How to install Oracle R Enterprise on Linux

Oracle R Enterprise

Oracle R Enterprise (ORE) makes open source R ready for enterprise. R commands and scripts can run on data stored in Oracle Database. ORE runs as an embedded component of Oracle Database.

Architecture 

As  shown in below figure, ORE has a client/server architecture.

ORE packages on the client side enables database tables to appear as native R data frames. On the server side R commands can be executed within SQL statements and PL/SQL blocks.

Installation Steps

On server side

1. Oracle database Enterprise Edition
2. Oracle R distribution (recommended, open source R distro is also supported but have to build from source)
3. Oracle R enterprise server
4. Oracle R supporting packages

On Client side

1. Oracle Database Client
2. Oracle R distribution
3. Oracle R supporting packages
4. Oracle R enterprise supporting packages

On server side

Need to make sure you are using the right combination of Oracle Database EE, Oracle R distribution and   Oracle R enterprise. I am installing below combination. Refer support matrix for details. Note that Oracle R enterprise runs on 64-bit platforms only.

 

• Install Oracle database Enterprise Edition

           I am not listing the steps here. Below section explains steps to set environment variables and verify database is up and running.

• Set environment variables 

After installing oracle database, set below environment variables
Refer Installation and Administration Guide.



$ bash
ORACLE_HOME=/scratch/rdbms12.1.0.2/app/oracle/product/12.1.0/dbhome_1; export ORACLE_HOME
ORACLE_SID=orcl12c ; export ORACLE_SID
PATH=$ORACLE_HOME/bin:$PATH;export PATH
NLS_LANG=AMERICAN_AMERICA.AL32UTF8;export NLS_LANG
LD_LIBRARY_PATH=$ORACLE_HOME/lib:$LD_LIBRARY_PATH;export LD_LIBRARY_PATH

echo $ORACLE_HOME
echo $ORACLE_SID
echo $PATH
echo $NLS_LANG
echo $LD_LIBRARY_PATH


Verify database is up and running.

$ sqlplus / as sysdba

exit

 

• Verify the environment

Refer install guide.

•  Install Oracle R distribution

I have to update my yum configuration to get this working. Oracle R distribution is part of addon channel. Addon repository url for Oracle Enterprise Linux  6 (64 bit) is give below.

http://public-yum.oracle.com/repo/OracleLinux/OL6/addons/x86_64/

$

I have added below section to my yum repo. Refer my previous blog entry for more details on configuring yum.

$ sudo su

$ cd /etc/yum.repos.d

$vi /etc/yum.repos.d

Add below section for addons channel. This was missing in my public-yum-ol6.repo.

[oel6_addons]
name=Oracle Linux $releasever Add ons ($basearch)
baseurl=http://public-yum.oracle.com/repo/OracleLinux/OL6/addons/x86_64/
gpgkey=http://public-yum.oracle.com/RPM-GPG-KEY-oracle-ol6
gpgcheck=1
enabled=1

Now run yum repolist. Here is a sample output.

Also add proxy and timeout params to /etc/yum.conf if you are behind a proxy server.

proxy=
timeout=300
 

 Without above parameters, got below error while running 'yum repolist'

$yum repolist

Loaded plugins: aliases, changelog, downloadonly, kabi, presto, refresh-packagekit, security, tmprepo, verify, versionlock
Loading support for kernel ABI
http://public-yum.oracle.com/repo/OracleLinux/OL6/UEK/latest/x86_64/repodata/repomd.xml: [Errno 14] PYCURL ERROR 7 - "couldn't connect to host"
Trying other mirror.
repo id                                repo name                                                                                       status
ol6_UEK_latest                         Latest Unbreakable Enterprise Kernel for Oracle Linux 6Server (x86_64)                          0
ol6_latest                             Oracle Linux 6Server Latest (x86_64)                                                            0
repolist: 0

After adding proxy and timeout, try yum repolist again

$ yum repolist

Loaded plugins: aliases, changelog, downloadonly, kabi, presto, refresh-packagekit, security, tmprepo, verify, versionlock
Loading support for kernel ABI

....

Now yum is configured properly. Proceed to install R distribution.

# yum install R-3.2.0

sample output below (truncated)

Loaded plugins: aliases, changelog, downloadonly, kabi, presto, refresh-packagekit, security, tmprepo, verify, versionlock
Loading support for kernel ABI
Setting up Install Process
Resolving Dependencies
--> Running transaction check..

.....truncated....

Installed:
  R.x86_64 0:3.2.0-2.el6

Dependency Installed:
  R-core.x86_64 0:3.2.0-2.el6    R-devel.x86_64 0:3.2.0-2.el6    libRmath.x86_64 0:3.2.0-2.el6    libRmath-devel.x86_64 0:3.2.0-2.el6

Complete!

• Install R enterprise

Download Oracle R Packages

Got to download link.

Accept license and download client, supporting and server packages(ORE 1.5).

$ cd /scratch/softwares/R/

$ ls

ore-server-linux-x86-64-1.5.zip
ore-supporting-linux-x86-64-1.5.zip

$ unzip  ore-server-linux-x86-64-1.5.zip

$ unzip  ore-supporting-linux-x86-64-1.5.zip

$ ./server.sh -i

This failed with below error

 ./server.sh -i --sys Chef1420

Oracle R Enterprise 1.5 Server.

