I can offer a work-around.
I have been encountering this same problem on one of two OS X systems, and one Solaris system. I've been corresponding with the RMySQL maintainer, David James (who I CC'd), and he knows everything that I do (and more, of course!). We don't have a proper solution yet, but here is a work-around that I found.
To get RMySQL working on the OS X system where it did not, I installed the gnugetopt package from fink, and then explicitly told RMySQL about it when installing RMySQL. In order to do this you first need to have a local copy of the RMySQL distribution file, RMySQL_0.5-3.tar.gz. Then, in the directory where that file resides define environment variables PKG_CPPFLAGS and PKG_LIBS so that:
[198]% printenv | grep PKG PKG_CPPFLAGS=-I/usr/local/mysql/include -I/sw/include/gnugetopt PKG_LIBS=-L/usr/local/mysql/lib -lmysqlclient -lgnugetopt
Then,
R CMD INSTALL --configure-args='--with-mysql-dir=/usr/local/mysql' RMySQL_0.5-3.tar.gz
Be sure to replace /usr/local/mysql with whatever is correct for you.
This is only a work-around; there are a number of reasons to believe that getopt_long should be present and available when RMySQL is installed--but as long as it's not, this is one way to get it.
I have mysql 4.0.16-standard (binary distribution downloaded from www.mysql.com), R 1.8.1 Patched (2004-01-12) (installed from source code), and OS X 10.2.8. The gcc is:
[205]% gcc -v Reading specs from /usr/libexec/gcc/darwin/ppc/3.3/specs Thread model: posix gcc version 3.3 20030304 (Apple Computer, Inc. build 1493)
On my other OS X system, where I did not encounter this problem, I'm still at R 1.8.0; the mysql is 4.0.15, and it is the version distributed by Server Logistics at http://www.macintoshhosting.net/mysql.php. That machine is OS X 10.3.something. I don't have the gcc version information handy.
David James has a successful installation with mysql installed from fink in 10.2.8, and R 1.8.1.
I hope this helps; stay tuned as I plan to keep working on this.
-Don
At 12:33 AM +1300 1/15/04, Geoff Grimwood wrote:
Hello,
I'm tearing my hair out over this. Any help will be very much appreciated. It's been two long nights battling with RMySQL.
library(RMySQL)Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library "/usr/local/lib/R/library/RMySQL/libs/RMySQL.so":
dlcompat: dyld: /usr/local/lib/R/bin/R.bin Undefined symbols:
_getopt_long
Error in library(RMySQL) : .First.lib failed
I am running Mac OS 10.2.8, R 1.8.1, RMySQL 0.5-3, MySQL 4.0.17. R and MySQL are well otherwise
I have moved away from the Fink sourced (ie /sw) version of R and MySQL to regular /usr/local types. Mainly because the Fink R is 1.7 and can't do the MySQL business. And I was wondering if the RMySQL install was comin to grief because it couldn't find the /sw mysql files.
Anyway, RMySQL seems to have install OK. I see it with installed.packages(). There was the apparent inability to find lmysqlclient and mysql.h but that seems to be a red herring (see below).
Regards
Geoff Grimwood Wellington New Zealand
[SIDLAW02:~/Desktop] geoff% sudo R CMD INSTALL --configure-args='--with-mysql-inc=/usr/local/mysql/include --with-mysql-lib=/usr/local/mysql/lib' RMySQL_0.5-3.tar.gz
* Installing *source* package 'RMySQL' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for mysql_init in -lmysqlclient... no
checking for mysql.h... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -no-cpp-precomp -I/usr/local/lib/R/include -I/usr/local/mysql/include -I/sw/include -fno-common -g -O2 -c RS-DBI.c -o RS-DBI.o
gcc -no-cpp-precomp -I/usr/local/lib/R/include -I/usr/local/mysql/include -I/sw/include -fno-common -g -O2 -c RS-MySQL.c -o RS-MySQL.o
gcc -bundle -flat_namespace -undefined suppress -L/sw/lib -L/usr/local/lib -o RMySQL.so RS-DBI.o RS-MySQL.o -L/usr/local/mysql/lib -lmysqlclient -lz -lcc_dynamic -L/usr/local/lib/R/bin -lR
[SNIP]
SIDLAW02:library/RMySQL/libs] geoff% ls -ltr total 500 -rwxr-xr-x 1 root staff 254816 Jan 14 23:45 RMySQL.so -rwxr-xr-x 1 root staff 249856 Jan 14 23:46 libmySQL.dll -rw-r--r-- 1 root staff 155 Jan 14 23:46 libMySQL_4.0.16.txt
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-- -------------------------------------- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA
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