2 Prerequisites

Install Oracle R Distribution on Linux 5

Oracle R Distribution for Linux 5 allows you to install a version of R 1.13.2 or a version of R 2.15.1 that is designed to work with Oracle R Enterprise. Oracle R Distribution supports Oracle Enterprise Linux 5 and Red Hat Enterprise Linux 5.

Go to http://public-yum.oracle.com/ and follow these steps to install R:

1. Become root; for example use

   sudo su -
   

2. Install the yum repository as follows:

   cd /etc/yum.repos.d
   

3. Use this command to get el5.repo:

   wget http://public-yum.oracle.com/public-yum-el5.repo
   

4. Open a text editor on the file just downloaded public-yum-el5.repo.

   Set

   • "enabled=1" for [el5_addons]

   • "enabled=1" for [el5_latest]

5. This step is optional.

   Type the following commands in a shell to check that your yum repository is configured correctly:

   sudo yum repolist
   

   The output should look like this:

   sudo yum repolist
   $ sudo yum repolist
   Loaded plugins: aliases, changelog, downloadonly, kabi, presto, refresh-packagekit, security, tmprepo, verify, versionlock
   Loading support for kernel ABI
   el5_latest                                              | 1.4 kB     00:00    
   el5_latest/pri                                          |  12 MB     00:07    
   el5_latest                                                           9713/9713
   ol6_UEK_latest                                          | 1.2 kB     00:00    
   ol6_UEK_latest/primary                                  | 4.3 MB     00:02    
   ol6_UEK_latest                                                      106/106
   ol6_addons                                               | 1.2 kB     00:00    
   ol6_addons/primary                                       |  11 kB     00:00    
   ol6_addons                                                            52/52
   ol6_latest                                               | 1.4 kB     00:00    
   ol6_latest/primary                                       |  23 MB     00:14    
   ol6_latest                                                       18112/18112
   repo id            repo name                                 status
   el5_latest         Oracle Linux 6Server Latest (x86_64)           9,713
   ol6_UEK_latest     Latest Unbreakable Enterprise Kernel for Oracle Linux 6Server (x86_64) 106 
   ol6_addons         Oracle Linux 6Server Add ons (x86_64)              52
   ol6_latest          Oracle Linux 6Server Latest (x86_64)             18,112
   repolist: 27,983
   
   

   Make sure that both the el5_addons and ol5_u6_base repository are listed. The list of repository can be different depending on the Linux version and current user's configuration of yum.

6. To install R, use the following command:

   yum install R.x86_64
   

You can quickly check that R was installed by starting R from the command line. You will see this startup message:

Oracle Distribution of R version 2.15.1  (--) -- "Roasted Marshmallows"
Copyright (C)  The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
 
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
 
  Natural language support but running in an English locale
 
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
 
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)
 
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
 
  Natural language support but running in an English locale
 
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
 
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Install Oracle R Distribution on Linux 6

Oracle R Distribution for Linux 6 allows you to install a version of R 2.15.1 that is designed to work with Oracle R Enterprise.

Go to http://public-yum.oracle.com/ and follow these steps to install R:

1. Become root; for example use

   sudo su -
   

2. Install the yum repository as follows:

   cd /etc/yum.repos.d
   

3. Use this command to get ol6.repo:

   wget http://public-yum.oracle.com/public-yum-ol6.repo
   

4. Open a text editor on the file just downloaded, public-yum-ol6.repo.

   Set

   • "enabled=1" for [ol6_addons]

   • "enabled=1" for [ol6_latest]

