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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