[R] Problem installing RODBC

[Marc Schwartz]

On Apr 19, 2010, at 7:02 PM, David Scott wrote:

> I have a problem with some missing headers when trying to install RODBC on my linux box.
> 
> > install.packages("RODBC",
> +                   lib="/usr/local/david/R")
> trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/RODBC_1.3-1.tar.gz'
> Content type 'application/x-gzip' length 990220 bytes (967 Kb)
> opened URL
> ==================================================
> downloaded 967 Kb
> 
> 
> Read .Rprofile
> * installing *source* package ‘RODBC’ ...
> checking for gcc... gcc -m32 -std=gnu99
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -m32 -std=gnu99 accepts -g... yes
> checking for gcc -m32 -std=gnu99 option to accept ANSI C... none needed
> checking how to run the C preprocessor... gcc -m32 -std=gnu99 -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking sql.h usability... no
> checking sql.h presence... no
> checking for sql.h... no
> checking sqlext.h usability... no
> checking sqlext.h presence... no
> checking for sqlext.h... no
> configure: error: "ODBC headers sql.h and sqlext.h not found"
> ERROR: configuration failed for package ‘RODBC’
> * removing ‘/usr/local/david/R/RODBC’
> 
> 
> Details of my setup are:
> 
> > R.version
>               _
> platform       i386-redhat-linux-gnu
> arch           i386
> os             linux-gnu
> system         i386, linux-gnu
> status
> major          2
> minor          10.0
> year           2009
> month          10
> day            26
> svn rev        50208
> language       R
> version.string R version 2.10.0 (2009-10-26)
> 
> I have the following mysql setup
> 
> mysql> status;
> --------------
> mysql  Ver 14.12 Distrib 5.0.88, for redhat-linux-gnu (i386) using readline 5.1
> 
> Connection id:		9
> Current database:	
> Current user:		root at localhost
> SSL:			Not in use
> Current pager:		stdout
> Using outfile:		''
> Using delimiter:	;
> Server version:		5.0.88 Source distribution
> Protocol version:	10
> Connection:		Localhost via UNIX socket
> Server characterset:	latin1
> Db     characterset:	latin1
> Client characterset:	latin1
> Conn.  characterset:	latin1
> UNIX socket:		/var/lib/mysql/mysql.sock
> Uptime:			95 days 19 hours 18 min 27 sec
> 
> 
> I am guessing my MySQL is getting a bit decrepit and needs updating, but welcome any suggestions about sorting this out.
> 
> 
> David Scott


The missing header files are contained in the unixODBC-devel RPM, which you will need to install and then you should be able to install RODBC. Recent RH/Fedora installations use 'yum' for package management, so something like:

  yum install unixODBC-devel

as root, should get you what you need.

Also, there is the R package RMySQL which provides an alternative interface to MySQL, if you should wish to investigate that approach.

Finally, there is the R-SIG-DB list which provides a focused audience for R and DB related matters:

  https://stat.ethz.ch/mailman/listinfo/r-sig-db

HTH,

Marc Schwartz