Troubleshooting

Table Of Contents

1. Installation Issues
2. Installing the database with "rake db:setup"
3. Installing Ruby on a server without root access
4. Runtime Issues

1. Installation Issues

i. Installing the database with "rake db:setup"

The Common Setup guide suggest running the two rake tasks db:load and db:seed. A typical Rails installation also comes with a rake task named db:setup which is supposed to do both, includig creating the MySQL database for you. However, please note that you might have to comment out all the other environments defined in database.yml while running this task, to leave only the one environment you are working on. It seems sometimes db:setup gets confused and will read the usernames and password fields of entries other than the one specified by RAILS_ENV.

ii. Installing Ruby on a server without root access

When installing Ruby, rvm will sometimes attempt to execute the commands on your system to install system packages (such as libyaml-devel, etc). If you're the owner of the system it will prompt you to enter an administrative password for 'yum' or 'apt-get'. However, if you're on a computer where you only have user access, you can't install these packages yourself. You may have to can ask the syadmins to do it.

Sometimes, like on supercomputer clusters, the packages that rvm wants to install are detected as 'missing' by rvm, but their files are still perfectly installed and available to you using a command such as module. In that case, if you know quite well that all the file can be found with module, issue the appropriate module load commands then you can trick rvm into not checking the packaging system for missing packages. Before compiling Ruby, edit the file $HOME/.rvm/scripts/functions/build_config and find an excerpt that looks like this:

  rvm_log "Checking requirements for ${rvm_autolibs_flag_runner}."
  if
    __rvm_requirements_run ${rvm_autolibs_flag_runner} "$@"
  then
    rvm_log "Requirements installation successful."
  else

Change the if condition so that it doesn't invoke the check command at all:

  rvm_log "Checking requirements for ${rvm_autolibs_flag_runner}."
  if
    true
    #__rvm_requirements_run ${rvm_autolibs_flag_runner} "$@"
  then
    rvm_log "Requirements installation successful."
  else

That way, rvm will always think your system has all the necessary package requirements to proceed. Make sure to undo this change after you've successfully compiled Ruby.

2. Runtime Issues

i. Mysql2 error

Some SQL queries performed by CBRAIN might fail with a message that contains these keywords:

(...) incompatible with sql_mode=only_full_group_by (...)

This happens more and more with modern servers. To fix this you need to change the configuration of the DB server, by removing the keyword ONLY_FULL_GROUP_BY from a setting called sql_mode. This sql_mode setting is a list of several keywords separated by commas. There are two ways you can do this:

• In the MySQL global configuration file (generally in /etc/my.cnf). The configuration file sometimes has the sql_mode setting explicitely stated in the [mysqld] section, and sometimes it isn't. If the setting isn't there, you can still create it yourself by first finding out the full value of sql_mode from the database's variable (see next bullet point) and removing ONLY_FULL_GROUP_BY.
• Directly in the database by changing the content of the "sql_mode" variable.