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We went back to look at why this happened and found https://github.com/freebsd/pkg/issues/1917 which we reported a long time ago. It seems that when py37-MarkupSafe became py37-markupsafe the FreeBSD package tool would mark the new package as manually installed (which it wasn't) so it sticked around ever since then for some people.
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Hence, a higher number means a more popular project.