Marc Schwartz wrote:
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: r...@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
Thanks Marc, super helpful and quick as well. Worked a treat.
David
--
_________________________________________________________________
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142, NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018
Director of Consulting, Department of Statistics
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