This post is a followup to a recent post I wrote. The issue at hand is that data are stored on a SQL server (Microsoft Server 2005 or version 9 of MS SQL Server to be exact) and that I would like to send queries from a command line interface, either from Mac OS X or a Linux system. The data queried from the server will most often be analyzed in R.
I will outline how to get all of this set up on a Mac OS X which should be similar to a Linux platform.
NOTE: Do not use the Macports version of the following packages – they are NOT needed and can be compiled from source without a problem.
Compile unixODBC (driver manager for different SQL servers)
First, Mac OS X comes with iODBC installed by default. However, FreeTDS is only tested on unixODBC so I’ll use this instead. I didn’t get any luck with iODBC but I didn’t give it nearly as much time as I did to get unixODBC working.
Install like usual: download, extract, ./configure, make, sudo make install. I used the default install directory /usr/local.
Compile FreeTDS (driver to communicate with MS SQL Server and Sybase databases)
First, I recommend getting the development version since all the recent updates are included. I had issues with locale Mac OS X and TDSVER=8.0 (anything higher than version 4.2 actually) specification using FreeTDS v0.82. To do so:
cvs -z3 -d:pserver:firstname.lastname@example.org:/cvsroot/freetds checkout -P freetds cd freetds ./autogen.sh ## generate the configure and make files ./configure --with-tdsver=8.0 --with-unixodbc=/usr/local make sudo make install
The configure line is taken from here. From that same documentation, we DON’T have to register the driver with the manager or add in the data source name for system wide access. I just dealt with local (home directory) files.
Recall from the previous post that I had issues with locale and TDSVER on Mac OS X. I emailed the mailing list and it was partially fixed (
freebcp doesn’t work but
isql works) in the development version of FreeTDS for TDSVER=8.0. My
[adrc] host = IP.ADDRESS port = 1433 tds version = 8.0 client charset = UTF-8 ##needed on MAC OS X
With this, I get query outputs in the command line:
$ bsqldb -S adrc -U USERNAME -P PASSWORD -h -t 't' -i katy.uds.sql | sed -n '2!p' > katy.uds.txt
isql (unixODBC), I have the following in my
[adrcDSN] Driver=/usr/local/lib/libtdsodbc.so ##Description=adrc Trace=No ##servername=adrc Server=IP.ADDRESS ##Address=IP.ADDRESS Port=1433 TDS_Version=8.0 Database=IBADataDictionary ## can have above database or not
isql adrcDSN USERNAME PASSWORD works and looks similar to this.
Note, throughout my process of debugging, I usually precede the commands osql, isql, and tsql with environment variables such as `TDSDUMP=stderr TDSVER=8.0 isql …’ to see what’s going on.
RODBC – accessing the databases in R
The installed RODBC on my R in Mac OS X uses iODBC by default. I compiled from source to get it to work with unixODBC:
R CMD INSTALL -l ~/Rlib RODBC_1.3-1.tar.gz ## in R library(RODBC, lib.loc="Rlib") ch <- odbcConnect("adrcDSN", "USERNAME", "PASSWORD")
I’ve outlined how to access MS SQL Server from the command line and in R, both of what I want. Only thing missing is getting output in emacs…