Database Connections

Connecting to Databases from R

Patterned after http://db.rstudio.com/

This walkthrough is for MacOS X users. Windows users may be able to achieve similar results through the use of Chocolatey, though research into the specific packages under Windows that match what homebrew installs is required.

These connectivity examples use DBI-compatible interfaces. DBI is a database interface specification that allows any compliant tool to communicate with databases without knowledge of the underlying database technology. Using DBI tooling allows both direct SQL queries through raw connections as well as tight integration with the tidyverse through the spiffy dbplyr package.

Database drivers must be written with DBI interfaces. Both native drivers and the generic (DBI-compliant) odbc connections are demonstrated. For Oracle and MS SQL Server, odbc is the only (free) connectivity option.

If you are only connecting to a single database type, the driver you choose is largely a matter of personal preference. If connecting to multiple different database types, using odbc will provide a more consistent interface. Connections made using odbc will appear in the connections tab of the RStudio IDE.

Install ODBC and Database Drivers

# install base odbc framework
brew install unixodbc

# Microsoft SQL Server, enabling it for use with odbc
brew install freetds --with-unixodbc
  
# PostgreSQL ODBC Drivers
brew install psqlodbc

# Maria/MySQL ODBC drivers
brew install mariadb-connector-c
brew install mariadb-connector-odbc

# SQLite ODBC Drivers
brew install sqliteodbc

Oracle Client Install

The Oracle client install is complicated. 😦

Download the Basic client and the ODBC drivers via
http://www.oracle.com/technetwork/topics/intel-macsoft-096467.html. A (free) Oracle account is required. Place both ZIP files in your ~/Downloads directory.

sudo unzip -o ~/Downloads/instantclient-basic-macos.x64-12.2.0.1.0-2.zip -d /opt/ora12
sudo unzip -o ~/Downloads/instantclient-odbc-macos.x64-12.2.0.1.0-2.zip -d /opt/ora12

# patch the Oracle ODBC install script to fix an incorrectly specified library
# extension (.so -> .dylib)
sudo patch ./oracle_odbc_update.patch /opt/ora12/instantclient_12_2/odbc_update_ini.sh > patch.diff
sudo /opt/ora12/instantclient_12_2/odbc_update_ini.sh /usr/local

ln -s `pwd`/libclntsh.dylib.12.1 /usr/local/lib
ln -s `pwd`/libclntshcore.dylib.12.1 /usr/local/lib

Configure ODBC Drivers

Set /usr/local/etc/odbcinst.ini to the following to allow easy reference to the database drivers by name rather than by full file path:

[SQLite]
Driver = /usr/local/lib/libsqlite3odbc.dylib

[PostgreSQL]
Driver = /usr/local/lib/psqlodbcw.so

[MySQL]
Driver = /usr/local/lib/libmysqlclient.dylib

[MariaSQL]
Driver = /usr/local/lib/libmaodbc.dylib

[SQL Server]
Driver = /usr/local/lib/libtdsodbc.so

[Oracle 12c]
Description     = Oracle ODBC driver for Oracle 12c
Driver          = /usr/local/lib/libsqora.dylib.12.2
Setup           =
FileUsage       =
CPTimeout       =
CPReuse         =

Configure R packages

Install all the relevant R packages. We use DBI as the primary database interface, with odbc for ODBC connectivity. Native drivers for PostgreSQL, MariaDB/MySQL, and SQLite are also installed. In production, you can choose either native or ODBC drivers as you see fit.

install.packages("DBI")         # DBI framework
install.packages("odbc")        # odbc framework

# Native drivers
install.packages("RPostgres")
install.packages("RMariaDB")    # covers MariaDB and MySQL
install.packages("RSQLite")