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Is there any software that I can run on either a Linux or a Windows server to check for domains that have out dated WordPress installations. I have seen a rise in hacked sites and in all cases the CMSes had not installed latest updates.

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Joomla! and WordPress have extensions that will notify you promptly if a new release is available for the current installation.

For Joomla! — Akeeba Admin Tools is highly recommended (the free version is good but the extra security features in the Pro version a more than worth it). While you on the JED you could also look at the Site Protection section to get an idea of what's there (personally though Admin Tools does everything all the others combined try to do).

For WordPress — we've used a few different solutions, the latest one we've used is the "Mail on Update" plugin, of course it pays to looks that various plugins available there's new stuff every week.

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If you use Nagios you can use cucumber-nagios to describe the following behaviour and automatically alert when you don't have the latest version. This example is written for WordPress, but it should easily be possible to write a similar statement for Joomla.

Feature: blog.example.com
  As an administrator
  I should be able to log in
  And I should be able to check for WordPress updates

  Scenario: Log in and check for updates
    When I go to "http://blog.example.com/wp-login.php"
    And I fill in "Username" with "admin"
    And I fill in "Password" with "password"
    And I press "Log In"
    And I go to "http://blog.example.com/wp-admin/network/update-core.php"
    Then I should see "You have the latest version of WordPress"

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