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I get this error in my logs a lot:

Deprecated function: Methods with the same name as their class will not be constructors in a future version of PHP; views_many_to_one_helper has a deprecated constructor in require_once() (line 127 of C:\...\sites\all\modules\contrib\ctools\ctools.module).

This is really not important to me and I don't want it filling up watchdog. Is there any easy way to tell Watchdog to not log these errors? Where can I change which errors get logged by watchdog?

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The Drupal watchdog includes the errors raised by PHP, such as the one you mention.

It might be possible to use hook_watchdog to filter out certain errors. However, it seems easier to change the PHP error level on your settings.php file, so that PHP does not complain about your ctools module.

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