List,
I am attempting to install RMySQL on a Kubuntu box.
mysql and R were installed using the adept package manager:
"apt-get install mysql-server"
"apt-get install r-base"
I can access mysql via the terminal and I can open R and perform various basic
tasks.
However, I cannot install the RMySQL package in R. I get the following error:
* Installing *source* package 'RMySQL' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for compress in -lz... yes
checking for getopt_long in -lc... yes
checking for mysql_init in -lmysqlclient... no
checking for mysql.h... no
checking for mysql_init in -lmysqlclient... no
checking for mysql_init in -lmysqlclient... no
checking for mysql_init in -lmysqlclient... no
checking for mysql_init in -lmysqlclient... no
checking for mysql_init in -lmysqlclient... no
checking for /usr/local/include/mysql/mysql.h... no
checking for /usr/include/mysql/mysql.h... no
checking for /usr/local/mysql/include/mysql/mysql.h... no
checking for /opt/include/mysql/mysql.h... no
checking for /include/mysql/mysql.h... no
Configuration error:
could not find the MySQL installation include and/or library
directories. Manually specify the location of the MySQL
libraries and the header files and re-run R CMD INSTALL.
INSTRUCTIONS:
1. Define and export the 2 shell variables PKG_CPPFLAGS and
PKG_LIBS to include the directory for header files (*.h)
and libraries, for example (using Bourne shell syntax):
export PKG_CPPFLAGS="-I<MySQL-include-dir>"
export PKG_LIBS="-L<MySQL-lib-dir> -lmysqlclient"
Re-run the R INSTALL command:
R CMD INSTALL RMySQL_<version>.tar.gz
2. Alternatively, you may pass the configure arguments
--with-mysql-dir=<base-dir> (distribution directory)
or
--with-mysql-inc=<base-inc> (where MySQL header files reside)
--with-mysql-lib=<base-lib> (where MySQL libraries reside)
in the call to R INSTALL --configure-args='...'
R CMD INSTALL --configure-args='--with-mysql-dir=DIR'
RMySQL_<version>.tar.gz
ERROR: configuration failed for package 'RMySQL'
** Removing '/usr/local/lib/R/site-library/RMySQL'
** Restoring previous '/usr/local/lib/R/site-library/RMySQL'
The downloaded packages are in
/tmp/RtmpDS6tND/downloaded_packages
Warning message:
installation of package 'RMySQL' had non-zero exit status in:
install.packages("
RMySQL")
I cannot find mysql.h or mysql.so anywhere. It was apparently installed in
/etc/mysql (that's where my.cnf is located, anyway) but I cannot figure out
where these headers and libraries are supposed to be.
Any help would be greatly appreciated. This is time critical! Never had any
problems with R on redhat, but we have moved over to Kubuntu for some reason,
and now of course issues come up when we need to use R to analyze data stored
in the mysql database!
Thanks in advance,
Pete
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