5. This step is optional.

   Type the following commands in a shell to check that your yum repository is configured correctly:

   sudo yum repolist
   $ sudo yum repolist
   Loaded plugins: aliases, changelog, downloadonly, kabi, presto, refresh-packagekit, security, tmprepo, verify, versionlock
   Loading support for kernel ABI
   el5_latest                                              | 1.4 kB     00:00    
   el5_latest/pri                                          |  12 MB     00:07    
   el5_latest                                                           9713/9713
   ol6_UEK_latest                                          | 1.2 kB     00:00    
   ol6_UEK_latest/primary                                  | 4.3 MB     00:02    
   ol6_UEK_latest                                                      106/106
   ol6_addons                                               | 1.2 kB     00:00    
   ol6_addons/primary                                       |  11 kB     00:00    
   ol6_addons                                                            52/52
   ol6_latest                                               | 1.4 kB     00:00    
   ol6_latest/primary                                       |  23 MB     00:14    
   ol6_latest                                                       18112/18112
   repo id            repo name                                 status
   el5_latest         Oracle Linux 6Server Latest (x86_64)           9,713
   ol6_UEK_latest     Latest Unbreakable Enterprise Kernel for Oracle Linux 6Server (x86_64) 106 
   ol6_addons         Oracle Linux 6Server Add ons (x86_64)              52
   ol6_latest          Oracle Linux 6Server Latest (x86_64)             18,112
   repolist: 27,983
   
   

   The list of repository can be different depending on the Linux version and current user's configuration of yum.

6. To install R, use the following command:

   yum install R.x86_64
   

You can quickly check that R was installed by starting R from the command line.

Oracle Distribution of R version 2.15.1  (--) -- "Roasted Marshmallows"
Copyright (C)  The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
 
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
 
  Natural language support but running in an English locale
 
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
 
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Install R on Red Hat Enterprise Linux 6

You must rebuild Linux 6 Oracle R Distribution RPMs from the source RPMs on Red Hat 6 before you install R.

Follow these steps to rebuild the RPMs on Red Hat Enterprise Linux 6:

1. Create an RPM build directory structure:

   mkdir -p ~/rpmbuild/{BUILD,RPMS,SOURCES,SPECS,SRPMS}
   

2. Set up RPM tools to use your own build tree (to avoid root login):

   echo '%_topdir %(echo $HOME)/rpmbuild' > ~/.rpmmacros
   

3. Download the R 2.15.1 SRPM (*.src.rpm) from Oracle's public yum at http://public-yum.oracle.com/repo/OracleLinux/OL6/addons/x86_64/R-2.15.1-1.el6.src.rpm.

   Save them to the rpmbuld/SRPMS directory.

4. Rebuild for Red Hat Enterprise Linux 6 using rpmbuild. For example,

   rpmbuild --rebuild~/SRPMS/R-2.15.1-1.el6.src.rpm
   

   Note that if any dependencies are missing you will need to yum install them as root.

5. The binary RPMs will be built and saved under ~/rpmbuild/RPMS.

6. Login as root: and run the commands to install. You use commands of the form

   rpm -i <path to rpmbuild/RPMS/<R-core RPM >
   

   For example,

   rpm -i /refresh/home/rpmbuild/RPMS/x86_64/R-core-2.15.1-1.el6.x86_64.rpm
   

You can quickly check that R was installed by starting R from the command line. R starts up with:

[oracle@celvpint1001 ~]$ R
 
Oracle Distribution of R version 2.15.1  (--) -- "Roasted Marshmallows"
Copyright (C)  The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

Using MKL

The Intel Math Kernel Library (MKL) includes highly vectorized and threaded Linear Algebra, Fast Fourier Transforms (FFT), Vector Math and Statistics functions. Oracle R Distribution includes support that dynamically picks up the Intel Math Kernel Library (MKL) if MKL is installed on your system.

Follow these steps to use MKL with Oracle R Distribution:

1. Add libmkl_rt.so, $R_HOME/lib, and $ORACLE_HOME/lib to the LD_LIBRARY_PATH system environment variable.

2. Start R and execute this Oracle R Distribution function Sys.BlasLapack():

   R> Sys.BlasLapack()
        $vendor
        [1] "Intel Math Kernel Library (Intel MKL)"
        $nthreads
        [1] -1
   

   The vendor value returned indicates the presence of MKL instead of R's internal BLAS.

3. In order to get the speedup provided by MKL, you must set the MKL_THREADING_LAYER environment variable to GNU before you invoke Oracle R Distribution on your system. In the Bash shell, set the variable as follows:

   export MKL_THREADING_LAYER=GNU