Installing ORE - Part C - Issue installing ORE on Windows Server

In my previous two blog posts (Part-A and Part-B) I detailed 4 steps for how you can install ORE on your servers and on your client machines.

I also mentioned a possible issue you may encounter if you try to install ORE on a Windows server. This blog post will look at this issue and how you can workaround it and get ORE installed.

The problem occurs when I when to install the ORE Supporting packages.

I was prompted to install these into a new library directory. If you get this error message then something is wrong and you should not proceed with installing these packages. If you do proceed and install them in a new library directory then they will not be seen by ORE and the database (as they were not installed in the $ORACLE_HOME/R/library) and when you go to run ORE from within R you will get errors like the following

package ‘Cairo’ successfully unpacked and MD5 sums checked

package ‘DBI’ successfully unpacked and MD5 sums checked

package ‘png’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘png’

package ‘ROracle’ successfully unpacked and MD5 sums checked

Warning: cannot remove prior installation of package ‘ROracle’

If I try the ore.connect I get the following errors.

ore.connect(user="RQUSER", sid="orcl", host="localhost", password="RQUSER", port=1521, all=TRUE)

Loading required package: ROracle

Error in .ore.oracleQuerySetup() :

ORACLE connection requires ROracle package

In addition: Warning message:

In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘ROracle’

To overcome this ORE install issue all you need to do is to close down your R Gui, then add the following lines to the Rprofile file. The Rprofile file is located in R\etc directory C:\Program Files\R\R-3.0.1\etc. Add the following lines:

# Add $ORACLE_HOME/R/library to .libPaths() for ORE packages

.libPaths("C:/app/oracle/product/11.2.0/dbhome_1/R/library")

The above line will tell R to look in or to include the R directory in the Oracle home as part of its search path. You many need to change the directory above to point to your Oracle home. When you log into the R Gui the path above will be included. Now you can install the packages and then import the packages. This time they will be installed in the $ORACLE_HOME/R/library.

When you open the R Gui and run the command to load the ORE package and to connect to your ORE schema you should not receive any error messages.

> library(ORE)

> ore.connect(user="RQUSER", sid="orcl", host="localhost", password="RQUSER", port=1521, all=TRUE)

Now you should have ORE installed and working on your Windows server.

Installing ORE - Part B

This is the second part of a two part blog post on installing ORE.

In reality there are 3 blog posts on installing ORE. The third and next blog post will be on a particular issue you might encounter on a Windows server and how you can over come the issue.

In the previous blog post I outlined the steps needed to install ORE on the database server and on the client machine. Click here to go to this post.

In this blog post I will show you how to setup a schema for ORE and how to get connected to the schema using ORE.

Step 3 : Setting up your Schema to use ORE / Tasks for your DBA

On the server when you unzipped the ORE download, you will find a demo_user.bat script (something similar like demo_user.sh on Linux).

After the script has performed some checks, you will be asked do you want to create a demo schema. Enter yes for this task to be completed and the RQUSER schema will be created in your schema. Then enter the password for the RQUSER.

The RQUSER can as a small set of system privileges that allow it to connect to and perform some functions on the database. This include:

GRANT CREATE TABLE TO RQUSER;

GRANT CREATE PROCEDURE TO RQUSER;

GRANT CREATE VIEW TO RQUSER;

GRANT CREATE MINING MODEL TO RQUSER;

NOTE: If you cannot connect to the database using the RQUSER and the password you set, then you might need to also grant CONNECT and RESOURCE to it too.

For every schema that you want to access using ORE you will need to grant the above to them.

In addition to these grants, if you want a schema to be able to create and drop R scripts in the database then you will need to grant them the addition role of RQADMIN.

sqlplus / AS SYSDBA

GRANT RQADMIN to RQUSER;

NB: You will need to grant RQADMIN to an schema where you want to use the embedded ORE in the database.

Step 4 : Connecting to the Database

If you have complete all of the above steps you are now ready to use ORE to connect to your database. The following is an example of the ore.connect command that you can use. It is assuming the RQUSER has the password RQUSER, and the the host is on the local machine (localhost). Replace localhost with the host name of your database server and also change the SID to that of your database.

ore.connect(user="rquser", sid="orcl", host="localhost", password="rquser", port=1521, all=TRUE);

If you get no errors and you get the R prompt back then you are connected to the RQUSER schema in your database.

