Re: [R] RMySQL Error Messages, crashing R

From: Jason Horn <>
Date: Tue 21 Feb 2006 - 00:09:49 EST


Thanks for the tip. I have tried rebuilding the RMySQL library, but it always fails. When I run:

R CMD INSTALL --configure-args='--with-mysql-inc=/usr/local/mysql/ include --with-mysql-lib=/usr/local/mysql/lib' /Users/jason/Desktop/ RMySQL_0.5-7.tar.gz.tar

I get ...

gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib - o RS-DBI.o RS-MySQL.o -L/usr/local/mysql/lib -lmysqlclient - lz -lcc_dynamic -F/Library/Frameworks/R.framework/.. -framework R ld: can't locate file for: -lcc_dynamic
make: *** [] Error 1
ERROR: compilation failed for package 'RMySQL'

The MySQL that I have is 5.0.18 that I downloaded as a binary directly from Is your mySQL installation from elsewhere? What do you mean "...that I installed through port."

It sounds like you have everything working. What commands did you use to get mySQL 5 installed? To get RMySQL compiled? Any help here is appreciated. I am heavily dependent on R working with mySQL for my project.


On Feb 19, 2006, at 11:21 PM, Phil Spector wrote:

> Jason -
> In order to get mysql5 to work with R.2.2 on Tiger, I had to
> rebuild
> the RMySQL library against the mysql libraries that I installed
> through port.
> (You didn't mention where you got your mysql from). The problem I saw
> was that I kept seeing the warning message, and R wouldn't connect
> to the database, but I'm pretty sure what you need to do is rebuild
> the R library
> against the system libraries that you've currently got installed.
> - Phil Spector
> Statistical Computing Facility
> Department of Statistics
> UC Berkeley
> On Sun, 19 Feb 2006, Jason Horn wrote:
>> I am having trouble getting RMySQL working with R. It did at one
>> point, work with an older 1.x version of R, but now with R2.2.1, I am
>> getting the following messages on my OS X 10.4.5 system:
>> RS-DBI driver warning: (MySQL mismatch between compiled version
>> 4.0.24 and runtime version 4.1.14)
>> if I then try to run any further db commands such as dbConnect, R
>> crashes with a bus error. When I started getting this error, I was
>> using MySQL 5. I have since removed that installation and instead
>> installed the older 4.0.24. I still get the error message. I have
>> also tried other versions of MySQL, but the error persists. I have
>> also tried installing RMySQL from sources, but it makes no
>> difference.
>> Does anyone know what this error message means. Are there any OS X
>> users that have with R 2.x working with RMySQL?
>> Please help!
>> - Jason
>> Jason Horn
>> Boston University Department of Biology
>> 5 Cumington Street Boston, MA 02215
>> office: 617 353 6987
>> cell: 401 588 2766
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> mailing list PLEASE do read the posting guide! Received on Tue Feb 21 00:14:35 2006

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