SEOptimer's Canonical Checker tool looks for the presence of the Canonical Tag in your site's HTML. Google recommends having this tag present on every page.
The Canonical Tag is a HTML Tag that tells Search Engines the primary URL of a page. URLs can have multiple versions due to things like parameters being passed or www and non-www versions, resulting in potential duplicate content. Google recommends all pages specify a Canonical for this reason.
You may need to determine what the primary preferred version of the page is. Often the CMS may manage this, or provide the ability to specify it.