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The only thing I can think of is that the commit was in a branch other than master. Does GitHub only watch the master branch for issue tags in commits?

The issue also doesn't have the commit attached to it, though the link to the issue from the commit works.

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migrated from superuser.com Jan 26 '13 at 2:43

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up vote 1 down vote accepted

GitHub will now only auto-close an issue via merged commit if it's brought into the default branch. This is usually, and by default, the master branch.

Until then the issue will remain open or one of the repo collaborators can manually close it.

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