To test that the connection was made you can run the following ORE command and then list the tables in the schema.

> ore.is.connected()

[1] TRUE

> ore.ls()

character(0)

The output of the last line above tells us that we do not have any tables in our RQUSER schema. I will have more blog posts on how you can use ORE and perform various ORE analytics in future posts.

There are a series of demonstrations that come with ORE. To access these type in the following command which will list the available ORE demos.

> demo(package="ORE")

The following command illustrates how you can run the ORE demo called basic.

> demo(basic, package="ORE")

Also check out the Part C blog post on how to resolve a potential install issue on a Windows server.

Installing ORE - Part A

This blog post will look at how you can go about installing ORE in your environment.

The install involves a 4 steps. The first step is the install on the Oracle Database server. The second step involves the install on your client machine. The third steps involves creating a schema for ORE. The fourth steps is connecting to the database using ORE.

In this Part A blog post I will cover the first two steps in this process. The other steps will be coved in another blog post.

NB : A the time of writing this blog post ORE 1.4 cannot be installed on a 12c database if it has a CDB/PDB configuration. If you want to use ORE with 12c then you need to do a traditional install that does not create a CDB with a PDB. The ORE team are working hard on this and I'm sure it will be available in the next release (or two or ...) of ORE.

Step 1 : Installing ORE on the Database Server

Before you being looking at ORE you need to ensure that you have the correct version of database. If you have version 11.2.0.3 or 11.2.0.4 then you can go ahead and perform the installation below. But if you have 11.2.0.1 or 11.2.0.2 then you will need to apply a patch to your database. See my note above about 12c.

Download the Oracle R Distribution from their website. Download here.

Although you can use the standard version of R, Oracle R Distribution comes with some highly tuned packages. If you are going to use the standard R download then you will need to ensure that you download the correct version. ORE 1.4 will require R version 3.0.1. Yes this is not the current version of R.

Accept at the defaults during the installation of ROracle, and within a minute or two ROracle will be installed.

Download the Oracle R Enterprise software. Download here. This will include the Server and Supporting downloads.

Uncompress the downloaded ORE files and go to the server directory. Here you will find the install.bat (other other similar name for your platform).

Make sure your ORACLE_HOME and ORACLE_SID environment variables are set.

A number of environment and environment variables are checked. When prompted accept the defaults.

When prompted for the password for the RQSYS user, enter an appropriate password and take careful note of it.

Now go back to the Oracle download page for ORE and download the supporting packages. Unzip the downloaded file. Noting the directory that they were installed in you can now load them in R. To do this open R and run the following commands. You will need to change the directory to where these are located on your server.

install.packages("C:/app/supporting/ROracle_1.1-11.zip", repos=NULL)

install.packages("C:/app/supporting/DBI_0.2-7.zip", repos=NULL)

install.packages("C:/app/supporting/png_0.1-7.zip", repos=NULL)

install.packages("C:/app/supporting/cairo_1.5-5.zip", repos=NULL)

Or you can use the R Gui to import these packages

WARNING:If you are installing on a Windows server you may encounter some issues when importing these packages. I will have a separate blog post on this soon.

NB: The ORE installation instructions make reference to Cario-_1.5-2.zip. This is incorrect. ORE 1.4 comes with Cario-_1.5-5.zip.

At this point, assuming you didn't have any errors, you now have ORE installed on your server.

Step 2 : Installing ORE on the Client

Download the Oracle R Distribution from their website. Download here.

NOTE: If your database and client are on the one machine then there is no need to install ROracle again.

The client install is much simpler and less involved. After you have installed ROracle the next step is to install the client packages for ORE. These can be downloaded from here.

After you have unzipped the file you can use the import packages from zip feature of the R Gui tool or using RStudio. Then import the supporting packages that you also installed as part of the server install.

Now you can install the supporting packages. Unzip them and then use the R Gui or RStudio to importing them. These supporting packages can be downloaded from here.

