Compilation fails for Percona Server

[tersmitten]

We are using Percona Server, the an enhanced, drop-in MySQL replacement.

Trying to install RMySQL results in the following error:

File mysql.h not found. Please install mysql development library, e.g: libmysqlclient-dev (deb) or mariadb-devel (rpm).

It seems that mysql.h is in /usr/include and the libmysqlclient so files are in /usr/lib.

Setting MYSQL_INC and PKG_LIBS like this:

Sys.setenv(MYSQL_INC = "/usr/include");
Sys.setenv(PKG_LIBS = "/usr/lib");

solves the problem for us, but wouldn't it be better to use mysql_config.

# mysql_config
Usage: /usr/bin/mysql_config [OPTIONS]
Options:
        --cflags         [-I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1]
        --include        [-I/usr/include]
        --libs           [-L/usr/lib -lmysqlclient -lpthread -lm -lrt -lssl -lcrypto -ldl]
        --libs_r         [-L/usr/lib -lmysqlclient_r -lpthread -lm -lrt -lssl -lcrypto -ldl]
        --plugindir      [/usr/lib/mysql/plugin]
        --socket         [/var/run/mysqld/mysqld.sock]
        --port           [0]
        --version        [5.5.35]
        --libmysqld-libs [-L/usr/lib -lmysqld]
        --variable=VAR   VAR is one of:
                pkgincludedir [/usr/include]
                pkglibdir     [/usr/lib]
                plugindir     [/usr/lib/mysql/plugin]

It seems to me that it could make the configure script much simpler.

[jeroen]

The problem is that mysql_config is not available on all systems. So we can add it to the configure script, but it would not make things simpler.

[jeroen]

Which operating system does this run on?

[tersmitten]

Ubuntu 12.04

[jeroen]

Fixed @ 26dac28. Can you help test?

[tersmitten]

Sure. I'll see if I can look into it this afternoon.

[tersmitten]

Seems to work!

> devtools::install_github("rstats-db/RMySQL")
Downloading github repo rstats-db/RMySQL@master
Installing RMySQL
Installing dependencies for RMySQL:
DBI
Installing package into ‘/data/home/mtersmitten/R/x86_64-pc-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/DBI_0.3.1.tar.gz'
Content type 'application/x-gzip' length 30106 bytes (29 Kb)
opened URL
==================================================
downloaded 29 Kb

* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (DBI)

The downloaded source packages are in
    ‘/tmp/RtmpIMAxKU/downloaded_packages’
'/usr/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmpIMAxKU/devtools3aa2e8bc3ca/rstats-db-RMySQL-6a33ac7'  \
  --library='/data/home/mtersmitten/R/x86_64-pc-linux-gnu-library/3.1' --install-tests 

* installing *source* package ‘RMySQL’ ...
Found mysql_config
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c RMySQL-init.c -o RMySQL-init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c connection.c -o connection.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c db-apply.c -o db-apply.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c driver.c -o driver.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c exception.c -o exception.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c fields.c -o fields.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c result.c -o result.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -g -fstack-protector --param=ssp-buffer-size=4 -Wformat-security -fPIC -g -static-libgcc -fno-omit-frame-pointer -DPERCONA_INNODB_VERSION=rel33.0  -fPIC -g -static-libgcc -fno-omit-frame-pointer -fno-strict-aliasing -DMY_PTHREAD_FASTMUTEX=1     -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RMySQL.so RMySQL-init.o connection.o db-apply.o driver.o exception.o fields.o result.o utils.o -L/usr/lib -lmysqlclient -lpthread -lm -lrt -lssl -lcrypto -ldl -L/usr/lib/R/lib -lR
installing to /data/home/mtersmitten/R/x86_64-pc-linux-gnu-library/3.1/RMySQL/libs
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (RMySQL)
> library(DBI)

>

library(DBI)