Bug #36598 compiling from source configures paths incorrectly

Description:

When I ran scripts/mysql_install_db I got the following error:

FATAL ERROR: Could not find /fill_help_tables.sql

The configure script in source install is ignoring the prefix of /usr/local/mysql that I set in configure. See below.

How to repeat:
I ran the following commands to compile from source:

cd /usr/local/src/mysql-5.1.24-rc
./configure --prefix=/usr/local/mysql --with-mysqld-user=mysql --with-ssl
make
make install
scripts/mysql_install_db

When I ran the last command above, scripts/mysql_install_db, I got the following error:

FATAL ERROR: Could not find /fill_help_tables.sql

I ran this to find out what the error could be:
/usr/local/libexec/mysqld –print-defaults

--port=3306 --socket=/tmp/mysql.sock --skip-locking --key_buffer=16M
--max_allowed_packet=1M --table_cache=64 --sort_buffer_size=512K
--net_buffer_length=8K --read_buffer_size=256K
--read_rnd_buffer_size=512K --myisam_sort_buffer_size=8M
--log-bin=mysql-bin --server-id=1 --user=mysql
--pid-file=/var/run/mysqld/mysqld.pid --socket=/var/run/mysqld/mysqld.sock
--port=3306 --basedir=/usr --datadir=/var/lib/mysql --tmpdir=/tmp
--language=/usr/share/mysql/english --skip-external-locking --bind-address=127.0.0.1
--key_buffer=16M --max_allowed_packet=16M --thread_stack=128K --thread_cache_size=8
--query_cache_limit=1M --query_cache_size=16M --expire_logs_days=10 --max_binlog_size=100M
--skip-bdb

Note that the path prefix of /usr/local/mysql is totally ignored!!!!

As a work around I had to do this:

./scripts/mysql_install_db --no-defaults --port=3306 --socket=/tmp/mysql.sock \
--skip-locking --key_buffer=16M --max_allowed_packet=1M --table_cache=64 \
--sort_buffer_size=512K --net_buffer_length=8K --read_buffer_size=256K  \
--read_rnd_buffer_size=512K --myisam_sort_buffer_size=8M --log-bin=mysql-bin \
--server-id=1 --user=mysql --pid-file=/var/run/mysqld/mysqld.pid \
--socket=/var/run/mysqld/mysqld.sock \
 --port=3306 --basedir=/usr/local/mysql --datadir=/usr/local/mysql/var \
--tmpdir=/tmp --language=/usr/local/mysql/share/mysql/english --skip-external-locking \
--bind-address=127.0.0.1 --key_buffer=16M --max_allowed_packet=16M \
--thread_stack=128K --thread_cache_size=8 --query_cache_limit=1M \
--query_cache_size=16M --expire_logs_days=10 --max_binlog_size=100M

Please fix your code! The above commands have worked in MySQL for 9 years.

Suggested fix:
Somebody needs to look at the configure script and fix it. The work around is above in the How to repeat section.

Many thanks for writing a bug report.

The problem here is, that you have somewhere on your system a second my.cnf with a given basedir. Please check /etc and /etc/mysql.

The problem is that there is lots of Linux software outside that will additionally install a my.cnf.

And MySQL is searching first at /etc and then at other places.

Where MySQL is searching you can see by using: ./libexec/mysqld --verbose --help

For example here on my computer:
$ ./libexec/mysqld --verbose --help | less
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf /home/myhome/mysql-5.1/etc/my.cnf ~/.my.cnf