That should be the client R software and ORE packages installed on your client machine. The next steps is to test a connection to your Oracle database using ORE. Before you can do that you will need to setup a Schema in the database to use R and also grant the necessary privileges to your other schemas that you want to access using R

Check out my next blog post (Installing ORE - Part B) for Steps 3 and 4.

Also check out the Part C blog post on how to resolve a potential install issue on a Windows server.

Oracle R Enterprise and Oracle 12c

A few of weeks ago we had the release of Oracle R Enterprise (ORE).

There has been some posts on the R/ORE on the Oracle discussion forums about installing ORE on Oracle 12c.

It turns out that the only way to install ORE on an Oracle 12c database is if you do a traditional install. What this means is that you do not have a CDB and PDBs configuration of Oracle 12c.

I'll assume that Oracle are currently working on this particular issue, as you can imagine that that there is considerable amount of complexity in getting ORE to work with the PDBs.

If you are not using Oracle 12c then you are OK, as long as you are using 11.2.0.3 or 11.2.0.4 versions of the database. If you are using a lower version of the 11.2 database then you need to apply a patch to allow ORE to run.

As they say I'm sure it will be "fixed in the next release" :-)

Oracle Advanced Analytics and Oracle Fusion Apps

At a recent Oracle User Group conference, I was part of a round table discussion on Apps and BI. Unfortunately most of the questions were focused on Apps and the new Fusion Applications from Oracle. I mentioned that there was data mining functionality (using the Oracle Advanced Analytics Option) built into the Fusion Apps, it seems to come as a surprise to the Apps people. They were not aware of this built in functionality and capabilities. Well Oracle Data Mining and Oracle Advanced Analytics has been built into the following Oracle Fusion Applications.

• Oracle Fusion HCM Workforce Predictions
• Oracle Fusion CRM Sales Prediction Engine
• Oracle Spend Classification
• Oracle Sales Prospector
• Oracle Adaptive Access Manager

Oracle Data Mining and Oracle Advanced Applications are also being used in the following applications:

• Oracle Airline Data Model
• Oracle Communications Data Model
• Oracle Retail Data Model
• Oracle Security Governor for Healthcare

I intend to submit a presentation on this topic to future Oracle User Group conferences as a way of spreading the Advanced Analytics message within the Oracle user community. If you would like me to present on this topic at your conference or SIG drop me an email and we can make the necessary arrangement :-)

Oracle 11.2g install on OLE 6.x

This notes are really just a reminder to myself of the typical "issues" that I encounter every time I do a new install of OEL 6.x and 11.2.0.4

These notes are in addition to the excellent installation instructions given by oracle-base.com: oel install, DB 11.2.0.x install

The notes listed below are just a reminder to myself of things that I seem to always have to look up. If you finish them useful then great.

1. Display issue & Installer not able to run

install says to do xhost +:0.0 this can give an error

instead do host +:0.0 and that should allow the installer to run

2. Now enough swap space when installer checks the pre-requisites

Need to add an addition 500M to the swap space

su (and then enter the password)

dd if=/dev/zero of=/tmp/swapfile bs=1M count=500

mkswap /tmp/swapfile

swapon /tmp/swapfile

exit (to return to the oracle user)

you can then turn off the extra space (if you really need to) after the install is finished

swapoff /tmp/swapfile

rm /tmp/swapfile

3. Post-Installation task

don't forget the final step, to set to restart flag

as root

vi /etc/oratab

change the following line to have the Y at the end (instead of the N)

DB11G:/u01/app/oracle/product/11.2.0/db_1:Y

4. Set up the automated start and stop of the DB

Again Oracle-Base gives an excellent set of instructions for doing this. Click here.

Oracle Text and Oracle Data Miner

This blog post is a follow up to comment on a previous blog post and to some emails.

Basically the people are asking about some messages they get when they open the Oracle Data Miner tool, that is part of SQL Developer.

If you are just using the SQL and PL/SQL functions in the database then you do not have to worried about Oracle Text. You will receive no warning message.

But if you use the Oracle Data Miner tool you will get a warning message.

Why do you get this message? Some of the functionality in the Oracle Data Miner tool relies on having Oracle Text enabled/installed in the database. You can locate this functionality under the Text section of the Component Workflow Editor palette of Oracle Data Miner.

