(no subject)

Mon, Feb 20, 2006 5:31 AM

Brian,

I am having exactly the same problem.  I am very interested to know  
if you have R 2.2.x, mySQL and RMySQL working together successfully  
(it sounds like you do).  If recompiling MySQL with gcc 3.3 was the  
solution, can you tell me how you managed to do it?  I have never  
tried to compile mySQL before, much less with a version of gcc that I  
don't have on my system (I currently have gcc 4.0.1 on my OS X 10.4.5  
system).  Any and all details are welcome.

Thanks,

-Jason

Jason Horn
Boston University Department of Biology
5 Cumington Street  Boston, MA 02215

jhorn at bu.edu
office: 617 353 6987
cell: 401 588 2766

Update on this thread:

It turned out that, not only did I need to install RMySQL from
sources, I also needed to reinstall MySQL from sources, using gcc 3.3
as the c and c++ compiler.  The binary version of MySQL 5.0.15 was
compiled using gcc 4.0, which caused some kind of conflict with R
relating to the C API (R complained as follows):

ld: truncated or malformed archive: /usr/local/mysql/lib/
libmysqlclient.a (ranlib structures in table of contents extends

past

the end of the table of contents, can't load from it)

Anyway, it all works now.  I am not sure whether it was the compiler
version that did the trick, of whether something else in my
configuration was different than in the MySQL binary (perhaps
relating to the ld flags) but it works.

FP

On Oct 20, 2005, at 1:22 AM, Prof Brian Ripley wrote:

On Thu, 20 Oct 2005, Parlamis Franklin wrote:

I upgraded R to 2.2.0 (Mac Cocoa GUI 1.13) this evening.  I am
running MySQL Standard version 4.1.14 locally, which I installed
several months ago from binaries on the MySQL web site (mysql-
standard-4.1.14-apple-darwin8.2.0-powerpc-64bit.dmg).  Before I
upgraded R, everything worked fine with RMySQL and DBI (all I used
was DBSendQuery, DBReadTable and DBWriteTable).

However, now when I load the DBI package I get the following error:

        Warning message:
        RS-DBI driver warning: (MySQL mismatch between compiled
version 4.0.24 and runtime version 4.1.14)

Then, if I attempt to use one of the DBI functions, say

DBReadTable,

R quits unexpectedly.  I reinstalled MySQL from binaries, and I

also

reinstalled the DBI and RMySQL packages from binaries.  Nothing has
helped.  I have never had MySQL 4.0.24 on my computer (4.1.14

was my

first and only install).

It is the (powerpc/2.2) RMySQL MacOS X binary that is compiled
against MySQL 4.0.24.  It seems you need to install RMySQL from the
sources.

This is not really a R-sig-DB topic but a MacOS one.

--
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595