[R-sig-DB] (no subject)

[Jason Horn]

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 using 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



	[[alternative HTML version deleted]]