Copyright (c) 2012, 2015 Oracle and/or its affiliates. All rights reserved.

Checking platform .................. Pass
Checking R ......................... Pass
Checking R libraries ............... Pass
Checking ORACLE_HOME ............... Pass
Checking ORACLE_SID ................ Pass
Checking sqlplus ................... Fail
  ERROR: invalid password

I have to pass @ to get it working.

eg:  ./server.sh -i --sys  mysyspassword@orcl12c

Refer this section for other inputs required to complete server.sh

Sample output below:

... truncated.......

  RQSYS PERMANENT tablespace ....... SYSAUX
  RQSYS TEMPORARY tablespace ....... TEMP

  ORE user type .................... New
  ORE user name .................... RUSER2
  ORE user PERMANENT tablespace .... USERS
  ORE user TEMPORARY tablespace .... TEMP
  Grant RQADMIN role ............... No

  Operation ........................ Install/Upgrade/Setup

Proceed? [yes]

Removing R libraries ............... Pass
Installing R libraries ............. Pass
Installing ORE libraries ........... Pass
Installing RQSYS data .............. Pass
Configuring ORE .................... Pass
Installing RQSYS code .............. Pass
Installing ORE packages ............ Pass
Creating ORE script ................ Pass
Installing migration scripts ....... Pass
Installing supporting packages ..... Pass
Creating ORE user .................. Pass
Granting ORE privileges ............ Pass

Done

On Client Side 

Install R Distribution on Linux

Refer similar step "On Server side" section to configure yum. And run below command.

$ yum install R-3.2.0

Install Oracle Database instant client

Go to database instant client download link.

accept license and download below zip files  (basic and sdk zip files)

1) instantclient-basic-linux.x64-12.1.0.2.0.zip

2) instantclient-sdk-linux.x64-12.1.0.2.0.zip

save above file to /scratch/R/client/

Unzip  above files

unzip instantclient-basic-linux.x64-12.1.0.2.0.zip

unzip instantclient-sdk-linux.x64-12.1.0.2.0.zip

Need to create symlink to .so files. Refer installation of zip file section for details.

cd /scratch/softwares/R/db_instant_client/instantclient_12_1

$ ln -s libclntsh.so.12.1 libclntsh.so
$ ln -s libocci.so.12.1 libocci.so

Need to set below env variables after installing ORE client packages.

$ bash

$ OCI_LIB64=/scratch/softwares/R/db_instant_client/instantclient_12_1;export OCI_LIB64
$ PATH=/scratch/softwares/R/db_instant_client/instantclient_12_1:$PATH;export PATH
$ LD_LIBRARY_PATH=/scratch/softwares/R/db_instant_client/instantclient_12_1;export LD_LIBRARY_PATH

Install R client packages

Go to download link.

Accept license and download ora client platform package.

ore-client-linux-x86-64-1.5.zip

unzip client zip

$ cd client

 $ sudo su

And run below commands. Basically need to replace three thing in the template commands specified here. (_version_ replaced to _1.5_ , arch replaced to x86_64,  platform replaced to linux)

R CMD INSTALL ORE_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREbase_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREcommon_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREdm_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREeda_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREembed_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREgraphics_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREmodels_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREpredict_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL OREstats_1.5_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL ORExml_1.5_R_x86_64-unknown-linux-gnu.tar.gz

Follow similar steps to install supporting packages also.

$ exit

$ cd ..

$ unzip ore-supporting-linux-x86-64-1.5.zip

$ cd supporting

replace arch -> x86_64

replace platform -> linux-gnu

R CMD INSTALL ROracle_1.2-1_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL DBI_0.3.1_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL png_0.1-7_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL Cairo_1.5-8_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL arules_1.1-9_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL statmod_1.4.21_R_x86_64-unknown-linux-gnu.tar.gz
R CMD INSTALL randomForest_4.6-10_R_x86_64-unknown-linux-gnu.tar.gz

 Basically need to replace arch and platform in the template commands specified here.

Connecting Oracle R Enterprise Client to Oracle R Enterprise Server

$ cd  /usr/lib64/R/bin

$ 

$ ./R

I got below error first time, while loading ORE package.

> library(ORE)

Loading required package: OREbase
Loading required package: OREcommon

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
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/lib64/R/library/ROracle/libs/ROracle.so':
  libclntsh.so.11.1: cannot open shared object file: No such file or directory
Error: package 'OREdm' could not be loaded

Looks like the shared object ROracle.so is referring to libclntsh.so.11.1 instead of libclntsh.so.12.1

bash-4.1$ pwd
/usr/lib64/R/library
bash-4.1$ grep -irsh "libclntsh.so.11.1" *
Binary file ROracle/libs/ROracle.so matches

As a work around, I have created a symlink, so that libclntsh.so.12.1 can be referred as libclntsh.so.11.1.

$ cd /scratch/softwares/R/db_instant_client/instantclient_12_1

 ln -s libclntsh.so.12.1 libclntsh.so.11.1

$ cd  /usr/lib64/R/bin

$ ./R

$ library(ORE)

Now libraries loaded successfully.

Connect to remote database 

> ore.connect(user="ruser2", sid="orcl12c", host="myhostnamehere", password="ruser2", port=1521, all=TRUE)

> ore.is.connected()
[1] TRUE

> ore.disconnect()