Error while installing RMySQL (MySQL 5.6.14 in Ubuntu 13.04)

Question

I'm trying to install RMySQL in Ubuntu 13.04 when using MySQL v5.6.14. Ubuntu does not have apt-get support for MySQL 5.6.14, so I had to install it manually. Now when I try to install RMySQL I get the following:

(It looks like the package files are not created? But I'm not sure why or how to debug it.)

elad@elad-ThinkPad-T430s:~/tmp$ sudo R CMD INSTALL --configure-args='--with-mysql-inc=/opt/mysql/server-5.6/include --with-mysql-lib=/opt/mysql/server-5.6/lib' RMySQL_0.9-3.tar.gz 
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for compress in -lz... yes
checking for getopt_long in -lc... yes
checking for mysql_init in -lmysqlclient... no
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mysql.h usability... no
checking mysql.h presence... no
checking for mysql.h... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/opt/mysql/server-5.6/include     -fpic  -O2 -pipe -g  -c RS-DBI.c -o RS-DBI.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/opt/mysql/server-5.6/include     -fpic  -O2 -pipe -g  -c RS-MySQL.c -o RS-MySQL.o
gcc -std=gnu99 -shared -o RMySQL.so RS-DBI.o RS-MySQL.o -L/opt/mysql/server-5.6/lib -lmysqlclient -lz -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/RMySQL/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘format’ from package ‘base’ in package ‘RMySQL’
Creating a generic function for ‘print’ from package ‘base’ in package ‘RMySQL’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'RMySQL', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/site-library/RMySQL/libs/RMySQL.so':
  libmysqlclient.so.18: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/RMySQL’
* restoring previous ‘/usr/local/lib/R/site-library/RMySQL’

Update:

This ended up being a LD_LIBRARY_PATH issue. Adding the following to /usr/bin/R solved it:

LD_LIBRARY_PATH=$LD_LIBRARY_PATH/opt/mysql/server-5.6/lib
export LD_LIBRARY_PATH

Answer 1

Did you run ldconfig after installing the library locally?

Does ldconfig -p return something regarding mysql?

On my box, with default MySQL libraries from Ubuntu [lines wrapped by hand]

edd@max:~$ ldconfig -p | grep mysql
        libmysqlclient.so.18 (libc6,x86-64) => \
               /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18
        libmysqlclient.so (libc6,x86-64) => \
               /usr/lib/x86_64-linux-gnu/libmysqlclient.so
edd@max:~$