c -o strbuf.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c subset.c -o subset.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c top.c -o top.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c trees.c -o trees.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c 
update.c -o update.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c utility.c -o utility.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DNDEBUG -I/usr/local/include   -ffloat-store -g -fpic  -g -O2  -c xval.c -o xval.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o C50.so attwinnow.o classify.o confmat.o construct.o contin.o discr.o formrules.o formtree.o getdata.o getnames.o global.o hash.o hooks.o implicitatt.o info.o mcost.o modelfiles.o p-thresh.o prune.o rc50.o redefine.o rsample.o rulebasedmodels.o rules.o ruletree.o siftrules.o sort.o strbuf.o subset.o top.o trees.o update.o utility.o xval.o -L/usr/lib64/R/lib -lR
installing to /example/dbhome_1/R/library/C50/libs
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'C50'
    finding HTML links ... done
    C5.0                                    html  
    C5.0Control                             html  
    churn                                   html  
    predict.C5.0                            html  
    summary.C5.0                            html  
    varImp.C5.0                             html  
** building package indices
** testing if installed package can be loaded
* DONE (C50)

Example 6-3 Installing a Package Using DCLI

This example shows the DLCI command for installing the C50 package. 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, see Oracle R Enterprise Installation and Administration Guide.

dcli -g nodes -l oracle R CMD INSTALL C50_0.1.0-19.tar.gz

Example 6-4 Using a C50 Package Function

This example shows starting R, connecting to Oracle R Enterprise on the server, loading the C50 package, and using a function in the package. The example starts R by executing the ORE command from the Linux command line. The example connects to Oracle R Enterprise and then loads the C50 package. It invokes the demo function to look for example programs in the package. Because the package does not have examples, this example then gets help for the C5.0 function. The example invokes example code from the help.

ORE

library(ORE)
ore.connect(user = "RQUSER", sid = "orcl", host = "myhost", 
            password = "rquserStrongPassword", port = 1521, all=TRUE)

library(C50)
demo(package = "C50")
?C5.0
data(churn)
treeModel <- C5.0(x = churnTrain[, -20], y = churnTrain$churn)
treeModel
Listing for Example 6-4 
$ ORE

R> library(ORE)
Loading required package: OREbase
 
Attaching package: 'OREbase'
 
The following objects are masked from 'package:base':
 
    cbind, data.frame, eval, interaction, order, paste, pmax, pmin,
    rbind, table
 
Loading required package: OREembed
Loading required package: OREstats
Loading required package: MASS
Loading required package: OREgraphics
Loading required package: OREeda
Loading required package: OREmodels
Loading required package: OREdm
Loading required package: lattice
Loading required package: OREpredict
Loading required package: ORExml
 
> ore.connect(user = "RQUSER", sid = "orcl", host = "myhost", 
+             password = "rquserStrongPassword", port = 1521, all=TRUE)
Loading required package: ROracle
Loading required package: DBI
 
R> library(C50)
R> demo(package = "C50")
no demos found
R> ?C5.0     # Output not shown.
R> data(churn)
R> treeModel <- C5.0(x = churnTrain[, -20], y = churnTrain$churn)
R> treeModel
Call:
C5.0.default(x = churnTrain[, -20], y = churnTrain$churn)
 
Classification Tree
Number of samples: 3333 
Number of predictors: 19 
 
Tree size: 27 
 
Non-standard options: attempt to group attributes

See Also: