What version of git-annex are you using? On what operating system?

6.20171001+gitg542d0649f-1~ndall+1

What steps will reproduce the problem?

$> git annex info     

git-annex: .git/annex/misctmp/mergedrefs.0: createDirectory: permission denied (Permission denied)
failed
git-annex: info: 1 failed

unless there is really a need to have this operations performed within the same repository/the same filesystem, I do not understand why generic $TMPDIR could not be used for such operations so no write access has to be demanded