Troubleshooting

Issues while running a patch

MySQL server has gone away

[PDOException] SQLSTATE[HY000]: General error: 2006 MySQL server has gone away

If you get this error the connection has timed out. In your MySQL config file, increase the value of wait_timeout to: wait_timeout= 200 Alternatively, run the patch without any migration using the option –skip-migration. To run the migrations use migartions:migrate command.

Patch fails during database migrations

Confirm all galaxies site databases can be accessed using the galaxy database manager username and password.

Suhosin

If you are using Suhosin you will have to adjust the command as follows: php -d suhosin.executor.include.whitelist=phar meteor.phar patch:apply --path=<JADU_HOME>

Issues after running a patch

If you encounter errors after completing a patch:

  1. Confirm all database migrations have run.
  2. Confirm all filesystem migrations have run.
  3. Delete jadu cache from JADU_HOME/var/cache/*
  4. On WISP systems, delete temporary asp.net files from C:\WINDOWS\Microsoft.NET\Framework\v4.0.30319\Temporary ASP.NET
  5. Confirm the group and associated permissions of patched files are correct.
  6. Clear OPcache if it is in use.
  7. Check all required XML config files have been created in JADU_HOME/config/
  8. When applying multiple patches, have they been applied in the correct order and are all Composer dependencies present.

Issues flagged by Version20150807120003

If XFP is installed, check that, if duplicate component names were flagged during migrations, that migrations were re-run after the flagged issues were resolved.

Images, JavaScript and CSS files return 500 server error in the Control Center

Add <remove fileExtension=".woff2" /> to JADU_HOME/public_html/jadu/web.config if its is missing.

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