[R-sig-DB] (no subject)
Jason Horn
jhorn @end|ng |rom bu@edu
Mon Feb 20 14:31:28 CET 2006
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
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