So if you are getting these warning messages then Oracle Text was not installed when the database was created.

How can you install Oracle Text? There are 2 scripts that you need to run.

For the first script you will need to log into SYS as SYSDBA and run the following script.

ctx/admin/catctx.sql password SYSAUX TEMP NOLOCK

This script will create a user called CTXSYS with the password of password (give above), with the default tablespace of SYSAUX, the temporary tablespace of TEMP and when the account is created don't lock it (NOLOCK).

This script will also install a number of CTX packages.

The next step is to log into the CTXSYS schema (using the password above) and run the following script.

/ctx/admin/defaults/dr0defin.sql

This takes a parameter to specify the language you want to use. For example "English", "AMERICAN", etc.

The final step is to connect as SYS again and lock the CTXSYS account.

alter user ctxsys account lock password expire;

If you are using Oracle 12c then the above steps will be automatically done for you during the process. If you are using an earlier version of the database or a database that has been upgraded through some version then Oracle Text may not have been installed. In this case you can run the able commands.

The ORE Packages

If you are interested in using ORE or just to get an idea of what does ORE give you that does not already exist in one of the other R packages then the table below lists the packages that come as part of ORE.

Before you can use then you will need to load these into your workspace. To do this you can issue the following command from the R prompt or from the prompt in RStudio.

> library(ORE)

RStudio is my preferred R interface and is widely used around the world.

ORE Installed Packages	Description
ORE	Oracle R Enterprise
OREbase	ORE - base
OREdm	The ORE functions that use the in-database Oracle Data Miner algorithms
OREeda	The ORE functions used for exploratory data analysis
OREgraphics	The ORE functions used for graphics
OREpredict	The ORE functions used for model predictions
OREstats	The ORE stats functions
ORExml	The ORE functions that convert R objects to XML
DBI	R Database Interface
ROracle	OCI based Oracle database interface for R
XML	Tools for parsing and generating XML within R and S-Plus.
bitops	Functions for Bitwise operations
png	Read and write PNG images

In addition to these core ORE packages, ORE also uses some R packages as part of the core ORE packages listed above. The following table lists the R packages that are used in the ORE packages. So make sure you have these packages installed. They should have come with your installation of R, but if something has happened then you can download them again.

R Packages used by ORE	Description
base	The R Base Package
boot	Bootstrap Functions (originally by Angelo Canty for S)
class	Functions for Classification
cluster	Cluster Analysis Extended Rousseeuw et al
codetools	Code Analysis Tools for R
compiler	The R Compiler Package
datasets	The R Datasets Package
foreign	Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ..
graphics	The R Graphics Package
grDevices	The R Graphics Devices and Support for Colours and Fonts
grid	The Grid Graphics Package
KernSmooth	Functions for kernel smoothing for Wand & Jones (1995)
lattice	Lattice Graphics
MASS	Support Functions and Datasets for Venables and Ripley's MASS
Matrix	Sparse and Dense Matrix Classes and Methods
methods	Formal Methods and Classes
mgcv	GAMs with GCV/AIC/REML smoothness estimation and GAMMs by PQL
nlme	Linear and Nonlinear Mixed Effects Models

I've been using R a lot over the past few years and I've had a number of projects involving R particularly over the past 12 month. I just found out that I will now have another short duration R project in May and June.

So watch out for lots more blog posts on R and ORE. Plus the usual blog posts on using Oracle Data Mining. ORE and Oracle Data Mining are very closely linked.

Gartner 2014 Advanced Analytics Quadrant

The Gartner 2014 Advanced Analytics Quadrant is out now. Well it is if you can find it.

Some of the companies have put it up on their websites to promote their position.

For some reason Oracle hasn't and I wonder why?

You can see that some typical technologies are missing from this, but this is to be expected. How much are companies really deploying these alternatives on real problems and in production. Perhaps the positioning of Revolution Analysis might be an indicator. At some point there might be a shift from investigative analysis into more main stream projects and then into production.

What is still evident from this years quadrant is that SAS and IBM (SPSS) still have very dominant positions and perhaps will have for some time to come.

It will be interesting how this will all play out over the next few years.

ODM Repository upgrade Issue with 4.0.1

An important announcement was made on the Oracle Data Mining discussion forum last night and I haven't seen anything on twitter about it yet (but maybe I missed it). It was about some ODM Repository migration issues that you might encounter with using ODM in SQL Developer 4.0.1 and using the Oracle Database 11.2.0.3.

Check out the full announcement here.

Make sure you have a full backup of your ODM schema and the repository before you perform your ODM repository upgrade.

As most people are still on Oracle 11g then this is a potential problem that most of you maybe facing.

I had a a repository migration issues last September during Oracle Open World. EA2 was release and in my eagerness to upgrade (and because I was writing my book on it) I had an issue where my repository go dropped and a new repository created. But nothing was migrated over to the new repository.

Guess what? I lost all my work. I was at OOW and my back ups were back home in Ireland. So you can imagine how I felt.

Here is a link to my blog post about it.

Oracle BigDataLite version 2.5.1 is now available

Back at the end of January Oracle finally go round to releasing the updated version of the Oracle BigDataLite virtual machine. Check out my previous blog post of this.

Yesterday (27th March) I say on Facebook that a new updated versions of the BigDataLite VM was released. I must have missed the tweet and other publicity on this somewhere :-(

This is a great VM that allows you to play with the various Big Data technologies without the hassle of going through the who install and configuration thing.

If you are interested in this then here are the details of what it contains and where you can find more details.

The following components are included on Oracle Big Data Lite Virtual Machine v 2.5:

Oracle Enterprise Linux 6.4

Oracle Database 12c Release 1 Enterprise Edition (12.1.0.1)

Cloudera’s Distribution including Apache Hadoop (CDH4.6)

Cloudera Manager 4.8.2

Cloudera Enterprise Technology, including:

   Cloudera RTQ (Impala 1.2.3)

   Cloudera RTS (Search 1.2)

Oracle Big Data Connectors 2.5

   Oracle SQL Connector for HDFS 2.3.0

   Oracle Loader for Hadoop 2.3.1

   Oracle Data Integrator 11g

   Oracle R Advanced Analytics for Hadoop 2.3.1

   Oracle XQuery for Hadoop 2.4.0

Oracle NoSQL Database Enterprise Edition 12cR1 (2.1.54)

Oracle JDeveloper 11g

Oracle SQL Developer 4.0

Oracle Data Integrator 12cR1/

Oracle R Distribution 3.0.1

Go to the Oracle Big Data Lite Virtual Machine landing page on OTN to download the latest release.

Predicting using ORE package

In a previous post I gave a an overview of the various in-database data mining algorithms that you can use in your Oracle R Enterprise scripts.

To create data mining models based on those algorithms you need to use the ore.odm functions.

After you have developed and tested your models you will select one of these to score your new data.

How can you do this using ORE? There is a suite of ORE functions called ore.predict that you can use to apply your data mining model to score or label new data.

The following table lists the ore.predict functions:

ORE Predict Function	Description
ore.predict-glm	Generalized linear model
ore.predict-kmeans	k-Means clustering mode
ore.predict-lm	Linear regression model
ore.predict-matrix	A matrix with no more than 1000 rows
ore.predict-multinom	Multinomial log-linear model
ore.predict-nnet	Neural network models
ore.predict-ore.model	An Oracle R Enterprise model
ore.predict-prcomp	Principal components analysis on a matrix
ore.predict-princomp	Principal components analysis on a numeric matrix
ore.predict-rpart	Recursive partitioning and regression tree model

As you will see from the above table there are more ore.predict functions than there are ore.odm functions. The reason for this is that ORE comes with some additional data mining algorithms. These are in addition to the sub-set of Oracle Data Mining algorithms that it uses. These include the ore.glm, ore.lm, ore.neural and ore.stepwise.

You also need to watch out for the data mining algorithms that are not used in prediction. These include the Minimum Description Length, Apriori and Non-Negative Matrix Factorization.

Remember that these ore.predict functions are run inside the Oracle Database. No data is extracted to the data analyst laptop or desktop. All the data stays in the database. The ORE functions are run in the database on the data in the database